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  • Molecular mechanisms of vancomycin resistance
    Protein Sci. (IF 2.42) Pub Date : 2020-01-23
    Peter J. Stogios; Alexei Savchenko

    Vancomycin and related glycopeptides are drugs of last resort for the treatment of severe infections caused by Gram‐positive bacteria such as Enterococcus species, Staphylococcus aureus, and Clostridium difficile. Vancomycin was long considered immune to resistance due to its bactericidal activity based on binding to the bacterial cell envelope rather than to a protein target as is the case for most antibiotics. However, two types of complex resistance mechanisms, each comprised of a multi‐enzyme pathway, emerged and are now widely disseminated in pathogenic species, thus threatening the clinical efficiency of vancomycin. Vancomycin forms an intricate network of hydrogen bonds with the d‐Ala‐d‐Ala region of Lipid II, interfering with the peptidoglycan layer maturation process. Resistance to vancomycin involves degradation of this natural precursor and its replacement with d‐Ala‐d‐lac or d‐Ala‐d‐Ser alternatives to which vancomycin has low affinity. Through extensive research over 30 years after the initial discovery of vancomycin resistance, remarkable progress has been made in molecular understanding of the enzymatic cascades responsible. Progress has been driven by structural studies of the key components of the resistance mechanisms which provided important molecular understanding such as, for example, the ability of this cascade to discriminate between vancomycin sensitive and resistant peptidoglycan precursors. Important structural insights have been also made into the molecular evolution of vancomycin resistance enzymes. Altogether this molecular data can accelerate inhibitor discovery and optimization efforts to reverse vancomycin resistance. Here, we overview our current understanding of this complex resistance mechanism with a focus on the structural and molecular aspects.

    更新日期:2020-01-23
  • The strengths and limitations of using biolayer interferometry to monitor equilibrium titrations of biomolecules
    Protein Sci. (IF 2.42) Pub Date : 2020-01-23
    Chamitha J. Weeramange; Max S. Fairlamb; Dipika Singh; Aron W. Fenton; Liskin Swint‐Kruse

    Every method used to quantify biomolecular interactions has its own strengths and limitations. To quantify protein‐DNA binding affinities, nitrocellulose filter binding assays with 32P‐labeled DNA quantify Kd values from 10−12 to 10−8 M but have several technical limitations. Here, we considered the suitability of biolayer interferometry (BLI), which monitors association and dissociation of a soluble macromolecule to an immobilized species; the ratio koff/kon determines Kd. However, for lactose repressor protein (LacI) and an engineered repressor protein (“LLhF”) binding immobilized DNA, complicated kinetic curves precluded this analysis. Thus, we determined whether the amplitude of the BLI signal at equilibrium related linearly to the fraction of protein bound to DNA. A key question was the effective concentration of immobilized DNA. Equilibrium titration experiments with DNA concentrations below Kd (equilibrium binding regime) must be analyzed differently than those with DNA near or above Kd (stoichiometric binding regime). For ForteBio streptavidin tips, the most frequent effective DNA concentration was ~2 × 10−9 M. Although variation occurred among different lots of sensor tips, binding events with Kd ≥ 10−8 M should reliably be in the equilibrium binding regime. We also observed effects from multi‐valent interactions: Tetrameric LacI bound two immobilized DNAs whereas dimeric LLhF did not. We next used BLI to quantify the amount of inducer sugars required to allosterically diminish protein‐DNA binding and to assess the affinity of fructose‐1‐kinase for the DNA‐LLhF complex. Overall, when experimental design corresponded with appropriate data interpretation, BLI was convenient and reliable for monitoring equilibrium titrations and thereby quantifying a variety of binding interactions.

    更新日期:2020-01-23
  • About three‐fourths of mouse proteins unexpectedly appear at a low position of SDS‐PAGE, often as additional isoforms, questioning whether all protein isoforms have been eliminated in gene‐knockout cells or organisms
    Protein Sci. (IF 2.42) Pub Date : 2020-01-23
    Jiayuan Qu; Ju Zhang; Lucas Zellmer; Yan He; Siqi Liu; Chenguang Wang; Chengfu Yuan; Ningzhi xu; Hai Huang; Dezhong J. Liao

    Most genes in evolutionarily complex genomes are expressed to multiple protein isoforms, but there is not yet any simple high‐throughput approach to identify these isoforms. Using an oversimplified top‐down LC–MS/MS strategy, we detected, around the 26‐kD position of SDS‐PAGE, proteins produced from 782 genes in a Cdk4−/− mouse embryonic fibroblast cell line. Interestingly, only 213 (27.24%, about one‐fourth) of these 782 genes have their proteins with a theoretical molecular mass (TMM) 10% smaller or larger than 26 kD, that is, between 23 and 29 kD, the range set as allowed variation in SDS‐PAGE. These 213 proteins are considered as the wild type (WT). The remaining three‐fourths includes proteins from 66 (9.44%) genes with a TMM smaller than 23 kD and proteins from 503 (64.32%, nearly two‐thirds) genes with a TMM larger than 29 kD; these proteins are categorized into a larger‐group or a smaller‐group, respectively, for their appearance at a higher or lower position of SDS‐PAGE. For instance, at this 26‐kD position we detected proteins from the Rps27a, Snrpf, Hist1h4a, and Rps25 genes whose proteins' TMM is 8.6, 9.7, 11.4, and 13.7 kD, respectively, and detected proteins from the Plelc1 and Prkdc genes, whose largest isoform is 533.9 and 471.1 kD, respectively. We extrapolate that many of those proteins migrating unexpectedly in SDS‐PAGE may be isoforms besides the WT protein. Moreover, we also detected a Cdk4 protein in this Cdk4−/− cell line, thus wondering whether some of other gene‐knockout cells or organisms show similar incompleteness of the knockout.

    更新日期:2020-01-23
  • Differences in the chitinolytic activity of mammalian chitinases on soluble and insoluble substrates
    Protein Sci. (IF 2.42) Pub Date : 2020-01-21
    Benjamin A. Barad; Lin Liu; Roberto E. Diaz; Ralp Basilio; Steven J. Van Dyken; Richard M. Locksley; James S. Fraser

    Chitin is an abundant polysaccharide used by many organisms for structural rigidity and water repulsion. As such, the insoluble crystalline structure of chitin poses significant challenges for enzymatic degradation. Acidic mammalian chitinase, a processive glycosyl hydrolase, is the primary enzyme involved in the degradation of environmental chitin in mammalian lungs. Mutations to acidic mammalian chitinase have been associated with asthma, and genetic deletion in mice increases morbidity and mortality with age. We initially set out to reverse this phenotype by engineering hyperactive acidic mammalian chitinase variants. Using a screening approach with commercial fluorogenic substrates, we identified mutations with consistent increases in activity. To determine whether the activity increases observed were consistent with more biologically relevant chitin substrates, we developed new assays to quantify chitinase activity with insoluble chitin, and identified a one‐pot fluorogenic assay that is sufficiently sensitive to quantify changes to activity due to the addition or removal of a carbohydrate‐binding domain. We show that the activity increases from our directed evolution screen were lost when insoluble substrates were used. In contrast, naturally occurring gain‐of‐function mutations gave similar results with oligomeric and insoluble substrates. We also show that activity differences between acidic mammalian chitinase and chitotriosidase are reduced with insoluble substrate, suggesting that previously reported activity differences with oligomeric substrates may have been driven by differential substrate specificity. These results highlight the need for assays against physiological substrates when engineering metabolic enzymes, and provide a new one‐pot assay that may prove to be broadly applicable to engineering glycosyl hydrolases.

    更新日期:2020-01-23
  • Misannotations of the genes encoding sugar N‐formyltransferases
    Protein Sci. (IF 2.42) Pub Date : 2020-01-20
    Nicholas M. Girardi; James B. Thoden; Hazel M. Holden

    Tens of thousands of bacterial genome sequences are now known due to the development of rapid and inexpensive sequencing technologies. An important key in utilizing these vast amounts of data in a biologically meaningful way is to infer the function of the proteins encoded in the genomes via bioinformatics techniques. Whereas these approaches are absolutely critical to the annotation of gene function, there are still issues of misidentifications, which must be experimentally corrected. For example, many of the bacterial DNA sequences encoding sugar N‐formyltransferases have been annotated as l‐methionyl‐tRNA transferases in the databases. These mistakes may be due in part to the fact that until recently the structures and functions of these enzymes were not well known. Herein we describe the misannotation of two genes, WP_088211966.1 and WP_096244125.1, from Shewanella spp. and Pseudomonas congelans, respectively. Although the proteins encoded by these genes were originally suggested to function as l‐methionyl‐tRNA transferases, we demonstrate that they actually catalyze the conversion of dTDP‐4‐amino‐4,6‐dideoxy‐d‐glucose to dTDP‐4‐formamido‐4,6‐dideoxy‐d‐glucose utilizing N10‐formyltetrahydrofolate as the carbon source. For this analysis, the genes encoding these enzymes were cloned and the corresponding proteins purified. X‐ray structures of the two proteins were determined to high resolution and kinetic analyses were conducted. Both enzymes display classical Michaelis–Menten kinetics and adopt the characteristic three‐dimensional structural fold previously observed for other sugar N‐formyltransferases. The results presented herein will aid in the future annotation of these fascinating enzymes.

    更新日期:2020-01-22
  • Allosteric inhibitors of Mycobacterium tuberculosis tryptophan synthase
    Protein Sci. (IF 2.42) Pub Date : 2020-01-20
    Karolina Michalska; Changsoo Chang; Natalia I. Maltseva; Robert Jedrzejczak; Gregory T. Robertson; Fabian Gusovsky; Patrick McCarren; Stuart L. Schreiber; Partha P. Nag; Andrzej Joachimiak

    Global dispersion of multidrug resistant bacteria is very common and evolution of antibiotic‐resistance is occurring at an alarming rate, presenting a formidable challenge for humanity. The development of new therapeuthics with novel molecular targets is urgently needed. Current drugs primarily affect protein, nucleic acid, and cell wall synthesis. Metabolic pathways, including those involved in amino acid biosynthesis, have recently sparked interest in the drug discovery community as potential reservoirs of such novel targets. Tryptophan biosynthesis, utilized by bacteria but absent in humans, represents one of the currently studied processes with a therapeutic focus. It has been shown that tryptophan synthase (TrpAB) is required for survival of Mycobacterium tuberculosis in macrophages and for evading host defense, and therefore is a promising drug target. Here we present crystal structures of TrpAB with two allosteric inhibitors of M. tuberculosis tryptophan synthase that belong to sulfolane and indole‐5‐sulfonamide chemical scaffolds. We compare our results with previously reported structural and biochemical studies of another, azetidine‐containing M. tuberculosis tryptophan synthase inhibitor. This work shows how structurally distinct ligands can occupy the same allosteric site and make specific interactions. It also highlights the potential benefit of targeting more variable allosteric sites of important metabolic enzymes.

    更新日期:2020-01-21
  • Structural insights into phosphopantetheinyl hydrolase PptH from Mycobacterium tuberculosis
    Protein Sci. (IF 2.42) Pub Date : 2020-01-20
    John Mosior; Ronnie Bourland; Shivatheja Soma; Carl Nathan; James Sacchettini

    The amidinourea 8918 was recently reported to inhibit the type II phosphopantetheinyl transferase (PPTase) of Mycobacterium tuberculosis (Mtb), PptT, a potential drug‐target that activates synthases and synthetases involved in cell wall biosynthesis and secondary metabolism. Surprisingly, high‐level resistance to 8918 occurred in Mtb harboring mutations within the gene adjacent to pptT, rv2795c, highlighting the role of the encoded protein as a potentiator of the bactericidal action of the amidinourea. Those studies revealed that Rv2795c (PptH) is a phosphopantetheinyl (PpT) hydrolase, possessing activity antagonistic with respect to PptT. We have solved the crystal structure of Mtb's phosphopantetheinyl hydrolase, making it the first phosphopantetheinyl (carrier protein) hydrolase structurally characterized. The 2.5 Å structure revealed the hydrolases' four‐layer (α/β/β/α) sandwich fold featuring a Mn‐Fe binuclear center within the active site. A structural similarity search confirmed that PptH most closely resembles previously characterized metallophosphoesterases (MPEs), particularly within the vicinity of the active site, suggesting that it may utilize a similar catalytic mechanism. In addition, analysis of the structure has allowed for the rationalization of the previously reported PptH mutations associated with 8918‐resistance. Notably, differences in the sequences and predicted structural characteristics of the PpT hydrolases PptH of Mtb and E. coli's acyl carrier protein hydrolase (AcpH) indicate that the two enzymes evolved convergently and therefore are representative of two distinct PpT hydrolase families.

    更新日期:2020-01-21
  • Solution structure for an Encephalitozoon cuniculi adrenodoxin‐like protein in the oxidized state
    Protein Sci. (IF 2.42) Pub Date : 2020-01-20
    Shareef Shaheen; Kayleigh F. Barrett; Sandhya Subramanian; Samuel L. M. Arnold; Joseph A. Laureanti; Peter J. Myler; Wesley C. Van Voorhis; Garry W. Buchko

    Encephalitozoon cuniculi is a unicellular, obligate intracellular eukaryotic parasite in the Microsporidia family and one of the agents responsible for microsporidosis infections in humans. Like most Microsporidia, the genome of E. cuniculi is markedly reduced and the organism contains mitochondria‐like organelles called mitosomes instead of mitochondria. Here we report the solution NMR structure for a protein physically associated with mitosome‐like organelles in E. cuniculi, the 128‐residue, adrenodoxin‐like protein Ec‐Adx (UniProt ID Q8SV19) in the [2Fe‐2S] ferredoxin superfamily. Oxidized Ec‐Adx contains a mixed four‐strand β‐sheet, β2‐β1‐β4‐β3 (↓↑↑↓), loosely encircled by three α‐helices and two 310‐helices. This fold is similar to the structure observed in other adrenodoxin and adrenodoxin‐like proteins except for the absence of a fifth anti‐parallel β‐strand next to β3 and the position of α3. Cross peaks are missing or cannot be unambiguously assigned for 20 amide resonances in the 1H‐15N HSQC spectrum of Ec‐Adx. These missing residues are clustered primarily in two regions, G48‐V61 and L94‐L98, containing the four cysteine residues predicted to ligate the paramagnetic [2Fe‐2S] cluster. Missing amide resonances in 1H‐15N HSQC spectra are detrimental to NMR‐based solution structure calculations because 1H‐1H NOE restraints are absent (glass half‐empty) and this may account for the absent β‐strand (β5) and the position of α3 in oxidized Ec‐Adx. On the other hand, the missing amide resonances unambiguously identify the presence, and immediate environment, of the paramagnetic [2Fe‐2S] cluster in oxidized Ec‐Adx (glass half‐full).

    更新日期:2020-01-21
  • Toward a structome of Acinetobacter baumannii drug targets
    Protein Sci. (IF 2.42) Pub Date : 2020-01-20
    Logan M. Tillery; Kayleigh F. Barrett; David M. Dranow; Justin Craig; Roger Shek; Ian Chun; Lynn K. Barrett; Isabelle Q. Phan; Sandhya Subramanian; Jan Abendroth; Donald D. Lorimer; Thomas E. Edwards; Wesley C. Van Voorhis

    Acinetobacter baumannii is well known for causing hospital‐associated infections due in part to its intrinsic antibiotic resistance as well as its ability to remain viable on surfaces and resist cleaning agents. In a previous publication, A. baumannii strain AB5075 was studied by transposon mutagenesis and 438 essential gene candidates for growth on rich‐medium were identified. The Seattle Structural Genomics Center for Infectious Disease entered 342 of these candidate essential genes into our pipeline for structure determination, in which 306 were successfully cloned into expression vectors, 192 were detectably expressed, 165 screened as soluble, 121 were purified, 52 crystalized, 30 provided diffraction data, and 29 structures were deposited in the Protein Data Bank. Here, we report these structures, compare them with human orthologs where applicable, and discuss their potential as drug targets for antibiotic development against A. baumannii.

    更新日期:2020-01-21
  • Curvature‐sensitive trans‐assembly of human Atg8‐family proteins in autophagy‐related membrane tethering
    Protein Sci. (IF 2.42) Pub Date : 2020-01-20
    Saki Taniguchi; Masayuki Toyoshima; Tomoyo Takamatsu; Joji Mima

    In macroautophagy, de novo formation of the double membrane‐bound organelles, termed autophagosomes, is essential for engulfing and sequestering the cytoplasmic contents to be degraded in the lytic compartments such as vacuoles and lysosomes. Atg8‐family proteins have been known to be responsible for autophagosome formation via membrane tethering and fusion events of precursor membrane structures. Nevertheless, how Atg8 proteins act directly upon autophagosome formation still remains enigmatic. Here, to further gain molecular insights into Atg8‐mediated autophagic membrane dynamics, we study the two representative human Atg8 orthologs, LC3B and GATE‐16, by quantitatively evaluating their intrinsic potency to physically tether lipid membranes in a chemically defined reconstitution system using purified Atg8 proteins and synthetic liposomes. Both LC3B and GATE‐16 retained the capacities to trigger efficient membrane tethering at the protein‐to‐lipid molar ratios ranging from 1:100 to 1:5,000. These human Atg8‐mediated membrane tethering reactions require trans‐assembly between the membrane‐anchored forms of LC3B and GATE‐16 and can be reversibly and strictly controlled by the membrane attachment and detachment cycles. Strikingly, we further uncovered distinct membrane curvature dependences of LC3B‐ and GATE‐16‐mediated membrane tethering reactions: LC3B can drive tethering more efficiently than GATE‐16 for highly‐curved small vesicles (e.g. 50 nm in diameter), although GATE‐16 turns out to be a more potent tether than LC3B for flatter large vesicles (e.g. 200 and 400 nm in diameter). Our findings establish curvature‐sensitive trans‐assembly of human Atg8‐family proteins in reconstituted membrane tethering, which recapitulates an essential subreaction of the biogenesis of autophagosomes in vivo.

    更新日期:2020-01-21
  • Conformational states of TNFR1 as a molecular switch for receptor function
    Protein Sci. (IF 2.42) Pub Date : 2020-01-20
    Chih Hung Lo; Evan C. Huber; Jonathan N. Sachs

    Tumor necrosis factor receptor 1 (TNFR1) is a transmembrane receptor which plays a key role in the regulation of the inflammatory pathway. While inhibition of TNFR1 has been the focus of many studies for treatment of autoimmune diseases such as rheumatoid arthritis, activation of the receptor is important for treatment of immunodeficiency diseases such as HIV and neurodegenerative diseases such as Alzheimer's disease where a boost in immune signaling is required. In addition, activation of other TNF receptors such as death receptor 5 or FAS receptor is important for cancer therapy. Here, we used a previously established TNFR1 FRET biosensor together with a fluorescence lifetime technology as a high‐throughput screening platform to identify a novel small molecule that activates TNFR1 by increasing inter‐monomeric spacing in a ligand‐independent manner. This shows that the conformational rearrangement of pre‐ligand assembled receptor dimers can determine the activity of the receptor. By probing the interaction between the receptor and its downstream signaling molecule (TRADD) our findings support a new model of TNFR1 activation in which varying conformational states of the receptor act as a molecular switch in determining receptor function.

    更新日期:2020-01-21
  • Site‐specific rapid deamidation and isomerization in human lens αA‐crystallin in vitro
    Protein Sci. (IF 2.42) Pub Date : 2020-01-16
    Takumi Takata; Seongmin Ha; Tamaki Koide; Noriko Fujii

    Recent studies have suggested that the isomerization/racemization of aspartate residues in proteins increases in aged tissues. One such residue is Asp151 in lens‐specific αA‐crystallin. Although many isomerization/racemization sites have been reported in various proteins, the factors that lead to those modifications in proteins in vivo remain obscure. Therefore, an in vitro system is needed to assess the mechanisms of modifications of Asp under various conditions. Deamidation of Asn to Asp in proteins occurs more rapidly than isomerization/racemization of Asp, although the reaction passes through the same intermediate in both pathways. Here, therefore, we replaced Asp151 in human lens αA‐crystallin with Asn by using site‐directed mutagenesis. The recombinant protein was expressed in Escherichia coli and used to investigate the deamidation/isomerization/racemization of Asn151 after incubation at 50°C for various durations and under different pH. After incubation, the mutant αA‐crystallin was subjected to enzymatic digestion followed by liquid chromatography–MS/MS to evaluate the ratio of modifications in Asn151‐containing peptides. The Asp151Asn αA‐crystallin mutant showed rapid deamidation to Asp with the formation of specific Asp isomers. In particular, deamidation increased greatly under basic conditions. By contrast, subunit–subunit interactions between αA‐crystallin and αB‐crystallin had little effect on the modification of Asn151. Our findings suggest that the Asp151Asn αA‐crystallin mutant represents a good in vitro model protein to assess deamidation, isomerization, and the racemization intermediates. Furthermore, our in vitro results show a different trend from in vivo data, implying the presence of specific factors that induce racemization from L‐Asp to D‐Asp residues in vivo.

    更新日期:2020-01-17
  • Structure of the BRK domain of the SWI/SNF chromatin remodeling complex subunit BRG1 reveals a potential role in protein–protein interactions
    Protein Sci. (IF 2.42) Pub Date : 2020-01-13
    Mark D. Allen; Mark Bycroft; Giovanna Zinzalla

    BRG1/SMARCA4 and its paralog BRM/SMARCA2 are the ATPase subunits of human SWI/SNF chromatin remodeling complexes. These multisubunit assemblies can act as either tumor suppressors or drivers of cancer, and inhibiting both BRG1 and BRM, is emerging as an effective therapeutic strategy in diverse cancers. BRG1 and BRM contain a BRK domain. The function of this domain is unknown, but it is often found in proteins involved in transcription and developmental signaling in higher eukaryotes, in particular in proteins that remodel chromatin. We report the NMR structure of the BRG1 BRK domain. It shows similarity to the glycine‐tyrosine‐phenylalanine (GYF) domain, an established protein–protein interaction module. Computational peptide‐binding‐site analysis of the BRK domain identifies a binding site that coincides with a highly conserved groove on the surface of the protein. This sets the scene for experiments to elucidate the role of this domain, and evaluate the potential of targeting it for cancer therapy.

    更新日期:2020-01-13
  • Structures of glyceraldehyde 3‐phosphate dehydrogenase in Neisseria gonorrhoeae and Chlamydia trachomatis
    Protein Sci. (IF 2.42) Pub Date : 2020-01-12
    Kayleigh F. Barrett; David M. Dranow; Isabelle Phan; Samantha A. Michaels; Shareef Shaheen; Edelmar D. Navaluna; Justin K. Craig; Logan M. Tillery; Ryan Choi; Thomas E. Edwards; Deborah G. Conrady; Jan Abendroth; Peter S. Horanyi; Donald D. Lorimer; Wesley C. Van Voorhis; Zhongsheng Zhang; Lynn K. Barrett; Sandhya Subramanian; Bart Staker; Erkang Fan; Peter Myler; Olusegun O. Soge; Kevin Hybiske; Kayode K. Ojo

    Neisseria gonorrhoeae (Ng) and Chlamydia trachomatis (Ct) are the most commonly reported sexually‐transmitted bacteria worldwide and usually present as co‐infections. Increasing resistance of Ng to currently recommended dual therapy of azithromycin and ceftriaxone presents therapeutic challenges for syndromic management of Ng‐Ct co‐infections. Development of a safe, effective and inexpensive dual therapy for Ng‐Ct co‐infections is an effective strategy for the global control and prevention of these two most prevalent bacterial sexually transmitted infections. Glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH) is a validated drug target with two approved drugs for indications other than antibacterials. Nonetheless, any new drugs targeting GAPDH in Ng and Ct must be specific inhibitors of bacterial GAPDH that do not inhibit human GAPDH, and structural information of Ng and Ct GAPDH will aid in finding such selective inhibitors. Here, we report the X‐ray crystal structures of Ng and Ct GAPDH. Analysis of the structures demonstrates significant differences in amino acid residues in the active sites of human GAPDH from those of the two bacterial enzymes suggesting design of compounds to selectively inhibit Ng and Ct is possible. We also describe an efficient in vitro assay of recombinant GAPDH enzyme activity amenable to high‐throughput drug screening to aid in identifying inhibitory compounds and begin to address selectivity.

    更新日期:2020-01-13
  • Substrate binding to Src: A new perspective on tyrosine kinase substrate recognition from NMR and molecular dynamics
    Protein Sci. (IF 2.42) Pub Date : 2019-11-21
    Mehul K. Joshi; Robert A. Burton; Heng Wu; Andrew M. Lipchik; Barbara P. Craddock; Huaping Mo; Laurie L. Parker; W. Todd Miller; Carol Beth Post

    Most signal transduction pathways in humans are regulated by protein kinases through phosphorylation of their protein substrates. Typical eukaryotic protein kinases are of two major types: those that phosphorylate‐specific sequences containing tyrosine (~90 kinases) and those that phosphorylate either serine or threonine (~395 kinases). The highly conserved catalytic domain of protein kinases comprises a smaller N lobe and a larger C lobe separated by a cleft region lined by the activation loop. Prior studies find that protein tyrosine kinases recognize peptide substrates by binding the polypeptide chain along the C‐lobe on one side of the activation loop, while serine/threonine kinases bind their substrates in the cleft and on the side of the activation loop opposite to that of the tyrosine kinases. Substrate binding structural studies have been limited to four families of the tyrosine kinase group, and did not include Src tyrosine kinases. We examined peptide‐substrate binding to Src using paramagnetic‐relaxation‐enhancement NMR combined with molecular dynamics simulations. The results suggest Src tyrosine kinase can bind substrate positioning residues C‐terminal to the phosphoacceptor residue in an orientation similar to serine/threonine kinases, and unlike other tyrosine kinases. Mutagenesis corroborates this new perspective on tyrosine kinase substrate recognition. Rather than an evolutionary split between tyrosine and serine/threonine kinases, a change in substrate recognition may have occurred within the TK group of the human kinome. Protein tyrosine kinases have long been therapeutic targets, but many marketed drugs have deleterious off‐target effects. More accurate knowledge of substrate interactions of tyrosine kinases has the potential for improving drug selectivity.

    更新日期:2020-01-13
  • Iterative annealing mechanism explains the functions of the GroEL and RNA chaperones
    Protein Sci. (IF 2.42) Pub Date : 2019-12-23
    D. Thirumalai; George H. Lorimer; Changbong Hyeon

    Molecular chaperones are ATP‐consuming machines, which facilitate the folding of proteins and RNA molecules that are kinetically trapped in misfolded states. Unassisted folding occurs by the kinetic partitioning mechanism according to which folding to the native state, with low probability as well as misfolding to one of the many metastable states, with high probability, occur rapidly. GroEL is an all‐purpose stochastic machine that assists misfolded substrate proteins to fold. The RNA chaperones such as CYT‐19, which are ATP‐consuming enzymes, help the folding of ribozymes that get trapped in metastable states for long times. GroEL does not interact with the folded proteins but CYT‐19 disrupts both the folded and misfolded ribozymes. The structures of GroEL and RNA chaperones are strikingly different. Despite these differences, the iterative annealing mechanism (IAM) quantitatively explains all the available experimental data for assisted folding of proteins and ribozymes. Driven by ATP binding and hydrolysis and GroES binding, GroEL undergoes a catalytic cycle during which it samples three allosteric states, T (apo), R (ATP bound), and R″ (ADP bound). Analyses of the experimental data show that the efficiency of the GroEL–GroES machinery and mutants is determined by the resetting rate k R ″ → T, which is largest for the wild‐type (WT) GroEL. Generalized IAM accurately predicts the folding kinetics of Tetrahymena ribozyme and its variants. Chaperones maximize the product of the folding rate and the steady‐state native state fold by driving the substrates out of equilibrium. Neither the absolute yield nor the folding rate is optimized.

    更新日期:2020-01-13
  • Structural and functional analysis of the Hsp70/Hsp40 chaperone system
    Protein Sci. (IF 2.42) Pub Date : 2019-10-07
    Qinglian Liu; Ce Liang; Lei Zhou

    As one of the most abundant and highly conserved molecular chaperones, the 70‐kDa heat shock proteins (Hsp70s) play a key role in maintaining cellular protein homeostasis (proteostasis), one of the most fundamental tasks for every living organism. In this role, Hsp70s are inextricably linked to many human diseases, most notably cancers and neurodegenerative diseases, and are increasingly recognized as important drug targets for developing novel therapeutics for these diseases. Hsp40s are a class of essential and universal partners for Hsp70s in almost all aspects of proteostasis. Thus, Hsp70s and Hsp40s together constitute one of the most important chaperone systems across all kingdoms of life. In recent years, we have witnessed significant progress in understanding the molecular mechanism of this chaperone system through structural and functional analysis. This review will focus on this recent progress, mainly from a structural perspective.

    更新日期:2020-01-13
  • Structural perspectives on HIV‐1 Vif and APOBEC3 restriction factor interactions
    Protein Sci. (IF 2.42) Pub Date : 2019-11-29
    Farshad C. Azimi; Jeffrey E. Lee

    Human immunodeficiency virus (HIV) is a retroviral pathogen that targets human immune cells such as CD4+ T cells, macrophages, and dendritic cells. The human apolipoprotein B mRNA‐ editing catalytic polypeptide 3 (APOBEC3 or A3) cytidine deaminases are a key class of intrinsic restriction factors that inhibit replication of HIV. When HIV‐1 enters the cell, the immune system responds by inducing the activation of the A3 family proteins, which convert cytosines to uracils in single‐stranded DNA replication intermediates, neutralizing the virus. HIV counteracts this intrinsic immune response by encoding a protein termed viral infectivity factor (Vif). Vif targets A3 to an E3 ubiquitin ligase complex for poly‐ubiquitination and proteasomal degradation. Vif is unique in that it can recognize and counteract multiple A3 restriction factor substrates. Structural biology studies have provided significant insights into the overall architectures and functions of Vif and A3 proteins; however, a structure of the Vif‐A3 complex has remained elusive. In this review, we summarize and reanalyze experimental data from recent structural, biochemical, and functional studies to provide key perspectives on the residues involved in Vif‐A3 protein–protein interactions.

    更新日期:2020-01-13
  • Stairway to translocation: AAA+ motor structures reveal the mechanisms of ATP‐dependent substrate translocation
    Protein Sci. (IF 2.42) Pub Date : 2019-10-17
    Stephanie N. Gates; Andreas Martin

    Translocases of the AAA+ (ATPases Associated with various cellular Activities) family are powerful molecular machines that use the mechano‐chemical coupling of ATP hydrolysis and conformational changes to thread DNA or protein substrates through their central channel for many important biological processes. These motors comprise hexameric rings of ATPase subunits, in which highly conserved nucleotide‐binding domains form active‐site pockets near the subunit interfaces and aromatic pore‐loop residues extend into the central channel for substrate binding and mechanical pulling. Over the past 2 years, 41 cryo‐EM structures have been solved for substrate‐bound AAA+ translocases that revealed spiral‐staircase arrangements of pore‐loop residues surrounding substrate polypeptides and indicating a conserved hand‐over‐hand mechanism for translocation. The subunits' vertical positions within the spiral arrangements appear to be correlated with their nucleotide states, progressing from ATP‐bound at the top to ADP or apo states at the bottom. Studies describing multiple conformations for a particular motor illustrate the potential coupling between ATP‐hydrolysis steps and subunit movements to propel the substrate. Experiments with double‐ring, Type II AAA+ motors revealed an offset of hydrolysis steps between the two ATPase domains of individual subunits, and the upper ATPase domains lacking aromatic pore loops frequently form planar rings. This review summarizes the critical advances provided by recent studies to our structural and functional understanding of hexameric AAA+ translocases, as well as the important outstanding questions regarding the underlying mechanisms for coordinated ATP‐hydrolysis and mechano‐chemical coupling.

    更新日期:2020-01-13
  • Structural basis of chemokine and receptor interactions: Key regulators of leukocyte recruitment in inflammatory responses
    Protein Sci. (IF 2.42) Pub Date : 2019-10-24
    Ram Prasad Bhusal; Simon R. Foster; Martin J. Stone

    In response to infection or injury, the body mounts an inflammatory immune response in order to neutralize pathogens and promote tissue repair. The key effector cells for these responses are the leukocytes (white blood cells), which are specifically recruited to the site of injury. However, dysregulation of the inflammatory response, characterized by the excessive migration of leukocytes to the affected tissues, can also lead to chronic inflammatory diseases. Leukocyte recruitment is regulated by inflammatory mediators, including an important family of small secreted chemokines and their corresponding G protein‐coupled receptors expressed in leukocytes. Unsurprisingly, due to their central role in the leukocyte inflammatory response, chemokines and their receptors have been intensely investigated and represent attractive drug targets. Nonetheless, the full therapeutic potential of chemokine receptors has not been realized, largely due to the complexities in the chemokine system. The determination of chemokine–receptor structures in recent years has dramatically shaped our understanding of the molecular mechanisms that underpin chemokine signaling. In this review, we summarize the contemporary structural view of chemokine–receptor recognition, and describe the various binding modes of peptide and small‐molecule ligands to chemokine receptors. We also provide some perspectives on the implications of these data for future research and therapeutic development.

    更新日期:2020-01-13
  • Comprehensive analysis of all evolutionary paths between two divergent PDZ domain specificities
    Protein Sci. (IF 2.42) Pub Date : 2019-11-14
    Joan Teyra; Andreas Ernst; Alex Singer; Frank Sicheri; Sachdev S. Sidhu

    To understand the molecular evolution of functional diversity in protein families, we comprehensively investigated the consequences of all possible mutation combinations separating two peptide‐binding domains with highly divergent specificities. We analyzed the Erbin PDZ domain (Erbin‐PDZ), which exhibits canonical type I specificity, and a synthetic Erbin‐PDZ variant (E‐14) that differs at six positions and exhibits an atypical specificity that closely resembles that of the natural Pdlim4 PDZ domain (Pdlim4‐PDZ). We constructed a panel of 64 PDZ domains covering all possible transitions between Erbin‐PDZ and E‐14 (i.e., the panel contained variants with all possible combinations of either the Erbin‐PDZ or E‐14 sequence at the six differing positions). We assessed the specificity profiles of the 64 PDZ domains using a C‐terminal phage‐displayed peptide library containing all possible genetically encoded heptapeptides. The specificity profiles clustered into six distinct groups, showing that intermediate domains can be nodes for the evolution of divergent functions. Remarkably, three substitutions were sufficient to convert the specificity of Erbin‐PDZ to that of Pdlim4‐PDZ, whereas Pdlim4‐PDZ contains 71 differences relative to Erbin‐PDZ. X‐ray crystallography revealed the structural basis for specificity transition: a single substitution in the center of the binding site, supported by contributions from auxiliary substitutions, altered the main chain conformation of the peptide ligand to resemble that of ligands bound to Pdlim4‐PDZ. Our results show that a very small set of mutations can dramatically alter protein specificity, and these findings support the hypothesis whereby complex protein functions evolve by gene duplication followed by cumulative mutations.

    更新日期:2020-01-13
  • Methyltransferase CheR binds to its chemoreceptor substrates independent of their signaling conformation yet modifies them differentially
    Protein Sci. (IF 2.42) Pub Date : 2019-11-11
    Mingshan Li; Gerald L. Hazelbauer

    Methylation of specific chemoreceptor glutamyl residues by methyltransferase CheR mediates sensory adaptation and gradient sensing in bacterial chemotaxis. Enzyme action is a function of chemoreceptor signaling conformation: kinase‐off receptors are more readily methylated than kinase‐on, a feature central to adaptational and gradient‐sensing mechanisms. Differential enzyme action could reflect differential binding, catalysis or both. We investigated by measuring CheR binding to kinase‐off and kinase‐on forms of Escherichia coli aspartate receptor Tar deleted of its CheR‐tethering, carboxyl terminus pentapeptide. This allowed characterization of the low‐affinity binding of enzyme to the substrate receptor body, otherwise masked by high‐affinity interaction with pentapeptide. We quantified the low‐affinity protein–protein interactions by determining kinetic rate constants of association and dissociation using bio‐layer interferometry and from those values calculating equilibrium constants. Whether Tar signaling conformations were shifted by ligand occupancy or adaptational modification, there was little or no difference between the two signaling conformations in kinetic or equilibrium parameters of enzyme‐receptor binding. Thus, differential methyltransferase action does not reflect differential binding. Instead, the predominant determinants of binding must be common to different signaling conformations. Characterization of the dependence of association rate constants on Deybe length, a measure of the influence of electrostatics, implicated electrostatic interactions as a common binding determinant. Taken together, our observations indicate that differential action of methyltransferase on kinase‐off and kinase‐on chemoreceptors is not the result of differential binding and suggest it reflects differential catalytic propensity. Differential catalysis rather than binding could well be central to other enzymes distinguishing alternative conformations of protein substrates.

    更新日期:2020-01-13
  • Building better enzymes: Molecular basis of improved non‐natural nucleobase incorporation by an evolved DNA polymerase
    Protein Sci. (IF 2.42) Pub Date : 2019-11-14
    Zahra Ouaray; Isha Singh; Millie M. Georgiadis; Nigel G. J. Richards

    Obtaining semisynthetic microorganisms that exploit the information density of “hachimoji” DNA requires access to engineered DNA polymerases. A KlenTaq variant has been reported that incorporates the “hachimoji” P:Z nucleobase pair with a similar efficiency to that seen for Watson–Crick nucleobase incorporation by the wild type (WT) KlenTaq DNA polymerase. The variant polymerase differs from WT KlenTaq by only four amino acid substitutions, none of which are located within the active site. We now report molecular dynamics (MD) simulations on a series of binary complexes aimed at elucidating the contributions of the four amino acid substitutions to altered catalytic activity. These simulations suggest that WT KlenTaq is insufficiently flexible to be able to bind AEGIS DNA correctly, leading to the loss of key protein/DNA interactions needed to position the binary complex for efficient incorporation of the “hachimoji” Z nucleobase. In addition, we test literature hypotheses about the functional roles of each amino acid substitution and provide a molecular description of how individual residue changes contribute to the improved activity of the KlenTaq variant. We demonstrate that MD simulations have a clear role to play in systematically screening DNA polymerase variants capable of incorporating different types of nonnatural nucleobases thereby limiting the number that need to be characterized by experiment. It is now possible to build DNA molecules containing nonnatural nucleobase pairs in addition to A:T and G:C. Exploiting this development in synthetic biology requires engineered DNA polymerases that can replicate nonnatural nucleobase pairs. Computational studies on a DNA polymerase variant reveal how amino acid substitutions outside of the active site yield an enzyme that replicates nonnatural nucleobase pairs with high efficiency. This work will facilitate efforts to obtain bacteria possessing an expanded genetic alphabet.

    更新日期:2020-01-13
  • GeTFEP: A general transfer free energy profile of transmembrane proteins
    Protein Sci. (IF 2.42) Pub Date : 2019-11-11
    Wei Tian; Hammad Naveed; Meishan Lin; Jie Liang

    Free energy of transferring amino acid side‐chains from aqueous environment into lipid bilayers, known as transfer free energy (TFE), provides important information on the thermodynamic stability of membrane proteins. In this study, we derived a TFE profile named General Transfer Free Energy Profile (GeTFEP) based on computation of the TFEs of 58 β‐barrel membrane proteins (βMPs). The GeTFEP agrees well with experimentally measured and computationally derived TFEs. Analysis based on the GeTFEP shows that residues in different regions of the transmembrane (TM) segments of βMPs have different roles during the membrane insertion process. Results further reveal the importance of the sequence pattern of TM strands in stabilizing βMPs in the membrane environment. In addition, we show that GeTFEP can be used to predict the positioning and the orientation of βMPs in the membrane. We also show that GeTFEP can be used to identify structurally or functionally important amino acid residue sites of βMPs. Furthermore, the TM segments of α‐helical membrane proteins can be accurately predicted with GeTFEP, suggesting that the GeTFEP is of general applicability in studying membrane protein.

    更新日期:2020-01-13
  • Effects of histatin 5 modifications on antifungal activity and kinetics of proteolysis
    Protein Sci. (IF 2.42) Pub Date : 2019-11-20
    Svetlana P. Ikonomova; Parisa Moghaddam‐Taaheri; Yan Wang; Mary T. Doolin; Kimberly M. Stroka; Bernhard Hube; Amy J. Karlsson

    Histatin 5 (Hst‐5) is an antimicrobial peptide with strong antifungal activity against Candida albicans, an opportunistic pathogen that is a common cause of oral thrush. The peptide is natively secreted by human salivary glands and shows promise as an alternative therapeutic against infections caused by C. albicans. However, Hst‐5 can be cleaved and inactivated by a family of secreted aspartic proteases (Saps) produced by C. albicans. Single‐residue substitutions can significantly affect the proteolytic resistance of Hst‐5 to Saps and its antifungal activity; the K17R substitution increases resistance to proteolysis, while the K11R substitution enhances antifungal activity. In this work, we showed that the positive effects of these two single‐residue modifications can be combined in a single peptide, K11R–K17R, with improved proteolytic resistance and antifungal activity. We also investigated the effect of additional single‐residue substitutions, with a focus on the effect of addition or removal of negatively charged residues, and found Sap‐dependent effects on degradation. Both single‐ and double‐substitutions affected the kinetics of proteolytic degradation of the intact peptide and of the fragments formed during degradation. Our results demonstrate the importance of considering proteolytic stability and not just antimicrobial activity when designing peptides for potential therapeutic applications.

    更新日期:2020-01-13
  • Identification of a PAI‐1‐binding site within an intrinsically disordered region of vitronectin
    Protein Sci. (IF 2.42) Pub Date : 2019-11-20
    Yuzhuo Chu; Joel C. Bucci; Cynthia B. Peterson

    The serine protease inhibitor, plasminogen activator inhibitor Type‐1 (PAI‐1) is a metastable protein that undergoes an unusual transition to an inactive conformation with a short half‐life of only 1–2 hr. Circulating PAI‐1 is bound to a cofactor vitronectin, which stabilizes PAI‐1 by slowing this latency conversion. A well‐characterized PAI‐1‐binding site on vitronectin is located within the somatomedin B (SMB) domain, corresponding to the first 44 residues of the protein. Another PAI‐1 recognition site has been identified with an engineered form of vitronectin lacking the SMB domain, yet retaining PAI‐1 binding capacity (Schar, Blouse, Minor, Peterson. J Biol Chem. 2008;283:28487–28496). This additional binding site is hypothesized to lie within an intrinsically disordered domain (IDD) of vitronectin. To localize the putative binding site, we constructed a truncated form of vitronectin containing 71 amino acids from the N‐terminus, including the SMB domain and an additional 24 amino acids from the IDD region. This portion of the IDD is rich in acidic amino acids, which are hypothesized to be complementary to several basic residues identified within an extensive vitronectin‐binding site mapped on PAI‐1 (Schar, Jensen, Christensen, Blouse, Andreasen, Peterson. J Biol Chem. 2008;283:10297–10309). Steady‐state and stopped‐flow fluorescence measurements demonstrate that the truncated form of vitronectin exhibits the same rapid biphasic association as full‐length vitronectin and that the IDD hosts the elusive second PAI‐1 binding site that lies external to the SMB domain of vitronectin.

    更新日期:2020-01-13
  • Identification of FAM181A and FAM181B as new interactors with the TEAD transcription factors
    Protein Sci. (IF 2.42) Pub Date : 2019-11-20
    Fedir Bokhovchuk; Yannick Mesrouze; Clara Delaunay; Typhaine Martin; Frédéric Villard; Marco Meyerhofer; Patrizia Fontana; Catherine Zimmermann; Dirk Erdmann; Pascal Furet; Clemens Scheufler; Tobias Schmelzle; Patrick Chène

    The Hippo pathway is a key signaling pathway in the control of organ size and development. The most distal elements of this pathway, the TEAD transcription factors, are regulated by several proteins, such as YAP (Yes‐associated protein), TAZ (transcriptional co‐activator with PDZ‐binding motif) and VGLL1‐4 (Vestigial‐like members 1–4). In this article, combining structural data and motif searches in protein databases, we identify two new TEAD interactors: FAM181A and FAM181B. Our structural data show that they bind to TEAD via an Ω‐loop as YAP/TAZ do, but only FAM181B possesses the LxxLF motif (x any amino acid) found in YAP/TAZ. The affinity of different FAM181A/B fragments for TEAD is in the low micromolar range and full‐length FAM181A/B proteins interact with TEAD in cells. These findings, together with a recent report showing that FAM181A/B proteins have a role in nervous system development, suggest a potential new involvement of the TEAD transcription factors in the development of this tissue.

    更新日期:2020-01-13
  • Oligomerization of RIG‐I and MDA5 2CARD domains
    Protein Sci. (IF 2.42) Pub Date : 2019-11-20
    Cassie M. Zerbe; David J. Mouser; James L. Cole

    The innate immune system is the first line of defense against invading pathogens. The retinoic acid‐inducible gene I (RIG‐I) like receptors (RLRs), RIG‐I and melanoma differentiation‐associated protein 5 (MDA5), are critical for host recognition of viral RNAs. These receptors contain a pair of N‐terminal tandem caspase activation and recruitment domains (2CARD), an SF2 helicase core domain, and a C‐terminal regulatory domain. Upon RLR activation, 2CARD associates with the CARD domain of MAVS, leading to the oligomerization of MAVS, downstream signaling and interferon induction. Unanchored K63‐linked polyubiquitin chains (polyUb) interacts with the 2CARD domain, and in the case of RIG‐I, induce tetramer formation. However, the nature of the MDA5 2CARD signaling complex is not known. We have used sedimentation velocity analytical ultracentrifugation to compare MDA5 2CARD and RIG‐I 2CARD binding to polyUb and to characterize the assembly of MDA5 2CARD oligomers in the absence of polyUb. Multi‐signal sedimentation velocity analysis indicates that Ub4 binds to RIG‐I 2CARD with a 3:4 stoichiometry and cooperatively induces formation of an RIG‐I 2CARD tetramer. In contrast, Ub4 and Ub7 interact with MDA5 2CARD weakly and form complexes with 1:1 and 2:1 stoichiometries but do not induce 2CARD oligomerization. In the absence of polyUb, MDA5 2CARD self‐associates to forms large oligomers in a concentration‐dependent manner. Thus, RIG‐I and MDA5 2CARD assembly processes are distinct. MDA5 2CARD concentration‐dependent self‐association, rather than polyUb binding, drives oligomerization and MDA5 2CARD forms oligomers larger than tetramer. We propose a mechanism where MDA5 2CARD oligomers, rather than a stable tetramer, function to nucleate MAVS polymerization.

    更新日期:2020-01-13
  • β‐amyloid model core peptides: Effects of hydrophobes and disulfides
    Protein Sci. (IF 2.42) Pub Date : 2019-11-25
    Laura M. L. Hawk; Jay M. Pittman; Patrick C. Moore; Atul K. Srivastava; Jonathan Zerweck; Joshua T. B. Williams; Andrew J. Hawk; Joseph R. Sachleben; Stephen C. Meredith

    The mechanism by which a disordered peptide nucleates and forms amyloid is incompletely understood. A central domain of β‐amyloid (Aβ21–30) has been proposed to have intrinsic structural propensities that guide the limited formation of structure in the process of fibrillization. In order to test this hypothesis, we examine several internal fragments of Aβ, and variants of these either cyclized or with an N‐terminal Cys. While Aβ21–30 and variants were always monomeric and unstructured (circular dichroism (CD) and nuclear magnetic resonance spectroscopy (NMRS)), we found that the addition of flanking hydrophobic residues in Aβ16–34 led to formation of typical amyloid fibrils. NMR showed no long‐range nuclear overhauser effect (nOes) in Aβ21–30, Aβ16–34, or their variants, however. Serial 1H‐15N‐heteronuclear single quantum coherence spectroscopy, 1H‐1H nuclear overhauser effect spectroscopy, and 1H‐1H total correlational spectroscopy spectra were used to follow aggregation of Aβ16–34 and Cys‐Aβ16–34 at a site‐specific level. The addition of an N‐terminal Cys residue (in Cys‐Aβ16–34) increased the rate of fibrillization which was attributable to disulfide bond formation. We propose a scheme comparing the aggregation pathways for Aβ16–34 and Cys‐Aβ16–34, according to which Cys‐Aβ16–34 dimerizes, which accelerates fibril formation. In this context, cysteine residues form a focal point that guides fibrillization, a role which, in native peptides, can be assumed by heterogeneous nucleators of aggregation.

    更新日期:2020-01-13
  • Molecular dynamics simulations of an engineered T4 lysozyme exclude helix to sheet transition, and provide insights into long distance, intra‐protein switchable motion
    Protein Sci. (IF 2.42) Pub Date : 2019-11-21
    Laurence Biggers; Hadeer Elhabashy; Edward Ackad; Mohammad S. Yousef

    An engineered variant of T4 lysozyme serves as a model for studying induced remote conformational changes in a full protein context. The design involves a duplicated surface helix, flanked by two loops, that switches between two different conformations spanning about 20 Å. Molecular dynamics simulations of the engineered protein, up to 1 μs, rule out α‐helix to β‐sheet transitions within the duplicated helix as suggested by others. These simulations highlight how the use of different force fields can lead to radical differences in the structure of the protein. In addition, Markov state modeling and transition path theory were employed to map a 6.6 μs simulation for possible early intermediate states and to provide insights into the onset of the switching motion. The putative intermediates involve the folding of one helical turn in the C‐terminal loop through energy driven, sequential rearrangement of nearby salt bridges around the key residue Arg63. These results provide a first step towards understanding the energetics and dynamics of a rather complicated intra‐protein motion.

    更新日期:2020-01-13
  • Differential effects of serine side chain interactions in amyloid formation by islet amyloid polypeptide
    Protein Sci. (IF 2.42) Pub Date : 2020-01-11
    Rehana Akter; Junjie Zou; Daniel P. Raleigh

    Islet amyloid polypeptide (IAPP), a 37 residue polypeptide, is the main protein component of islet amyloid deposits produced in the pancreas in Type 2 diabetes. Human IAPP contains five serine residues at positions 19, 20, 28, 29, and 34. Models of the IAPP amyloid fibril indicate a structure composed of two closely aligned columns of IAPP monomers with each monomer contributing to two intermolecular β‐strands. Ser 19 and Ser 20 are in the partially ordered β‐turn region, which links the two strands, whereas Ser 28, Ser 29, and Ser 34 are in the core region of the amyloid fibril. Ser 29 is involved in contacts between the two columns of monomers and is the part of the steric zipper interface. We undertook a study of individual serine substitutions with the hydrophobic isostere 2‐aminobutyric acid (2‐Abu) to examine the site‐specific role of serine side chains in IAPP amyloid formation. All five variants formed amyloid. The Ser 19 to 2‐Abu mutant accelerates amyloid formation by a factor of 3 to 4, while the Ser 29 to 2‐Abu mutation modestly slows the rate of amyloid formation. 2‐Abu replacements at the other sites had even smaller effects. The data demonstrate that the cross‐column interactions made by residue 29 are not essential for amyloid formation and also show that cross‐strand networks of hydrogen‐bonded Ser side chains, so called Ser‐ladders, are not required for IAPP amyloid formation. The effect of the Ser 19 to 2‐Abu mutant suggests that residues in this region are important for amyloid formation by IAPP.

    更新日期:2020-01-13
  • Protein kinases phosphorylate long disordered regions in intrinsically disordered proteins
    Protein Sci. (IF 2.42) Pub Date : 2019-11-28
    Ryotaro Koike; Mutsuki Amano; Kozo Kaibuchi; Motonori Ota

    Phosphorylation is a major post‐translational modification that plays a central role in signaling pathways. Protein kinases phosphorylate substrates (phosphoproteins) by adding phosphate at Ser/Thr or Tyr residues (phosphosites). A large amount of data identifying and describing phosphosites in phosphoproteins has been reported but the specificity of phosphorylation is not fully resolved. In this report, data of kinase‐substrate pairs identified by the Kinase‐Interacting Substrate Screening (KISS) method were used to analyze phosphosites in intrinsically disordered regions (IDRs) of intrinsically disordered proteins. We compared phosphorylated and nonphosphorylated IDRs and found that the phosphorylated IDRs were significantly longer than nonphosphorylated IDRs. The phosphorylated IDR is often the longest IDR (71%) in a phosphoprotein when only a single phosphosite exists in the IDR, and when the phosphoprotein has multiple phosphosites in an IDR(s), the phosphosites are primarily localized in a single IDR (78%) and this IDR is usually the longest one (81%). We constructed a stochastic model of phosphorylation to estimate the effect of IDR length. The model that accounted for IDR length produced more realistic results when compared with a model that excluded the IDR length. We propose that the IDR length is a significant determinant for locating kinase phosphorylation sites in phosphoproteins.

    更新日期:2020-01-13
  • Hydrophobic residues of melittin mediate its binding to αA−crystallin
    Protein Sci. (IF 2.42) Pub Date : 2019-12-18
    Lisa M. Ramirez; Alexander Shekhtman; Jayanti Pande

    The molecular chaperone αA‐crystallin, mainly localized in the human ocular lens, is believed to protect the lens from opacification and cataract, by suppressing the aggregation of the other lens proteins. The present study provides structural and thermodynamic insights into the ability of human αA‐crystallin (HAA) to bind to its partially unfolded clients in the lens, using a small peptide, melittin from bee venom, as a model client. We characterized the thermodynamic parameters of the binding process between melittin and HAA through isothermal titration calorimetry (ITC), and found the binding to be endothermic and entropy‐driven. We identified the amino acids in melittin important for binding to HAA by saturation‐transfer difference (STD) nuclear magnetic resonance (NMR) experiments, and analysis of NMR line broadening upon titration of melittin with HAA. Our results suggest that hydrophobic residues Ile17 and Ile20 on the C‐terminal region of melittin are in close contact with HAA in the melittin‐HAA complex. Information obtained from NMR experiments was used to generate structural models of the melittin‐HAA complex by molecular docking with high‐ambiguity driven docking (HADDOCK). Structural models of the melittin‐HAA complex reveal important principles underlying the interaction of HAA with its clients.

    更新日期:2020-01-13
  • Type I fatty acid synthase trapped in the octanoyl‐bound state
    Protein Sci. (IF 2.42) Pub Date : 2020-01-11
    Alexander Rittner; Karthik S. Paithankar; Aaron Himmler; Martin Grininger

    De novo fatty acid biosynthesis in humans is accomplished by a multidomain protein, the Type I fatty acid synthase (FAS). Although ubiquitously expressed in all tissues, fatty acid synthesis is not essential in normal healthy cells due to sufficient supply with fatty acids by the diet. However, FAS is overexpressed in cancer cells and correlates with tumor malignancy, which makes FAS an attractive selective therapeutic target in tumorigenesis. Herein, we present a crystal structure of the condensing part of murine FAS, highly homologous to human FAS, with octanoyl moieties covalently bound to the transferase (MAT—malonyl‐/acetyltransferase) and the condensation (KS—β‐ketoacyl synthase) domain. The MAT domain binds the octanoyl moiety in a novel (unique) conformation, which reflects the pronounced conformational dynamics of the substrate‐binding site responsible for the MAT substrate promiscuity. In contrast, the KS binding pocket just subtly adapts to the octanoyl moiety upon substrate binding. Besides the rigid domain structure, we found a positive cooperative effect in the substrate binding of the KS domain by a comprehensive enzyme kinetic study. These structural and mechanistic findings contribute significantly to our understanding of the mode of action of FAS and may guide future rational inhibitor designs.

    更新日期:2020-01-13
  • Context and number of noncanonical repeat variable diresidues impede the design of TALE proteins with improved DNA targeting
    Protein Sci. (IF 2.42) Pub Date : 2019-12-24
    James T. Anderson; Julia M. Rogers; Luis A. Barrera; Martha L. Bulyk

    Transcription activator‐like effector (TALE) proteins have been used extensively for targeted binding of fusion proteins to loci of interest in (epi)genome engineering. Such approaches typically utilize four canonical TALE repeat variable diresidue (RVD) types, corresponding to the identities of two key amino acids, to target each nucleotide. Alternate RVDs with improved specificity are desired. Here, we focused on seven noncanonical RVDs that have been suggested to have improved specificity for their target nucleotides. We used custom protein binding microarrays to characterize the DNA‐binding activity of 65 TALEs containing these alternate or corresponding canonical RVDs at multiple positions to ~5,000 unique DNA sequences per protein. We found that none of the noncanonical thymine‐targeting RVDs displayed stronger preference for thymine than did the canonical RVD. Of the noncanonical RVDs with putatively improved specificity for guanine, only EN and NH showed greater discrimination of guanine over adenine. This improved specificity, however, comes at a cost: more substitutions of a noncanonical RVD for a canonical RVD generally decreased the protein's DNA‐binding activity. Our results highlight the need to investigate RVD‐nucleotide specificities in multiple protein contexts and suggest that a balance between canonical and noncanonical RVDs is needed to build TALEs with improved specificity.

    更新日期:2020-01-13
  • PhoH2 proteins couple RNA helicase and RNAse activities
    Protein Sci. (IF 2.42) Pub Date : 2020-01-07
    Emma S. V. Andrews; Vickery L. Arcus

    PhoH2 proteins are found in a very diverse range of microorganisms that span bacteria and archaea. These proteins are composed of two domains: an N‐terminal PIN‐domain fused with a C‐terminal PhoH domain. Collectively this fusion functions as an RNA helicase and ribonuclease. In other genomic contexts, PINdomains and PhoHdomains are separate but adjacent suggesting association to achieve similar function. Exclusively among the mycobacteria, PhoH2 proteins are encoded in the genome with an upstream gene, phoAT, which is thought to play the role of an antitoxin (in place of the traditional VapB antitoxin that lies upstream of the 47 other PINdomains in the mycobacterial genome). This review examines PhoH2 proteins as a whole and describes the bioinformatics, biochemical, structural, and biological properties of the two domains that make up PhoH2: PIN and PhoH. We review the transcriptional regulators of phoH2 from two mycobacterial species and speculate on the function of PhoH2 proteins in the context of a Type II toxin–antitoxin system which are thought to play a role in the stress response in bacteria.

    更新日期:2020-01-07
  • Hexameric structure of the ATPase motor subunit of magnesium chelatase in chlorophyll biosynthesis
    Protein Sci. (IF 2.42) Pub Date : 2020-01-07
    Yong‐Shan Gao; Yan‐Li Wang; Xiao Wang; Lin Liu

    Magnesium chelatase (MgCh) is a heterotrimeric enzyme complex, composed of two AAA+ family subunits that can assembly into a double ring structure and a large catalytic subunit. The small AAA+ subunit has ATPase activity and can self‐oligomerize into a ring structure, while the other AAA+ subunit lacks independent ATPase activity. Previous structural studies of the ATPase motor subunit of MgCh from a bacteriochlorophyll‐synthesizing bacterium have identified a unique ATPase clade, but the model of oligomeric assembly is unclear. Here we present the hexameric structure of the MgCh ATPase motor subunit from the chlorophyll‐synthesizing cyanobacterium Synechocystis sp. PCC 6803. This structure reveals details of how the hexameric ring is assembled, and thus provides a basis for further studying the heterotrimeric complex.

    更新日期:2020-01-07
  • X‐ray crystallographic structure of BshB, the zinc‐dependent deacetylase involved in bacillithiol biosynthesis
    Protein Sci. (IF 2.42) Pub Date : 2019-12-31
    Robert L. Woodward; Michaela M. Castleman; Chelsea E. Meloche; Mary E. Karpen; Clare G. Carlson; William H. Yobi; Jacqueline C. Jepsen; Benjamin W. Lewis; Brooke N. Zarnosky; Paul D. Cook

    Many gram‐positive bacteria produce bacillithiol to aid in the maintenance of redox homeostasis and degradation of toxic compounds, including the antibiotic fosfomycin. Bacillithiol is produced via a three‐enzyme pathway that includes the action of the zinc‐dependent deacetylase BshB. Previous studies identified conserved aspartate and histidine residues within the active site that are involved in metal binding and catalysis, but the enzymatic mechanism is not fully understood. Here we report two X‐ray crystallographic structures of BshB from Bacillus subtilis that provide insight into the BshB catalytic mechanism.

    更新日期:2019-12-31
  • Regulation of bifunctional proteins in cells: Lessons from the phospholipase Cβ/G protein pathway
    Protein Sci. (IF 2.42) Pub Date : 2019-12-31
    Lela Jackson; Androniqi Qifti; Katherine M. Pearce; Suzanne Scarlata

    Some proteins can serve multiple functions depending on different cellular conditions. An example of a bifunctional protein is inositide‐specific mammalian phospholipase Cβ (PLCβ). PLCβ is activated by G proteins in response to hormones and neurotransmitters to increase intracellular calcium. Recently, alternate cellular function(s) of PLCβ have become uncovered. However, the conditions that allow these different functions to be operative are unclear. Like many mammalian proteins, PLCβ has a conserved catalytic core along with several regulatory domains. These domains modulate the intensity and duration of calcium signals in response to external sensory information, and allow this enzyme to inhibit protein translation in a noncatalytic manner. In this review, we first describe PLCβ's cellular functions and regulation of the switching between these functions, and then discuss the thermodynamic considerations that offer insight into how cells manage multiple and competitive associations allowing them to rapidly shift between functional states.

    更新日期:2019-12-31
  • Structural characterization of aminoglycoside 4′‐O‐adenylyltransferase ANT(4′)‐IIb from Pseudomonas aeruginosa
    Protein Sci. (IF 2.42) Pub Date : 2019-12-31
    Cameron Semper; Peter Stogios; Djalal Meziane‐Cherif; Elena Evdokimova; Patrice Courvalin; Alexei Savchenko

    Aminoglycosides were one of the first classes of broad‐spectrum antibacterial drugs clinically used to effectively combat infections. The rise of resistance to these drugs, mediated by enzymatic modification, has since compromised their utility as a treatment option, prompting intensive research into the molecular function of resistance enzymes. Here, we report the crystal structure of aminoglycoside nucleotidyltransferase ANT(4′)‐IIb in apo and tobramycin‐bound forms at a resolution of 1.6 å and 2.15 å, respectively. ANT(4′)‐IIb was discovered in the opportunistic pathogen Pseudomonas aeruginosa and conferred resistance to amikacin and tobramycin. Analysis of the ANT(4′)‐IIb structures revealed a two‐domain organization featuring a mixed β‐sheet and an α‐helical bundle. ANT(4′)‐IIb monomers form a dimer required for its enzymatic activity, as coordination of the aminoglycoside substrate relies on residues contributed by both monomers. Despite harbouring appreciable primary sequence diversity compared to previously characterized homologues, the ANT(4′)‐IIb structure demonstrates a surprising level of structural conservation highlighting the high plasticity of this general protein fold. Site‐directed mutagenesis of active site residues and kinetic analysis provides support for a catalytic mechanism similar to those of other nucleotidyltransferases. Using the molecular insights provided into this ANT(4′)‐IIb‐represented enzymatic group, we provide a hypothesis for the potential evolutionary origin of these aminoglycoside resistance determinants.

    更新日期:2019-12-31
  • A python script to design site‐directed mutagenesis primers
    Protein Sci. (IF 2.42) Pub Date : 2019-12-27
    Chuyun Bi; Xiaofang Huang; Dan Tang; Yuanyuan Shi; Lixiang Zhou; Yunzhuo Hu; Xuanyang Chen; Shiqian Qi; Shiqiang Lin

    Primer design is essential to conduct whole plasmid site‐directed mutagenesis for protein study. Traditionally, primers of mutagenesis are designed manually that is time‐consuming and fallible. Here, we present a Python script for searching primers by presetting parameters of nucleotide composition and percentage of guanine‐cytosine (GC content). The running results showed that the script is able to search primers with mutations of target residue automatically. This script may facilitate primer design for whole plasmid site‐directed mutagenesis and aid protein mutant construction.

    更新日期:2019-12-27
  • Design and structure of two new protein cages illustrate successes and ongoing challenges in protein engineering
    Protein Sci. (IF 2.42) Pub Date : 2019-12-26
    Kevin A. Cannon; Rachel U. Park; Scott E. Boyken; Una Nattermann; Sue Yi; David Baker; Neil P. King; Todd O. Yeates

    In recent years, new protein engineering methods have produced more than a dozen symmetric, self‐assembling protein cages whose structures have been validated to match their design models with near‐atomic accuracy. However, many protein cage designs that are tested in the lab do not form the desired assembly, and improving the success rate of design has been a point of recent emphasis. Here we present two protein structures solved by X‐ray crystallography of designed protein oligomers that form two‐component cages with tetrahedral symmetry. To improve on the past tendency toward poorly soluble protein, we used a computational protocol that favors the formation of hydrogen‐bonding networks over exclusively hydrophobic interactions to stabilize the designed protein–protein interfaces. Preliminary characterization showed highly soluble expression, and solution studies indicated successful cage formation by both designed proteins. For one of the designs, a crystal structure confirmed at high resolution that the intended tetrahedral cage was formed, though several flipped amino acid side chain rotamers resulted in an interface that deviates from the precise hydrogen‐bonding pattern that was intended. A structure of the other designed cage showed that, under the conditions where crystals were obtained, a noncage structure was formed wherein a porous 3D protein network in space group I213 is generated by an off‐target twofold homomeric interface. These results illustrate some of the ongoing challenges of developing computational methods for polar interface design, and add two potentially valuable new entries to the growing list of engineered protein materials for downstream applications.

    更新日期:2019-12-27
  • Developments, applications, and prospects of cryo‐electron microscopy
    Protein Sci. (IF 2.42) Pub Date : 2019-12-26
    Xu Benjin; Liu Ling

    Cryo‐electron microscopy (cryo‐EM) is a structural biological method that is used to determine the 3D structures of biomacromolecules. After years of development, cryo‐EM has made great achievements, which has led to a revolution in structural biology. In this article, the principle, characteristics, history, current situation, workflow, and common problems of cryo‐EM are systematically reviewed. In addition, the new development direction of cryo‐EM—cryo‐electron tomography (cryo‐ET), is discussed in detail. Also, cryo‐EM is prospected from the following aspects: the structural analysis of small proteins, the improvement of resolution and efficiency, and the relationship between cryo‐EM and drug development. This review is dedicated to giving readers a comprehensive understanding of the development and application of cryo‐EM, and to bringing them new insights.

    更新日期:2019-12-27
  • Solution Structure of the Nucleotide hydrolase BlsM: Implication of its Substrate Specificity
    Protein Sci. (IF 2.42) Pub Date : 2019-12-26
    Minhee Kang; Kiran Doddapaneni; Samantha Sarni; Zach Heppner; Vicki Wysocki; Zhengrong Wu

    Biosynthesis of the peptidyl nucleoside antifungal agent blasticidin S in Streptomyces griseochromogenes requires the hydrolytic function of a nucleotide hydrolase, BlsM, to excise the free cytosine from the 5’‐monophosphate cytosine nucleotide. In addition to its hydrolytic activity, interestingly, BlsM has also been shown to possess a novel cytidine deaminase activity, converting cytidine and deoxycytidine to uridine and deoxyuridine. To gain insight into the substrate specificity of BlsM and the mechanism by which it performs these dual function, the solution structure of BlsM was determined by multi‐dimensional nuclear magnetic resonance (NMR) approaches. BlsM displays a nucleoside deoxyribosyltransferase‐like dimeric topology, with each monomer consisting of a five‐stranded β‐sheet that is sandwiched by five α‐helixes. Compared with the purine nucleotide hydrolase RCL, each monomer of BlsM has a smaller active site pocket, enclosed by a group of conserved hydrophobic residues from both monomers. The smaller size of active site is consistent with its substrate specificity for a pyrimidine, whereas a much more open active site, as in RCL might be required to accommodate a larger purine ring. In addition, BlsM confers its substrate specificity for a ribosyl‐nucleotide through a key residue, Phe19. When mutated to a tyrosine, F19Y reverses its substrate preference. While significantly impaired in its hydrolytic capability, F19Y exhibited a pronounced deaminase activity on CMP, presumably due to an altered substrate orientation as a result of a steric clash between the 2’‐hydroxyl of CMP and the ζ‐OH group of F19Y. Finally, Glu105 appears to be critical for the dual function of BlsM.

    更新日期:2019-12-27
  • Structure of the full length Serratia marcescens acetyltransferase AAC(3)‐Ia in complex with coenzyme A
    Protein Sci. (IF 2.42) Pub Date : 2019-12-26
    Georgy Popov; Elena Evdokimova; Peter J. Stogios; Alexei Savchenko

    Acyl‐coenzyme A‐dependent N‐acetyltransferases (AACs) catalyse the modification of aminoglycosides rendering the bacteria carrying such enzymes resistant to this class of antibiotics. Here we present the crystal structure of AAC(3)‐Ia enzyme from Serratia marcescens in complex with coenzyme A determined to 1.8 å resolution. This enzyme served as an architype for the AAC enzymes targeting the amino group at position 3 of aminoglycoside main aminocyclitol ring. The structure of this enzyme has been previously determined only in truncated form and was interpreted as distinct from subsequently characterised AACs. The reason for the unusual arrangement of secondary structure elements of AAC(3)‐Ia was not further investigated. By determining the full length structure of AAC(3)‐Ia we establish that this enzyme adopts the canonical AAC fold conserved across this family and it does not undergo through significant rearrangement of secondary structure elements upon ligand binding as was proposed previously. In addition, our results suggest that the C‐terminal tail in AAC(3)‐Ia monomer forms intramolecular hydrogen bonds that contributes to formation of stable dimer, representing the predominant oligomeric state for this enzyme.

    更新日期:2019-12-27
  • Glutaminyl‐tRNA Synthetase from Pseudomonas aeruginosa: Characterization, structure, and development as a screening platform
    Protein Sci. (IF 2.42) Pub Date : 2019-12-24
    Yaritza Escamilla; Casey A. Hughes; Jan Abendroth; David M. Dranow; Samantha Balboa; Frank B. Dean; James M. Bullard

    Pseudomonas aeruginosa has a high potential for developing resistance to multiple antibiotics. The gene (glnS) encoding glutaminyl‐tRNA synthetase (GlnRS) from P. aeruginosa was cloned and the resulting protein characterized. GlnRS was kinetically evaluated and the KM and kcatobs, governing interactions with tRNA, were 1.0 μM and 0.15 s−1, respectively. The crystal structure of the α2 form of P. aeruginosa GlnRS was solved to 1.9 Å resolution. The amino acid sequence and structure of P. aeruginosa GlnRS were analyzed and compared to that of GlnRS from Escherichia coli. Amino acids that interact with ATP, glutamine, and tRNA are well conserved and structure overlays indicate that both GlnRS proteins conform to a similar three‐dimensional structure. GlnRS was developed into a screening platform using scintillation proximity assay technology and used to screen ~2,000 chemical compounds. Three inhibitory compounds were identified and analyzed for enzymatic inhibition as well as minimum inhibitory concentrations against clinically relevant bacterial strains. Two of the compounds, BM02E04 and BM04H03, were selected for further studies. These compounds displayed broad‐spectrum antibacterial activity and exhibited moderate inhibitory activity against mutant efflux deficient strains of P. aeruginosa and E. coli. Growth of wild‐type strains was unaffected, indicating that efflux was likely responsible for the lack of sensitivity. The global mode of action was determined using time‐kill kinetics. BM04H03 did not inhibit the growth of human cell cultures at any concentration and BM02E04 only inhibit cultures at the highest concentration tested (400 μg/ml). In conclusion, GlnRS from P. aeruginosa is shown to have a structure similar to that of E. coli GlnRS and two natural product compounds were identified as inhibitors of P. aeruginosa GlnRS with the potential for utility as lead candidates in antibacterial drug development in a time of increased antibiotic resistance.

    更新日期:2019-12-25
  • Structural and biochemical analysis of the metallo‐β‐lactamase L1 from emerging pathogen Stenotrophomonas maltophilia revealed the subtle but distinct di‐metal scaffold for catalytic activity
    Protein Sci. (IF 2.42) Pub Date : 2019-12-24
    Youngchang Kim; Natalia Maltseva; Mateusz Wilamowski; Christine Tesar; Michael Endres; Andrzej Joachimiak

    Emergence of Enterobacteriaceae harboring metallo‐β‐lactamases (MBL) has raised global threats due to their broad antibiotic resistance profiles and the lack of effective inhibitors against them. We have been studied one of the emerging environmental MBL, the L1 from Stenotrophomonas maltophilia K279a. We determined several crystal structures of L1 complexes with three different classes of β‐lactam antibiotics (penicillin G, moxalactam, meropenem, and imipenem), with the inhibitor captopril and different metal ions (Zn+2, Cd+2, and Cu+2). All hydrolyzed antibiotics and the inhibitor were found binding to two Zn+2 ions mainly through the opened lactam ring and some hydrophobic interactions with the binding pocket atoms. Without a metal ion, the active site is very similarly maintained as that of the native form with two Zn+2 ions, however, the protein does not bind the substrate moxalactam. When two Zn+2 ions were replaced with other metal ions, the same di‐metal scaffold was maintained and the added moxalactam was found hydrolyzed in the active site. Differential scanning fluorimetry and isothermal titration calorimetry were used to study thermodynamic properties of L1 MBL compared with New Deli Metallo‐β‐lactamase‐1 (NDM‐1). Both enzymes are significantly stabilized by Zn+2 and other divalent metals but showed different dependency. These studies also suggest that moxalactam and its hydrolyzed form may bind and dissociate with different kinetic modes with or without Zn+2 for each of L1 and NDM‐1. Our analysis implicates metal ions, in forming a distinct di‐metal scaffold, which is central to the enzyme stability, promiscuous substrate binding and versatile catalytic activity.

    更新日期:2019-12-25
  • Crystal structure of a Vip3B family insecticidal protein reveals a new fold and a unique tetrameric assembly
    Protein Sci. (IF 2.42) Pub Date : 2019-12-23
    Meiying Zheng; Artem G. Evdokimov; Farhad Moshiri; Casey Lowder; Jeff Haas

    Vegetatively expressed insecticidal proteins (VIPs) produced by Bacillus thuringiensis fall into several classes of which the third, VIP3, is known for their activity against several key Lepidopteran pests of commercial broad acre crops and because their mode of action does not overlap with that of crystalline insecticidal proteins. The details of the VIP3 structure and mode of action have remained obscure for the quarter century that has passed since their discovery. In the present article, we report the first crystal structure of a full‐length VIP3 protein. Crystallization of this target required multiple rounds of construct optimization and screening—over 200 individual sequences were expressed and tested. This protein adopts a novel global fold that combines domains with hitherto unreported topology and containing elements seemingly borrowed from carbohydrate‐binding domains, lectins, or from other insecticidal proteins.

    更新日期:2019-12-23
  • The antimicrobial peptide database provides a platform for decoding the design principles of naturally occurring antimicrobial peptides
    Protein Sci. (IF 2.42) Pub Date : 2019-08-10
    Guangshun Wang

    This article is written for the 2020 tool issue of Protein Science. It briefly introduces the widely used antimicrobial peptide database, initially online in 2003. After a description of the main features of each database version and some recent additions, the focus is on the peptide design parameters for each of the four unified classes of natural antimicrobial peptides (AMPs). The amino acid signature in AMPs varies substantially, leading to a variety of structures for functional and mechanistic diversity. Also, Nature is a master of combinatorial chemistry by deploying different amino acids onto the same structural scaffold to tune peptide functions. In addition, the single‐domain AMPs may be posttranslationally modified, self‐assembled, or combined with other AMPs for function. Elucidation of the design principles of natural AMPs will facilitate future development of novel molecules for various applications.

    更新日期:2019-12-21
  • SimpleDSFviewer: A tool to analyze and view differential scanning fluorimetry data for characterizing protein thermal stability and interactions
    Protein Sci. (IF 2.42) Pub Date : 2019-08-19
    Changye Sun; Yong Li; Edwin A. Yates; David G. Fernig

    Differential scanning fluorimetry (DSF) is a widely used thermal shift assay for measuring protein stability and protein–ligand interactions that are simple, cheap, and amenable to high throughput. However, data analysis remains a challenge, requiring improved methods. Here, the program SimpleDSFviewer, a user‐friendly interface, is described to help the researchers who apply DSF technique in their studies. SimpleDSFviewer integrates melting curve (MC) normalization, smoothing, and melting temperature (Tm) analysis and directly previews analyzed data, providing an efficient analysis tool for DSF. SimpleDSFviewer is developed in Matlab, and it is freely available for all users to use in Matlab workspace or with Matlab Runtime. It is easy to use and an efficient tool for researchers to preview and analyze their data in a very short time.

    更新日期:2019-12-21
  • KEGG Mapper for inferring cellular functions from protein sequences
    Protein Sci. (IF 2.42) Pub Date : 2019-08-29
    Minoru Kanehisa; Yoko Sato

    KEGG is a reference knowledge base for biological interpretation of large‐scale molecular datasets, such as genome and metagenome sequences. It accumulates experimental knowledge about high‐level functions of the cell and the organism represented in terms of KEGG molecular networks, including KEGG pathway maps, BRITE hierarchies, and KEGG modules. By the process called KEGG mapping, a set of protein coding genes in the genome, for example, can be converted to KEGG molecular networks enabling interpretation of cellular functions and other high‐level features. Here we report a new version of KEGG Mapper, a suite of KEGG mapping tools available at the KEGG website (https://www.kegg.jp/ or https://www.genome.jp/kegg/), together with the KOALA family tools for automatic assignment of KO (KEGG Orthology) identifiers used in the mapping.

    更新日期:2019-12-21
  • Collection of antimicrobial peptides database and its derivatives: Applications and beyond
    Protein Sci. (IF 2.42) Pub Date : 2019-09-30
    Faiza Hanif Waghu; Susan Idicula‐Thomas

    Collection of antimicrobial peptides (CAMP), CAMPSign, and ClassAMP are open‐access resources that have been developed to enhance research on antimicrobial peptides (AMPs). Comprehensive information on AMPs and machine learning‐based predictive models are made available for users through these resources. As of date, CAMPR3 has 10,247 sequences, 757 structures, and 114 family‐specific signatures of AMPs along with associated tools for AMP sequence and structure analysis. CAMPSign uses family‐specific sequence conservation, in the form of patterns and hidden Markov models for identification of AMPs. ClassAMP can be used to classify AMPs as antibacterial, antifungal, or antiviral based on sequence information. Here we describe CAMP and its derivatives and illustrate, with a few examples, the contribution of these online resources to the advancement of our current understanding of AMPs.

    更新日期:2019-12-21
  • Integration of the Rosetta suite with the python software stack via reproducible packaging and core programming interfaces for distributed simulation
    Protein Sci. (IF 2.42) Pub Date : 2019-12-02
    Alexander S. Ford; Brian D. Weitzner; Christopher D. Bahl

    The Rosetta software suite for macromolecular modeling is a powerful computational toolbox for protein design, structure prediction, and protein structure analysis. The development of novel Rosetta‐based scientific tools requires two orthogonal skill sets: deep domain‐specific expertise in protein biochemistry and technical expertise in development, deployment, and analysis of molecular simulations. Furthermore, the computational demands of molecular simulation necessitate large scale cluster‐based or distributed solutions for nearly all scientifically relevant tasks. To reduce the technical barriers to entry for new development, we integrated Rosetta with modern, widely adopted computational infrastructure. This allows simplified deployment in large‐scale cluster and cloud computing environments, and effective reuse of common libraries for simulation execution and data analysis. To achieve this, we integrated Rosetta with the Conda package manager; this simplifies installation into existing computational environments and packaging as docker images for cloud deployment. Then, we developed programming interfaces to integrate Rosetta with the PyData stack for analysis and distributed computing, including the popular tools Jupyter, Pandas, and Dask. We demonstrate the utility of these components by generating a library of a thousand de novo disulfide‐rich miniproteins in a hybrid simulation that included cluster‐based design and interactive notebook‐based analyses. Our new tools enable users, who would otherwise not have access to the necessary computational infrastructure, to perform state‐of‐the‐art molecular simulation and design with Rosetta.

    更新日期:2019-12-21
  • RCSB Protein Data Bank: Enabling biomedical research and drug discovery
    Protein Sci. (IF 2.42) Pub Date : 2019-11-29
    David S. Goodsell; Christine Zardecki; Luigi Di Costanzo; Jose M. Duarte; Brian P. Hudson; Irina Persikova; Joan Segura; Chenghua Shao; Maria Voigt; John D. Westbrook; Jasmine Y. Young; Stephen K. Burley

    Analyses of publicly available structural data reveal interesting insights into the impact of the three‐dimensional (3D) structures of protein targets important for discovery of new drugs (e.g., G‐protein‐coupled receptors, voltage‐gated ion channels, ligand‐gated ion channels, transporters, and E3 ubiquitin ligases). The Protein Data Bank (PDB) archive currently holds > 155,000 atomic‐level 3D structures of biomolecules experimentally determined using crystallography, nuclear magnetic resonance spectroscopy, and electron microscopy. The PDB was established in 1971 as the first open‐access, digital‐data resource in biology, and is now managed by the Worldwide PDB partnership (wwPDB; wwPDB.org). US PDB operations are the responsibility of the Research Collaboratory for Structural Bioinformatics PDB (RCSB PDB). The RCSB PDB serves millions of RCSB.org users worldwide by delivering PDB data integrated with ∼40 external biodata resources, providing rich structural views of fundamental biology, biomedicine, and energy sciences. Recently published work showed that the PDB archival holdings facilitated discovery of ∼90% of the 210 new drugs approved by the US Food and Drug Administration 2010–2016. We review user‐driven development of RCSB PDB services, examine growth of the PDB archive in terms of size and complexity, and present examples and opportunities for structure‐guided drug discovery for challenging targets (e.g., integral membrane proteins).

    更新日期:2019-12-21
  • SASBDB: Towards an automatically curated and validated repository for biological scattering data
    Protein Sci. (IF 2.42) Pub Date : 2019-10-11
    Alexey G. Kikhney; Clemente R. Borges; Dmitry S. Molodenskiy; Cy M. Jeffries; Dmitri I. Svergun

    Small‐angle scattering (SAS) of X‐rays and neutrons is a fundamental tool to study the nanostructural properties, and in particular, biological macromolecules in solution. In structural biology, SAS recently transformed from a specialization into a general technique leading to a dramatic increase in the number of publications reporting structural models. The growing amount of data recorded and published has led to an urgent need for a global SAS repository that includes both primary data and models. In response to this, a small‐angle scattering biological data bank (SASBDB) was designed in 2014 and is available for public access at www.sasbdb.org. SASBDB is a comprehensive, free and searchable repository of SAS experimental data and models deposited together with the relevant experimental conditions, sample details and instrument characteristics. SASBDB is rapidly growing, and presently has over 1,000 entries containing more than 1,600 models. We describe here the overall organization and procedures of SASBDB paying most attention to user‐relevant information during submission. Perspectives of further developments, in particular, with OneDep system of the Protein Data Bank, and also widening of SASBDB including new types of data/models are discussed.

    更新日期:2019-12-21
  • Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations
    Protein Sci. (IF 2.42) Pub Date : 2019-12-04
    Ji Young Lee; James M. Krieger; Hongchun Li; Ivet Bahar

    Recent years have seen progress in druggability simulations, that is, molecular dynamics simulations of target proteins in solutions containing drug‐like probe molecules to characterize their drug‐binding abilities, if any. An important consecutive step is to analyze the trajectories to construct pharmacophore models (PMs) to use for virtual screening of libraries of small molecules. While considerable success has been observed in this type of computer‐aided drug discovery, a systematic tool encompassing multiple steps from druggability simulations to pharmacophore modeling, to identifying hits by virtual screening of libraries of compounds, has been lacking. We address this need here by developing a new tool, Pharmmaker, building on the DruGUI module of our ProDy application programming interface. Pharmmaker is composed of a suite of steps: (Step 1) identification of high affinity residues for each probe molecule type; (Step 2) selecting high affinity residues and hot spots in the vicinity of sites identified by DruGUI; (Step 3) ranking of the interactions between high affinity residues and specific probes; (Step 4) obtaining probe binding poses and corresponding protein conformations by collecting top‐ranked snapshots; and (Step 5) using those snapshots for constructing PMs. The PMs are then used as filters for identifying hits in structure‐based virtual screening. Pharmmaker, accessible online at http://prody.csb.pitt.edu/pharmmaker, can be used in conjunction with other tools available in ProDy.

    更新日期:2019-12-21
  • Cryo‐EM map interpretation and protein model‐building using iterative map segmentation
    Protein Sci. (IF 2.42) Pub Date : 2019-10-24
    Thomas C. Terwilliger; Paul D. Adams; Pavel V. Afonine; Oleg V. Sobolev

    A procedure for building protein chains into maps produced by single‐particle electron cryo‐microscopy (cryo‐EM) is described. The procedure is similar to the way an experienced structural biologist might analyze a map, focusing first on secondary structure elements such as helices and sheets, then varying the contour level to identify connections between these elements. Since the high density in a map typically follows the main‐chain of the protein, the main‐chain connection between secondary structure elements can often be identified as the unbranched path between them with the highest minimum value along the path. This chain‐tracing procedure is then combined with finding side‐chain positions based on the presence of density extending away from the main path of the chain, allowing generation of a Cα model. The Cα model is converted to an all‐atom model and is refined against the map. We show that this procedure is as effective as other existing methods for interpretation of cryo‐EM maps and that it is considerably faster and produces models with fewer chain breaks than our previous methods that were based on approaches developed for crystallographic maps.

    更新日期:2019-12-21
  • A three‐dimensional potential of mean force to improve backbone and sidechain hydrogen bond geometry in Xplor‐NIH protein structure determination
    Protein Sci. (IF 2.42) Pub Date : 2019-10-27
    Charles D. Schwieters; Guillermo A. Bermejo; G. Marius Clore

    We introduce a new hydrogen bonding potential of mean force generated from high‐quality crystal structures for use in Xplor‐NIH structure calculations. This term applies to hydrogen bonds involving both backbone and sidechain atoms. When used in structure refinement calculations of 10 example protein systems with experimental distance, dihedral and residual dipolar coupling restraints, we demonstrate that the new term has superior performance to the previously developed hydrogen bonding potential of mean force used in Xplor‐NIH.

    更新日期:2019-12-21
  • VarSite: Disease variants and protein structure
    Protein Sci. (IF 2.42) Pub Date : 2019-10-27
    Roman A. Laskowski; James D. Stephenson; Ian Sillitoe; Christine A. Orengo; Janet M. Thornton

    VarSite is a web server mapping known disease‐associated variants from UniProt and ClinVar, together with natural variants from gnomAD, onto protein 3D structures in the Protein Data Bank. The analyses are primarily image‐based and provide both an overview for each human protein, as well as a report for any specific variant of interest. The information can be useful in assessing whether a given variant might be pathogenic or benign. The structural annotations for each position in the protein include protein secondary structure, interactions with ligand, metal, DNA/RNA, or other protein, and various measures of a given variant's possible impact on the protein's function. The 3D locations of the disease‐associated variants can be viewed interactively via the 3dmol.js JavaScript viewer, as well as in RasMol and PyMOL. Users can search for specific variants, or sets of variants, by providing the DNA coordinates of the base change(s) of interest. Additionally, various agglomerative analyses are given, such as the mapping of disease and natural variants onto specific Pfam or CATH domains. The server is freely accessible to all at: https://www.ebi.ac.uk/thornton-srv/databases/VarSite.

    更新日期:2019-12-21
  • Molstack: A platform for interactive presentations of electron density and cryo‐EM maps and their interpretations
    Protein Sci. (IF 2.42) Pub Date : 2019-10-25
    Przemyslaw J. Porebski; Grzegorz Bokota; Barat S. Venkataramany; Wladek Minor

    In the Special Issue on Tools for Protein Science in 2018, we presented Molstack: a concept of a cloud‐based platform for sharing electron density maps and their interpretations. Molstack is a web platform that allows the interactive visualization of density maps through the simultaneous presentation of multiple datasets and models in a way that allows for easy pairwise comparison. We anticipated that the users of this conceptually simple platform would find many different uses for their projects, and we were not mistaken. We have observed researchers use Molstack to present experimental evidence for their models in the form of electron density maps, omit maps, and anomalous difference density maps. Users also employed Molstack to present alternative interpretations of densities, including rerefinements and speculative interpretations. While we anticipated these types of projects to be the main use cases, we were pleased to see Molstack used to display superpositions of different models, as a tool for story‐driven presentations, and for collaboration as well. Here, we present developments in the platform that were driven by user feedback, highlight several cases that used Molstack to enhance the publication, and discuss possible directions for the platform.

    更新日期:2019-12-21
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