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Natural compound plumbagin based inhibition of hIAPP revealed by Markov state models based on MD data along with experimental validations Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-03-18 Faisal Nabi, Owais Ahmad, Adeeba Khan, Md Nadir Hassan, Malik Hisamuddin, Sadia Malik, Ali Chaari, Rizwan Hasan Khan
Human islet amyloid polypeptide (amylin or hIAPP) is a 37 residue hormone co-secreted with insulin from β cells of the pancreas. In patients suffering from type-2 diabetes, amylin self-assembles into amyloid fibrils, ultimately leading to the death of the pancreatic cells. However, a research gap exists in preventing and treating such amyloidosis. Plumbagin, a natural compound, has previously been
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Computational analyses of drug resistance mutations in katG and emb complexes in Mycobacterium tuberculosis Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-03-14 Aadam Basrai, Tom L. Blundell, Arun Prasad Pandurangan
The number of antibiotic resistant pathogens is increasing rapidly, and with this comes a substantial socioeconomic cost that threatens much of the world. To alleviate this problem, we must use antibiotics in a more responsible and informed way, further our understanding of the molecular basis of drug resistance, and design new antibiotics. Here, we focus on a key drug‐resistant pathogen, Mycobacterium
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Efficient and accurate binding free energy calculation of Aβ9–40 protofilament propagation Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-03-14 Christina V. Frost, Nadine Schwierz, Martin Zacharias
Self‐assembled aggregation of peptides and proteins into regular amyloid fibrils is associated with several neurodegenerative diseases. In case of Alzheimer's disease proteolytic cleavage products of the amyloid precursor protein form pathological amyloid‐beta fibrils in a nucleation and propagation phase. The molecular details and thermodynamic driving forces of amyloid formation are not well understood
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Expression and functional analysis of a recombinant aquaporin Z from Antarctic Pseudomonas sp. AMS3 Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-03-13 S. Balakrishnan, R. N. Z. R. A. Rahman, N. D. M. Noor, W. Latip, M. S. M. Ali
Aquaporin (AQP) is a water channel protein from the family of transmembrane proteins which facilitates the movement of water across the cell membrane. It is ubiquitous in nature, however the understanding of the water transport mechanism, especially for AQPs in microbes adapted to low temperatures, remains limited. AQP also has been recognized for its ability to be used for water filtration, but knowledge
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Post‐translational modification sites are present in hydrophilic cavities of alpha‐synuclein, tau, FUS, and TDP‐43 fibrils: A molecular dynamics study Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-03-09 Noah Nathan Kochen, Darren Seaney, Vivek Vasandani, Marguerite Murray, Anthony R. Braun, Jonathan N. Sachs
Hydration plays a crucial role in the refolding of intrinsically disordered proteins into amyloid fibrils; however, the specific interactions between water and protein that may contribute to this process are still unknown. In our previous studies of alpha‐synuclein (aSyn), we have shown that waters confined in fibril cavities are stabilizing features of this pathological fold; and that amino acids
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Allosteric pathways of SARS and SARS‐CoV‐2 spike protein identified by neural relational inference Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-03-09 Yao Hu, Mingwei Li, Qian Wang
The receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) spike protein must undergo a crucial conformational transition to invade human cells. It is intriguing that this transition is accompanied by a synchronized movement of the entire spike protein. Therefore, it is possible to design allosteric regulators targeting non‐RBD but hindering the conformational
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Issue Information ‐ Table of Content Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-03-07
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AbDPP: Target‐oriented antibody design with pretraining and prior biological structure knowledge Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-03-05 Chenglei Yu, Xiangtian Lin, Yuxuan Cheng, Jiahong Xu, Hao Wang, Yuyao Yan, Yanting Huang, Lanxuan Liu, Wei Zhao, Qin Zhao, John Wang, Lei Zhang
Antibodies represent a crucial class of complex protein therapeutics and are essential in the treatment of a wide range of human diseases. Traditional antibody discovery methods, such as hybridoma and phage display technologies, suffer from limitations including inefficiency and a restricted exploration of the immense space of potential antibodies. To overcome these limitations, we propose a novel
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Pyroglutamylation modulates electronic properties and the conformational ensemble of the amyloid β‐peptide Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-03-04 Darcy S. Davidson, Justin A. Lemkul
Alzheimer's disease (AD) is a neurodegenerative disorder that is characterized by the formation of extracellular amyloid‐β (Aβ) plaques. The underlying cause of AD is unknown, however, post‐translational modifications (PTMs) of Aβ have been found in AD patients and are thought to play a role in protein aggregation. One such PTM is pyroglutamylation, which can occur at two sites in Aβ, Glu3 and Glu11
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HSV‐1 ICP0 dimer domain adopts a novel β‐barrel fold Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-02-19 Erick McCloskey, Maithri Kashipathy, Anne Cooper, Philip Gao, David K. Johnson, Kevin P. Battaile, Scott Lovell, David J. Davido
Infected cell protein 0 (ICP0) is an immediate‐early regulatory protein of herpes simplex virus 1 (HSV‐1) that possesses E3 ubiquitin ligase activity. ICP0 transactivates viral genes, in part, through its C‐terminal dimer domain (residues 555–767). Deletion of this dimer domain results in reduced viral gene expression, lytic infection, and reactivation from latency. Since ICP0's dimer domain is associated
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Ternary complexes of isopentenyl phosphate kinase from Thermococcus paralvinellae reveal molecular determinants of non-natural substrate specificity Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-02-09 Bryce P. Johnson, Prashant S. Mandal, Sara M. Brown, Leonard M. Thomas, Shanteri Singh
Isopentenyl phosphate kinases (IPKs) have recently garnered attention for their central role in biocatalytic “isoprenol pathways,” which seek to reduce the synthesis of the isoprenoid precursors to two enzymatic steps. Furthermore, the natural promiscuity of IPKs toward non-natural alkyl-monophosphates (alkyl-Ps) as substrates has hinted at the isoprenol pathways' potential to access novel isoprenoids
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Application of AlphaFold models in evaluating ligandable cysteines across E3 ligases Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-02-09 Patrick Koldenhof, Martijn P. Bemelmans, Brahma Ghosh, Kelly L. Damm-Ganamet, Herman W. T. van Vlijmen, Vineet Pande
Proteolysis Targeting Chimeras (PROTACs) are an emerging therapeutic modality and chemical biology tools for Targeted Protein Degradation (TPD). PROTACs contain a ligand targeting the protein of interest, a ligand recruiting an E3 ligase and a linker connecting these two ligands. There are over 600 E3 ligases known so far, but only a handful have been exploited for TPD applications. A key reason for
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Computational evidences of a misfolding event in an aggregation-prone light chain preceding the formation of the non-native pathogenic dimer Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-02-05 Fausta Desantis, Mattia Miotto, Edoardo Milanetti, Giancarlo Ruocco, Lorenzo Di Rienzo
Antibody light chain amyloidosis is a disorder in which protein aggregates, mainly composed of immunoglobulin light chains, deposit in diverse tissues impairing the correct functioning of organs. Interestingly, due to the high susceptibility of antibodies to mutations, AL amyloidosis appears to be strongly patient-specific. Indeed, every patient will display their own mutations that will make the proteins
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III. Geometrical framework for thinking about globular proteins: Turns in proteins Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-01-30 Tatjana Škrbić, Achille Giacometti, Trinh X. Hoang, Amos Maritan, Jayanth R. Banavar
We have shown recently that the notion of poking pairwise interactions along a chain provides a unifying framework for understanding the formation of both secondary and the tertiary protein structure based on symmetry and geometry. α-helices and β-sheets are found to be special geometries that have systematic poking contacts in a repetitive manner with the contacts being local along the α-helix and
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Substrate selectivity and unique sequence signatures in SWEET/semiSWEET homologs of four taxonomic groups: Sequence analysis and phylogenetic studies Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-01-19 Ankita Gupta, Ramasubbu Sankararamakrishnan
The recently discovered SWEET (Sugar Will Eventually be Exported Transporter) proteins are involved in the selective transport of monosaccharides and disaccharides. The prokaryotic counterparts, semiSWEETs, form dimers with each monomer forming a triple-helix transmembrane bundle (THB). The longer eukaryotic SWEETs have seven transmembrane helices with two THBs and a linker helix. Structures of semiSWEETs/SWEETs
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AlphaFold2‐guided description of CoBaHMA, a novel family of bacterial domains within the heavy‐metal‐associated superfamily Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-01-23 Geoffroy Gaschignard, Maxime Millet, Apolline Bruley, Karim Benzerara, Manuela Dezi, Feriel Skouri‐Panet, Elodie Duprat, Isabelle Callebaut
AbstractThree‐dimensional (3D) structure information, now available at the proteome scale, may facilitate the detection of remote evolutionary relationships in protein superfamilies. Here, we illustrate this with the identification of a novel family of protein domains related to the ferredoxin‐like superfold, by combining (i) transitive sequence similarity searches, (ii) clustering approaches, and
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Crystal structure of GTP‐dependent dephospho‐coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-01-18 Akiko Kita, Yuna Ishida, Takahiro Shimosaka, Yuta Michimori, Kira Makarova, Eugene Koonin, Haruyuki Atomi, Kunio Miki
AbstractThe biosynthesis pathways of coenzyme A (CoA) in most archaea involve several unique enzymes including dephospho‐CoA kinase (DPCK) that converts dephospho‐CoA to CoA in the final step of CoA biosynthesis in all domains of life. The archaeal DPCK is unrelated to the analogous bacterial and eukaryotic enzymes and shows no significant sequence similarity to any proteins with known structures.
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Critical micellar concentration determination of pure phospholipids and lipid‐raft and their mixtures with cholesterol Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-01-18 Sofia Serravalle, Martina Pisano, Michele F. M. Sciacca, Nancy Salamone, Luciano Sicali, Giuseppe Mazzara, Luca Costa, Carmelo La Rosa
AbstractPhospholipids in biological membranes establish a chemical equilibrium between free phospholipids in the aqueous phase (CMC) and self‐assembled phospholipids in vesicles, keeping the CMC constant. The CMC is different for each phospholipid, depends on the amount of cholesterol, and, according to the lipid‐chaperone hypothesis, controls the interaction between free phospholipids and amyloidogenic
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Random, de novo, and conserved proteins: How structure and disorder predictors perform differently Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-01-16 Lasse Middendorf, Lars A. Eicholt
AbstractUnderstanding the emergence and structural characteristics of de novo and random proteins is crucial for unraveling protein evolution and designing novel enzymes. However, experimental determination of their structures remains challenging. Recent advancements in protein structure prediction, particularly with AlphaFold2 (AF2), have expanded our knowledge of protein structures, but their applicability
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Transient excited states of the metamorphic protein Mad2 and their implications for function Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-01-15 Shefali Jain, Ashok Sekhar
AbstractThe spindle checkpoint complex is a key surveillance mechanism in cell division that prevents premature separation of sister chromatids. Mad2 is an integral component of this spindle checkpoint complex that recognizes cognate substrates such as Mad1 and Cdc20 in its closed (C‐Mad2) conformation by fastening a “seatbelt” around short peptide regions that bind to the substrate recognition site
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A monomeric structure of human TMEM63A protein Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-01-13 Xuening Wu, Tiantian Shang, Xinyi Lü, Deyi Luo, Dongxue Yang
OSCA/TMEM63 is a newly identified family of mechanically activated (MA) ion channels in plants and animals, respectively, which convert physical forces into electrical signals or trigger intracellular cascades and are essential for eukaryotic physiology. OSCAs and related TMEM16s and transmembrane channel-like (TMC) proteins form homodimers with two pores. However, the molecular architecture of the
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Structural and thermodynamic properties of conserved water molecules in Mpro native: A combined approach by MD simulation and Grid Inhomogeneous Solvation Theory Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-01-11 Hridoy R. Bairagya, Alvea Tasneem, Debapriyo Sarmadhikari
The new viral strains of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) are continuously rising, becoming more virulent, and transmissible. Therefore, the development of new antiviral drugs is essential. Due to its significant role in the viral life cycle of SARS-CoV-2, the main protease (Mpro) enzyme is a leading target for antiviral drug design. The Mpro monomer consists of domain DI
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E. James Milner-White (1945–2023) Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-01-10 David P. Leader
This is a short appreciation of the contributions made by E. James Milner-White to the field of protein structure, in particular his description of small hydrogen-bonded motifs.
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Dissecting the geometric and hydrophobic constraints of stapled peptides Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-01-09 Jianguo Li, Yaw Sing Tan, Chandra S Verma
Stapled peptides are a promising class of molecules with potential as highly specific probes of protein–protein interactions and as therapeutics. Hydrocarbon stapling affects the peptide properties through the interplay of two factors: enhancing the overall hydrophobicity and constraining the conformational flexibility. By constructing a series of virtual peptides, we study the role of each factor
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Globin phylogeny, evolution and function, the newest update Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-01-09 Claudio David Schuster, Franco Salvatore, Luc Moens, Marcelo Adrián Martí
Our globin census update allows us to refine our vision of globin origin, evolution, and structure to function relationship in the context of the currently accepted tree of life. The modern globin domain originates as a single domain, three-over-three α-helical folded structure before the diversification of the kingdoms of life (Bacteria, Archaea, Eukarya). Together with the diversification of prokaryotes
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Mechanistic study of the transmission pattern of the SARS-CoV-2 omicron variant Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-01-05 Ke An, Xianzhi Yang, Mengqi Luo, Junfang Yan, Peiyi Xu, Honghui Zhang, Yuqing Li, Song Wu, Arieh Warshel, Chen Bai
The omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) characterized by 30 mutations in its spike protein, has rapidly spread worldwide since November 2021, significantly exacerbating the ongoing COVID-19 pandemic. In order to investigate the relationship between these mutations and the variant's high transmissibility, we conducted a systematic analysis of the mutational
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A conserved but structurally divergent loop in acyl protein thioesterase 1 regulates its catalytic activity, ligand binding, and folded stability Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-01-05 William Trey Harris, Isabelle Altieri, Isabella Gieck, R. Jeremy Johnson
Human acyl protein thioesterases (APTs) catalyze the depalmitoylation of S-acylated proteins attached to the plasma membrane, facilitating reversible cycles of membrane anchoring and detachment. We previously showed that a bacterial APT homologue, FTT258 from the gram-negative pathogen Francisella tularensis, exists in equilibrium between a closed and open state based on the structural dynamics of
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Issue Information ‐ Table of Content Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2024-01-08
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Sequence-dependent and -independent information in a combined random energy model for protein folding and coding Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-12-29 Antônio F. Pereira de Araújo
Random energy models (REMs) provide a simple description of the energy landscapes that guide protein folding and evolution. The requirement of a large energy gap between the native structure and unfolded conformations, considered necessary for cooperative, protein-like, folding behavior, indicates that proteins differ markedly from random heteropolymers. It has been suggested, therefore, that natural
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Synergy and anti-cooperativity in allostery: Molecular dynamics study of WT and oncogenic KRAS-RGL1 Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-12-28 Aysima Hacisuleyman, Burak Erman
This study focuses on investigating the effects of an oncogenic mutation (G12V) on the stability and interactions within the KRAS-RGL1 protein complex. The KRAS-RGL1 complex is of particular interest due to its relevance to KRAS-associated cancers and the potential for developing targeted drugs against the KRAS system. The stability of the complex and the allosteric effects of specific residues are
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Structural flexibility and heterogeneity of recombinant human glial fibrillary acidic protein (GFAP) Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-12-27 Dea Gogishvili, Eva Illes-Toth, Matthew J. Harris, Christopher Hopley, Charlotte E. Teunissen, Sanne Abeln
Glial fibrillary acidic protein (GFAP) is a promising biomarker for brain and spinal cord disorders. Recent studies have highlighted the differences in the reliability of GFAP measurements in different biological matrices. The reason for these discrepancies is poorly understood as our knowledge of the protein's 3-dimensional conformation, proteoforms, and aggregation remains limited. Here, we investigate
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Initiation factor 3 bound to the 30S ribosomal subunit in an initial step of translation Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-12-26 Adwaith B. Uday, Rishi Kumar Mishra, Tanweer Hussain
Bacterial ribosomes require three initiation factors IF1, IF2, and IF3 during the initial steps of translation. These IFs ensure correct base pairing of the initiator tRNA anticodon with the start codon in the mRNA located at the P-site of the 30S ribosomal subunit. IF3 is one of the first IFs to bind to the 30S and plays a crucial role in the selection of the correct start codon and codon: anticodon
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Proteomic analysis and protein structure prediction of Shigella phage Sfk20 based on a comparative study using structure prediction approaches Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-12-25 Bani Mallick, Aninda Dutta, Payel Mondal, Moumita Dutta
Bacteriophages are the natural predators of bacteria and are available abundantly everywhere in nature. Lytic phages can specifically infect their bacterial host (through attachment to the receptor) and use their host replication machinery to replicate rapidly, a feature that enables them to kill a disease-causing bacteria. Hence, phage attachment to the host bacteria is the first important step of
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The role of lysine acetylation in the function of mitochondrial ribosomal protein L12 Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-12-25 Katelynn V. Paluch, Karlie R. Platz, Emma J. Rudisel, Ryan R. Erdmann, Taylor R. Laurin, Kristin E. Dittenhafer-Reed
Mitochondria play a central role in energy production and cellular metabolism. Mitochondria contain their own small genome (mitochondrial DNA, mtDNA) that carries the genetic instructions for proteins required for ATP synthesis. The mitochondrial proteome, including the mitochondrial transcriptional machinery, is subject to post-translational modifications (PTMs), including acetylation and phosphorylation
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Retraction: Citius, Altius, Fortius. J. Lange, G. Vriend. Proteins: Structure, Function, and Bioinformatics. 2020. https://doi.org/10.1002/prot.12345 Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-12-18
The above article, published online on 12 June 2020 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the authors, the journal's Editor-in-Chief Dr. Nikolay Dokholyan, and John Wiley & Sons, Inc. The above article is a humorous editorial contribution surrounding a specialized topic, and was not intended for full online publication as part of the journal's scholarly
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Issue Information ‐ Table of Content Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-12-15
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Predicting the functional state of protein kinases using interpretable graph neural networks from sequence and structural data Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-12-11 Ashwin Ravichandran, Juan C. Araque, John W. Lawson
Protein kinases are central to cellular activities and are actively pursued as drug targets for several conditions including cancer and autoimmune diseases. Despite the availability of a large structural database for kinases, methodologies to elucidate the structure–function relationship of these proteins (without manual intervention) are lacking. Such techniques are essential in structural biology
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An intrinsic network of polar interactions is responsible for binding of UL49.5 C-degron by the CRL2KLHDC3 ubiquitin ligase Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-12-08 Magdalena J. Ślusarz, Andrea D. Lipińska
Bovine herpesvirus type 1 (BoHV-1) is a pathogen of cattle responsible for infectious bovine rhinotracheitis. The BoHV-1 UL49.5 is a transmembrane protein that binds to the transporter associated with antigen processing (TAP) and downregulates cell surface expression of the antigenic peptide complexes with the major histocompatibility complex class I (MHC-I). KLHDC3 is a kelch domain-containing protein
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Transmembrane proteins—Different anchoring systems Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-12-07 Irena Roterman, Katarzyna Stapor, Leszek Konieczny
Transmembrane proteins are active in amphipathic environments. To stabilize the protein in such surrounding the exposure of hydrophobic residues on the protein surface is required. Transmembrane proteins are responsible for the transport of various molecules. Therefore, they often represent structures in the form of channels. This analysis focused on the stability and local flexibility of transmembrane
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Comparison of structural networks across homologous proteins Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-12-07 Vasam Manjveekar Prabantu, Vasundhara Gadiyaram, Saraswathi Vishveshwara, Narayanaswamy Srinivasan
Protein sequence determines its structure and function. The indirect relationship between protein function and structure lies deep-rooted in the structural topology that has evolved into performing optimal function. The evolution of structure and its interconnectivity has been conventionally studied by comparing the root means square deviation between protein structures at the backbone level. Two factors
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Prediction of interactions between cell surface proteins by machine learning Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-12-05 Zhaoqian Su, Brian Griffin, Scott Emmons, Yinghao Wu
Cells detect changes in their external environments or communicate with each other through proteins on their surfaces. These cell surface proteins form a complicated network of interactions in order to fulfill their functions. The interactions between cell surface proteins are highly dynamic and, thus, challenging to detect using traditional experimental techniques. Here, we tackle this challenge using
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Structural implications of amyloidogenic rare variants Ser282Leu and Gln356Arg identified in h-BRCA1 Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-12-01 Neha Mishra, Suchita Dubey, Anchala Kumari, Mudassar Ali Khan, Ekaterina S. Kuligina, Elena V. Preobrazhenskaya, Alexandr A. Romanko, Lumbini R. Yadav, Rajiv Sarin, Evgeny N. Imyanitov, Ashok K. Varma
Preliminary studies have shown BRCA1 (170–1600) residues to be intrinsically disordered with unknown structural details. However, thousands of clinically reported variants have been identified in this central region of BRCA1. Therefore, we aimed to characterize h-BRCA1(260–553) to assess the structural basis for pathogenicity of two rare missense variants Ser282Leu, Gln356Arg identified from the Indian
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The N-terminal intrinsically disordered region of Ncb5or docks with the cytochrome b5 core to form a helical motif that is of ancient origin Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-12-01 David R. Benson, Bin Deng, Maithri M. Kashipathy, Scott Lovell, Kevin P. Battaile, Anne Cooper, Philip Gao, Aron W. Fenton, Hao Zhu
NADH cytochrome b5 oxidoreductase (Ncb5or) is a cytosolic ferric reductase implicated in diabetes and neurological conditions. Ncb5or comprises cytochrome b5 (b5) and cytochrome b5 reductase (b5R) domains separated by a CHORD-Sgt1 (CS) linker domain. Ncb5or redox activity depends on proper inter-domain interactions to mediate electron transfer from NADH or NADPH via FAD to heme. While full-length human
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Role of surface glycans in enveloped RNA virus infections: A structural perspective Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-11-22 Bhawna Pandey, Srividhya S., Ananya Chatterjee, Vidya Mangala Prasad
Enveloped RNA viruses have been causative agents of major pandemic outbreaks in the recent past. Glycans present on these virus surface proteins are critical for multiple processes during the viral infection cycle. Presence of glycans serves as a key determinant of immunogenicity, but intrinsic heterogeneity, dynamics, and evolutionary shifting of glycans in heavily glycosylated enveloped viruses confounds
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Cover Image, Volume 91, Issue 12 Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-11-23 Burcu Ozden, Andriy Kryshtafovych, Ezgi Karaca
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CASP15 cryo-EM protein and RNA targets: Refinement and analysis using experimental maps Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-11-23 Thomas Mulvaney, Rachael C. Kretsch, Luc Elliott, Joseph G. Beton, Andriy Kryshtafovych, Daniel J. Rigden, Rhiju Das, Maya Topf
CASP assessments primarily rely on comparing predicted coordinates with experimental reference structures. However, experimental structures by their nature are only models themselves—their construction involves a certain degree of subjectivity in interpreting density maps and translating them to atomic coordinates. Here, we directly utilized density maps to evaluate the predictions by employing a method
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Cover Image, Volume 91, Issue 12 Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-11-23 Rhiju Das, Rachael C. Kretsch, Adam J. Simpkin, Thomas Mulvaney, Phillip Pham, Ramya Rangan, Fan Bu, Ronan M. Keegan, Maya Topf, Daniel J. Rigden, Zhichao Miao, Eric Westhof
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Issue Information ‐ Table of Content Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-11-25
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Biotin protein ligase as you like it: Either extraordinarily specific or promiscuous protein biotinylation Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-11-23 John E. Cronan
Biotin (vitamin H or B7) is a coenzyme essential for all forms of life. Biotin has biological activity only when covalently attached to a few key metabolic enzyme proteins. Most organisms have only one attachment enzyme, biotin protein ligase (BPL), which attaches biotin to all target proteins. The sequences of these proteins and their substrate proteins are strongly conserved throughout biology. Structures
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Benchmarking the accuracy of structure-based binding affinity predictors on Spike–ACE2 deep mutational interaction set Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-11-22 Burcu Ozden, Eda Şamiloğlu, Atakan Özsan, Mehmet Erguven, Can Yükrük, Mehdi Koşaca, Melis Oktayoğlu, Muratcan Menteş, Nazmiye Arslan, Gökhan Karakülah, Ayşe Berçin Barlas, Büşra Savaş, Ezgi Karaca
Since the start of COVID-19 pandemic, a huge effort has been devoted to understanding the Spike (SARS-CoV-2)–ACE2 recognition mechanism. To this end, two deep mutational scanning studies traced the impact of all possible mutations across receptor binding domain (RBD) of Spike and catalytic domain of human ACE2. By concentrating on the interface mutations of these experimental data, we benchmarked six
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The enigmatic HCN channels: A cellular neurophysiology perspective Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-11-19 Poonam Mishra, Rishikesh Narayanan
What physiological role does a slow hyperpolarization-activated ion channel with mixed cation selectivity play in the fast world of neuronal action potentials that are driven by depolarization? That puzzling question has piqued the curiosity of physiology enthusiasts about the hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, which are widely expressed across the body and especially
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Interfacial residues in protein–protein complexes are in the eyes of the beholder Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-11-19 Jayadevan Parvathy, Arangasamy Yazhini, Narayanaswamy Srinivasan, Ramanathan Sowdhamini
Interactions between proteins are vital in almost all biological processes. The characterization of protein–protein interactions helps us understand the mechanistic basis of biological processes, thereby enabling the manipulation of proteins for biotechnological and clinical purposes. The interface residues of a protein–protein complex are assumed to have the following two properties: (a) they always
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Identification of sequence determinants for the ABHD14 enzymes Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-11-16 Kaveri Vaidya, Golding Rodrigues, Sonali Gupta, Archit Devarajan, Mihika Yeolekar, M. S. Madhusudhan, Siddhesh S. Kamat
Over the course of evolution, enzymes have developed remarkable functional diversity in catalyzing important chemical reactions across various organisms, and understanding how new enzyme functions might have evolved remains an important question in modern enzymology. To systematically annotate functions, based on their protein sequences and available biochemical studies, enzymes with similar catalytic
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Effects of ion type and concentration on the structure and aggregation of the amyloid peptide Aβ16−22$$ {\boldsymbol{\beta}}_{16-22} $$ Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-11-14 Eva Smorodina, Batuhan Kav, Hebah Fatafta, Birgit Strodel
Among the various factors controlling the amyloid aggregation process, the influences of ions on the aggregation rate and the resulting structures are important aspects to consider, which can be studied by molecular simulations. There is a wide variety of protein force fields and ion models, raising the question of which model to use in such studies. To address this question, we perform molecular dynamics
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Signatures of tRNAGlx-specificity in proteobacterial glutamyl-tRNA synthetases Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-11-12 Saumya Dasgupta, Aditya Dev, Nipa Chongdar, Premananda Basak, Shubhra Ghosh Dastidar, Gautam Basu
The canonical function of glutamyl-tRNA synthetase (GluRS) is to glutamylate tRNAGlu. Yet not all bacterial GluRSs glutamylate tRNAGlu; many glutamylate both tRNAGlu and tRNAGln, while some glutamylate only tRNAGln and not the cognate substrate tRNAGlu. Understanding the basis of the unique specificity of tRNAGlx is important. Mutational studies have hinted at hotspot residues, both on tRNAGlx and
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Community analysis of large-scale molecular dynamics simulations elucidated dynamics-driven allostery in tyrosine kinase 2 Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-11-10 Nastazia Lesgidou, Metaxia Vlassi
TYK2 is a nonreceptor tyrosine kinase, member of the Janus kinases (JAK), with a central role in several diseases, including cancer. The JAKs' catalytic domains (KD) are highly conserved, yet the isolated TYK2-KD exhibits unique specificities. In a previous work, using molecular dynamics (MD) simulations of a catalytically impaired TYK2-KD variant (P1104A) we found that this amino acid change of its
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MPA-Pred: A machine learning approach for predicting the binding affinity of membrane protein–protein complexes Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-11-10 Fathima Ridha, M. Michael Gromiha
Membrane protein–protein interactions are essential for several functions including cell signaling, ion transport, and enzymatic activity. These interactions are mainly dictated by their binding affinities. Although several methods are available for predicting the binding affinity of protein–protein complexes, there exists no specific method for membrane protein–protein complexes. In this work, we
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Location of S-nitrosylated cysteines in protein three-dimensional structures Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-11-08 Oliviero Carugo
Although S-nitrosylation of cysteines is a common protein posttranslational modification, little is known about its three-dimensional structural features. This paper describes a systematic survey of the data available in the Protein Data Bank. Several interesting observations could be made. (1) As a result of radiation damage, S-nitrosylated cysteines (Snc) are frequently reduced, at least partially
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Rational design of antibody-like peptides for targeting the human complement fragment protein C5a Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-11-07 Manaswini Ghosh, Sucharita Shadangi, Soumendra Rana
Human complement fragment 5a (C5a) is one of the most potent glycoproteins generated downstream of C3a and C4a during late-stage activation of the complement signaling cascade. C5a recruits receptors like C5aR1 and C5aR2 and is established to play a critical role in complement-mediated inflammation. Thus, excessive C5a in the plasma due to aberrant activation of the complement contributes to the pathophysiology
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A structural analysis of the nsp9 protein from the coronavirus MERS CoV reveals a conserved RNA binding interface Proteins Struct. Funct. Bioinform. (IF 2.9) Pub Date : 2023-11-06 Gayathri Mani, Serene El-Kamand, Bing Wang, David L. Baker, Sandro F. Ataide, Irina Artsimovitch, Liza Cubeddu, Roland Gamsjaeger
Middle East respiratory syndrome coronavirus (MERS CoV) and severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) are RNA viruses from the Betacoronavirus family that cause serious respiratory illness in humans. One of the conserved non-structural proteins encoded for by the coronavirus family is non-structural protein 9 (nsp9). Nsp9 plays an important role in the RNA capping process of the