Understanding the determinants of antibody specificity is one of the challenging tasks in antibody development. Monospecific antibodies are still dominant in approved antibody therapeutics but there is a significant body of work to show that multispecific antibodies can increase the overall therapeutic effect. Dual‐specific or “Two‐in‐One” antibodies can bind to two different antigens separately with

CAPRI challenges offer a variety of blind tests for protein‐protein interaction prediction. In CAPRI Rounds 38‐45, we generated a set of putative binding modes for each target with an FFT‐based docking algorithm, and then scored and ranked these binding modes with a proprietary scoring function, ITScorePP. We have also developed a novel web server, Rebipp. The algorithm utilizes information retrieval

Taking advantage of the known planarity of the N‐acetyl group of N‐acetylglucosamine, an analysis of the quality of carbohydrate structures found in the protein databank was performed. Few obvious defects of the local geometry of the carbonyl group were observed. However, the N‐acetyl group was often found in the less favorable cis conformation (12% of the cases). It was also found severely twisted

Supply of iron into human cells is achieved by iron carrier protein transferrin and its receptor, that upon complex formation get internalized by endocytosis. Similarly, the iron needs to be delivered into the brain, and necessitates the transport across the blood‐brain barrier. While there are still unanswered questions about these mechanisms, extensive efforts have been made to use the system for

Understanding how each residue position contributes to protein function has been a long‐standing goal in protein science. Substitution studies have historically focused on conserved protein positions. However, substitutions of nonconserved positions can also modify function. Indeed, we recently identified nonconserved positions that have large substitution effects in human liver pyruvate kinase (hLPYK)

Tyrosine phosphorylation, a highly regulated post‐translational modification, is carried out by the enzyme tyrosine kinase (TK). TKs are important mediators in signaling cascades, facilitating diverse biological processes in response to stimuli. TKs may acquire mutations leading to malignancy and are viable targets for anti‐cancer drugs. Mast/stem cell growth factor receptor KIT is a TK involved in

Years of evolution have kept actin conserved throughout various clades of life. It is an essential protein starring in many cellular processes. In a primitive eukaryote named Entamoeba histolytica , actin directs the process of phagocytosis. A finely tuned coordination between various actin‐binding proteins (ABPs) choreographs this process and forms one of the virulence factors for this protist pathogen

Ancestral sequence reconstruction has had recent success in decoding the origins and the determinants of complex protein functions. However, phylogenetic analyses of remote homologues must handle extreme amino acid sequence diversity resulting from extended periods of evolutionary change. We exploited the wealth of protein structures to develop an evolutionary model based on protein secondary structure

Protein‐protein interactions (PPIs) are ubiquitous and functionally of great importance in biological systems. Hence, the accurate prediction of PPIs by protein‐protein docking and scoring tools is highly desirable in order to characterize their structure and biological function. Ab initio docking protocols are divided into the sampling of docking poses to produce at least one near‐native structure

Sortases are a group of enzymes displayed on the cell‐wall of Gram‐positive bacteria. They are responsible for the attachment of virulence factors onto the peptidoglycan in a transpeptidation reaction through recognition of a pentapeptide substrate. Most housekeeping sortases recognize one specific pentapeptide motif; however, Streptococcus pyogenes sortase A (SpSrtA WT) recognizes LPETG, LPETA and

The ryanodine receptors (RyR) are essential to calcium signaling in striated muscles. A deep understanding of the complex Ca2+‐activation/inhibition mechanism of RyRs requires detailed structural and dynamic information for RyRs in different functional states (e.g., with Ca2+ bound to activating or inhibitory sites). Recently, high‐resolution structures of the RyR isoform 1 (RyR1) were solved by cryo‐electron

Amyloid‐beta (Aβ) protein is related to Alzheimer's disease (AD), and various experiments have shown that oligomers as small as dimers are cytotoxic. Recent studies have concluded that interactions of Aβ with neuronal cell membranes lead to disruption of membrane integrity, toxicity and play a key role in the development of AD. Molecular dynamics (MD) simulations have been used to investigate Aβ in

Proteins are the active players in performing essential molecular activities throughout biology, and their dynamics has been broadly demonstrated to relate to their mechanisms. The intrinsic fluctuations have often been used to represent their dynamics and then compared to the experimental B‐factors. However, proteins do not move in a vacuum and their motions are modulated by solvent which can impose

Pentapeptide repeat proteins (PRPs) represent a large superfamily with more than 38 000 sequences in nearly 3500 species, the majority belonging to cyanobacteria but represented among all branches of life. PRPs contain at least eight consecutive pentapeptide repeats with the consensus (A/C/S/V/T/L/I)(D/N/S/K/E/I/R)(L/F)(S/T/R/E/Q/K/V/D)(G/D/E/N/R/Q/K). PRPs fold into right‐handed quadrilateral β helices

Coronavirus disease 2019 (COVID‐19) is a pandemic infectious disease caused by novel Severe Acute Respiratory Syndrome coronavirus‐2 (SARS CoV‐2). The SARS CoV‐2 is transmitted more rapidly and readily than SARS CoV. Both, SARS CoV and SARS CoV‐2 via their glycosylated spike proteins recognize the human angiotensin converting enzyme‐2 (ACE‐2) receptor. We generated multiple sequence alignments and

Protein domains exist by themselves or in combination with other domains to form complex multi‐domain proteins. Defining domain boundaries in proteins is essential for understanding their evolution and function but is not trivial. More specifically, partitioning domains that interact by forming a single β‐sheet is known to be particularly troublesome for automatic structure‐based domain decomposition

Intrinsically disordered regions (IDR) play an important role in key biological processes and are closely related to human diseases. IDRs have great potential to serve as targets for drug discovery, most notably in disordered binding regions. Accurate prediction of IDRs is challenging because their genome wide occurrence and a low ratio of disordered residues make them difficult targets for traditional

2020 is a leap year. That means that we have one day extra and, if the Olympic games had survived the corona crisis, we would all be watching television and ask the eternal question whether Olympic records will for ever be broken and broken again, or that there are limits to human biology1. In this article we ask the same question, but rather than discussing aspects of Citius, Altius, and Fortius of

Mutual information and entropy transfer analysis employed on two inactive states of human beta‐2 adrenergic receptor (β2‐AR) unraveled distinct communication pathways. Previously, a so‐called “highly” inactive state of the receptor was observed during 1.5 μs long MD simulation where the largest intracellular loop (ICL3) was swiftly packed onto G‐protein binding cavity, becoming entirely inaccessible

A fully atomistic (AT) modeling of biological macromolecules at relevant length‐ and time‐scales is often cumbersome or not even desirable, both in terms of computational effort required and a posteriori analysis. This difficulty can be overcome with the use of multiresolution models, in which different regions of the same system are concurrently described at different levels of detail. In enzymes

Mixed lineage leukemia protein (MLL1 protein) recognizes CpG site via its CXXC domain and is frequently associated with leukemia. The specific recognition is abolished by C1188D mutation which also prevents MLL‐related leukemia. In this paper, multiple molecular dynamic simulations were performed to investigate the mechanism of recognition and influences of C1188D mutation. Started from fully dissociated

The Nest is a concave‐shaped structural motif in proteins formed by consecutive enantiomeric left‐handed (L) and right‐handed (R) helical conformation of the backbone. This important motif subsumes many turn and helix capping structures and binds electron‐rich ligands. Simple Nests are either RL or LR. Larger Nests (>2 residues long) may be RLR, LRL, RLRL, etc., being considered as composed of overlapping

Structural characterization of alternatively folded and partially disordered protein conformations remains challenging. Outer surface protein A (OspA) is a pivotal protein in Borrelia infection, which is the etiological agent of Lyme disease. OspA exists in equilibrium with intermediate conformations, in which the central and the C‐terminal regions of the protein have lower stabilities than the N‐terminal

Protein docking algorithms aim to predict the 3D structure of a protein complex from the structures of its separated components. In the past, most docking algorithms focused on docking pairs of proteins to form dimeric complexes. However, attention is now turning towards the more difficult problem of using docking methods to predict the structures of multi‐component complexes. In both cases, however

Voltage‐gated sodium channels (NavChs) are biological pores that control the flow of sodium ions through the cell membrane. In humans, mutations in genes encoding NavChs can disrupt physiological cellular activity thus leading to a wide spectrum of diseases. Here, we present a topological connection between the functional architecture of a NavAb bacterial channel and accumulation of atomic hydropathicity

Multicopper oxidases (MCOs) use copper ions as cofactors to oxidize a variety of substrates while reducing oxygen to water. MCOs have been identified in various taxa, with notable occurrences in fungi. The role of these fungal MCOs in lignin degradation sparked an interest due to their potential for application in biofuel production and various other industries. MCOs consist of different protein domains

The N‐ terminal cleavage of fusion tags to restore the native N‐ terminus of recombinant proteins is a challenging task and up to today, protocols need to be optimized for different proteins individually. Within this work, we present a novel protease that was designed in‐silico to yield enhanced promiscuity toward different N‐ terminal amino acids. Two mutations in the active‐site amino acids of human

The aggregation of Aβ42 peptides is considered as one of the main causes for the development of Alzheimer's disease. In this context, Zn2+ and Cu2+ play a significant role in regulating the aggregation mechanism, due to changes in the structural and the solvation free energy of Aβ42. In practice, experimental studies are not able to determine the latter properties, since the Aβ42–Zn2+ and Aβ42–Cu2+

The infinitesimally small sequence space naturally scouted in the millions of years of evolution suggests that the natural proteins are constrained by some functional prerequisites and should differ from randomly generated sequences. We have developed a protein sequence fitness scoring function that implements sequence and corresponding secondary structural information at tripeptide levels to differentiate

Ensemble docking has provided an inexpensive method to account for receptor flexibility in molecular docking for virtual screening. Unfortunately, as there is no rigorous theory to connect the docking scores from multiple structures to measured activity, researchers have not yet come up with effective ways to use these scores to classify compounds into actives and inactives. This shortcoming has led

Protein thermostability is important to evolution, diseases, and industrial applications. Proteins use diverse molecular strategies to achieve stability at high temperature, yet reducing the entropy of unfolding seems required. We investigated five small α-proteins and five β-proteins with known, distinct structures and thermostability (Tm ) using multi-seed molecular dynamics simulations at 300, 350

Cyanophages, widespread in aquatic systems, are a class of viruses that specifically infect cyanobacteria. Though they play important roles in modulating the homeostasis of cyanobacterial populations, little is known about the freshwater cyanophages, especially those hypothetical proteins of unknown function. Mic1 is a freshwater siphocyanophage isolated from the Lake Chaohu. It encodes three hypothetical

ClpS2 is a small protein under development as a probe for selectively recognizing N‐terminal amino acids of N‐degron peptide fragments. To understand the structural basis of ClpS2 specificity for an N‐terminal amino acid, all atom molecular dynamics (MD) simulations were conducted using the sequence of a bench‐stable mutant of ClpS2, called PROSS. We predicted that a single amino acid leucine to asparagine

Conversion of 10‐hydroxygeraniol to 10‐oxogeranial is a crucial step in iridoid biosynthesis. This reaction is catalyzed by a zinc‐dependent alcohol dehydrogenase, 10‐hydroxygeraniol dehydrogenase, belonging to the family of medium‐chain dehydrogenase/reductase (MDR). Here, we report the crystal structures of a novel 10‐hydroxygeraniol dehydrogenase from Catharanthus roseus in its apo and nicotinamide

Integration of template‐based modeling, global sampling and precise scoring is crucial for the development of molecular docking programs with improved accuracy. We combined template‐based modeling and ab‐initio docking protocol as hybrid docking strategy called CoDock for the docking and scoring experiments of the seventh CAPRI edition. For CAPRI rounds 38‐45, we obtained acceptable or better models

Targets in the protein docking experiment CAPRI (Critical Assessment of Predicted Interactions) generally present new challenges and contribute to new developments in methodology. In rounds 38 to 45 of CAPRI, most targets could be effectively predicted using template-based methods. However, the server ClusPro required structures rather than sequences as input, and hence we had to generate and dock

Protein docking is essential for structural characterization of protein interactions. Besides providing the structure of protein complexes, modeling of proteins and their complexes is important for understanding the fundamental principles and specific aspects of protein interactions. The accuracy of protein modeling, in general, is still less than that of the experimental approaches. Thus, it is important

Structural information about protein-protein interactions, often missing at the interactome scale, is important for mechanistic understanding of cells and rational discovery of therapeutics. Protein docking provides a computational alternative for such information. However, ranking near-native docked models high among a large number of candidates, often known as the scoring problem, remains a critical

There have been several studies suggesting that protein structures solved by NMR spectroscopy and x-ray crystallography show significant differences. To understand the origin of these differences, we assembled a database of high-quality protein structures solved by both methods. We also find significant differences between NMR and crystal structures-in the root-mean-square deviations of the Cα atomic

Internal structure similarity in proteins can be observed at the domain and at subdomain levels. From an evolutionary perspective, structurally similar elements may arise divergently by gene duplication and fusion events but may also be the product of convergent evolution under physicochemical constraints. The characterization of proteins that contain repeated structural elements has implications for

Immune checkpoint blockade of signaling pathways such as PD-1/PD-L1 has recently opened up a new avenue for highly efficient immunotherapeutic strategies to treat cancer. Since tumor microenvironments are characterized by lower pH (5.5-7.0), pH-dependent protein-ligand interactions can be exploited as efficient means to regulate drug affinity and specificity for a variety of malignancies. In this article

Kinesin dimer walks processively along a microtubule (MT) protofilament in a hand-over-hand manner, transiting alternately between one-head-bound (1HB) and two-heads-bound (2HB) states. In 1HB state, one head bound by adenosine diphosphate (ADP) is detached from MT and the other head is bound to MT. Here, using all-atom molecular dynamics simulations we determined the position and orientation of the

Cytochromes P450 are versatile heme-based enzymes responsible for vital life processes. Of these, P450cam (substrate camphor) has been most studied. Despite this, precise mechanisms of the key O─O cleavage step remain partly elusive to date; effects observed in various enzyme mutants remain partly unexplained. We have carried out extended (to 1000 ns) MM-MD and follow-on quantum mechanics/molecular

Musashi-2 (MSI2) belongs to Musashi family of RNA binding proteins (RBP). Like Musashi-1 (MSI1), it is overexpressed in a variety of cancers and is a promising therapeutic target. Both MSI proteins contain two N-terminal RNA recognition motifs and play roles in posttranscriptional regulation of target mRNAs. Previously, we have identified several inhibitors of MSI1, all of which bind to MSI2 as well

Hydrostatic pressure has a vital role in the biological adaptation of the piezophiles, organisms that live under high hydrostatic pressure. However, the mechanisms by which piezophiles are able to adapt their proteins to high hydrostatic pressure is not well understood. One proposed hypothesis is that the volume changes of unfolding (ΔVTot ) for proteins from piezophiles is distinct from those of nonpiezophilic

FimH is a bacterial adhesin protein located at the tip of Escherichia coli fimbria that functions to adhere bacteria to host cells. Thus, FimH is a critical factor in bacterial infections such as urinary tract infections and is of interest in drug development. It is also involved in vaccine development and as a model for understanding shear-enhanced catch bond cell adhesion. To date, over 60 structures

Ste24 enzymes, a family of eukaryotic integral membrane proteins, are zinc metalloproteases (ZMPs) originally characterized as "CAAX proteases" targeting prenylated substrates, including a-factor mating pheromone in yeast and prelamin A in humans. Recently, Ste24 was shown to also cleave nonprenylated substrates. Reduced activity of the human ortholog, HsSte24, is linked to multiple disease states

In this paper, using Word2vec, a widely-used natural language processing method, we demonstrate that protein domains may have a learnable implicit semantic "meaning" in the context of their functional contributions to the multi-domain proteins in which they are found. Word2vec is a group of models which can be used to produce semantically meaningful embeddings of words or tokens in a fixed-dimension

The analysis of amino acid coevolution has emerged as a practical method for protein structural modeling by providing structural contact information from alignments of amino acid sequences. In parallel, chemical cross-linking/mass spectrometry (XLMS) has gained attention as a universally applicable method for obtaining low-resolution distance constraints to model the quaternary arrangements of proteins

Nostoc sp. PCC 7120 are filamentous cyanobacteria capable of both oxygenic photosynthesis and nitrogen fixation, with the latter taking place in specialized cells known as heterocysts that terminally differentiate from vegetative cells under conditions of nitrogen starvation. Cyanobacteria have existed on earth for more than 2 billion years and are thought to be responsible for oxygenation of the earth's

The nondiscriminating aspartyl‐tRNA synthetase (ND‐AspRS), found in many archaea and bacteria, covalently attaches aspartic acid to tRNAAsp and tRNAAsn generating a correctly charged Asp‐tRNAAsp and an erroneous Asp‐tRNAAsn. This relaxed tRNA specificity is governed by interactions between the tRNA and the enzyme. In an effort to assess the contributions of the anticodon‐binding domain to tRNA specificity