Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.

We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average ~70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target.

Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment.

We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers).

Geometrical Conversion of the EGFR Extracellular Domain by Adiabatic Mapping Combining Normal Mode Analysis of the Elastic Network Model and Energy Optimization.

The activation of epidermal growth factor receptor (EGFR) involves the geometrical conversion of the extracellular domain (ECD) from the tethered to the extended forms with the dynamic rearrangement of the relative positions of four subdomains (SDs); however, this conversion process has not yet been thoroughly understood. We compare the two different forms of the X-ray crystal structures of ECD and simulate the ECD conversion process using adiabatic mapping that combines normal mode analysis of the elastic network model (ENM-NMA) and energy optimization. A comparison of the crystal structures reveals the rigidity of the intradomain geometry of the SD-I and -III backbone regardless of the form.

Residue-residue interactions regulating the Ca2+-induced EF-hand conformation changes in calmodulin.

Calmodulin (CaM) is a Ca2+-binding messenger protein having four Ca2+-binding motifs named 'EF-hand'; the EF-hand motifs undergo a conformation change induced by Ca2+-binding. In order to study how Ca2+-binding induces the conformation change of EF-hand motifs and which residues are involved in the reaction, two 1μ second long MD simulations were independently performed from the apo- and holo-CaM and their structures and interactions were compared. The Ca2+-binding weakens the helix-helix interaction in all EF-hand, however, the holo-CaM MD adopted the close-like form.

Comprehensive analysis of the Co-structures of dipeptidyl peptidase IV and its inhibitor.

Background: We comprehensively analyzed X-ray cocrystal structures of dipeptidyl peptidase IV (DPP-4) and its inhibitor to clarify whether DPP-4 alters its general or partial structure according to the inhibitor used and whether DPP-4 has a common rule for inhibitor binding.

Results: All the main and side chains in the inhibitor binding area were minimally altered, except for a few side chains, despite binding to inhibitors of various shapes. Some residues (Arg125, Glu205, Glu206, Tyr662 and Asn710) in the area had binding modes to fix a specific atom of inhibitor to a particular spatial position in DPP-4.

CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies.

Molecular recognition study on the binding of calcium to calbindin D9k based on 3D reference interaction site model theory.

Ca(2+)-binding proteins are widely distributed throughout cells and play various important roles. Calbindin D9k is a member of the EF-hand Ca(2+)-binding protein family. In this study, we examined the binding of Ca(2+) to calbindin D9k in terms of the free energy of solvation, as obtained by 3D reference interaction site model theory, which describes the statistical mechanics of liquids.

Quality assessment methods for 3D protein structure models based on a residue-residue distance matrix prediction.

In the absence of experimentally determined three dimensional (3D) structures of proteins, the prediction of protein structures using computational methods is a standard alternative approach in bioinformatics. When using the predicted protein models to compute the native structure of an unknown target protein, estimating the actual quality of the protein models is important for selecting the best or near-best model. Moreover, estimates of the differences between the protein models and the native protein structure are obviously useful to end users who can then decide on the utility of the models for their specific problems.

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.

Community-wide blind prediction experiments such as CAPRI and CASP provide an objective measure of the current state of predictive methodology. Here we describe a community-wide assessment of methods to predict the effects of mutations on protein-protein interactions. Twenty-two groups predicted the effects of comprehensive saturation mutagenesis for two designed influenza hemagglutinin binders and the results were compared with experimental yeast display enrichment data obtained using deep sequencing.

United3D: a protein model quality assessment program that uses two consensus based methods.

In protein structure prediction, such as template-based modeling and free modeling (ab initio modeling), the step that assesses the quality of protein models is very important. We have developed a model quality assessment (QA) program United3D that uses an optimized clustering method and a simple Cα atom contact-based potential. United3D automatically estimates the quality scores (Qscore) of predicted protein models that are highly correlated with the actual quality (GDT_TS).

LB3D: a protein three-dimensional substructure search program based on the lower bound of a root mean square deviation value.

Searching for protein structure-function relationships using three-dimensional (3D) structural coordinates represents a fundamental approach for determining the function of proteins with unknown functions. Since protein structure databases are rapidly growing in size, the development of a fast search method to find similar protein substructures by comparison of protein 3D structures is essential. In this article, we present a novel protein 3D structure search method to find all substructures with root mean square deviations (RMSDs) to the query structure that are lower than a given threshold value.

Community-wide assessment of protein-interface modeling suggests improvements to design methodology.

The CAPRI (Critical Assessment of Predicted Interactions) and CASP (Critical Assessment of protein Structure Prediction) experiments have demonstrated the power of community-wide tests of methodology in assessing the current state of the art and spurring progress in the very challenging areas of protein docking and structure prediction. We sought to bring the power of community-wide experiments to bear on a very challenging protein design problem that provides a complementary but equally fundamental test of current understanding of protein-binding thermodynamics. We have generated a number of designed protein-protein interfaces with very favorable computed binding energies but which do not appear to be formed in experiments, suggesting that there may be important physical chemistry missing in the energy calculations.

New protein structure model evaluation methods that include a side-chain consensus score for the protein modeling.

Selecting the best quality model from a set of predicted structures is one of the most important aspects of protein structure prediction. We have developed model quality assessment programs that select high quality models which account for both the Calpha backbone and side-chain atom positions. The new methods are based on the consensus method with consideration of the side-chain environment of a protein structure and the secondary structure agreement.

HUMAN FAMSD-BASE: high quality protein structure model database for the human genome using the FAMSD homology modeling method.

Almost all proteins express their biological functions through the structural conformation of their specific amino acid sequences. Therefore, acquiring the three-dimensional structures of proteins is very important to elucidate the role of a particular protein. We had built protein structure model databases, which is called RIKEN FAMSBASE (http://famshelp.

Method for predicting homology modeling accuracy from amino acid sequence alignment: the power function.

We have devised a power function (PF) that can predict the accuracy of a three-dimensional (3D) structure model of a protein using only amino acid sequence alignments. This Power Function (PF) consists of three parts; (1) the length of a model, (2) a homology identity percent value and (3) the agreement rate between PSI-PRED secondary structure prediction and the secondary structure judgment of a reference protein. The PF value is mathematically computed from the execution process of homology search tools, such as FASTA or various BLAST programs, to obtain the amino acid sequence alignments.

FAMSD: A powerful protein modeling platform that combines alignment methods, homology modeling, 3D structure quality estimation and molecular dynamics.

The prediction of a protein three-dimensional (3D) structure is one of the most important challenges in computational structural biology. We have developed an automatic protein 3D structure prediction method called FAMSD. FAMSD is based on a comparative modeling method which consists of the following four steps: (1) generating and selecting sequence alignments between target and template proteins; (2) constructing 3D structure models based on each selected alignment; (3) selecting the best 3D structure model and (4) refining the selected model.

Dynamic influence of the two membrane-proximal immunoglobulin-like domains upon the peptide-binding platform domain in class I and class II major histocompatibility complexes: normal mode analysis.

Major histocompatibility complexes (MHCs) mainly fall into class I and class II. The two classes have similar structures, with two membrane-proximal immunoglobulin-like domains and a peptide-binding platform domain, though their organizations are different. We simulated the dynamics of a whole and partial model deficient in either of the two membrane-proximal domains for class I and class II using normal mode analysis.

Bioinformatics based Ligand-Docking and in-silico screening.

We report a novel method, ChooseLD (CHOOse biological information Semi-Empirically on the Ligand Docking), which uses simulated annealing (SA) based on bioinformatics for protein-ligand flexible docking. The fingerprint alignment score (FPAScore) value is used to determine the docking conformation of the ligand. This method includes the matching of chemical descriptors such as fingerprints (FPs) and the root mean square deviation (rmsd) calculation of the coordinates of atoms of the chemical descriptors.

Dynamic interaction among the platform domain and two membrane-proximal immunoglobulin-like domains of class I major histocompatibility complex: normal mode analysis.

Class I major histocompatibility complex (MHC) molecules have three domains, a platform domain and two membrane-proximal immunoglobulin-like domains, an alpha3 domain and a beta2-immunoglobulin (beta2m). To understand the dynamic interactions among the three domains, we simulated the behavior of a partial model deficient in beta2m and another model deficient in the alpha3 domain, by normal mode analysis. As a result, the partial model deficient in beta2m was more flexible in interdomain conformation than the other model.

The SKE-DOCK server and human teams based on a combined method of shape complementarity and free energy estimation.

We participated in rounds 6-12 of the critical assessment of predicted interaction (CAPRI) contest as the SKE-DOCK server and human teams. The SKE-DOCK server is based on simple geometry docking and a knowledge base scoring function. The procedure is summarized in the following three steps: (1) protein docking according to shape complementarity, (2) evaluating complex models, and (3) repacking side-chain of models.

Topology of AspT, the aspartate:alanine antiporter of Tetragenococcus halophilus, determined by site-directed fluorescence labeling.

The gram-positive lactic acid bacterium Tetragenococcus halophilus catalyzes the decarboxylation of L-aspartate (Asp) with release of L-alanine (Ala) and CO(2). The decarboxylation reaction consists of two steps: electrogenic exchange of Asp for Ala catalyzed by an aspartate:alanine antiporter (AspT) and intracellular decarboxylation of the transported Asp catalyzed by an L-aspartate-beta-decarboxylase (AspD). AspT belongs to the newly classified aspartate:alanine exchanger family (transporter classification no.

Identification of amino acid residues of Salmonella SlyA that are critical for transcriptional regulation.

The type III secretion system encoded by Salmonella pathogenicity island 2 (SPI-2) is essential for the intracellular survival and replication of Salmonella enterica. The expression of SPI-2 genes is dependent on a two-component regulatory system, SsrA (SpiR)/SsrB, encoded in the SPI-2 region. This paper shows that SlyA regulates transcription of the sensor kinase SsrA by binding to the ssrA promoter, indicating that SlyA is directly involved in the regulation of SPI-2 gene expression.

FAMS complex: a fully automated homology modeling system for protein complex structures.

The formation of a protein-protein complex is responsible for many biological functions; therefore, three-dimensional structures of protein complexes are essential for deeper understandings of protein functions and the mechanisms of diseases at the atomic level. However, compared with individual proteins, complex structures are difficult to solve experimentally because of technical limitations. Thus a method that can predict protein complex structures would be invaluable.

Protein structure prediction in CASP6 using CHIMERA and FAMS.

In CASP6, the CHIMERA-group predicted full-atom models of all targets using SKE-CHIMERA, a Web-user interface system for protein structure prediction that allows human intervention at necessary stages; we used a lot of information from our own data and from publicly available data. Using SKE-CHIMERA, we iterated manual step (template selection and alignment by the in-house program CHIMERA) and automatic step (three-dimensional model building by the in-house program FAMS). The official CASP6 assessment showed that CHIMERA-group was one of the most successful predictors in homology modeling, especially for FR/H (Fold Recognition/Homologous).