A combinatorial distance-constraint approach to predicting protein tertiary models from known secondary structure

Destructuration of Canola Protein Gels during In Situ Gastrointestinal Digestion Studied by X-ray Scattering

We are studying the destructuration of canola protein gels, as a solid food model, during in situ gastrointestinal digestion using synchrotron small-angle X-ray scattering (SAXS). Digestion of two gels, prepared by heating pH 8 and pH 11 solutions, was carried out by diffusion of enzymatic juices into the gel from the top of the capillary and monitored for several tens of hours. Very similar time evolutions of SAXS curves occur at different positions of the gel in the capillary, with a delay determined by the distance from the surface initially in contact with the digestive juice. The main phenomena observed are (i) at the scale of the protein conformation (1-5 nm). The scattering curve is a power law, the exponent of which measures the compactness (related to the degree of unfolding). It can be plotted as a function of the characteristic size of proteins/and interprotein distances and as a function of the scattering intensity. Such diagrams clearly show successive digestion processes. For the pH 11 gel, in which proteins are initially hardly unfolded, the digestive processes are unfolding (1st step), recompaction-aggregation phenomena (2nd step) due to gastrointestinal pH conditions and enzymatic cleavage, further unfolding-disaggregation (3rd step), and final protein cleavage (4th step) down to small peptides. For the pH 8 gel, proteins are initially unfolded, and only the last three steps are observed, showing the influence of easier access for the enzymes. (ii) At the scale of large aggregates (10-50 nm), we observe for both gels a decrease in the size and/or number of these aggregates during digestion and alteration of their interfaces. (iii) At the scale of the secondary protein structure, wide-angle X-ray scattering is very useful for detecting the degradation of the secondary protein structure at different steps of digestion.

Identification of SARS-CoV-2 Nucleocapsid and Spike T-Cell Epitopes for Assessing T-Cell Immunity

Developing optimal T-cell response assays to severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is critical for measuring the duration of immunity to this disease and assessing the efficacy of vaccine candidates. These assays need to target conserved regions of SARS-CoV-2 global variants and avoid cross-reactivity to seasonal human coronaviruses. To contribute to this effort, we employed an in silico immunoinformatics analysis pipeline to identify immunogenic peptides resulting from conserved and highly networked regions with topological importance from the SARS-CoV-2 nucleocapsid and spike proteins. A total of 57 highly networked T-cell epitopes that are conserved across geographic viral variants were identified from these viral proteins, with a binding potential to diverse HLA alleles and 80 to 100% global population coverage. Importantly, 18 of these T-cell epitope derived peptides had limited homology to seasonal human coronaviruses making them promising candidates for SARS-CoV-2-specific T-cell immunity assays. Moreover, two of the NC-derived peptides elicited effector/polyfunctional responses of CD8+ T cells derived from SARS-CoV-2 convalescent patients.IMPORTANCE The development of specific and validated immunologic tools is critical for understanding the level and duration of the cellular response induced by SARS-CoV-2 infection and/or vaccines against this novel coronavirus disease. To contribute to this effort, we employed an immunoinformatics analysis pipeline to define 57 SARS-CoV-2 immunogenic peptides within topologically important regions of the nucleocapsid (NC) and spike (S) proteins that will be effective for detecting cellular immune responses in 80 to 100% of the global population. Our immunoinformatics analysis revealed that 18 of these peptides had limited homology to circulating seasonal human coronaviruses and therefore are promising candidates for distinguishing SARS-CoV-2-specific immune responses from pre-existing coronavirus immunity. Importantly, CD8+ T cells derived from SARS-CoV-2 survivors exhibited polyfunctional effector responses to two novel NC-derived peptides identified as HLA-binders. These studies provide a proof of concept that our immunoinformatics analysis pipeline identifies novel immunogens which can elicit polyfunctional SARS-CoV-2-specific T-cell responses.

Importance of the Linker Region in Matrix Metalloproteinase-1 Domain Interactions

Collagenolysis is catalyzed by enzymes from the matrix metalloproteinase (MMP) family, where one of the most studied is MMP-1. The X-ray crystallographic structure of MMP-1 complexed with a collagen-model triple-helical peptide (THP) provided important atomistic information, but few details on the effects of the conformational flexibility on catalysis. In addition, the role of the linker region between the catalytic (CAT) and hemopexin-like (HPX) domains was not defined. In order to reveal the dynamics and correlations of MMP-1 comprehensive atomistic molecular dynamics simulations of an MMP-1•THP complex was performed. To examine the role of the linker region for MMP-1 function simulations with linker regions from MT1-MMP/MMP-14 and MMP-13 replacing the MMP-1 linker region were performed. The MD studies were in good agreement with the experimental observation that in the MMP-1•THP X-ray crystallographic structure MMP-1 is in a "closed" conformation. MD revealed that the interactions of the THP with the both the CAT and HPX domains of MMP-1 are dynamic in nature, and the linker region of MMP-1 influences the interactions and dynamics of both the CAT and HPX domains and collagen binding to MMP-1.

VMD DisRg: New User-Friendly Implement for calculation distance and radius of gyration in VMD program

Molecular dynamic simulation is a practical and powerful technique for analysis of protein structure. Several programs have been developed to facilitate the mentioned investigation, under them the visual molecular dynamic or VMD is the most frequently used programs. One of the beneficial properties of the VMD is its ability to be extendable by designing new plug-in. We introduce here a new facility of the VMD for distance analysis and radius of gyration of biopolymers such as protein and DNA.

AVAILABILITY

The database is available for free at http://trc.ajums.ac.ir/HomePage.aspx/?TabID/=12618/&Site/=trc.ajums.ac/&Lang/=fa-IR.

CALCOM: a software for calculating the center of mass of proteins

The center of mass of a protein is an artificial point useful for detecting important and simple features of proteins structure, shape and association.CALCOM is a software which calculates the center of mass of a protein, starting from PDB protein structure files. In the case of protein complexes and of protein-small ligand complexes, the position of protein residues or of ligand atoms respect to each protein subunit can be evaluated, as well as the distance among the center of mass of the protein subunits, in order to compare different conformations and evaluate the relative motion of subunits.

AVAILABILITY

THE SERVICE IS AVAILABLE AT THE URL: http://bioinformatica.isa.cnr.it/CALCOM/.

Strict rules determine arrangements of strands in sandwich proteins

From a computer analysis of the spatial organization of the secondary structures of beta-sandwich proteins, we find certain sets of consecutive strands that are connected by hydrogen bonds, which we call "strandons." The analysis of the arrangements of strandons in 491 protein structures that come from 69 different superfamilies reveals strict regularities in the arrangements of strandons and the formation of what we call "canonical supermotifs." Six such supermotifs account for approximately 90% of all observed structures. Simple geometric rules are described that dictate the formation of these supermotifs.

Detecting compensatory covariation signals in protein evolution using reconstructed ancestral sequences

When protein sequences divergently evolve under functional constraints, some individual amino acid replacements that reverse the charge (e.g. Lys to Asp) may be compensated by a replacement at a second position that reverses the charge in the opposite direction (e.g. Glu to Arg). When these side-chains are near in space (proximal), such double replacements might be driven by natural selection, if either is selectively disadvantageous, but both together restore fully the ability of the protein to contribute to fitness (are together "neutral"). Accordingly, many have sought to identify pairs of positions in a protein sequence that suffer compensatory replacements, often as a way to identify positions near in space in the folded structure. A "charge compensatory signal" might manifest itself in two ways. First, proximal charge compensatory replacements may occur more frequently than predicted from the product of the probabilities of individual positions suffering charge reversing replacements independently. Conversely, charge compensatory pairs of changes may be observed to occur more frequently in proximal pairs of sites than in the average pair. Normally, charge compensatory covariation is detected by comparing the sequences of extant proteins at the "leaves" of phylogenetic trees. We show here that the charge compensatory signal is more evident when it is sought by examining individual branches in the tree between reconstructed ancestral sequences at nodes in the tree. Here, we find that the signal is especially strong when the positions pairs are in a single secondary structural unit (e.g. alpha helix or beta strand) that brings the side-chains suffering charge compensatory covariation near in space, and may be useful in secondary structure prediction. Also, "node-node" and "node-leaf" compensatory covariation may be useful to identify the better of two equally parsimonious trees, in a way that is independent of the mathematical formalism used to construct the tree itself. Further, compensatory covariation may provide a signal that indicates whether an episode of sequence evolution contains more or less divergence in functional behavior. Compensatory covariation analysis on reconstructed evolutionary trees may become a valuable tool to analyze genome sequences, and use these analyses to extract biomedically useful information from proteome databases.

A novel method for sampling alpha-helical protein backbones

We present a novel technique of sampling the configurations of helical proteins. Assuming knowledge of native secondary structure, we employ assembly rules gathered from a database of existing structures to enumerate the geometrically possible three-dimensional arrangements of the constituent helices. We produce a library of possible folds for 25 helical protein cores. In each case, our method finds significant numbers of conformations close to the native structure. In addition, we assign coordinates to all atoms for four of the 25 proteins and show that this has a small effect on the number of near-native conformations. In the context of database driven exhaustive enumeration our method performs extremely well, yielding significant percentages of conformations (between 0.02% and 82%) within 6 A of the native structure. The method's speed and efficiency make it a valuable tool for predicting protein structure.

Ab initio construction of protein tertiary structures using a hierarchical approach

We present a hierarchical method to predict protein tertiary structure models from sequence. We start with complete enumeration of conformations using a simple tetrahedral lattice model. We then build conformations with increasing detail, and at each step select a subset of conformations using empirical energy functions with increasing complexity. After enumeration on lattice, we select a subset of low energy conformations using a statistical residue-residue contact energy function, and generate all-atom models using predicted secondary structure. A combined knowledge-based atomic level energy function is then used to select subsets of the all-atom models. The final predictions are generated using a consensus distance geometry procedure. We test the feasibility of the procedure on a set of 12 small proteins covering a wide range of protein topologies. A rigorous double-blind test of our method was made under the auspices of the CASP3 experiment, where we did ab initio structure predictions for 12 proteins using this approach. The performance of our methodology at CASP3 is reasonably good and completely consistent with our initial tests.

Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions

The problem of protein tertiary structure prediction from primary sequence can be separated into two subproblems: generation of a library of possible folds and specification of a best fold given the library. A distance geometry procedure based on random pairwise metrization with good sampling properties was used to generate a library of 500 possible structures for each of 11 small helical proteins. The input to distance geometry consisted of sets of restraints to enforce predicted helical secondary structure and a generic range of 5 to 11 A between predicted contact residues on all pairs of helices. For each of the 11 targets, the resulting library contained structures with low RMSD versus the native structure. Near-native sampling was enhanced by at least three orders of magnitude compared to a random sampling of compact folds. All library members were scored with a combination of an all-atom distance-dependent function, a residue pair-potential, and a hydrophobicity function. In six of the 11 cases, the best-ranking fold was considered to be near native. Each library was also reduced to a final ab initio prediction via consensus distance geometry performed over the 50 best-ranking structures from the full set of 500. The consensus results were of generally higher quality, yielding six predictions within 6.5 A of the native fold. These favorable predictions corresponded to those for which the correlation between the RMSD and the scoring function were highest. The advantage of the reported methodology is its extreme simplicity and potential for including other types of structural restraints.