Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment

The discovery that the functions of most eukaryotic gene products are mediated through multi-protein complexes makes the prediction of protein interactions one of the most important current challenges in structural biology. Rigid-body docking methods can generate a large number of alternative candidates, but it is difficult to discriminate the near-native interactions from the large number of false positives. Many different scoring functions have been developed for this purpose, but in most cases, experimental and biological information is still required for accurate predictions. We explore here the use of evolutionary restraints in evaluating rigid-body docking geometries. In order to identify potential interface residues we identify functional residues based on the comparison of observed amino acid substitutions with those predicted from local environment. The interface residues identified by this method are correctly located in 85% of the cases. These predicted interface residues are used to define distance restraints that help to score rigid-body docking solutions. We have developed the pyDockRST software, which uses the percentage of satisfied distance restraints, together with the electrostatics and desolvation binding energy, to identify correct docking orientations. This methodology dramatically improves the docking results when compared to the use of energy criteria alone, and is able to find the correct orientation within the top 20 docking solutions in 80% of the cases.     

Quantifying Structural and Functional Restraints on Amino Acid Substitutions in Evolution of Proteins

One of Oleg Ptitsyn's most important papers (Shakhnovich, E., Abkevich, V., and Ptitsyn, O. (1996) Nature, 379, 96-98) describes how knowledge of structure and function can be used to understand better the nature of amino acid substitutions in families and superfamilies of proteins. The selective advantages of retaining structure and function during evolution can be expressed as restraints on the amino acid substitutions that are accepted.     

A structural dissection of amino acid substitutions in helical transmembrane proteins

The evolution of protein folds is under strong constraints from their surrounding environment. Although folding in water‐soluble proteins is driven primarily by hydrophobic forces, the nature of the forces that determine the folding and stability of transmembrane proteins are still not fully understood. Furthermore, the chemically heterogeneous lipid bilayer has a non‐uniform effect on protein structure. In this article, we attempt to get an insight into the nature of this effect by examining the impact of various types of local structure environment on amino acid substitution, based on alignments of high‐resolution structures of polytopic helical transmembrane proteins combined with sequences of close homologs. Compared to globular proteins, burying amino acid sidechains, especially hydrophilic ones, led to a lower increase in conservation in both the lipid‐water interface region and the hydrocarbon core region. This observation is due to surface residues in HTM proteins especially in the HC region being relatively highly conserved, suggesting higher evolutionary constraints from their specific interactions with the surrounding lipid molecules. Polar and small residues, particularly Pro and Gly, show a noticeable increase in conservation as they are positioned more towards the centre of the membrane, which is consistent with their recognized key roles in structural stability. In addition, the examination of hydrogen bonds in the membrane environment identified some exposed hydrophilic residues being better conserved when not hydrogen‐bonded to other residues, supporting the importance of lipid‐protein sidechain interactions. The conclusions presented in this study highlight the distinct features of substitution matrices that take into account the membrane environment, and their potential role in improving sequence‐structure alignments of transmembrane proteins. Proteins 2010; © 2010 Wiley‐Liss, Inc.     

CODA: a combined algorithm for predicting the structurally variable regions of protein models

CODA, an algorithm for predicting the variable regions in proteins, combines FREAD a knowledge based approach, and PETRA, which constructs the region ab initio. FREAD selects from a database of protein structure fragments with environmentally constrained substitution tables and other rule-based filters. FREAD was parameterized and tested on over 3000 loops. The average root mean square deviation ranged from 0.78 A for three residue loops to 3.5 A for eight residue loops on a nonhomologous test set. CODA clusters the predictions from the two independent programs and makes a consensus prediction that must pass a set of rule-based filters. CODA was parameterized and tested on two unrelated separate sets of structures that were nonhomologous to one another and those found in the FREAD database. The average root mean square deviation in the test set ranged from 0.76 A for three residue loops to 3.09 A for eight residue loops. CODA shows a general improvement in loop prediction over PETRA and FREAD individually. The improvement is far more marked for lengths six and upward, probably as the predictive power of PETRA becomes more important. CODA was further tested on several model structures to determine its applicability to the modeling situation. A web server of CODA is available at http://www-cryst.bioc.cam.ac.uk/~charlotte/Coda/search_coda.html.     

Nonrandom amino acid substitution and estimation of the number of nucleotide substitutions in evolution

Summary A method of estimating the number of nucleotide substitutions from amino acid sequence data is developed by using Dayhoff's mutation probability matrix. This method takes into account the effect of nonrandom amino acid substitutions and gives an estimate which is similar to the value obtained by Fitch's counting method, but larger than the estimate obtained under the assumption of random substitutions (Jukes and Cantor's formula). Computer simulations based on Dayhoff's mutation probability matrix have suggested that Jukes and Holmquist's method of estimating the number of nucleotide substitutions gives an overestimate when amino acid substitution is not random and the variance of the estimate is generally very large. It is also shown that when the number of nucleotide substitutions is small, this method tends to give an overestimate even when amino acid substitution is purely at random.     

Structural effects of amino acid substitutions on the P21 proteins: Evidence for a malignant conformation

The conformational effects of different amino acid substitutions for Gly at position 12 in theras-oncogene-encoded P21 proteins have been investigated using conformational energy calculations. Mutations that cause amino acid substitutions for Gly 12 result in a protein that produces malignant transformation of cells. It had previously been shown that substitution of Val, Lys, or Ser for Gly at position 12 results in a major conformational change, and that the preferred lowest energy structure for each of the substituted peptides is identical. It is now found that substitution for Gly 12 of other amino acids that have widely disparate helix-nucleating potentials and completely different side chains (Asp, Asn, Cys, Phe, Tle, Leu, and Ala) all produce this identical lowest energy conformation. This finding is consistent with the recent results of site-specific mutagenesis experiments showing that P21 proteins containing these amino acids at position 12 all promote malignant transformation of cells and suggests the existence of a malignancy-causing conformation for the P21 proteins.     

Three amino acid substitutions contributing to thermostability of phosphoglucose isomerase in the Glanville fritillary butterfly

Temperature is one of the most important environmental factors that affect organisms, especially ectotherms, due to its effects on protein stability. Understanding the general rules that govern thermostability changes in proteins to adapt high-temperature environments is crucial. Here, we report the amino acid substitutions of phosphoglucose isomerase (PGI) related to thermostability in the Glanville fritillary butterfly (Melitaea cinxia, Lepidoptera: Nymphalidae). The PGI encoded by the most common allele in M. cinxia in the Chinese population (G3-PGI), which is more thermal tolerant, is more stable under heat stress than that in the Finnish population (D1-PGI). There are 5 amino acid substitutions between G3-PGI and D1-PGI. Site-directed mutagenesis revealed that the combination of amino acid substitutions of H35Q, M49T, and I64V may increase PGI thermostability. These substitutions alter the 3D structure to increase the interaction between 2 monomers of PGI. Through molecular dynamics simulations, it was found that the amino acid at site 421 is more stable in G3-PGI, confining the motion of the α-helix 420–441 and stabilizing the interaction between 2 PGI monomers. The strategy for high-temperature adaptation through these 3 amino acid substitutions is also adopted by other butterfly species (Boloria eunomia, Aglais urticae, Colias erate, and Polycaena lua) concurrent with M. cinxia in the Tianshan Mountains of China, i.e., convergent evolution in butterflies.     

Prediction of amino acid residues participated in substrate recognition by cytochrome P450 subfamilies with broad substrate specificity

Cytochromes P450 comprise a large superfamily and several of their isoforms play a crucial role in metabolism of xenobiotics, including drugs. Although these enzymes demonstrate broad and cross‐substrate specificity, different cytochrome P450 subfamilies exhibit certain selectivity for some types of substrates. Analysis of amino acid residues of the active sites of six cytochrome subfamilies (CYP1А, CYP2А, CYP2С, CYP2D, CYP2E and CYP3А) enables to define subfamily‐specific patterns that consist of four residues. These residues are located on the periphery of the active sites of these cytochromes. We suggest that they can form a primary binding site at the entrance to the active site, defining cytochrome substrate recognition. Copyright © 2013 John Wiley & Sons, Ltd.     

Analysis of GTPases carrying hydrophobic amino acid substitutions in lieu of the catalytic glutamine: implications for GTP hydrolysis

Ras superfamily GTP-binding proteins regulate important signaling events in the cell. Ras, which often serves as a prototype, efficiently hydrolyzes GTP in conjunction with its regulator GAP. A conserved glutamine plays a vital role in GTP hydrolysis in most GTP-binding proteins. Mutating this glutamine in Ras has oncogenic effects, since it disrupts GTP hydrolysis. The analysis presented here is of GTP-binding proteins that are a paradox to oncogenic Ras, since they have the catalytic glutamine (Glncat) substituted by a hydrophobic amino acid, yet can hydrolyze GTP efficiently. We term these proteins HAS-GTPases. Analysis of the amino acid sequences of HAS-GTPases reveals prominent presence of insertions around the GTP-binding pocket. Homology modeling studies suggest an interesting means to achieve catalysis despite the drastic hydrophobic substitution replacing the key Glncat of Ras-like GTPases. The substituted hydrophobic residue adopts a "retracted conformation," where it is positioned away from the GTP, as its role in catalysis would be unproductive. This conformation is further stabilized by interactions with hydrophobic residues in its vicinity. These interacting residues are strongly conserved and hydrophobic in all HAS-GTPases, and correspond to residues Asp92 and Tyr96 of Ras. An experimental support for the "retracted conformation" of Switch II arises from the crystal structures of Ylqf and hGBP1. This conformation allows us to hypothesize that, unlike in classical GTPases, catalytic residues could be supplied by regions other than the Switch II (i.e., either the insertions or a neighboring domain).     

Exploring the effects of sparse restraints on protein structure prediction

One of the main barriers to accurate computational protein structure prediction is searching the vast space of protein conformations. Distance restraints or inter‐residue contacts have been used to reduce this search space, easing the discovery of the correct folded state. It has been suggested that about 1 contact for every 12 residues may be sufficient to predict structure at fold level accuracy. Here, we use coarse‐grained structure‐based models in conjunction with molecular dynamics simulations to examine this empirical prediction. We generate sparse contact maps for 15 proteins of varying sequence lengths and topologies and find that given perfect secondary‐structural information, a small fraction of the native contact map (5%‐10%) suffices to fold proteins to their correct native states. We also find that different sparse maps are not equivalent and we make several observations about the type of maps that are successful at such structure prediction. Long range contacts are found to encode more information than shorter range ones, especially for α and αβ‐proteins. However, this distinction reduces for β‐proteins. Choosing contacts that are a consensus from successful maps gives predictive sparse maps as does choosing contacts that are well spread out over the protein structure. Additionally, the folding of proteins can also be used to choose predictive sparse maps. Overall, we conclude that structure‐based models can be used to understand the efficacy of structure‐prediction restraints and could, in future, be tuned to include specific force‐field interactions, secondary structure errors and noise in the sparse maps.     

Amino acid substitutions outside a preselected antigenic region in hemoglobin affect the binding to monoclonal antibodies obtained by immunization with the synthetic region

It is often assumed that amino acid substitutions outside a protein antigenic site have no effect on the reactivity of a protein variant with antibodies, especially monoclonal antibodies (mAbs). Substitutions that exert an effect on the reactivity of a protein variant with mAbs are frequently considered to be within the antigenic site of the mAb. To test this assumption, two mAbs [IgG_l(k) and IgG_2a (k)] were prepared by immunization with a synthetic peptide corresponding to region 63–78 of the chain of human hemoglobin (Hb). The peptide was used as an immunogen in its free form (i.e., without conjugation to a carrier), so that the results will not be made ambiguous by peptide modification nor by an immune response to sites spanning peptide and protein carrier. In addition to their reaction with human Hb, the mAbs were also studied with four primate Hbs which had no substitutions within region 63–78 and only a limited number of substitutions which occurred outside of, and at considerable distances in three-dimensional (3D) structure from, this region. Inhibition studies revealed substantial differences in the binding affinities of some of the primate Hbs, relative to human Hb. Some of the substitutions caused major decreases in binding, although they were at considerable distances in the 3D structure from the indicated site residues. It is concluded that substitutions in a protein, even when distant from an antigenic site, can exert major influences on the protein's reactivity with anti-site mAbs.     

Effect of constituting amino acid residue numbers on molecularly imprinted chiral recognition sites

In the present study, the effect of constituting amino acid residue numbers of oligopeptide derivatives, which are candidate materials to construct molecular recognition sites, on chiral recognition ability was investigated. Chiral recognition sites were formed from oligopeptide derivatives, of which constituting amino acid residue numbers were three to six, by adopting an alternative molecular imprinting. It was made clear that the number four, in other words, the tetrapeptide derivative, is the best candidate material to form a chiral recognition site.     

Functional consequences of amino acid substitutions to GerVB, a component of the Bacillus megaterium spore germinant receptor

The extreme metabolic dormancy and resistance properties of spores formed by members of the Bacillus and Clostridium genera are lost upon exposure to a variety of small-molecule germinants. Germinants are known to interact in an as yet undefined manner with cognate receptor complexes that reside in the inner membrane that surrounds the spore protoplast. The receptor itself is a complex of at least three proteins, and in this study we identify amino acid residues, predicted to lie in loop regions of GerVB on the exterior aspect of the membrane, that influence the Bacillus megaterium spore germination response. Three consecutive residues adjacent to putative transmembrane domain 10 (TM10) were demonstrated to mediate to various degrees the proline germinative response while also influencing germination in response to leucine, glucose, and inorganic salts, suggesting that this region may be part of a ligand binding pocket. Alternatively, substitutions in this region may affect the conformation of associated functionally important TM regions. Leucine- and KBr-mediated germination was also influenced by substitutions in other outer loop regions. These observations, when considered with accompanying kinetic analyses that demonstrate cooperativity between germinants, suggest that binding sites for the respective germinants are in close spatial proximity in the receptor but do not overlap. Additionally, proline recognition was conferred to a chimeric receptor when TM regions associated with the putative binding loop were present, indicating that residues in TM9 and/or TM10 of GerVB are also of functional importance in the proline-induced germinative response.     

Conformational effects of amino acid substitutions at positions 10, 12, and 13 in the P21 protein

Substitutions of amino acids for Gly 12 or Gly 13 in theras oncogene-encoded P21 proteins have been demonstrated to produce unique structural changes in these proteins that correlate with their ability to produce cell transformation. For example, the P21 proteins with Arg 12 or Val 13 are both known to be actively transforming. Recent site-specific mutagenesis experiments on the transforming Arg 12 protein have found that the substitution of Val for Gly 10 has no effect on transforming activity whereas the substitution of Val for Gly 13 led to a loss of transforming activity. In this study, we examine the structural effects of these substitutions on the amino terminal hydrophobic decapeptide (Leu 6-Gly 15) of P21 using conformational energy analysis. The results show that the transforming proteins with Gly 10 and Arg 12 or Val 10 and Arg 12 can both adopt the putative malignancy-causing conformation, whereas, for the nontransforming protein with Arg 12 and Val 13, this conformation is energetically disallowed. These results further support the theory that due to structural changes the transforming P21 proteins are unable to bind to some regulatory cellular element which may be the recently identified binding protein responsible for the induction of increased GTPase activity in normal P21 compared with transforming mutants.     

甜菜夜蛾拓扑异构酶I氨基酸突变对其DNA解旋活性的影响

【目的】为了探究甜菜夜蛾 Spodoptera exigua 拓扑异构酶I（topoisomerase I, Top I）氨基酸突变对其DNA解旋活性的影响。【方法】通过克隆甜菜夜蛾 Top I 基因,构建原核表达载体,采用完全重叠PCR定点突变技术,向甜菜夜蛾Top I 的V420, L530, A653和S729（根据人Top I 氨基酸序列编号）4个位点引入突变,将改造成功的重组 Top I 基因转化至大肠杆菌BL21 (DE3)中,诱导重组蛋白表达、纯化,测定Top I突变对其解旋活性的影响。【结果】完全重叠PCR能实现甜菜夜蛾 Top I 定点突变。重组蛋白在体外得到稳定的表达,表达产物经SDS-PAGE电泳分析在96.0 kDa处出现特异性条带。通过对重组蛋白分离纯化并测定对质粒pBR322解旋酶活性,发现引入V420I, L530P和A653T突变后Top I的比活力显著降低,而引入S729T突变后比活力与野生型蛋白无显著差异。【结论】本研究证明在甜菜夜蛾Top I中引入V420I, L530P和A653T突变后,其对底物pBR322的解旋活性显著降低,为后期探索甜菜夜蛾Top I的定点突变与其对喜树碱及其衍生物敏感性的关系奠定了基础。     

Context-specific amino acid substitution matrices and their use in the detection of protein homologs

The sequence homology detection relies on score matrices, which reflect the frequency of amino acid substitutions observed in a dataset of homologous sequences. The substitution matrices in popular use today are usually constructed without consideration of the structural context in which the substitution takes place. Here, we present amino acid substitution matrices specific for particular polar-nonpolar environment of the amino acid. As expected, these matrices [context-specific substitution matrices (CSSMs)] show striking differences from the popular BLOSUM62 matrix, which does not include structural information. When incorporated into BLAST and PSI-BLAST, CSSM outperformed BLOSUM matrices as assessed by ROC curve analyses of the number of true and false hits and by the accuracy of the sequence alignments to the hit sequences. These findings are also of relevance to profile-profile-based methods of homology detection, since CSSMs may help build a better profile. Profiles generated for protein sequences in PDB using CSSM-PSI-BLAST will be made available for searching via RPSBLAST through our web site http://lmbbi.nci.nih.gov/.     

Approaches to predicting effects of single amino acid substitutions on the function of a protein

The relative activities of 313 mutants of the gene V protein of bacteriophage f1, assayed in vivo, have been used to evaluate two approaches to predicting the effects of single amino acid substitutions on the function of a protein. First, we tested methods that only depend on the properties of the wild-type and substituting amino acids. None of the properties or measures of the functional equivalence of amino acids we tested, including the frequency of exchange of amino acids among homologous proteins as well as changes in side-chain size, hydrophobicity, and charge, were found to be more than weakly correlated with the activities of mutants. The principal reason for this poor correlation was found to be that the effect of a particular substitution varies considerably from site to site. We then tested an approach using the activities of several mutants with substitutions at a site to predict the activity of another mutant, and we find that this is a relatively good indicator of whether the other mutant at that site will be functional. A predictive scheme was developed that combines the weak information from the models depending on the properties of the wild-type and substituting amino acids with the stronger information from the tolerance of a site to substitution. Although this scheme requires no knowledge of the structure of a mutant protein, it is useful in predicting the activities of mutants.     

Molecular distribution of amino acid substitutions on neuraminidase from the 2009 (H1N1) human influenza pandemic virus

The pandemic influenza AH1N1 (2009) caused an outbreak of human infection that spread to the world. Neuraminidase (NA) is anantigenic surface glycoprotein, which is essential to the influenza infection process, and is the target of anti-flu drugs oseltamivirand zanamivir. Currently, NA inhibitors are the pillar pharmacological strategy against seasonal and global influenza. Althoughmutations observed after NA-inhibitor treatment are characterized by changes in conserved amino acids of the enzyme catalyticsite, it is possible that specific amino acid substitutions (AASs) distant from the active site such as H274Y, could confer oseltamiviror zanamivir resistance. To better understand the molecular distribution pattern of NA AASs, we analyzed NA AASs from allavailable reported pandemic AH1N1 NA sequences, including those reported from America, Africa, Asia, Europe, Oceania, andspecifically from Mexico. The molecular distributions of the AASs were obtained at the secondary structure domain level for boththe active and catalytic sites, and compared between geographic regions. Our results showed that NA AASs from America, Asia,Europe, Oceania and Mexico followed similar molecular distribution patterns. The compiled data of this study showed that highlyconserved amino acids from the NA active site and catalytic site are indeed being affected by mutations. The reported NA AASsfollow a similar molecular distribution pattern worldwide. Although most AASs are distributed distantly from the active site, thisstudy shows the emergence of mutations affecting the previously conserved active and catalytic site. A significant number ofunique AASs were reported simultaneously on different continents.     

Ligand recognition by peptidoglycan recognition protein-S (PGRP-S): structure of the complex of camel PGRP-S with heptanoic acid at 2.15 Å resolution

Peptidoglycan recognition proteins (PGRPs) are important components of the innate immune system which provide the first line of defense against invading microbes. There are four members in the family of PGRPs in animals of which PGRP-S is a common domain. It is responsible for the binding to microbial cell wall molecules. In order to understand the mode of binding of PGRP-S to the components of the bacterial cell wall, the structure of the complex of camel PGRP-S (CPGRP-S) with heptanoic acid has been determined at 2.15 Å resolution. The structure determination showed the presence of four crystallographically independent protein molecules which are designated as A, B, C, and D. These four protein molecules associate in the form of two homodimers which are represented as A-B and C-D dimers. The association between molecules A and B gives rise to a shallow cleft on the surface at one end of the dimeric interface. One molecule of heptanoic acid is observed at this binding site in the A-B dimer. The association of C and D molecules results in the formation of a long zig-zag tunnel along with the C-D interface. In the cleft at the C-D interface, three molecules of hydrogen peroxide along with other non-water solvent molecules have been observed. The analysis of the several complexes of CPGRP-S with fatty acids and non-fatty acids such as peptidoglycan, lipopolysaccharide, and lipoteichoic acid shows that the fatty acids bind at the A-B site while non-fatty acids interact through C-D interface.