ECMIS: computational approach for the identification of hotspots at protein-protein interfaces

Background

Various methods have been developed to computationally predict hotspot residues at novel protein-protein interfaces. However, there are various challenges in obtaining accurate prediction. We have developed a novel method which uses different aspects of protein structure and sequence space at residue level to highlight interface residues crucial for the protein-protein complex formation.

Results

ECMIS (Energetic Conservation Mass Index and Spatial Clustering) algorithm was able to outperform existing hotspot identification methods. It was able to achieve around 80% accuracy with incredible increase in sensitivity and outperforms other existing methods. This method is even sensitive towards the hotspot residues contributing only small-scale hydrophobic interactions.

Conclusion

Combination of diverse features of the protein viz. energy contribution, extent of conservation, location and surrounding environment, along with optimized weightage for each feature, was the key for the success of the algorithm. The academic version of the algorithm is available at http://caps.ncbs.res.in/download/ECMIS/ECMIS.zip.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-303) contains supplementary material, which is available to authorized users.     

Efficient prediction of human protein-protein interactions at a global scale

Background

Our knowledge of global protein-protein interaction (PPI) networks in complex organisms such as humans is hindered by technical limitations of current methods.

Results

On the basis of short co-occurring polypeptide regions, we developed a tool called MP-PIPE capable of predicting a global human PPI network within 3 months. With a recall of 23% at a precision of 82.1%, we predicted 172,132 putative PPIs. We demonstrate the usefulness of these predictions through a range of experiments.

Conclusions

The speed and accuracy associated with MP-PIPE can make this a potential tool to study individual human PPI networks (from genomic sequences alone) for personalized medicine.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0383-1) contains supplementary material, which is available to authorized users.     

Homology-based modeling of 3D structures of protein-protein complexes using alignments of modified sequence profiles

Customary practice in predicting 3D structures of protein-protein complexes is employment of various docking methods when the structures of separate monomers are known a priori. The alternative approach, i.e. the template-based prediction with pure sequence information as a starting point, is still considered as being inferior mostly due to presumption that the pool of available structures of protein-protein complexes, which can serve as putative templates, is not sufficiently large. Recently, however, several labs have developed databases containing thousands of 3D structures of protein-protein complexes, which enable statistically reliable testing of homology-based algorithms. In this paper we report the results on homology-based modeling of 3D structures of protein complexes using alignments of modified sequence profiles. The method, called HOMology-BAsed COmplex Prediction (HOMBACOP), has two distinctive features: (I) extra weight on aligning interfacial residues in the dynamical programming algorithm, and (II) increased gap penalties for the interfacial segments. The method was tested against our recently developed ProtCom database and against the Boston University protein-protein BENCHMARK. In both cases, models generated were compared to the models built on basis of customarily protein structure initiative (PSI)-BLAST sequence alignments. It was found that existence of homologous (by the means of PSI-BLAST) templates (44% of cases) enables both methods to produce models of good quality, with the profiles method outperforming the PSI-BLAST models (with respect to the percentage of correctly predicted residues on the complex interface and fraction of native interfacial contacts). The models were evaluated according to the CAPRI assessment criteria and about two thirds of the models were found to fall into acceptable and medium-quality categories. The same comparison of a larger set of 463 protein complexes showed again that profiles generate better models. We further demonstrate, using our ProtCom database, the suitability of the profile alignment algorithm in detecting remote homologues between query and template sequences, where the PSI-BLAST method fails.     

An intuitive graphical webserver for multiple-choice protein sequence search

Every day tens of thousands of sequence searches and sequence alignment queries are submitted to webservers. The capitalized word “BLAST” becomes a verb, describing the act of performing sequence search and alignment. However, if one needs to search for sequences that contain, for example, two hydrophobic and three polar residues at five given positions, the query formation on the most frequently used webservers will be difficult. Some servers support the formation of queries with regular expressions, but most of the users are unfamiliar with their syntax. Here we present an intuitive, easily applicable webserver, the Protein Sequence Analysis server, that allows the formation of multiple choice queries by simply drawing the residues to their positions; if more than one residue are drawn to the same position, then they will be nicely stacked on the user interface, indicating the multiple choice at the given position. This computer-game-like interface is natural and intuitive, and the coloring of the residues makes possible to form queries requiring not just certain amino acids in the given positions, but also small nonpolar, negatively charged, hydrophobic, positively charged, or polar ones. The webserver is available at http://psa.pitgroup.org.     

Architectures and functional coverage of protein-protein interfaces

The diverse range of cellular functions is performed by a limited number of protein folds existing in nature. One may similarly expect that cellular functional diversity would be covered by a limited number of protein-protein interface architectures. Here, we present 8205 interface clusters, each representing a unique interface architecture. This data set of protein-protein interfaces is analyzed and compared with older data sets. We observe that the number of both biological and crystal interfaces increases significantly compared to the number of Protein Data Bank entries. Furthermore, we find that the number of distinct interface architectures grows at a much faster rate than the number of folds and is yet to level off. We further analyze the growth trend of the functional coverage by constructing functional interaction networks from interfaces. The functional coverage is also found to steadily increase. Interestingly, we also observe that despite the diversity of interface architectures, some are more favorable and frequently used, and of particular interest, are the ones that are also preferred in single chains.     

蛋白质-蛋白质界面热点残基预测及其在线工具

蛋白质-蛋白质结合热点是界面中对结合自由能有着显著贡献的一小簇残基。捕捉和揭示这类热点残基可以加深对蛋白质间相互作用机制的理解,为蛋白质工程和药物设计提供指导。但实验技术费时费力且代价昂贵。计算工具可用于辅助和补充实验上的尝试。该文较详细、系统地介绍了蛋白质界面热点的特性、计算预测的策略与技术,并应用实例进一步说明这些方法学的特征;还介绍了界面热点的数据库和一些主要的在线预测工具,旨在为设计、挑选和应用这类工具解决特定问题的研究人员提供指南。     

Assessing predictions of protein-protein interaction: the CAPRI experiment

The Critical Assessment of PRedicted Interactions (CAPRI) experiment was designed in 2000 to test protein docking algorithms in blind predictions of the structure of protein-protein complexes. In four years, 17 complexes offered by crystallographers as targets prior to publication, have been subjected to structure prediction by docking their two components. Models of these complexes were submitted by predictor groups and assessed by comparing their geometry to the X-ray structure and by evaluating the quality of the prediction of the regions of interaction and of the pair wise residue contacts. Prediction was successful on 12 of the 17 targets, most of the failures being due to large conformation changes that the algorithms could not cope with. Progress in the prediction quality observed in four years indicates that the experiment is a powerful incentive to develop new procedures that allow for flexibility during docking and incorporate nonstructural information. We therefore call upon structural biologists who study protein-protein complexes to provide targets for further rounds of CAPRI predictions.     

A holistic molecular docking approach for predicting protein-protein complex structure

A holistic protein-protein molecular docking approach, HoDock, was established, composed of such steps as binding site prediction, initial complex structure sampling, refined complex structure sampling, structure clustering, scoring and final structure selection. This article explains the detailed steps and applications for CAPRI Target 39. The CAPRI result showed that three predicted binding site residues, A191HIS, B512ARG and B531ARG, were correct, and there were five submitted structures with a high fraction of correct receptor-ligand interface residues, indicating that this docking approach may improve prediction accuracy for protein-protein complex structures.     

MPtopo: A database of membrane protein topology

The reliability of the transmembrane (TM) sequence assignments for membrane proteins (MPs) in standard sequence databases is uncertain because the vast majority are based on hydropathy plots. A database of MPs with dependable assignments is necessary for developing new computational tools for the prediction of MP structure. We have therefore created MPtopo, a database of MPs whose topologies have been verified experimentally by means of crystallography, gene fusion, and other methods. Tests using MPtopo strongly validated four existing MP topology-prediction algorithms. MPtopo is freely available over the internet and can be queried by means of an SQL-based search engine.     

Interactome Mapping: Using Protein Microarray Technology to Reconstruct Diverse Protein Networks

A major focus of systems biology is to characterize interactions between cellular components, in order to develop an accurate picture of the intricate networks within biological systems. Over the past decade, protein microarrays have greatly contributed to advances in proteomics and are becoming an important platform for systems biology. Protein microarrays are highly flexible, ranging from large-scale proteome microarrays to smaller customizable microarrays, making the technology amenable for detection of a broad spectrum of biochemical properties of proteins. In this article, we will focus on the numerous studies that have utilized protein microarrays to reconstruct biological networks including protein-DNA interactions, posttranslational protein modifications (PTMs), lectin-glycan recognition, pathogen-host interactions and hierarchical signaling cascades. The diversity in applications allows for integration of interaction data from numerous molecular classes and cellular states, providing insight into the structure of complex biological systems. We will also discuss emerging applications and future directions of protein microarray technology in the global frontier.     

Computer modeling studies of the structure of a repressor

Due to advances in molecular biology the DNA sequences of structural genes coding for proteins are often known before a protein is characterized or even isolated. The function of a protein whose amino acid sequence has been deduced from a DNA sequence may not even be known. This has created greater interest in the development of methods to predict the tertiary structures of proteins. The a priori prediction of a protein's structure from its amino acid sequence is not yet possible. However, since proteins with similar amino acid sequences are observed to have similar three-dimensional structures, it is possible to use an analogy with a protein of known structure to draw some conclusions about the structure and properties of an uncharacterized protein. The process of predicting the tertiary structure of a protein relies very much upon computer modeling and analysis of the structure. The prediction of the structure of the bacteriophage 434 cro repressor is used as an example illustrating current procedures.     

Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect.

Data sets of 362 structurally nonredundant protein-protein interfaces and of 57 symmetry-related oligomeric interfaces have been used to explore whether the hydrophobic effect that guides protein folding is also the main driving force for protein-protein associations. The buried nonpolar surface area has been used to measure the hydrophobic effect. Our analysis indicates that, although the hydrophobic effect plays a dominant role in protein-protein binding, it is not as strong as that observed in the interior of protein monomers. Comparison of interiors of the monomers with those of the interfaces reveals that, in general, the hydrophobic amino acids are more frequent in the interior of the monomers than in the interior of the protein-protein interfaces. On the other hand, a higher proportion of charged and polar residues are buried at the interfaces, suggesting that hydrogen bonds and ion pairs contribute more to the stability of protein binding than to that of protein folding. Moreover, comparison of the interior of the interfaces to protein surfaces indicates that the interfaces are poorer in polar/charged than the surfaces and are richer in hydrophobic residues. The interior of the interfaces appears to constitute a compromise between the stabilization contributed by the hydrophobic effect on the one hand and avoiding patches on the protein surfaces that are too hydrophobic on the other. Such patches would be unfavorable for the unassociated monomers in solution. We conclude that, although the types of interactions are similar between protein-protein interfaces and single-chain proteins overall, the contribution of the hydrophobic effect to protein-protein associations is not as strong as to protein folding. This implies that packing patterns and interatom, or interresidue, pairwise potential functions, derived from monomers, are not ideally suited to predicting and assessing ligand associations or design. These would perform adequately only in cases where the hydrophobic effect at the binding site is substantial.     

简单的一致性方法预测蛋白质二级结构

蛋白质二级结构预测对于我们了解蛋白质空间结构是至关重要的一步。文章提出了一种简单的二级结构预测方法,该方法采用多数投票法将现有的3种较好的二级结构预测方法的预测结果汇集形成一致性预测结果。从PDB数据库中随机选取近两年新测定结构的57条相似性小于30%的蛋白质,对该方法的预测结果进行测试,其Q3准确率比3种独立的方法提高了1.12—2.29%,相关系数及SOV准确率也有相应的提高。并且各项准确率均比同样采用一致性方法的Jpred二级结构预测程序准确率要高。这种预测方法虽然原理简单,但无须使用额外的参数,计算量小,易于实现,最重要的前提就是必须选用目前准确性比较出色的蛋白质二级结构预测方法。     

Apolipoprotein E-low density lipoprotein receptor binding: study of protein-protein interaction in rationally selected docked complexes

Apolipoprotein E (apoE) is an important protein involved in lipid metabolism due to its interaction with members of the low-density lipoprotein receptor (LDLR) family. To further understand the molecular basis for this receptor-binding activity, an apoE fragment containing the receptor binding region (residues 135-151) was docked onto the fifth LDLR ligand binding repeat (LR5) by computational methods. A subset of structures generated by the docking was rationally selected on the grounds of experimental data combined with modeling and was used for further analysis. The application and comparison of two different experimental structures for the apoE fragment underlines the local structural changes occurring in apoE when switching from a receptor-inactive to a receptor-active conformation. The body of interactions occurring at the interface between the two proteins is in very good agreement with the biochemical data available for both apoE and LDLR. Charged residues are involved in numerous ionic interactions and might therefore be important for the specificity of the interaction between apoE and LR5. In addition, the interface also features a tryptophan and a stacking of histidine residues, revealing that the association between the two proteins is not entirely governed by ionic interactions. In particular, the presence of histidine residues in the interface gives a structural basis for the pH-regulated release mechanism of apoE in the endosomes. The proposed molecular basis for apoE binding to LDLR could aid the design of strategies for targeting alterations in lipid transport and metabolism.     

Interaction cutoff effect on ruggedness of protein-protein energy landscape

The concept of the energy landscape is important for better understanding of protein-protein interactions and for designing adequate docking procedures. The intermolecular landscape has a rugged terrain that impedes search procedures. Its inherent ruggedness is related to the conformational characteristics of the molecules and to the form of the potential function--more rugged for short-range potentials and less rugged for "soft," typically long-range potentials. Our study determined that the landscape ruggedness is further substantially exacerbated by truncation of the potentials. This additional ruggedness appears below certain critical interaction ranges that depend on the form of the potential. The theoretical model describing the cutoff effect on the landscape ruggedness is confirmed by the energy calculation on a dataset of protein-protein complexes. The negative effect of the potentials cutoff is well known. However, revealing its physical basis in terms of the energy landscape is important for better understanding of intermolecular interactions.     

New benchmark metrics for protein-protein docking methods

With the development of many computational methods that predict the structural models of protein-protein complexes, there is a pressing need to benchmark their performance. As was the case for protein monomers, assessing the quality of models of protein complexes is not straightforward. An effective scoring scheme should be able to detect substructure similarity and estimate its statistical significance. Here, we focus on characterizing the similarity of the interfaces of the complex and introduce two scoring functions. The first, the interfacial Template Modeling score (iTM-score), measures the geometric distance between the interfaces, while the second, the Interface Similarity score (IS-score), evaluates their residue-residue contact similarity in addition to their geometric similarity. We first demonstrate that the IS-score is more suitable for assessing docking models than the iTM-score. The IS-score is then validated in a large-scale benchmark test on 1562 dimeric complexes. Finally, the scoring function is applied to evaluate docking models submitted to the Critical Assessment of Prediction of Interactions (CAPRI) experiments. While the results according to the new scoring scheme are generally consistent with the original CAPRI assessment, the IS-score identifies models whose significance was previously underestimated.     

The ROP2 family of Toxoplasma gondii rhoptry proteins: proteomic and genomic characterization and molecular modeling

Four rhoptry proteins (ROP) of Toxoplasma gondii previously identified with mAb have been affinity purified and analyzed by MS; the data obtained allowed the genomic sequences to be assigned to these proteins. As previously suggested for some of them by antibody crossreactivity, these proteins were shown to belong to a family, the prototype of which being ROP2. We describe here the proteins ROP2, 4, 5, and 7. These four proteins correspond to the most abundant products of a gene family that comprises several members which we have identified in genomic and EST libraries. Eight additional sequences were found and we have cloned four of them. All members of the ROP2 family contain a protein-kinase-like domain, but only some of them possess a bona fide kinase catalytic site. Molecular modeling of the kinase domain demonstrates the conservation of residues critical for the stabilization of the protein-kinase fold, especially within a hydrophobic segment described so far as transmembrane and which appears as an helix buried inside the protein. The concomitant synthesis of these ROPs by T. gondii tachyzoites suggests a specific role for each of these proteins, especially in the early interaction with the host cell upon invasion.     

SHMTool: a webserver for comparative analysis of somatic hypermutation datasets

The somatic hypermutation (SHM) of Immunoglobulin variable (V) regions is a key process in the generation of antibody diversity. The growing number of datasets of point mutations that occur during SHM in mice and humans often include comparisons between wild-type and individuals or strains genetically defective in the repair mechanisms that contribute to SHM. However, it has been difficult to compare the results of different studies because the analyses have not been standardized for criteria such as correction for base composition and the inclusion of unique mutations. If many mutations are involved, the analysis can also be time consuming. To overcome these problems and facilitate a standardized analysis and display of similar data, we present a webserver (SHMTool) for comparing SHM datasets, available at http://scb.aecom.yu.edu/shmtool.