Peptide segments in protein-protein interfaces

An efficient computational protocol for template-based design of peptides that inhibit interactions involving SARS-CoV-2 proteins

The RNA-dependent RNA polymerase (RdRp) complex of SARS-CoV-2 lies at the core of its replication and transcription processes. The interfaces between holo-RdRp subunits are highly conserved, facilitating the design of inhibitors with high affinity for the interaction interface hotspots. We, therefore, take this as a model protein complex for the application of a structural bioinformatics protocol to design peptides that inhibit RdRp complexation by preferential binding at the interface of its core subunit nonstructural protein, nsp12, with accessory factor nsp7. Here, the interaction hotspots of the nsp7-nsp12 subunit of RdRp, determined from a long molecular dynamics trajectory, are used as a template. A large library of peptide sequences constructed from multiple hotspot motifs of nsp12 is screened in-silico to determine sequences with high geometric complementarity and interaction specificity for the binding interface of nsp7 (target) in the complex. Two lead designed peptides are extensively characterized using orthogonal bioanalytical methods to determine their suitability for inhibition of RdRp complexation. Binding affinity of these peptides to accessory factor nsp7, determined using a surface plasmon resonance (SPR) assay, is slightly better than that of nsp12: dissociation constant of 133nM and 167nM, respectively, compared to 473nM for nsp12. A competitive ELISA is used to quantify inhibition of nsp7-nsp12 complexation, with one of the lead peptides giving an IC50 of 25μM . Cell penetrability and cytotoxicity are characterized using a cargo delivery assay and MTT cytotoxicity assay, respectively. Overall, this work presents a proof-of-concept of an approach for rational discovery of peptide inhibitors of SARS-CoV-2 protein-protein interactions.

Interaction Energetics and Druggability of the Protein-Protein Interaction between Kelch-like ECH-Associated Protein 1 (KEAP1) and Nuclear Factor Erythroid 2 Like 2 (Nrf2)

Development of small molecule inhibitors of protein-protein interactions (PPIs) is hampered by our poor understanding of the druggability of PPI target sites. Here, we describe the combined application of alanine-scanning mutagenesis, fragment screening, and FTMap computational hot spot mapping to evaluate the energetics and druggability of the highly charged PPI interface between Kelch-like ECH-associated protein 1 (KEAP1) and nuclear factor erythroid 2 like 2 (Nrf2), an important drug target. FTMap identifies four binding energy hot spots at the active site. Only two of these are exploited by Nrf2, which alanine scanning of both proteins shows to bind primarily through E79 and E82 interacting with KEAP1 residues S363, R380, R415, R483, and S508. We identify fragment hits and obtain X-ray complex structures for three fragments via crystal soaking using a new crystal form of KEAP1. Combining these results provides a comprehensive and quantitative picture of the origins of binding energy at the interface. Our findings additionally reveal non-native interactions that might be exploited in the design of uncharged synthetic ligands to occupy the same site on KEAP1 that has evolved to bind the highly charged DEETGE binding loop of Nrf2. These include π-stacking with KEAP1 Y525 and interactions at an FTMap-identified hot spot deep in the binding site. Finally, we discuss how the complementary information provided by alanine-scanning mutagenesis, fragment screening, and computational hot spot mapping can be integrated to more comprehensively evaluate PPI druggability.

Benchmarking the PEPOP methods for mimicking discontinuous epitopes

Background

Computational methods provide approaches to identify epitopes in protein Ags to help characterizing potential biomarkers identified by high-throughput genomic or proteomic experiments. PEPOP version 1.0 was developed as an antigenic or immunogenic peptide prediction tool. We have now improved this tool by implementing 32 new methods (PEPOP version 2.0) to guide the choice of peptides that mimic discontinuous epitopes and thus potentially able to replace the cognate protein Ag in its interaction with an Ab. In the present work, we describe these new methods and the benchmarking of their performances.

Results

Benchmarking was carried out by comparing the peptides predicted by the different methods and the corresponding epitopes determined by X-ray crystallography in a dataset of 75 Ag-Ab complexes. The Sensitivity (Se) and Positive Predictive Value (PPV) parameters were used to assess the performance of these methods. The results were compared to that of peptides obtained either by chance or by using the SUPERFICIAL tool, the only available comparable method.

Conclusion

The PEPOP methods were more efficient than, or as much as chance, and 33 of the 34 PEPOP methods performed better than SUPERFICIAL. Overall, “optimized” methods (tools that use the traveling salesman problem approach to design peptides) can predict peptides that best match true epitopes in most cases.

Small protein-protein interfaces rich in electrostatic are often linked to regulatory function

Protein-protein interaction (PPI) is critical for several biological functions in living cells through the formation of an interface. Therefore, it is of interest to characterize protein-protein interfaces using an updated non-redundant structural dataset of 2557 homo (identical subunits) and 393 hetero (different subunits) dimer protein complexes determined by X-ray crystallography. We analyzed the interfaces using van der Waals (vdW), hydrogen bonding and electrostatic energies. Results show that on average homo and hetero interfaces are similar. Hence, we further grouped the 2950 interfaces based on percentage vdW to total energies into dominant (≥60%) and sub-dominant (<60%) vdW interfaces. Majority (92%) of interfaces have dominant vdW energy with large interface size (146 ± 87 (homo) and 137 ± 76 (hetero) residues) and interface area (1622 ± 1135 Ų (homo) and 1579 ± 1060 Ų (hetero)). However, a proportion (8%) of interfaces have sub-dominant vdW energy with small interface size (85 ± 46 (homo) and 88 ± 36 (hetero) residues) and interface area (823 ± 538 Ų (homo) and 881 ± 377 Ų (hetero)). It is found that large interfaces have two-fold more interface area and interface size than small interfaces with increasing hydrogen bonding energy to interface size. However, small interfaces have three-fold more electrostatics energy than large interfaces with increasing electrostatics to interface size. Thus, 8% of complexes having small interfaces with limited interface area and sub-dominant vdW energy are rich in electrostatics. It is interesting to observe that complexes having small interfaces are often associated with regulatory function. Hence, the observed structural features with known molecular function provide insights for the better understanding of PPI.Communicated by Ramaswamy H. Sarma.

Inferring and Using Protein Quaternary Structure Information from Crystallographic Data

A precise knowledge of the quaternary structure of proteins is essential to illuminate both their function and their evolution. The major part of our knowledge on quaternary structure is inferred from X-ray crystallography data, but this inference process is hard and error-prone. The difficulty lies in discriminating fortuitous protein contacts, which make up the lattice of protein crystals, from biological protein contacts that exist in the native cellular environment. Here, we review methods devised to discriminate between both types of contacts and describe resources for downloading protein quaternary structure information and identifying high-confidence quaternary structures. The use of high-confidence datasets of quaternary structures will be critical for the analysis of structural, functional, and evolutionary properties of proteins.

Protein-protein interfaces are vdW dominant with selective H-bonds and (or) electrostatics towards broad functional specificity

Several catalysis, cellular regulation, immune function, cell wall assembly, transport, signaling and inhibition occur through Protein- Protein Interactions (PPI). This is possible with the formation of specific yet stable protein-protein interfaces. Therefore, it is of interest to understand its molecular principles using structural data in relation to known function. Several interface features have been documented using known X-ray structures of protein complexes since 1975. This has improved our understanding of the interface using structural features such as interface area, binding energy, hydrophobicity, relative hydrophobicity, salt bridges and hydrogen bonds. The strength of binding between two proteins is dependent on interface size (number of residues at the interface) and thus its corresponding interface area. It is known that large interfaces have high binding energy (sum of (van der Waals) vdW, H-bonds, electrostatics). However, the selective role played by each of these energy components and more especially that of vdW is not explicitly known. Therefore, it is important to document their individual role in known protein-protein structural complexes. It is of interest to relate interface size with vdW, H-bonds and electrostatic interactions at the interfaces of protein structural complexes with known function using statistical and multiple linear regression analysis methods to identify the prominent force. We used the manually curated non-redundant dataset of 278 hetero-dimeric protein structural complexes grouped using known functions by Sowmya et al. (2015) to gain additional insight to this phenomenon using a robust inter-atomic non-covalent interaction analyzing tool PPCheck (Anshul and Sowdhamini, 2015). This dataset consists of obligatory (enzymes, regulator, biological assembly), immune and nonobligatory (enzyme and regulator inhibitors) complexes. Results show that the total binding energy is more for large interfaces. However, this is not true for its individual energy factors. Analysis shows that vdW energies contribute to about 75% ± 11% on average among all complexes and it also increases with interface size (r2 ranging from 0.67 to 0.89 with p<0.01) at 95% confidence limit irrespective of molecular function. Thus, vdW is both dominant and proportional at the interface independent of molecular function. Nevertheless, H bond energy contributes to 15% ± 6.5% on average in these complexes. It also moderately increases with interface size (r2 ranging from 0.43 to 0.61 with p<0.01) only among obligatory and immune complexes. Moreover, there is about 11.3% ± 8.7% contribution by electrostatic energy. It increases with interface size specifically among non-obligatory regulator-inhibitors (r2 = 0.44). It is implied that both H-bonds and electrostatics are neither dominant nor proportional at the interface. Nonetheless, their presence cannot be ignored in binding. Therefore, H-bonds and (or) electrostatic energy having specific role for improved stability in complexes is implied. Thus, vdW is common at the interface stabilized further with selective H-bonds and (or) electrostatic interactions at an atomic level in almost all complexes. Comparison of this observation with residue level analysis of the interface is compelling. The role by H-bonds (14.83% ± 6.5% and r2 = 0.61 with p<0.01) among obligatory and electrostatic energy (8.8% ± 4.77% and r2 = 0.63 with p <0.01) among non-obligatory complexes within interfaces (class A) having more non-polar residues than surface is influencing our inference. However, interfaces (class B) having less non-polar residues than surface show 1.5 fold more electrostatic energy on average. The interpretation of the interface using inter-atomic (vdW, H-bonds, electrostatic) interactions combined with inter-residue predominance (class A and class B) in relation to known function is the key to reveal its molecular principles with new challenges.

A structural dissection of large protein-protein crystal packing contacts

With the rapid increase in crystal structures of protein-protein complexes deposited in the Protein Data Bank (PDB), more and more crystal contacts have been shown to have similar or even larger interface areas than biological interfaces. However, little attention has been paid to these large crystal packing contacts and their structural principles remain unknown. To address this issue, we used a comparative feature analysis to analyze the geometric and physicochemical properties of large crystal packing contacts by comparing two types of specific protein-protein interactions (PPIs), weak transient complexes and permanent homodimers. Our results show that although large crystal packing contacts have a similar interface area and contact size as permanent homodimers, they tend to be more planar, loosely packed and less hydrophobic than permanent homodimers and cannot form a central core region that is fully buried during interaction. However, the properties of large crystal packing contacts, except for the interface area and contact size, more closely resemble those of weak transient complexes. The large overlap between biological and large crystal packing contacts indicates that interface properties are not efficient indicators for classification of biological interfaces from large crystal packing contacts and finding other specific features urgently needed.

Flexibility and small pockets at protein-protein interfaces: New insights into druggability

The transient assembly of multiprotein complexes mediates many aspects of cell regulation and signalling in living organisms. Modulation of the formation of these complexes through targeting protein-protein interfaces can offer greater selectivity than the inhibition of protein kinases, proteases or other post-translational regulatory enzymes using substrate, co-factor or transition state mimetics. However, capitalising on protein-protein interaction interfaces as drug targets has been hindered by the nature of interfaces that tend to offer binding sites lacking the well-defined large cavities of classical drug targets. In this review we posit that interfaces formed by concerted folding and binding (disorder-to-order transitions on binding) of one partner and other examples of interfaces where a protein partner is bound through a continuous epitope from a surface-exposed helix, flexible loop or chain extension may be more tractable for the development of "orthosteric", competitive chemical modulators; these interfaces tend to offer small-volume but deep pockets and/or larger grooves that may be bound tightly by small chemical entities. We discuss examples of such protein-protein interaction interfaces for which successful chemical modulators are being developed.

Structural, evolutionary, and assembly principles of protein oligomerization

In the protein universe, 30-50% of proteins self-assemble to form symmetrical complexes consisting of multiple copies of themselves, called homomers. The prevalence of homomers motivates us to review many of their properties. In Section 1, we describe the methods and challenges associated with quaternary structure inference-these methods are indeed at the basis of any analysis on homomers. In Section 2, we describe the morphological properties of homomers, as well as the database 3DComplex, which provides a taxonomy for both homomeric and heteromeric protein complexes. In Section 3, we review interface properties of homomeric complexes. In Section 4, we then present recent findings on the evolution of homomer interfaces, which we link in Section 5 to the evolution of homomers as entire entities. In Section 6, we discuss mechanisms involved in their assembly and how these mechanisms can be linked to evolution.

2P2Idb: a structural database dedicated to orthosteric modulation of protein-protein interactions

Protein–protein interactions are considered as one of the next generation of therapeutic targets. Specific tools thus need to be developed to tackle this challenging chemical space. In an effort to derive some common principles from recent successes, we have built 2P2Idb (freely accessible at http://2p2idb.cnrs-mrs.fr), a hand-curated structural database dedicated to protein–protein interactions with known orthosteric modulators. It includes all interactions for which both the protein–protein and protein–ligand complexes have been structurally characterized. A web server provides links to related sites of interest, binding affinity data, pre-calculated structural information about protein–protein interfaces and 3D interactive views through java applets. Comparison of interfaces in 2P2Idb to those of representative datasets of heterodimeric complexes has led to the identification of geometrical parameters and residue properties to assess the druggability of protein–protein complexes. A tool is proposed to calculate a series of biophysical and geometrical parameters that characterize protein–protein interfaces. A large range of descriptors are computed including, buried accessible surface area, gap volume, non-bonded contacts, hydrogen-bonds, atom and residue composition, number of segments and secondary structure contribution. All together the 2P2I database represents a structural source of information for scientists from academic institutions or pharmaceutical industries.

Insights from the structural analysis of protein heterodimer interfaces

Protein heterodimer complexes are often involved in catalysis, regulation, assembly, immunity and inhibition. This involves the formation of stable interfaces between the interacting partners. Hence, it is of interest to describe heterodimer interfaces using known structural complexes. We use a non-redundant dataset of 192 heterodimer complex structures from the protein databank (PDB) to identify interface residues and describe their interfaces using amino-acids residue property preference. Analysis of the dataset shows that the heterodimer interfaces are often abundant in polar residues. The analysis also shows the presence of two classes of interfaces in heterodimer complexes. The first class of interfaces (class A) with more polar residues than core but less than surface is known. These interfaces are more hydrophobic than surfaces, where protein-protein binding is largely hydrophobic. The second class of interfaces (class B) with more polar residues than core and surface is shown. These interfaces are more polar than surfaces, where binding is mainly polar. Thus, these findings provide insights to the understanding of protein-protein interactions.

PRICE (PRotein Interface Conservation and Energetics): a server for the analysis of protein-protein interfaces

Residues in a protein-protein interface that are important for forming and stabilizing the interaction can usually be identified by looking at patterns of evolutionary conservation in groups of homologous proteins and also by the computational identification of binding hotspots. The PRICE (PRotein Interface Conservation and Energetics) server takes the coordinates of a protein-protein complex, dissects the interface into core and rim regions, and calculates (1) the degree of conservation (measured as the sequence entropy), as well as (2) the change in free energy of binding (∆∆G, due to alanine scanning mutagenesis) of interface residues. Results are displayed as color-coded plots and also made available for download. This enables the computational identification of binding hot spots, based on which further experiments can be designed. The method will aid in protein functional prediction by correct assignment of hot regions involved in binding. Consideration of sequence entropies for residues with large ∆∆G values may provide an indication of the biological relevance of the interface. Finally, the results obtained on a test set of alanine mutants has been compared to those obtained using other servers/methods. The PRICE server is a web application available at http://www.boseinst.ernet.in/resources/bioinfo/stag.html.

Deciphering the shape and deformation of secondary structures through local conformation analysis

Background

Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation.

Results

Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface) reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations.

Conclusion

The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons.

Can self-inhibitory peptides be derived from the interfaces of globular protein-protein interactions?

In this study, we assess on a large scale the possibility of deriving self-inhibitory peptides from protein domains with globular architectures. Such inhibitory peptides would inhibit interactions of their origin domain by mimicking its mode of binding to cognate partners, and could serve as promising leads for rational design of inhibitory drugs. For our large-scale analysis, we analyzed short linear segments that were cut out of protein interfaces in silico in complex structures of protein-protein docking Benchmark 3.0 and CAPRI targets from rounds 1-19. Our results suggest that more than 50% of these globular interactions are dominated by one short linear segment at the domain interface, which provides more than half of the original interaction energy. Importantly, in many cases the derived peptides show strong energetic preference for their original binding mode independently of the context of their original domain, as we demonstrate by extensive computational peptide docking experiments. As an in depth case study, we computationally design a candidate peptide to inhibit the EphB4-EphrinB2 interaction based on a short peptide derived from the G-H loop in EphrinB2. Altogether, we provide an elaborate framework for the in silico selection of candidate inhibitory molecules for protein-protein interactions. Such candidate molecules can be readily subjected to wet-laboratory experiments and provide highly promising starting points for subsequent drug design.

Conserved residue clusters at protein-protein interfaces and their use in binding site identification

BACKGROUND

Biological evolution conserves protein residues that are important for structure and function. Both protein stability and function often require a certain degree of structural co-operativity between spatially neighboring residues and it has previously been shown that conserved residues occur clustered together in protein tertiary structures, enzyme active sites and protein-DNA interfaces. Residues comprising protein interfaces are often more conserved compared to those occurring elsewhere on the protein surface. We investigate the extent to which conserved residues within protein-protein interfaces are clustered together in three-dimensions.

RESULTS

Out of 121 and 392 interfaces in homodimers and heterocomplexes, 96.7 and 86.7%, respectively, have the conserved positions clustered within the overall interface region. The significance of this clustering was established in comparison to what is seen for the subsets of the same size of randomly selected residues from the interface. Conserved residues occurring in larger interfaces could often be sub-divided into two or more distinct sub-clusters. These structural cluster(s) comprising conserved residues indicate functionally important regions within the protein-protein interface that can be targeted for further structural and energetic analysis by experimental scanning mutagenesis. Almost 60% of experimental hot spot residues (with DeltaDeltaG > 2 kcal/mol) were localized to these conserved residue clusters. An analysis of the residue types that are enriched within these conserved subsets compared to the overall interface showed that hydrophobic and aromatic residues are favored, but charged residues (both positive and negative) are less common. The potential use of this method for discriminating binding sites (interfaces) versus random surface patches was explored by comparing the clustering of conserved residues within each of these regions--in about 50% cases the true interface is ranked among the top 10% of all surface patches.

CONCLUSIONS

Protein-protein interaction sites are much larger than small molecule biding sites, but still conserved residues are not randomly distributed over the whole interface and are distinctly clustered. The clustered nature of evolutionarily conserved residues within interfaces as compared to those within other surface patches not involved in binding has important implications for the identification of protein-protein binding sites and would have applications in docking studies.

Atomic analysis of protein-protein interfaces with known inhibitors: the 2P2I database

Background

In the last decade, the inhibition of protein-protein interactions (PPIs) has emerged from both academic and private research as a new way to modulate the activity of proteins. Inhibitors of these original interactions are certainly the next generation of highly innovative drugs that will reach the market in the next decade. However, in silico design of such compounds still remains challenging.

Methodology/Principal Findings

Here we describe this particular PPI chemical space through the presentation of 2P2I_DB, a hand-curated database dedicated to the structure of PPIs with known inhibitors. We have analyzed protein/protein and protein/inhibitor interfaces in terms of geometrical parameters, atom and residue properties, buried accessible surface area and other biophysical parameters. The interfaces found in 2P2I_DB were then compared to those of representative datasets of heterodimeric complexes. We propose a new classification of PPIs with known inhibitors into two classes depending on the number of segments present at the interface and corresponding to either a single secondary structure element or to a more globular interacting domain. 2P2I_DB complexes share global shape properties with standard transient heterodimer complexes, but their accessible surface areas are significantly smaller. No major conformational changes are seen between the different states of the proteins. The interfaces are more hydrophobic than general PPI's interfaces, with less charged residues and more non-polar atoms. Finally, fifty percent of the complexes in the 2P2I_DB dataset possess more hydrogen bonds than typical protein-protein complexes. Potential areas of study for the future are proposed, which include a new classification system consisting of specific families and the identification of PPI targets with high druggability potential based on key descriptors of the interaction.

Conclusions

2P2I database stores structural information about PPIs with known inhibitors and provides a useful tool for biologists to assess the potential druggability of their interfaces. The database can be accessed at http://2p2idb.cnrs-mrs.fr.

Computational analysis and determination of a highly conserved surface exposed segment in H5N1 avian flu and H1N1 swine flu neuraminidase

Background

Catalytic activity of influenza neuraminidase (NA) facilitates elution of progeny virions from infected cells and prevents their self-aggregation mediated by the catalytic site located in the body region. Research on the active site of the molecule has led to development of effective inhibitors like oseltamivir, zanamivir etc, but the high rate of mutation and interspecies reassortment in viral sequences and the recent reports of oseltamivir resistant strains underlines the importance of determining additional target sites for developing future antiviral compounds. In a recent computational study of 173 H5N1 NA gene sequences we had identified a 50-base highly conserved region in 3'-terminal end of the NA gene.

Results

We extend the graphical and numerical analyses to a larger number of H5N1 NA sequences (514) and H1N1 swine flu sequences (425) accessed from GenBank. We use a 2D graphical representation model for the gene sequences and a Graphical Sliding Window Method (GSWM) for protein sequences scanning the sequences as a block of 16 amino acids at a time. Using a protein sequence descriptor defined in our model, the protein sliding scan method allowed us to compare the different strains for block level variability, which showed significant statistical correlation to average solvent accessibility of the residue blocks; single amino acid position variability results in no correlation, indicating the impact of stretch variability in chemical environment. Close to the C-terminal end the GSWM showed less descriptor-variability with increased average solvent accessibility (ASA) that is also supported by conserved predicted secondary structure of 3' terminal RNA and visual evidence from 3D crystallographic structure.

Conclusion

The identified terminal segment, strongly conserved in both RNA and protein sequences, is especially significant as it is surface exposed and structural chemistry reveals the probable role of this stretch in tetrameric stabilization. It could also participate in other biological processes associated with conserved surface residues. A RNA double hairpin secondary structure found in this segment in a majority of the H5N1 strains also supports this observation. In this paper we propose this conserved region as a probable site for designing inhibitors for broad-spectrum pandemic control of flu viruses with similar NA structure.

The subunit interfaces of weakly associated homodimeric proteins

We analyzed subunit interfaces in 315 homodimers with an X-ray structure in the Protein Data Bank, validated by checking the literature for data that indicate that the proteins are dimeric in solution and that, in the case of the "weak" dimers, the homodimer is in equilibrium with the monomer. The interfaces of the 42 weak dimers, which are smaller by a factor of 2.4 on average than in the remainder of the set, are comparable in size with antibody-antigen or protease-inhibitor interfaces. Nevertheless, they are more hydrophobic than in the average transient protein-protein complex and similar in amino acid composition to the other homodimer interfaces. The mean numbers of interface hydrogen bonds and hydration water molecules per unit area are also similar in homodimers and transient complexes. Parameters related to the atomic packing suggest that many of the weak dimer interfaces are loosely packed, and we suggest that this contributes to their low stability. To evaluate the evolutionary selection pressure on interface residues, we calculated the Shannon entropy of homologous amino acid sequences at 60% sequence identity. In 93% of the homodimers, the interface residues are better conserved than the residues on the protein surface. The weak dimers display the same high degree of interface conservation as other homodimers, but their homologs may be heterodimers as well as homodimers. Their interfaces may be good models in terms of their size, composition, and evolutionary conservation for the labile subunit contacts that allow protein assemblies to share and exchange components, allosteric proteins to undergo quaternary structure transitions, and molecular machines to operate in the cell.

Accessibility and partner number of protein residues, their relationship and a webserver, ContPlot for their display

Background

Depending on chemical features residues have preferred locations – interior or exterior – in protein structures, which also determine how many other residues are found around them. The close packing of residues is the hallmark of protein interior and protein-protein interaction sites.

Results

The average values of accessible surface area (ASA) and partner number (PN, the number of other residues within a distance of 4.5 Å from any atom of a given residue) of different residues have been determined and a webserver, ContPlot has been designed to display these values (relative to the average values) along the protein sequence. This would be useful to visually identify residues that are densely packed, or those involved in protein-protein interactions. The skewness observed in the distribution of PNs is indicative of the hydrophobic or hydrophilic nature of the residue. The variation of ASA with PN can be analytically expressed in terms of a cubic equation. These equations (one for each residue) can be used to estimate the ASA of a polypeptide chain using the PNs of the individual residues in the structure.

Conclusion

The atom-based PNs (obtained by counting surrounding atoms) are highly correlated to the residue-based PN, indicating that the latter can adequately capture the atomic details of packing. The average values of ASA and PN associated with each residue should be useful in protein structure prediction or fold-recognition algorithm. ContPlot would provide a handy tool to assess the importance of a residue in the protein structure or interaction site.

Dissection, residue conservation, and structural classification of protein-DNA interfaces

The basic DNA-binding modules of 128 protein-DNA interfaces have been analyzed. Although these are less planar, like the protein-protein interfaces, the protein-DNA interfaces can also be dissected into core regions in which all the fully-buried atoms are located, and rim regions having atoms with residual accessibilities. The sequence entropy of the core residues is smaller than those in the rim, indicating that the former are better conserved and possibly contribute more towards the binding free energy, as has been implicated in protein-protein interactions. On the protein side, 1014 A(2) of the surface is buried of which 63% belong to the core. There are some differences in the propensities of residues to occur in the core and the rim. In the DNA strands, the nucleotide(s) containing fully-buried atoms in all three components usually occupy central positions of the binding region. A new classification scheme for the interfaces has been introduced based on the composition of secondary structural elements of residues and the results compared with the conventional classification of DNA-binding proteins, as well as the protein class of the molecule. It appears that a common framework may be developed to understand both protein-protein and protein-DNA interactions.

Cavities and atomic packing in protein structures and interfaces

A comparative analysis of cavities enclosed in a tertiary structure of proteins and interfaces formed by the interaction of two protein subunits in obligate and non-obligate categories (represented by homodimeric molecules and heterocomplexes, respectively) is presented. The total volume of cavities increases with the size of the protein (or the interface), though the exact relationship may vary in different cases. Likewise, for individual cavities also there is quantitative dependence of the volume on the number of atoms (or residues) lining the cavity. The larger cavities tend to be less spherical, solvated, and the interfaces are enriched in these. On average 15 A(3) of cavity volume is found to accommodate single water, with another 40-45 A(3) needed for each additional solvent molecule. Polar atoms/residues have a higher propensity to line solvated cavities. Relative to the frequency of occurrence in the whole structure (or interface), residues in beta-strands are found more often lining the cavities, and those in turn and loop the least. Any depression in one chain not complemented by a protrusion in the other results in a cavity in the protein-protein interface. Through the use of the Voronoi volume, the packing of residues involved in protein-protein interaction has been compared to that in the protein interior. For a comparable number of atoms the interface has about twice the number of cavities relative to the tertiary structure.

Protein–protein interaction and quaternary structure

Protein–protein recognition plays an essential role in structure and function. Specific non-covalent interactions stabilize the structure of macromolecular assemblies, exemplified in this review by oligomeric proteins and the capsids of icosahedral viruses. They also allow proteins to form complexes that have a very wide range of stability and lifetimes and are involved in all cellular processes. We present some of the structure-based computational methods that have been developed to characterize the quaternary structure of oligomeric proteins and other molecular assemblies and analyze the properties of the interfaces between the subunits. We compare the size, the chemical and amino acid compositions and the atomic packing of the subunit interfaces of protein–protein complexes, oligomeric proteins, viral capsids and protein–nucleic acid complexes. These biologically significant interfaces are generally close-packed, whereas the non-specific interfaces between molecules in protein crystals are loosely packed, an observation that gives a structural basis to specific recognition. A distinction is made within each interface between a core that contains buried atoms and a solvent accessible rim. The core and the rim differ in their amino acid composition and their conservation in evolution, and the distinction helps correlating the structural data with the results of site-directed mutagenesis and in vitro studies of self-assembly.

Secondary structure based analysis and classification of biological interfaces: identification of binding motifs in protein–protein interactions

MOTIVATION

The increasing amount of data on protein-protein interaction needs to be rationalized for deriving guidelines for the alteration or design of an interface between two proteins.

RESULTS

We present a detaild structural analysis and comparison of homo- versus heterodimeric protein-protein interfaces. Regular secondary structures (helices and strands) are the main components of the former, whereas non-regular structures (turns, loops, etc.) frequently mediate interactions in the latter. Interface helices get longer with increasing interface area, but only in heterocomplexes. On average, the homodimers have longer helical segments and prominent helix-helix pairs. There is a surprising distinction in the relative orientation of interface helices, with a tendency for aligned packing in homodimers and a clear preference for packing at 90 degrees in heterodimers. Arg and the aromatic residues have a higher preference to occur in all secondary structural elements (SSEs) in the interface. Based on the dominant SSE, the interfaces have been grouped into four classes: alpha, beta, alphabeta and non-regular. Identity between protein and interface classes is the maximum for alpha proteins, but rather mediocre for the other protein classes. The interface classes of the two chains forming a heterodimer are often dissimilar. Eleven binding motifs can capture the prominent architectural features of most of the interfaces.