Abstract
Protein–protein interactions (PPIs) play crucial roles in diverse cellular processes. There are different types of PPIs based on the composition, affinity and whether the association is permanent or transient. Analyzing the diversity of PPIs at the atomic level is crucial for uncovering the key features governing the interactions involved in PPI. A systematic physico-chemical and conformational studies were implemented on interfaces involved in different PPIs, including crystal packing, weak transient heterodimers, weak transient homodimers, strong transient heterodimers and homodimers. The comparative analysis shows that the interfaces tend to be larger, less planar, and more tightly packed with the increase of the interaction strength. Meanwhile the strong interactions undergo greater conformational changes than the weak ones involving main chains as well as side chains. Finally, using 18 features derived from our analysis, we developed a support vector regression model to predict the binding affinity with a promising result, which further demonstrate the reliability of our studies. We believe this study will provide great help in more thorough understanding the mechanism of diverse PPIs.
Similar content being viewed by others
References
Bahadur RP, Chakrabarti P, Rodier F, Janin J (2004) A dissection of specific and non-specific protein–protein interfaces. J Mol Biol 336:943–955
Bernauer J, Bahadur RP, Rodier F, Janin J, Poupon A (2008) DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein–protein interactions. Bioinformatics 24:652–658
Krissinel E, Henrick K (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372:774–797
Ponstingl H, Henrick K, Thornton JM (2000) Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins 41:47–57
Zhu H, Domingues FS, Sommer I, Lengauer T (2006) Noxclass: prediction of protein–protein interaction types. BMC Bioinformatics 7:27
Nooren IM, Thornton JM (2003) Diversity of protein–protein interactions. EMBO J 22:3486–3492
Ozbabacan SE, Engin HB, Gursoy A, Keskin O (2011) Transient protein–protein interactions. Protein Eng 24:635–648
Perkins JR, Diboun I, Dessailly BH, Lees JG, Orengo C (2010) Transient protein–protein interactions: structural, functional, and network properties. Structure 18:1233–1243
Jones S, Thornton JM (1996) Principles of protein–protein interactions. Proc Natl Acad Sci USA 93:13–20
Nooren IM, Thornton JM (2003) Structural characterisation and functional significance of transient protein–protein interactions. J Mol Biol 325:991–1018
De S, Krishnadev O, Srinivasan N, Rekha N (2005) Interaction preferences across protein–protein interfaces of obligatory and non-obligatory components are different. BMC Struct Biol 5:15
Guharoy M, Chakrabarti P (2007) Secondary structure based analysis and classification of biological interfaces: identification of binding motifs in protein–protein interactions. Bioinformatics 23:1909–1918
Dey S, Pal A, Chakrabarti P, Janin J (2010) The subunit interfaces of weakly associated homodimeric proteins. J Mol Biol 398:146–160
La D, Kong M, Hoffman W, Choi YI, Kihara D (2013) Predicting permanent and transient protein–protein interfaces. Proteins 81:805–818
Kastritis PL, Moal IH, Hwang H, Weng Z, Bates PA, Bonvin AM, Janin J (2011) A structure-based benchmark for protein–protein binding affinity. Protein Sci 20:482–491
Wang R, Fang X, Lu Y, Wang S (2004) The PDBbind database: collection of binding affinities for protein–ligand complexes with three-dimensional structures. J Med Chem 47:2977–2980
Bahadur RP, Chakrabarti P, Rodier F, Janin J (2003) Dissecting subunit interfaces in homodimeric proteins. Proteins 53:708–719
Hubbard SJ, Thornton JM (1993) NACCESS: computer program. University College London, London
Ruvinsky AM, Kirys T, Tuzikov AV, Vakser IA (2011) Side-chain conformational changes upon protein–protein association. J Mol Biol 408:356–365
Kortemme T, Baker D (2002) A simple physical model for binding energy hot spots in protein–protein complexes. Proc Natl Acad Sci USA 99:14116–14121
Saha RP, Bahadur RP, Pal A, Mandal S, Chakrabarti P (2006) ProFace: a server for the analysis of the physicochemical features of protein–protein interfaces. BMC Struct Biol 6:11
Gutteridge A, Thornton J (2004) Conformational change in substrate binding, catalysis and product release: an open and shut case? FEBS Lett 567:67–73
Gutteridge A, Thornton J (2005) Conformational changes observed in enzyme crystal structures upon substrate binding. J Mol Biol 346:21–28
Echols N, Milburn D, Gerstein M (2003) MolMovDB: analysis and visualization of conformational change and structural flexibility. Nucleic Acids Res 31:478–482
Hayward S, Lee RA (2002) Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50. J Mol Graph Model 21:181–183
Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE (2000) Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 33:889–897
Melo F, Feytmans E (1997) Novel knowledge-based mean force potential at atomic level. J Mol Biol 267:207–222
Su Y, Zhou A, Xia X, Li W, Sun Z (2009) Quantitative prediction of protein–protein binding affinity with a potential of mean force considering volume correction. Protein Sci 18:2550–2558
Böhm HJ (1998) Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs. J Comput Aided Mol Des 12:309–323
Englebienne P, Moitessier N (2009) Docking ligands into flexible and solvated macromolecules. 4. Are popular scoring functions accurate for this class of proteins? J Chem Inf Model 49:1568–1580
Oda A, Tsuchida K, Takakura T, Yamaotsu N, Hirono S (2006) Comparison of consensus scoring strategies for evaluating computational models of protein–ligand complexes. J Chem Inf Model 46:380–391
Ballester PJ, Mitchell JB (2010) A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking. Bioinformatics 26:1169–1175
Li XL, Zhu M, Li XL, Wang HQ, Wang SL (2012) Protein–protein binding affinity prediction based on an SVR ensemble. Intell Comput Technol 7389:145–151
Janin J, Rodier F (1995) Protein–protein interaction at crystal contacts. Proteins 23:580–587
Lo Conte L, Chothia C, Janin J (1999) The atomic structure of protein–protein recognition sites. J Mol Biol 285:2177–2198
Laskowski RA (1995) SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph 13:323–330
Obiero J, Pittet V, Bonderoff SA, Sanders DA (2010) Thioredoxin system from Deinococcus radiodurans. J Bacteriol 192:494–501
Betts MJ, Sternberg MJ (1999) An analysis of conformational changes on protein–protein association: implications for predictive docking. Protein Eng 12:271–283
Janin J, Chothia C (1990) The structure of protein–protein recognition sites. J Biol Chem 265:16027–16030
Chrencik JE, Brooun A, Recht MI, Kraus ML, Koolpe M, Kolatkar AR, Bruce RH, Martiny-Baron G, Widmer H, Pasquale EB, Kuhn P (2006) Structure and thermodynamic characterization of the EphB4/Ephrin-B2 antagonist peptide complex reveals the determinants for receptor specificity. Structure 14:321–330
Grant BJ, Gorfe AA, McCammon JA (2010) Large conformational changes in proteins: signaling and other functions. Curr Opin Struct Biol 20:142–147
Zhou P, Wang C, Tian F, Ren Y, Yang C, Huang J (2013) Biomacromolecular quantitative structure–activity relationship (BioQSAR): a proof-of-concept study on the modeling, prediction and interpretation of protein–protein binding affinity. J Comput Aided Mol Des 27:67–78
Moal IH, Agius R, Bates PA (2011) Protein–protein binding affinity prediction on a diverse set of structures. Bioinformatics 27:3002–3009
Acknowledgments
This work was funded by the National Natural Science Foundation of China (No. 20905054 and 21175095).
Author information
Authors and Affiliations
Corresponding authors
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Luo, J., Guo, Y., Zhong, Y. et al. A functional feature analysis on diverse protein–protein interactions: application for the prediction of binding affinity. J Comput Aided Mol Des 28, 619–629 (2014). https://doi.org/10.1007/s10822-014-9746-y
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10822-014-9746-y