High-resolution Global Peptide-protein Docking Using Fragments-based PIPER-FlexPepDock

Overview

Journal PLoS Comput Biol

Specialty Biology

Date 2017 Dec 28

PMID 29281622

Citations 59

Authors

Nawsad Alam

Oriel Goldstein

Bing Xia

Kathryn A Porter

Dima Kozakov

Ora Schueler-Furman

Affiliations

Soon will be listed here.

Abstract

Peptide-protein interactions contribute a significant fraction of the protein-protein interactome. Accurate modeling of these interactions is challenging due to the vast conformational space associated with interactions of highly flexible peptides with large receptor surfaces. To address this challenge we developed a fragment based high-resolution peptide-protein docking protocol. By streamlining the Rosetta fragment picker for accurate peptide fragment ensemble generation, the PIPER docking algorithm for exhaustive fragment-receptor rigid-body docking and Rosetta FlexPepDock for flexible full-atom refinement of PIPER docked models, we successfully addressed the challenge of accurate and efficient global peptide-protein docking at high-resolution with remarkable accuracy, as validated on a small but representative set of peptide-protein complex structures well resolved by X-ray crystallography. Our approach opens up the way to high-resolution modeling of many more peptide-protein interactions and to the detailed study of peptide-protein association in general. PIPER-FlexPepDock is freely available to the academic community as a server at http://piperfpd.furmanlab.cs.huji.ac.il.

Citing Articles

Efficient Refinement of Complex Structures of Flexible Histone Peptides Using Post-Docking Molecular Dynamics Protocols.

Bayarsaikhan B, Zsido B, Borzsei R, Hetenyi C Int J Mol Sci. 2024; 25(11).

PMID: 38892133 PMC: 11172440. DOI: 10.3390/ijms25115945.

Leveraging machine learning models for peptide-protein interaction prediction.

Yin S, Mi X, Shukla D RSC Chem Biol. 2024; 5(5):401-417.

PMID: 38725911 PMC: 11078210. DOI: 10.1039/d3cb00208j.

Peptriever: a Bi-Encoder approach for large-scale protein-peptide binding search.

Gurvich R, Markel G, Tanoli Z, Meirson T Bioinformatics. 2024; 40(5).

PMID: 38710496 PMC: 11112044. DOI: 10.1093/bioinformatics/btae303.

A New Advanced Approach: Design and Screening of Affinity Peptide Ligands Using Computer Simulation Techniques.

Wei Z, Chen M, Lu X, Liu Y, Peng G, Yang J Curr Top Med Chem. 2024; 24(8):667-685.

PMID: 38549525 DOI: 10.2174/0115680266281358240206112605.

Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools.

Vincenzi M, Mercurio F, Leone M Int J Mol Sci. 2024; 25(3).

PMID: 38339078 PMC: 10855943. DOI: 10.3390/ijms25031798.

References

London N, Movshovitz-Attias D, Schueler-Furman O . The structural basis of peptide-protein binding strategies. Structure. 2010; 18(2):188-99. DOI: 10.1016/j.str.2009.11.012. View

de Vries S, Rey J, Schindler C, Zacharias M, Tuffery P . The pepATTRACT web server for blind, large-scale peptide-protein docking. Nucleic Acids Res. 2017; 45(W1):W361-W364. PMC: 5570166. DOI: 10.1093/nar/gkx335. View

Venkatraman V, Yang Y, Sael L, Kihara D . Protein-protein docking using region-based 3D Zernike descriptors. BMC Bioinformatics. 2009; 10:407. PMC: 2800122. DOI: 10.1186/1471-2105-10-407. View

Kurcinski M, Jamroz M, Blaszczyk M, Kolinski A, Kmiecik S . CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site. Nucleic Acids Res. 2015; 43(W1):W419-24. PMC: 4489223. DOI: 10.1093/nar/gkv456. View

Berman H, Westbrook J, Feng Z, Gilliland G, Bhat T, Weissig H . The Protein Data Bank. Nucleic Acids Res. 1999; 28(1):235-42. PMC: 102472. DOI: 10.1093/nar/28.1.235. View

Gray J, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl C . Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol. 2003; 331(1):281-99. DOI: 10.1016/s0022-2836(03)00670-3. View

Pawson T, Nash P . Assembly of cell regulatory systems through protein interaction domains. Science. 2003; 300(5618):445-52. DOI: 10.1126/science.1083653. View

Trellet M, Melquiond A, Bonvin A . A unified conformational selection and induced fit approach to protein-peptide docking. PLoS One. 2013; 8(3):e58769. PMC: 3596317. DOI: 10.1371/journal.pone.0058769. View

Kozakov D, Beglov D, Bohnuud T, Mottarella S, Xia B, Hall D . How good is automated protein docking?. Proteins. 2013; 81(12):2159-66. PMC: 3934018. DOI: 10.1002/prot.24403. View

10.

Vanhee P, Verschueren E, Baeten L, Stricher F, Serrano L, Rousseau F . BriX: a database of protein building blocks for structural analysis, modeling and design. Nucleic Acids Res. 2010; 39(Database issue):D435-42. PMC: 3013806. DOI: 10.1093/nar/gkq972. View

11.

Davis I, Arendall 3rd W, Richardson D, Richardson J . The backrub motion: how protein backbone shrugs when a sidechain dances. Structure. 2006; 14(2):265-74. DOI: 10.1016/j.str.2005.10.007. View

12.

Park H, Lee G, Heo L, Seok C . Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments. PLoS One. 2014; 9(11):e113811. PMC: 4242723. DOI: 10.1371/journal.pone.0113811. View

13.

Trabuco L, Lise S, Petsalaki E, Russell R . PepSite: prediction of peptide-binding sites from protein surfaces. Nucleic Acids Res. 2012; 40(Web Server issue):W423-7. PMC: 3394340. DOI: 10.1093/nar/gks398. View

14.

Brooks B, Brooks 3rd C, MacKerell Jr A, Nilsson L, Petrella R, Roux B . CHARMM: the biomolecular simulation program. J Comput Chem. 2009; 30(10):1545-614. PMC: 2810661. DOI: 10.1002/jcc.21287. View

15.

Webb B, Sali A . Comparative Protein Structure Modeling Using MODELLER. Curr Protoc Bioinformatics. 2014; 47:5.6.1-32. DOI: 10.1002/0471250953.bi0506s47. View

16.

Moncalian G, Cardenes N, Deribe Y, Spinola-Amilibia M, Dikic I, Bravo J . Atypical polyproline recognition by the CMS N-terminal Src homology 3 domain. J Biol Chem. 2006; 281(50):38845-53. DOI: 10.1074/jbc.M606411200. View

17.

Lavi A, Ngan C, Movshovitz-Attias D, Bohnuud T, Yueh C, Beglov D . Detection of peptide-binding sites on protein surfaces: the first step toward the modeling and targeting of peptide-mediated interactions. Proteins. 2013; 81(12):2096-105. PMC: 4183195. DOI: 10.1002/prot.24422. View

18.

Berman H, Battistuz T, Bhat T, Bluhm W, Bourne P, Burkhardt K . The Protein Data Bank. Acta Crystallogr D Biol Crystallogr. 2002; 58(Pt 6 No 1):899-907. DOI: 10.1107/s0907444902003451. View

19.

Song Y, DiMaio F, Wang R, Kim D, Miles C, Brunette T . High-resolution comparative modeling with RosettaCM. Structure. 2013; 21(10):1735-42. PMC: 3811137. DOI: 10.1016/j.str.2013.08.005. View

20.

Li Y, Suino K, Daugherty J, Xu H . Structural and biochemical mechanisms for the specificity of hormone binding and coactivator assembly by mineralocorticoid receptor. Mol Cell. 2005; 19(3):367-80. DOI: 10.1016/j.molcel.2005.06.026. View