Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations
Abstract
We find that peptides mediate up to 40% of known protein-protein interactions in higher eukaryotes and play a key role in cellular signaling, protein trafficking, immunology, and oncology. However, it is challenging to predict peptide-protein binding with conventional computational modeling approaches, due to slow dynamics and high peptide flexibility. Here, we present a prototype of the approach which combines global peptide docking using ClusPro PeptiDock and all-atom enhanced simulations using Gaussian accelerated molecular dynamics (GaMD). For three distinct model peptides, the lowest backbone root-mean-square deviations (RMSDs) of their bound conformations relative to X-ray structures obtained from PeptiDock were 3.3–4.8 Å, being medium quality predictions according to the Critical Assessment of PRediction of Interactions (CAPRI) criteria. GaMD simulations refined the peptide-protein complex structures with significantly reduced peptide backbone RMSDs of 0.6–2.7 Å, yielding two high quality (sub-angstrom) and one medium quality models. Furthermore, the GaMD simulations identified important low-energy conformational states and revealed the mechanism of peptide binding to the target proteins. Therefore, PeptiDock+GaMD is a promising approach for exploring peptide-protein interactions.
- Authors:
-
- Univ. of Kansas, Lawrence, KS (United States)
- Stony Brook Univ., NY (United States). Laufer Center for Physical and Quantitative Biology
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1577835
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Frontiers in Molecular Biosciences
- Additional Journal Information:
- Journal Volume: 6; Journal ID: ISSN 2296-889X
- Publisher:
- Frontiers Media SA
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Wang, Jinan, Alekseenko, Andrey, Kozakov, Dima, and Miao, Yinglong. Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations. United States: N. p., 2019.
Web. doi:10.3389/fmolb.2019.00112.
Wang, Jinan, Alekseenko, Andrey, Kozakov, Dima, & Miao, Yinglong. Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations. United States. https://doi.org/10.3389/fmolb.2019.00112
Wang, Jinan, Alekseenko, Andrey, Kozakov, Dima, and Miao, Yinglong. Wed .
"Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations". United States. https://doi.org/10.3389/fmolb.2019.00112. https://www.osti.gov/servlets/purl/1577835.
@article{osti_1577835,
title = {Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations},
author = {Wang, Jinan and Alekseenko, Andrey and Kozakov, Dima and Miao, Yinglong},
abstractNote = {We find that peptides mediate up to 40% of known protein-protein interactions in higher eukaryotes and play a key role in cellular signaling, protein trafficking, immunology, and oncology. However, it is challenging to predict peptide-protein binding with conventional computational modeling approaches, due to slow dynamics and high peptide flexibility. Here, we present a prototype of the approach which combines global peptide docking using ClusPro PeptiDock and all-atom enhanced simulations using Gaussian accelerated molecular dynamics (GaMD). For three distinct model peptides, the lowest backbone root-mean-square deviations (RMSDs) of their bound conformations relative to X-ray structures obtained from PeptiDock were 3.3–4.8 Å, being medium quality predictions according to the Critical Assessment of PRediction of Interactions (CAPRI) criteria. GaMD simulations refined the peptide-protein complex structures with significantly reduced peptide backbone RMSDs of 0.6–2.7 Å, yielding two high quality (sub-angstrom) and one medium quality models. Furthermore, the GaMD simulations identified important low-energy conformational states and revealed the mechanism of peptide binding to the target proteins. Therefore, PeptiDock+GaMD is a promising approach for exploring peptide-protein interactions.},
doi = {10.3389/fmolb.2019.00112},
journal = {Frontiers in Molecular Biosciences},
number = ,
volume = 6,
place = {United States},
year = {Wed Oct 30 00:00:00 EDT 2019},
month = {Wed Oct 30 00:00:00 EDT 2019}
}
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Molecular Simulations Identify Binding Poses and Approximate Affinities of Stapled α-Helical Peptides to MDM2 and MDMX
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Position of Transmembrane Helix 6 Determines Receptor G Protein Coupling Specificity
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Characterization of Domain–Peptide Interaction Interface: Prediction of SH3 Domain-Mediated Protein–Protein Interaction Network in Yeast by Generic Structure-Based Models
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Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations
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Unconstrained enhanced sampling for free energy calculations of biomolecules: a review
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Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
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Current status and future challenges in T-cell receptor/peptide/MHC molecular dynamics simulations
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- Briefings in Bioinformatics, Vol. 16, Issue 6
ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT
journal, April 2017
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- Bioinformatics, Vol. 33, Issue 20
PepX: a structural database of non-redundant protein–peptide complexes
journal, October 2009
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- Nucleic Acids Research, Vol. 38, Issue suppl_1
CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site
journal, May 2015
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- Nucleic Acids Research, Vol. 43, Issue W1
GalaxyPepDock: a protein–peptide docking tool based on interaction similarity and energy optimization
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High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock
journal, December 2017
- Alam, Nawsad; Goldstein, Oriel; Xia, Bing
- PLOS Computational Biology, Vol. 13, Issue 12
Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors
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Molecular Basis of Ligand Dissociation in β-Adrenergic Receptors
journal, September 2011
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A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking
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Optimal Clustering for Detecting Near-Native Conformations in Protein Docking
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Protein-Protein Interaction Investigated by Steered Molecular Dynamics: The TCR-pMHC Complex
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Works referencing / citing this record:
Computational modeling of cyclic peptide inhibitor–MDM2/MDMX binding through global docking and Gaussian accelerated molecular dynamics simulations
journal, June 2020
- Wang, Yeng-Tseng; Cheng, Tian-Lu
- Journal of Biomolecular Structure and Dynamics
Computational modeling of cyclic peptide inhibitor–MDM2/MDMX binding through global docking and Gaussian accelerated molecular dynamics simulations
text, January 2020
- Wang, Yeng-Tseng; Cheng, Tian-Lu
- Taylor & Francis
Computational modeling of cyclic peptide inhibitor–MDM2/MDMX binding through global docking and Gaussian accelerated molecular dynamics simulations
text, January 2020
- Wang, Yeng-Tseng; Cheng, Tian-Lu
- Taylor & Francis