Coarse-Grained Modeling of Peptide Docking Associated with Large Conformation Transitions of the Binding Protein: Troponin I Fragment–Troponin C System

Wabik, Jacek; Kurcinski, Mateusz; Kolinski, Andrzej

doi:10.3390/molecules200610763

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Coarse-Grained Modeling of Peptide Docking Associated with Large Conformation Transitions of the Binding Protein: Troponin I Fragment–Troponin C System

Jacek Wabik

Mateusz Kurcinski

and

Andrzej Kolinski

Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland

Author to whom correspondence should be addressed.

Academic Editor: Rino Ragno

Molecules 2015, 20(6), 10763-10780; https://doi.org/10.3390/molecules200610763

Received: 31 March 2015 / Revised: 14 May 2015 / Accepted: 21 May 2015 / Published: 11 June 2015

(This article belongs to the Special Issue Molecular Docking in Drug Design)

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Abstract

Most of the current docking procedures are focused on fine conformational adjustments of assembled complexes and fail to reproduce large-scale protein motion. In this paper, we test a new modeling approach developed to address this problem. CABS-dock is a versatile and efficient tool for modeling the structure, dynamics and interactions of protein complexes. The docking protocol employs a coarse-grained representation of proteins, a simplified model of interactions and advanced protocols for conformational sampling. CABS-dock is one of the very few tools that allow unrestrained docking with large conformational freedom of the receptor. In an example application we modeled the process of complex assembly between two proteins: Troponin C (TnC) and the N-terminal helix of Troponin I (TnI N-helix), which occurs in vivo during muscle contraction. Docking simulations illustrated how the TnC molecule undergoes significant conformational transition on complex formation, a phenomenon that can be modeled only when protein flexibility is properly accounted for. This way our procedure opens up a new possibility for studying mechanisms of protein complex assembly, which may be a supporting tool for rational drug design. View Full-Text

Keywords: protein docking; flexible docking; coarse-grained modeling; molecular mechanisms

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Wabik, J.; Kurcinski, M.; Kolinski, A. Coarse-Grained Modeling of Peptide Docking Associated with Large Conformation Transitions of the Binding Protein: Troponin I Fragment–Troponin C System. Molecules 2015, 20, 10763-10780. https://doi.org/10.3390/molecules200610763

AMA Style

Wabik J, Kurcinski M, Kolinski A. Coarse-Grained Modeling of Peptide Docking Associated with Large Conformation Transitions of the Binding Protein: Troponin I Fragment–Troponin C System. Molecules. 2015; 20(6):10763-10780. https://doi.org/10.3390/molecules200610763

Chicago/Turabian Style

Wabik, Jacek, Mateusz Kurcinski, and Andrzej Kolinski. 2015. "Coarse-Grained Modeling of Peptide Docking Associated with Large Conformation Transitions of the Binding Protein: Troponin I Fragment–Troponin C System" Molecules 20, no. 6: 10763-10780. https://doi.org/10.3390/molecules200610763

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Coarse-Grained Modeling of Peptide Docking Associated with Large Conformation Transitions of the Binding Protein: Troponin I Fragment–Troponin C System

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