Vaiwala, R and Ayappa, KG (2021) A generic force field for simulating native protein structures using dissipative particle dynamics. In: Soft Matter, 17 (42). pp. 9772-9785.
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Abstract
A coarse-grained force field for molecular dynamics simulations of the native structures of proteins in a dissipative particle dynamics (DPD) framework is developed. The parameters for bonded interactions are derived by mapping the bonds and angles for 20 amino acids onto target distributions obtained from fully atomistic simulations in explicit solvent. A dual-basin potential is introduced for stabilizing backbone angles, to cover a wide spectrum of protein secondary structures. The backbone dihedral potential enables folding of the protein from an unfolded initial state to the folded native structure. The proposed force field is validated by evaluating the structural properties of several model peptides and proteins including the SARS-CoV-2 fusion peptide, consisting of α-helices, β-sheets, loops and turns. Detailed comparisons with fully atomistic simulations are carried out to assess the ability of the proposed force field to stabilize the different secondary structures present in proteins. The compact conformations of the native states were evident from the radius of gyration and the high intensity peaks of the root mean square deviation histograms, which were found to be within 0.4 nm. The Ramachandran-like energy landscape on the phase space of backbone angles (θ) and dihedrals (�) effectively captured the conformational phase space of α-helices at �(�= 50°,θ= 90°) and β-strands at �(�= ±180°,θ= 90-120°). Furthermore, the residue-residue native contacts were also well reproduced by the proposed DPD model. The applicability of the model to multidomain complexes was assessed using lysozyme and a large α-helical bacterial pore-forming toxin, cytolysin A. Our study illustrates that the proposed force field is generic, and can potentially be extended for efficientin silicoinvestigations of membrane bound polypeptides and proteins using DPD simulations. © The Royal Society of Chemistry 2021.
| Item Type: | Journal Article |
|---|---|
| Publication: | Soft Matter |
| Publisher: | Royal Society of Chemistry |
| Additional Information: | The copyright for this article belongs to Authors |
| Keywords: | Dihedral angle; Molecular dynamics; Peptides; SARS, Atomistic simulations; Backbone angles; Coarse-grained force fields; Dissipative particle dynamics; Dynamic framework; Forcefields; Native proteins; Native structures; Phase spaces; Proteins structures, Phase space methods |
| Department/Centre: | Division of Interdisciplinary Sciences > Centre for Biosystems Science and Engineering Division of Mechanical Sciences > Chemical Engineering |
| Date Deposited: | 22 Nov 2021 10:57 |
| Last Modified: | 22 Nov 2021 10:57 |
| URI: | http://eprints.iisc.ac.in/id/eprint/70539 |
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