title: Effects of different force fields on the structural character of α synuclein β-hairpin peptide (35-56) in aqueous environment.
abstract: The hallmark of Parkinson's disease (PD) is the intracellular protein aggregation forming Lewy Bodies (LB) and Lewy neuritis which comprise mostly of a protein, alpha synuclein (α-syn). Molecular dynamics (MD) simulation methods can augment experimental techniques to understand misfolding and aggregation pathways with atomistic resolution. The quality of MD simulations for proteins and peptides depends greatly on the accuracy of empirical force fields. The aim of this work is to investigate the effects of different force fields on the structural character of β hairpin fragment of α-syn (residues 35-56) peptide in aqueous solution. Six independent MD simulations are done in explicit solvent using, AMBER03, AMBER99SB, GROMOS96 43A1, GROMOS96 53A6, OPLS-AA, and CHARMM27 force fields with CMAP corrections. The performance of each force field is assessed from several structural parameters such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), formation of β-turn, the stability of folded β-hairpin structure, and the favourable conformations obtained for different force fields. In this study, CMAP correction of CHARMM27 force field is found to overestimate the helical conformation, while GROMOS96 53A6 is found to most successfully capture the conformational dynamics of α-syn β-hairpin fragment as elicited from NMR.
authors.affiliation: a Structural Biology and Bioinformatics Division , Indian Institute of Chemical Biology, Council of Scientific and Industrial Research , 4 Raja S. C. Mullick Road, Kolkata 700032 , India.
authors.forename: Sangeeta
authors.initials: S
authors.lastname: Kundu
mesh_terms: D016229:Amyloid beta-Peptides / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D006860:Hydrogen Bonding; D016631:Lewy Bodies / Q000737:chemistry / Q000378:metabolism; D009682:Magnetic Resonance Spectroscopy; D056004:Molecular Dynamics Simulation; D010300:Parkinson Disease / Q000378:metabolism* / Q000473:pathology; D066263:Protein Aggregation, Pathological; D017433:Protein Structure, Secondary; D012997:Solvents / Q000737:chemistry*; D013816:Thermodynamics; D014867:Water / Q000737:chemistry; D051844:alpha-Synuclein / Q000737:chemistry* / Q000378:metabolism
chemical_list: D016229:Amyloid beta-Peptides; D012997:Solvents; D051844:alpha-Synuclein; D014867:Water
keywords: Parkinson’s disease; aggregation; alpha synculein; molecular dynamics simulation