Ultraviolet spectroscopy of protein backbone transitions in aqueous solution: combined QM and MM simulations.

ABSTRACT: A generalized approach combining quantum mechanics (QM) and molecular mechanics (MM) calculations is developed to simulate the n --> pi* and pi --> pi* backbone transitions of proteins in aqueous solution. These transitions, which occur in the ultraviolet (UV) at 180-220 nm, provide a sensitive probe for secondary structures. The excitation Hamiltonian is constructed using high-level electronic structure calculations of N-methylacetamide (NMA). Its electrostatic fluctuations are modeled using a new algorithm, EHEF, which combines a molecular dynamics (MD) trajectory obtained with a MM forcefield and electronic structures of sampled MD snapshots calculated by QM. The lineshapes and excitation splittings induced by the electrostatic environment in the experimental UV linear absorption (LA) a

SUBMITTER: Jiang J 

PROVIDER: S-EPMC2888931 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature