Paper Citing NAMD - Abstract
Jiang, Jun; Abramavicius, Darius; Bulheller, Benjamin M.; Hirst, Jonathan D.; Mukamel, Shaul
Ultraviolet Spectroscopy of Protein Backbone Transitions in Aqueous Solution: Combined QM and MM Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:8270-8277, JUN 24 2010
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) and circular dichroism (CD) spectra of several proteins in aqueous solution are reproduced by our calculations. The distinct CD features of alpha-helix and beta-sheet protein structures are observed in the simulations and can be assigned to different backbone geometries. The fine structure of the UV spectra is accurately characterized and enables us to identify signatures of secondary structures.
