Langevin modes of macromolecules: applications to crambin and DNA hexamers.
Langevin modes describe the behavior of atoms moving on a harmonic potential surface subject to viscous damping described by a classical Langevin equation. We present applications to the protein crambin and to the DNA duplex d(CpGpCpGpCpG)2 and its complex with ethidium. Our friction matrix is weighted according to surface area exposed to solvent, and results are reported for various values of the solvent viscosity and models for hydrodynamic interactions. Even for relatively small solvent friction (eta = 0.3 cp) a substantial number of modes are overdamped, and time correlation functions decay smoothly without the oscillations characteristic of gas-phase calculations. Perturbation theory starting from the gas-phase modes is accurate for many low-frequency modes (which are overdamped in the presence of solvent), but fails badly for higher modes. For correlation functions of interest to fluorescence depolarization or nmr relaxation, the plateau values are insensitive to solvent viscosity, but the relaxation times are not. The advantages and limitations of this analysis of macromolecular motions are discussed.
Kottalam
J
J
Department of Molecular Biology, Research Institute of Scripps Clinic, La Jolla, California 93037.
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DA
D004247:DNA; D046911:Macromolecular Substances; D008433:Mathematics; D009838:Oligodeoxyribonucleotides; D010940:Plant Proteins; D014783:Viscosity
D046911:Macromolecular Substances; D009838:Oligodeoxyribonucleotides; D010940:Plant Proteins; C024934:crambin protein, Crambe abyssinica; D004247:DNA