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Langevin modes of macromolecules: Applications to crambin and DNA hexamers
Author(s) -
Kottalam J.,
Case D. A.
Publication year - 1990
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360291008
Subject(s) - chemistry , langevin equation , relaxation (psychology) , macromolecule , chemical physics , viscosity , solvent , thermodynamics , rotational diffusion , molecular physics , molecule , statistical physics , physics , social psychology , biochemistry , organic chemistry , psychology
Langevin modes described 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 hydro‐dynamic interactions. Even for relatively small solvent friction (η = 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.