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 weigh...

Full description

Saved in:
Bibliographic Details
Published inBiopolymers Vol. 29; no. 10-11; p. 1409
Main Authors Kottalam, J, Case, D A
Format Journal Article
LanguageEnglish
Published United States 15.08.1990
Subjects
DNA
Macromolecular Substances
Mathematics
Oligodeoxyribonucleotides
Plant Proteins
Viscosity
Online AccessGet more information

Cover

More Information
Summary: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.
ISSN:0006-3525
DOI:10.1002/bip.360291008