Premium
Frictional models for stochastic simulations of proteins
Author(s) -
Venable Richard M.,
Pastor Richard W.
Publication year - 1988
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.360270609
Subject(s) - chemistry , parametrization (atmospheric modeling) , radius , ribonuclease , diffusion , range (aeronautics) , lysozyme , atom (system on chip) , constant (computer programming) , thermodynamics , molecular dynamics , hydrodynamic radius , solvent , chemical physics , computational chemistry , physics , aqueous solution , quantum mechanics , rna , materials science , organic chemistry , computer security , computer science , composite material , embedded system , biochemistry , micelle , programming language , gene , radiative transfer
As a first step toward a systematic parametrization of friction constants of atoms in proteins, a model in which frictional resistance is placed explicitly on each atom accessible to solvent is used to calculate overall translational and rotational diffusion constants. It is found that these quantities are relatively insensitive to the precise value of the atomic friction constant, as long as the effective hydrodynamic radius of the surface atoms is approximately 1 Å. However, if only protein atoms are included in the calculation, no reasonable range atomic of radii can reproduce the experimental translational diffusion constant to better than 20% for lysozyme and 5% for ribonuclease. When a hydration shell of approximately 70% coverage for lysozyme and 20% for ribonuclease is included, there is quantitative agreement with experimental results. The sensitivity of peptide diffusion to levels of hydration is also investigated; it is found that for glycine, two bound waters are required to provide agreement with experiment. These findings imply that the effects of solvent damping will be underestimated in stochastic simulations of proteins and peptides unless bound waters are taken into account.