Bias-free separation of internal and overall motion of biomolecules

Citation
U. Schieborr et H. Ruterjans, Bias-free separation of internal and overall motion of biomolecules, PROTEINS, 45(3), 2001, pp. 207-218
Citations number
23
Language
INGLESE
art.tipo
Article
Categorie Soggetti
Biochemistry & Biophysics
Journal title
PROTEINS-STRUCTURE FUNCTION AND GENETICS
ISSN journal
0887-3585 → ACNP
Volume
45
Issue
3
Year of publication
2001
Pages
207 - 218
Database
ISI
SICI code
0887-3585(20011115)45:3<207:BSOIAO>2.0.ZU;2-U
Abstract
Collective internal motions are known to be important for the function of b iological macromolecules. It has been discussed in the past whether the app lication of superimposing algorithms to remove the overall motion from a st ructural ensemble introduces artificial correlations between distant atoms. Here we present a new method to eliminate residual rotation and translatio n from cartesian modes derived from a normal mode analysis or from a princi pal component analysis. Bias-free separation is based on the idea that the addition of modes of pure rotation/translation can compensate the residual overall motion. Removal of overall motion must reduce the "total amount of motion" (TAM) in the mode. Our algorithm allows to back-calculate revised c ovariance matrices. The approach was applied to two model systems that show residual overall motion, when analyzed using all atoms as reference for th e superimposing algorithm. In both cases, our algorithm was capable of elim inating residual covariances caused by the overall motion, while retaining internal covariances even for very distant atoms. A structural ensemble obt ained for a 13-ns molecular dynamics simulation of the protein Ribonuclease T1 showed a covariance matrix of the corrected modes with significantly sh arper contours after applying the bias-free separation. (C) 2001 Wiley-Liss , Inc.