Multi-basin dynamics of a protein in aqueous solution
Abstract
A molecular dynamics simulation of crambin in aqueous solution shows that motions are characteristic of non-linear systems. The authors describe typical non-linear excitations, such as intermittency, for various representations of the protein dynamics and structure. The protein backbone dihedral angles show fast correlated transitions from one minimum well to another. Each transition is followed by small overdamped oscillations. Equal-time cross correlations of all ({phi},{psi}) angles show that correlations are extended along the backbone chain. An analysis based on a generalized least squares fitting of the protein fluctuations along vectors show that a small set of molecule optimal dynamic coordinates (MODC) describe most of the protein fluctuations. In addition, the MODC describe a trajectory where the protein conformation jumps from one minimum well to another. An extension of the MODC describing 2- and 3-dimensional cuts of the protein configurational space clearly shows a trajectory around multiple basins of attraction.
- Authors:
-
- Los Alamos National Lab., NM (United States). Theoretical Biology and Biophysics Group
- Publication Date:
- Research Org.:
- Los Alamos National Lab., NM (United States)
- OSTI Identifier:
- 10186930
- Report Number(s):
- LA-UR-94-3138; CONF-9405240-1
ON: DE95000860; TRN: AHC29426%%40
- DOE Contract Number:
- W-7405-ENG-36
- Resource Type:
- Technical Report
- Resource Relation:
- Conference: Non-linear exitations in biomolecules,Les Houches (France),30 May - 4 Jun 1994; Other Information: PBD: [1994]
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIPS; PROTEIN STRUCTURE; EXPERIMENTAL DATA; MATHEMATICAL MODELS; 550200; BIOCHEMISTRY
Citation Formats
Garcia, A.E. Multi-basin dynamics of a protein in aqueous solution. United States: N. p., 1994.
Web. doi:10.2172/10186930.
Garcia, A.E. Multi-basin dynamics of a protein in aqueous solution. United States. doi:10.2172/10186930.
Garcia, A.E. Sat .
"Multi-basin dynamics of a protein in aqueous solution". United States.
doi:10.2172/10186930. https://www.osti.gov/servlets/purl/10186930.
@article{osti_10186930,
title = {Multi-basin dynamics of a protein in aqueous solution},
author = {Garcia, A.E.},
abstractNote = {A molecular dynamics simulation of crambin in aqueous solution shows that motions are characteristic of non-linear systems. The authors describe typical non-linear excitations, such as intermittency, for various representations of the protein dynamics and structure. The protein backbone dihedral angles show fast correlated transitions from one minimum well to another. Each transition is followed by small overdamped oscillations. Equal-time cross correlations of all ({phi},{psi}) angles show that correlations are extended along the backbone chain. An analysis based on a generalized least squares fitting of the protein fluctuations along vectors show that a small set of molecule optimal dynamic coordinates (MODC) describe most of the protein fluctuations. In addition, the MODC describe a trajectory where the protein conformation jumps from one minimum well to another. An extension of the MODC describing 2- and 3-dimensional cuts of the protein configurational space clearly shows a trajectory around multiple basins of attraction.},
doi = {10.2172/10186930},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Sat Oct 01 00:00:00 EDT 1994},
month = {Sat Oct 01 00:00:00 EDT 1994}
}
-
FISSION PRODUCT RUTHENIUM: NOTES ON ITS CHEMISTRY IN CERTAIN AQUEOUS SOLUTIONS AND ON THE PREPARATION OF LABELLED AND CARRIER-FREE SOLUTIONS FOR EXPERIMENTAL WORK. PART I. RUTHENIUM CHEMISTRY IN CERTAIN AQUEOUS MEDIA. PART II. PREPARATIONS OF LABELLED RUTHENIUM COMPOUNDS. PART III. PREPARATIONS OF CARRIER-FREE RUTHENIUM SOLUTION
Information is presented to assist those engaged in the disposal and in the biological fate of fission product ruthenium. (auth)