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Mathematical and computational model...

Baker, Nathan Andrew.

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Mathematical and computational modeling of biomolecular systems.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Mathematical and computational modeling of biomolecular systems./
Author:	Baker, Nathan Andrew.
Description:	87 p.
Notes:	Chairs: James Andrew McCammon; Michael J. Holst.
Contained By:	Dissertation Abstracts International62-03B.
Subject:	Biophysics, General. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3007138
ISBN:	0493163549

Mathematical and computational modeling of biomolecular systems.
Baker, Nathan Andrew.

Mathematical and computational modeling of biomolecular systems. - 87 p.

Chairs: James Andrew McCammon; Michael J. Holst.

Thesis (Ph.D.)--University of California, San Diego, 2001.

This thesis describes the development and application of computational and mathematical models for biomolecular systems. The work presented in this dissertation can be roughly divided into two broad categories: development of new methods to elucidate biomolecular electrostatics and the investigation of dynamical properties of biological systems.

ISBN: 0493163549Subjects--Topical Terms:

1019105
Biophysics, General.

Mathematical and computational modeling of biomolecular systems.
LDR:03574nam 2200325 a 45 001 935961
005 20110510
008 110510s2001 eng d
020 $a 0493163549
035 $a (UnM)AAI3007138
035 $a AAI3007138
040 $a UnM $c UnM
100 1 $a Baker, Nathan Andrew. $3 1259661
245 1 0 $a Mathematical and computational modeling of biomolecular systems.
300 $a 87 p.
500 $a Chairs: James Andrew McCammon; Michael J. Holst.
500 $a Source: Dissertation Abstracts International, Volume: 62-03, Section: B, page: 1408.
502 $a Thesis (Ph.D.)--University of California, San Diego, 2001.
520 $a This thesis describes the development and application of computational and mathematical models for biomolecular systems. The work presented in this dissertation can be roughly divided into two broad categories: development of new methods to elucidate biomolecular electrostatics and the investigation of dynamical properties of biological systems.
520 $a Here we present the application of new adaptive finite element methods and new “parallel focusing” multigrid techniques to enable the solution of the Poisson-Boltzmann equation for supramolecular structures which are orders of magnitude larger in size than systems suitable for current solver technology. As a demonstration of these new methods, electrostatic potentials have been calculated for several moderate-size proteins, including HIV integrase, fasciculin-2, and acetylcholinesterase, as well as large microtubule and ribosome structures.
520 $a As part of the investigation of the dynamics of biological processes, the effects of stochastic gating of enzyme reactivity on substrate selectivity were examined. Recently, a new mechanism for reaction selectivity, arising from conformational gating of the reactions, has been reported in the acetylcholinesterase system. A distribution of reaction rates is derived for several limiting cases of substrate size. It is shown that the gated rate distribution shows much stronger steric selectivity than the usual Boltzmann dependence.
520 $a Finally, the dynamical properties of a protein toxin are studied to determine the effects structural fluctuations may have on its biological activity. Fasciculin-2 (FAS2) is a potent protein inhibitor of the hydrolytic enzyme acetylcholinesterase. A 2 nanosecond isobaric-isothermal ensemble molecular dynamics simulation of this toxin was performed to examine the dynamic structural properties which may play a role in this inhibition. Conformational fluctuations of the FAS2 protein were examined by a variety of techniques to identify flexible residues and determine their characteristic motion. The tips of the toxin “finger” loops and the turn connecting loops I and II were found to fluctuate, while the rest of the protein remained fairly rigid throughout the simulation. The implications of these fluctuations for biological activity are discussed. Finally, the structural fluctuations were compared to NMR data of fluctuations on a similar timescale in a related three-finger toxin. The molecular dynamics results were in good qualitative agreement with the experimental measurements. (Abstract shortened by UMI.)
590 $a School code: 0033.
650 4 $a Biophysics, General. $3 1019105
650 4 $a Chemistry, Physical. $3 560527
690 $a 0494
690 $a 0786
710 2 0 $a University of California, San Diego. $3 1018093
773 0 $t Dissertation Abstracts International $g 62-03B.
790 $a 0033
790 1 0 $a Holst, Michael J., $e advisor
790 1 0 $a McCammon, James Andrew, $e advisor
791 $a Ph.D.
792 $a 2001
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3007138