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Membrane-peptide interactions studie...

Grossfield, Alan Marc.

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Membrane-peptide interactions studied by computer simulation.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Membrane-peptide interactions studied by computer simulation./
Author:	Grossfield, Alan Marc.
Description:	187 p.
Notes:	Adviser: Thomas B. Woolf.
Contained By:	Dissertation Abstracts International61-10B.
Subject:	Biophysics, General. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=9993111
ISBN:	0493004998

Membrane-peptide interactions studied by computer simulation.
Grossfield, Alan Marc.

Membrane-peptide interactions studied by computer simulation. - 187 p.

Adviser: Thomas B. Woolf.

Thesis (Ph.D.)--The Johns Hopkins University, 2001.

In order to understand the behavior of membrane-bound molecules—such as sidechain analogs and other small molecules, peptides, and proteins—we must develop a better understanding of the interactions between them and the membranes. One powerful tool for doing this is computer simulation. To use simulations, we must first decide how to represent the various components of the calculation. This work presents calculations using two different membrane representations: an all-atom environment, sampled by molecular dynamics, and a newly developed lattice dipole model. We ran molecular dynamics calculations of two tryptophan analogs embedded in lipid bilayers, in order to rationalize the placement of tryptophan residues in membrane proteins, and the experimentally observed behavior of those analogs. The simulations seem to indicate that, although the isolated analogs have free energy minima when packing in the acyl chains, tryptophan residues appear in the headgroup region because they make the most favorable interactions with that environment. The lattice dipole model is intended to calculate reasonably accurate solvation free energies for membrane-bound molecules without the computational cost of all-atom molecular dynamics. Once fully developed, this model could be used to investigate the effects of membrane width and headgroup type on membrane protein structure, predict membrane protein structure, or serve as a boundary for an aperiodic molecular dynamics simulation. The present work presents the theory, development, and testing of this model. Taken together, these projects indicate that computer simulations can be used to improve our understanding of membranes and membrane proteins.

ISBN: 0493004998Subjects--Topical Terms:

1019105
Biophysics, General.

Membrane-peptide interactions studied by computer simulation.
LDR:02567nam 2200265 a 45 001 936489
005 20110510
008 110510s2001 eng d
020 $a 0493004998
035 $a (UnM)AAI9993111
035 $a AAI9993111
040 $a UnM $c UnM
100 1 $a Grossfield, Alan Marc. $3 1260179
245 1 0 $a Membrane-peptide interactions studied by computer simulation.
300 $a 187 p.
500 $a Adviser: Thomas B. Woolf.
500 $a Source: Dissertation Abstracts International, Volume: 61-10, Section: B, page: 5194.
502 $a Thesis (Ph.D.)--The Johns Hopkins University, 2001.
520 $a In order to understand the behavior of membrane-bound molecules—such as sidechain analogs and other small molecules, peptides, and proteins—we must develop a better understanding of the interactions between them and the membranes. One powerful tool for doing this is computer simulation. To use simulations, we must first decide how to represent the various components of the calculation. This work presents calculations using two different membrane representations: an all-atom environment, sampled by molecular dynamics, and a newly developed lattice dipole model. We ran molecular dynamics calculations of two tryptophan analogs embedded in lipid bilayers, in order to rationalize the placement of tryptophan residues in membrane proteins, and the experimentally observed behavior of those analogs. The simulations seem to indicate that, although the isolated analogs have free energy minima when packing in the acyl chains, tryptophan residues appear in the headgroup region because they make the most favorable interactions with that environment. The lattice dipole model is intended to calculate reasonably accurate solvation free energies for membrane-bound molecules without the computational cost of all-atom molecular dynamics. Once fully developed, this model could be used to investigate the effects of membrane width and headgroup type on membrane protein structure, predict membrane protein structure, or serve as a boundary for an aperiodic molecular dynamics simulation. The present work presents the theory, development, and testing of this model. Taken together, these projects indicate that computer simulations can be used to improve our understanding of membranes and membrane proteins.
590 $a School code: 0098.
650 4 $a Biophysics, General. $3 1019105
690 $a 0786
710 2 0 $a The Johns Hopkins University. $3 1017431
773 0 $t Dissertation Abstracts International $g 61-10B.
790 $a 0098
790 1 0 $a Woolf, Thomas B., $e advisor
791 $a Ph.D.
792 $a 2001
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=9993111