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Using molecular dynamics simulations...

Friedel, Miriam R.

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Using molecular dynamics simulations of proteins to understand the effects of confinement.

Record Type:	Electronic resources : Monograph/item
Title/Author:	Using molecular dynamics simulations of proteins to understand the effects of confinement./
Author:	Friedel, Miriam R.
Description:	191 p.
Notes:	Source: Dissertation Abstracts International, Volume: 67-09, Section: B, page: 5124.
Contained By:	Dissertation Abstracts International67-09B.
Subject:	Physics, General. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3232997
ISBN:	9780542855962

Using molecular dynamics simulations of proteins to understand the effects of confinement.
Friedel, Miriam R.

Using molecular dynamics simulations of proteins to understand the effects of confinement. - 191 p.

Source: Dissertation Abstracts International, Volume: 67-09, Section: B, page: 5124.

Thesis (Ph.D.)--University of California, Santa Barbara, 2006.

Although the information necessary for a protein to fold is encoded in its amino acid sequence, the environment in which it folds can have a significant impact on the folding process. To date, the majority of protein folding studies (theoretical, computational and experimental) have been carried out in an idealized, dilute environment. In this work, we use molecular dynamics simulations of minimalist model proteins and peptides to examine the impact of two types of confinement on protein folding and peptide assembly. First, we utilize a spherical potential to emulate the cellular confinement and crowding that proteins experience when folding in vivo. Using this potential, we examine the impact on the thermodynamics and kinetics of both protein folding and peptide assembly. Then, we examine how tethering a protein to a surface impacts its stability and folding mechanism. Both types of confinement can have a significant impact on the thermodynamic stability, unfolded state, and mechanisms of folding and assembly, but they do so in unique ways. In addition to examining in detail the specific ways confinement impacts protein folding, we will also discuss the implications of our results for various biological problems and technological applications.

ISBN: 9780542855962Subjects--Topical Terms:

1018488
Physics, General.

Using molecular dynamics simulations of proteins to understand the effects of confinement.
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245 1 0 $a Using molecular dynamics simulations of proteins to understand the effects of confinement.
300 $a 191 p.
500 $a Source: Dissertation Abstracts International, Volume: 67-09, Section: B, page: 5124.
500 $a Adviser: Philip A. Pincus.
502 $a Thesis (Ph.D.)--University of California, Santa Barbara, 2006.
520 $a Although the information necessary for a protein to fold is encoded in its amino acid sequence, the environment in which it folds can have a significant impact on the folding process. To date, the majority of protein folding studies (theoretical, computational and experimental) have been carried out in an idealized, dilute environment. In this work, we use molecular dynamics simulations of minimalist model proteins and peptides to examine the impact of two types of confinement on protein folding and peptide assembly. First, we utilize a spherical potential to emulate the cellular confinement and crowding that proteins experience when folding in vivo. Using this potential, we examine the impact on the thermodynamics and kinetics of both protein folding and peptide assembly. Then, we examine how tethering a protein to a surface impacts its stability and folding mechanism. Both types of confinement can have a significant impact on the thermodynamic stability, unfolded state, and mechanisms of folding and assembly, but they do so in unique ways. In addition to examining in detail the specific ways confinement impacts protein folding, we will also discuss the implications of our results for various biological problems and technological applications.
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