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Physical, organizational and evolutionary principles of protein sequence-structure relationships.

Record Type:	Electronic resources : Monograph/item
Title/Author:	Physical, organizational and evolutionary principles of protein sequence-structure relationships.
Author:	Xia, Yu.
Description:	157 p.
Notes:	Adviser: Michael Levitt.
Notes:	Source: Dissertation Abstracts International, Volume: 64-03, Section: B, page: 1133.
Contained By:	Dissertation Abstracts International64-03B.
Subject:	Biophysics, General.
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3085380
ISBN:	0496331876

Physical, organizational and evolutionary principles of protein sequence-structure relationships.
Xia, Yu.

Physical, organizational and evolutionary principles of protein sequence-structure relationships. [electronic resource] - 157 p.

Adviser: Michael Levitt.

Thesis (Ph.D.)--Stanford University, 2003.

We study the physical, organizational and evolutionary principles that govern the mapping and dynamics of protein sequence-structure relationships, in particular, the dominant folding energetics of proteins, the determination of the three-dimensional protein structure from primary sequence information alone, the large-scale organization in protein sequence space, and structure-based protein sequence evolution. In the first part of the thesis, we study the local rules of protein sequence-structure relationships that describe how three-dimensional structural information is encoded in the primary sequence of a protein. We describe a unified framework to derive energy parameters optimally from a set of known native protein structures, demonstrate the power of such knowledge-based energy functions in a hierarchical approach for ab initio protein structure prediction, and test the predictive power of our method in a double-blind community-wide experiment. In the second part of the thesis, we study the global rules of protein sequence-structure relationships that describe the large-scale organization and structure-constrained evolutionary dynamics in protein sequence space, with the aid of simple exact models for proteins. We study the global organization of the sequence space that is compatible with a target structure, and show how protein energetics affects the global organization and evolutionary dynamics of the sequence space. We discover the different roles of mutation and recombination in the evolutionary origin of protein thermodynamic behavior. Finally, we present a coherent and comprehensive analysis on the sequence space organization and evolution of protein folding under either kinetic or thermodynamic control. We find that there are important similarities as well as differences between organization and evolution in sequence space of protein folding under kinetic and thermodynamic control, which in turn explains the similarities and differences of protein thermodynamic and kinetic behavior in terms of their evolutionary origins.

ISBN: 0496331876Subjects--Topical Terms:

226901
Biophysics, General.

Physical, organizational and evolutionary principles of protein sequence-structure relationships.
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520 # $a We study the physical, organizational and evolutionary principles that govern the mapping and dynamics of protein sequence-structure relationships, in particular, the dominant folding energetics of proteins, the determination of the three-dimensional protein structure from primary sequence information alone, the large-scale organization in protein sequence space, and structure-based protein sequence evolution. In the first part of the thesis, we study the local rules of protein sequence-structure relationships that describe how three-dimensional structural information is encoded in the primary sequence of a protein. We describe a unified framework to derive energy parameters optimally from a set of known native protein structures, demonstrate the power of such knowledge-based energy functions in a hierarchical approach for ab initio protein structure prediction, and test the predictive power of our method in a double-blind community-wide experiment. In the second part of the thesis, we study the global rules of protein sequence-structure relationships that describe the large-scale organization and structure-constrained evolutionary dynamics in protein sequence space, with the aid of simple exact models for proteins. We study the global organization of the sequence space that is compatible with a target structure, and show how protein energetics affects the global organization and evolutionary dynamics of the sequence space. We discover the different roles of mutation and recombination in the evolutionary origin of protein thermodynamic behavior. Finally, we present a coherent and comprehensive analysis on the sequence space organization and evolution of protein folding under either kinetic or thermodynamic control. We find that there are important similarities as well as differences between organization and evolution in sequence space of protein folding under kinetic and thermodynamic control, which in turn explains the similarities and differences of protein thermodynamic and kinetic behavior in terms of their evolutionary origins.
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