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Collagen structure and preferential ...

Rainey, Jan Kristian.

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Collagen structure and preferential assembly explored by parallel microscopy and bioinformatics.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Collagen structure and preferential assembly explored by parallel microscopy and bioinformatics./
Author:	Rainey, Jan Kristian.
Description:	259 p.
Notes:	Adviser: M. Cynthia Goh.
Contained By:	Dissertation Abstracts International64-04B.
Subject:	Biophysics, General. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=NQ78310
ISBN:	0612783103

Collagen structure and preferential assembly explored by parallel microscopy and bioinformatics.
Rainey, Jan Kristian.

Collagen structure and preferential assembly explored by parallel microscopy and bioinformatics. - 259 p.

Adviser: M. Cynthia Goh.

Thesis (Ph.D.)--University of Toronto (Canada), 2003.

Although its self-assembly is ubiquitous for most animals and has been extensively studied for decades, collagen remains a rather enigmatic protein. The preferential assembly process of one particular collagen construct, fibrous long spacing collagen formed with added α<sub>1</sub>-acid glycoprotein, is detailed. Stable intermediate structures are resolved by atomic force microscopy, demonstrating for the first time the onset of the periodic surface protrusions separated by 270 nm that are characteristic of this form of collagen. A preliminary fibrillogenesis mechanism is proposed on the basis of this data, but the ongoing problem of the lack of a high-resolution structure for the collagen monomer makes detailed analysis difficult. Therefore, a diversion into bioinformatics styled analyses is presented. In the first analysis, the collagen triple-helix is parameterized using all available high-resolution crystal structure data. This provides a general framework for prediction of any triple-helical peptide structure and is shown using a nonredundant data set to generate a prediction agreeing exceptionally well with the highest resolution structure solved to date. From a preferential assembly standpoint, only the terminal atoms of each residue are important—it is these that modulate supramolecular assembly through either attractive or repulsive interactions. However, the large size (&sim;3150 amino acids) of the collagen monomer makes prediction of all side chain atoms undesirable. Following the success of backbone dependent rotamer libraries, a second statistically derived parameter set is developed. It allows prediction of terminal side-chain atom positions given only a polypeptide backbone. This is validated by comparing numerous predictions to experimental structures for a large set of protein structures, showing excellent potential as a general predictive method for efficiently positioning side-chains. Combining the two parameter sets, any triple-helical structure may be readily predicted. A model of the human type I collagen monomer is introduced and its utility is demonstrated through correlation with atomic force microscopy data. This allows both the interpretation of height data, and the clarification of the preliminary assembly mechanism proposed towards the beginning of the Thesis for fibrous long spacing collagen.

ISBN: 0612783103Subjects--Topical Terms:

1019105
Biophysics, General.

Collagen structure and preferential assembly explored by parallel microscopy and bioinformatics.
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100 1 $a Rainey, Jan Kristian. $3 1253317
245 1 0 $a Collagen structure and preferential assembly explored by parallel microscopy and bioinformatics.
300 $a 259 p.
500 $a Adviser: M. Cynthia Goh.
500 $a Source: Dissertation Abstracts International, Volume: 64-04, Section: B, page: 1651.
502 $a Thesis (Ph.D.)--University of Toronto (Canada), 2003.
520 $a Although its self-assembly is ubiquitous for most animals and has been extensively studied for decades, collagen remains a rather enigmatic protein. The preferential assembly process of one particular collagen construct, fibrous long spacing collagen formed with added α<sub>1</sub>-acid glycoprotein, is detailed. Stable intermediate structures are resolved by atomic force microscopy, demonstrating for the first time the onset of the periodic surface protrusions separated by 270 nm that are characteristic of this form of collagen. A preliminary fibrillogenesis mechanism is proposed on the basis of this data, but the ongoing problem of the lack of a high-resolution structure for the collagen monomer makes detailed analysis difficult. Therefore, a diversion into bioinformatics styled analyses is presented. In the first analysis, the collagen triple-helix is parameterized using all available high-resolution crystal structure data. This provides a general framework for prediction of any triple-helical peptide structure and is shown using a nonredundant data set to generate a prediction agreeing exceptionally well with the highest resolution structure solved to date. From a preferential assembly standpoint, only the terminal atoms of each residue are important—it is these that modulate supramolecular assembly through either attractive or repulsive interactions. However, the large size (&sim;3150 amino acids) of the collagen monomer makes prediction of all side chain atoms undesirable. Following the success of backbone dependent rotamer libraries, a second statistically derived parameter set is developed. It allows prediction of terminal side-chain atom positions given only a polypeptide backbone. This is validated by comparing numerous predictions to experimental structures for a large set of protein structures, showing excellent potential as a general predictive method for efficiently positioning side-chains. Combining the two parameter sets, any triple-helical structure may be readily predicted. A model of the human type I collagen monomer is introduced and its utility is demonstrated through correlation with atomic force microscopy data. This allows both the interpretation of height data, and the clarification of the preliminary assembly mechanism proposed towards the beginning of the Thesis for fibrous long spacing collagen.
590 $a School code: 0779.
650 4 $a Biophysics, General. $3 1019105
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710 2 0 $a University of Toronto (Canada). $3 1017674
773 0 $t Dissertation Abstracts International $g 64-04B.
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792 $a 2003
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=NQ78310