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Global, Local, and Topological Struc...

Dundas, Joseph.

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Global, Local, and Topological Structural Comparison of Biomolecules.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Global, Local, and Topological Structural Comparison of Biomolecules./
Author:	Dundas, Joseph.
Description:	116 p.
Notes:	Source: Dissertation Abstracts International, Volume: 72-04, Section: B, page: 1865.
Contained By:	Dissertation Abstracts International72-04B.
Subject:	Biology, Molecular. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3446108
ISBN:	9781124499994

Global, Local, and Topological Structural Comparison of Biomolecules.
Dundas, Joseph.

Global, Local, and Topological Structural Comparison of Biomolecules. - 116 p.

Source: Dissertation Abstracts International, Volume: 72-04, Section: B, page: 1865.

Thesis (Ph.D.)--University of Illinois at Chicago, 2011.

Alignment of protein structures can help to infer protein function and can reveal ancient evolutionary relationships. In this thesis, I discuss computational methods we developed for structural alignment of both global backbones and local surfaces of proteins that do not depend on the ordering of residues in the primary sequence. The algorithm for global alignment is based on fragment assembly, and takes advantage of an approximation algorithm for solving the maximum weight independent set problem. I show how this algorithm can be applied to discover proteins related by complex topological rearrangement, including circularly permuted proteins as well as proteins related by complex higher order permutations. The algorithm for local surface alignment is based on solving the bi-partite graph matching problem through comparison of surface pockets and voids, such as those computed from the underlying alpha complex of protein structure. I also describe how multiple matched surfaces can be used to automatically generate signature pockets and basis set that represent the ensemble of conformations of protein binding surfaces with a specific biological function of binding activity. This is followed by illustrative examples of signature pockets and basis sets computed for the evolutionarily related metzincin metalloendopeptidase (MEP) family of enzymes. I will then give an example of signature pockets on a set of enzymes that are from different evolutionary origin but have evolved to bind the same NAD cofactor. For both the MEP family of enzymes and the NAD binding proteins, I will give a discussion how how they can be used for discriminating MEP and NAD binding enzymes from other enzymes.

ISBN: 9781124499994Subjects--Topical Terms:

1017719
Biology, Molecular.

Global, Local, and Topological Structural Comparison of Biomolecules.
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100 1 $a Dundas, Joseph. $3 1682246
245 1 0 $a Global, Local, and Topological Structural Comparison of Biomolecules.
300 $a 116 p.
500 $a Source: Dissertation Abstracts International, Volume: 72-04, Section: B, page: 1865.
500 $a Adviser: Jie Liang.
502 $a Thesis (Ph.D.)--University of Illinois at Chicago, 2011.
520 $a Alignment of protein structures can help to infer protein function and can reveal ancient evolutionary relationships. In this thesis, I discuss computational methods we developed for structural alignment of both global backbones and local surfaces of proteins that do not depend on the ordering of residues in the primary sequence. The algorithm for global alignment is based on fragment assembly, and takes advantage of an approximation algorithm for solving the maximum weight independent set problem. I show how this algorithm can be applied to discover proteins related by complex topological rearrangement, including circularly permuted proteins as well as proteins related by complex higher order permutations. The algorithm for local surface alignment is based on solving the bi-partite graph matching problem through comparison of surface pockets and voids, such as those computed from the underlying alpha complex of protein structure. I also describe how multiple matched surfaces can be used to automatically generate signature pockets and basis set that represent the ensemble of conformations of protein binding surfaces with a specific biological function of binding activity. This is followed by illustrative examples of signature pockets and basis sets computed for the evolutionarily related metzincin metalloendopeptidase (MEP) family of enzymes. I will then give an example of signature pockets on a set of enzymes that are from different evolutionary origin but have evolved to bind the same NAD cofactor. For both the MEP family of enzymes and the NAD binding proteins, I will give a discussion how how they can be used for discriminating MEP and NAD binding enzymes from other enzymes.
590 $a School code: 0799.
650 4 $a Biology, Molecular. $3 1017719
650 4 $a Biology, Bioinformatics. $3 1018415
690 $a 0307
690 $a 0715
710 2 $a University of Illinois at Chicago. $3 1020478
773 0 $t Dissertation Abstracts International $g 72-04B.
790 1 0 $a Liang, Jie, $e advisor
790 $a 0799
791 $a Ph.D.
792 $a 2011
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3446108