Sequence Order Independent Comparison of Protein Global Backbone Structures and Local Binding Surfaces for Evolutionary and Functional Inference View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2011-03-29

AUTHORS

Joe Dundas , Bhaskar DasGupta , Jie Liang

ABSTRACT

Alignment of protein structures can help to infer protein functions and can reveal ancient evolutionary relationship. We 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 sequences. The algorithm for global structural alignment is based on fragment assembly, and takes advantage of an approximation algorithm for solving the maximum weight independent set problem. We 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 the protein structure. We also describe how multiple matched surfaces can be used to automatically generate signature pockets and a basis set that represents 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 a basis set computed for NAD binding proteins, along with a discussion on how they can be used for discriminating NAD-binding enzymes from other enzymes. More... »

PAGES

125-143

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-94-007-0881-5_7

DOI

http://dx.doi.org/10.1007/978-94-007-0881-5_7

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1019444394


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