NDLI: Graphical models of residue coupling in protein families

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Graphical models of residue coupling in protein families

Content Provider	ACM Digital Library
Author	Thomas, John Ramakrishnan, Naren Bailey-Kellogg, Chris
Abstract	Identifying residue coupling relationships within a protein family can provide important insights into the family's evolutionary record, and has significant applications in analyzing and optimizing sequence-structure-function relationships. We present the first algorithm to infer an undirected graphical model representing residue coupling in protein families. Such a model, which we call a residue coupling network, serves as a compact description of the joint amino acid distribution, focused on the independences among residues. This stands in contrast to current methods, which manipulate dense representations of co-variation and are focused on assessing dependence, which can conflate direct and indirect relationships. Our probabilistic model provides a sound basis for predictive (will this newly designed protein be folded and functional?), diagnostic (why is this protein not stable or functional?), and abductive reasoning (what if I attempt to graft features of one protein family onto another?). Further, our algorithm can readily incorporate, as priors, hypotheses regarding possible underlying mechanistic/energetic explanations for coupling. The resulting approach constitutes a powerful and discriminatory mechanism to identify residue coupling from protein sequences and structures. Analysis results on the G-protein coupled receptor (GPCR) and PDZ domain families demonstrate the ability of our approach to effectively uncover and exploit models of residue coupling.
Starting Page	12
Ending Page	20
Page Count	9
File Format	PDF
ISBN	1595932135
DOI	10.1145/1134030.1134033
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2005-08-21
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Graphical models Sequence-structure-function relationships Evolutionary co-variation Residue coupling networks
Content Type	Text
Resource Type	Article

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