Publication:
Predicting important residues and ınteraction pathways in proteins using Gaussian network model: binding and stability of HLA proteins

Thumbnail Image

School / College / Institute

Program

KU-Authors

KU Authors

Co-Authors

Haliloğlu, Türkan
Gül, Ahmet

Publication Date

Language

Embargo Status

NO

Journal Title

Journal ISSN

Volume Title

Alternative Title

Abstract

A statistical thermodynamics approach is proposed to determine structurally and functionally important residues in native proteins that are involved in energy exchange with a ligand and other residues along an interaction pathway. The structure-function relationships, ligand binding and allosteric activities of ten structures of HLA Class I proteins of the immune system are studied by the Gaussian Network Model. Five of these models are associated with inflammatory rheumatic disease and the remaining five are properly functioning. In the Gaussian Network Model, the protein structures are modeled as an elastic network where the inter-residue interactions are harmonic. Important residues and the interaction pathways in the proteins are identified by focusing on the largest eigenvalue of the residue interaction matrix. Predicted important residues match those known from previous experimental and clinical work. Graph perturbation is used to determine the response of the important residues along the interaction pathway. Differences in response patterns of the two sets of proteins are identified and their relations to disease are discussed.

Source

Publisher

Public Library of Science

Subject

Mathematical and computational biology

Citation

Has Part

Source

PLOS Computational Biology

Book Series Title

Edition

DOI

10.1371/journal.pcbi.1000845

item.page.datauri

Link

Rights

Copyrights Note

Endorsement

Review

Supplemented By

Referenced By

0

Views

4

Downloads

View PlumX Details