Coarse-grained elastic networks, normal mode analysis and robotics-inspired methods for modeling protein conformational transitions

Ibrahim Al-Bluwi, Marc Vaisset, Thierry Simeon, Juan Cortes

Research output: Chapter in Book/Report/Conference proceedingConference contribution

5 Scopus citations

Abstract

This paper presents a method, inspired by robot motion planning algorithms, to model conformational transitions in proteins. The capacity of normal mode analysis to predict directions of collective large-amplitude motions is exploited to bias the conformational exploration. A coarse-grained elastic network model built on short fragments of three residues is proposed for the rapid computation of normal modes. The accurate reconstruction of the all-atom model from the coarsegrained one is achieved using closed-form inverse kinematics. Results show the capacity of the method to model conformational transitions of proteins within a few hours of computing time on a single processor. Tests on a set of ten proteins demonstrate that the computing time scales linearly with the protein size, independently of the protein topology. Further experiments on adenylate kinase show that main features of the transition between the open and closed conformations of this protein are well captured in the computed path.

Original languageEnglish (US)
Title of host publicationProceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012
Pages40-47
Number of pages8
DOIs
StatePublished - 2012
Event2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012 - Philadelphia, PA, United States
Duration: Oct 4 2012Oct 7 2012

Publication series

NameProceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012

Conference

Conference2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012
CountryUnited States
CityPhiladelphia, PA
Period10/4/1210/7/12

All Science Journal Classification (ASJC) codes

  • Biomedical Engineering
  • Health Informatics

Keywords

  • Protein conformational transitions
  • elastic network models
  • inverse kinematics
  • motion planning algorithms
  • normal mode analysis

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