Protein flexibility predictions using graph theory

Donald J. Jacobs, A. J. Rader, Leslie A. Kuhn, M. F. Thorpe

Research output: Contribution to journalArticle

549 Scopus citations

Abstract

Techniques from graph theory are applied to analyze the bond networks in proteins and identify the flexible and rigid regions. The bond network consists of distance constraints defined by the covalent and hydrogen bonds and salt bridges in the protein, identified by geometric and energetic criteria. We use an algorithm that counts the degrees of freedom within this constraint network and that identifies all the rigid and flexible substructures in the protein, including overconstrained regions (with more crosslinking bonds than are needed to rigidify the region) and underconstrained or flexible regions, in which dihedral bond rotations can occur. The number of extra constraints or remaining degrees of bond-rotational freedom within a substructure quantifies its relative rigidity/flexibility and provides a flexibility index for each bond in the structure. This novel computational procedure, first used in the analysis of glassy materials, is approximately a million times faster than molecular dynamics simulations and captures the essential conformational flexibility of the protein main and side-chains from analysis of a single, static three-dimensional structure. This approach is demonstrated by comparison with experimental measures of flexibility for three proteins in which hinge and loop motion are essential for biological function: HIV protease, adenylate kinase, and dihydrofolate reductase.

Original languageEnglish (US)
Pages (from-to)150-165
Number of pages16
JournalProteins: Structure, Function and Genetics
Volume44
Issue number2
DOIs
StatePublished - Aug 1 2001

Keywords

  • Adenylate kinase
  • Conformational change
  • Coupled/collective motions
  • Dihedral angle constraints and rotations
  • Dihydrofolate reductase
  • Distance constraints
  • Hydrogen-bond networks
  • Mobility and dynamics
  • Structural stability

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

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  • Cite this

    Jacobs, D. J., Rader, A. J., Kuhn, L. A., & Thorpe, M. F. (2001). Protein flexibility predictions using graph theory. Proteins: Structure, Function and Genetics, 44(2), 150-165. https://doi.org/10.1002/prot.1081