Biophysics

, Volume 59, Issue 1, pp 28–34 | Cite as

Method of prediction and optimization of conformational motion of proteins based on mass transportation principle

  • A. A. Koshevoy
  • E. O. Stepanov
  • Yu. B. Porozov
Molecular Biophysics

Abstract

The paper highlights approaches to fast prediction of protein conformational mobility. A new mathematical model based on the transportation principle is proposed. We describe an algorithm and soft-ware developed for a construction of the possible trajectories of the large-scale conformational motions of proteins (i.e. movements that occur within relatively large time intervals of the order of milliseconds). The modeling showed that the proposed method provides adequate, in terms of current knowledge of the biology and physics of proteins, results and allows simulation of large-scale conformational transitions for less time.

Keywords

conformational motion of protein transportation principle optimization coarse-grained methods 

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Copyright information

© Pleiades Publishing, Inc. 2014

Authors and Affiliations

  • A. A. Koshevoy
    • 1
  • E. O. Stepanov
    • 2
    • 3
  • Yu. B. Porozov
    • 1
  1. 1.ITMO UniversitySt. PetersburgRussia
  2. 2.St. Petersburg Department of Steklov Institute of MathematicsRussian Academy of SciencesSt. PetersburgRussia
  3. 3.St. Petersburg State UniversityPeterhof, St. PetersburgRussia

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