4.3 Article

Structural features that predict real-value fluctuations of globular proteins

Journal

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Volume 80, Issue 5, Pages 1425-1435

Publisher

WILEY
DOI: 10.1002/prot.24040

Keywords

protein flexibility; protein dynamics; structure-dynamics relationship; support vector regression; molecular dynamics; fluctuation prediction

Funding

  1. EU (Foundation for Polish Science MPD)
  2. National Science Foundation [IIS0915801, DMS0800568, EF0850009]
  3. National Institutes of Health [R01GM075004, R01GM097528]
  4. Direct For Biological Sciences
  5. Emerging Frontiers [0850009] Funding Source: National Science Foundation
  6. Div Of Information & Intelligent Systems
  7. Direct For Computer & Info Scie & Enginr [0915801] Funding Source: National Science Foundation

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It is crucial to consider dynamics for understanding the biological function of proteins. We used a large number of molecular dynamics (MD) trajectories of nonhomologous proteins as references and examined static structural features of proteins that are most relevant to fluctuations. We examined correlation of individual structural features with fluctuations and further investigated effective combinations of features for predicting the real value of residue fluctuations using the support vector regression (SVR). It was found that some structural features have higher correlation than crystallographic B-factors with fluctuations observed in MD trajectories. Moreover, SVR that uses combinations of static structural features showed accurate prediction of fluctuations with an average Pearson's correlation coefficient of 0.669 and a root mean square error of 1.04 angstrom. This correlation coefficient is higher than the one observed in predictions by the Gaussian network model (GNM). An advantage of the developed method over the GNMs is that the former predicts the real value of fluctuation. The results help improve our understanding of relationships between protein structure and fluctuation. Furthermore, the developed method provides a convienient practial way to predict fluctuations of proteins using easily computed static structural features of proteins. Proteins 2012; (c) 2012 Wiley Periodicals, Inc.

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