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Flexibility-rigidity index for protein-nucleic acid flexibility and fluctuation analysis.
Opron, Kristopher; Xia, Kelin; Burton, Zach; Wei, Guo-Wei.
Afiliação
  • Opron K; Department of Biochemistry and Molecular Biology, Michigan State University, Michigan, 48824.
  • Xia K; Department of Mathematics, Michigan State University, Michigan, 48824.
  • Burton Z; Department of Biochemistry and Molecular Biology, Michigan State University, Michigan, 48824.
  • Wei GW; Mathematical Biosciences Institute, The Ohio State University, Columbus, Ohio, 43210.
J Comput Chem ; 37(14): 1283-95, 2016 May 30.
Article em En | MEDLINE | ID: mdl-26927815
Protein-nucleic acid complexes are important for many cellular processes including the most essential functions such as transcription and translation. For many protein-nucleic acid complexes, flexibility of both macromolecules has been shown to be critical for specificity and/or function. The flexibility-rigidity index (FRI) has been proposed as an accurate and efficient approach for protein flexibility analysis. In this article, we introduce FRI for the flexibility analysis of protein-nucleic acid complexes. We demonstrate that a multiscale strategy, which incorporates multiple kernels to capture various length scales in biomolecular collective motions, is able to significantly improve the state of art in the flexibility analysis of protein-nucleic acid complexes. We take the advantage of the high accuracy and O(N) computational complexity of our multiscale FRI method to investigate the flexibility of ribosomal subunits, which are difficult to analyze by alternative approaches. An anisotropic FRI approach, which involves localized Hessian matrices, is utilized to study the translocation dynamics in an RNA polymerase.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Ácidos Nucleicos / Proteínas Idioma: En Ano de publicação: 2016 Tipo de documento: Article

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Ácidos Nucleicos / Proteínas Idioma: En Ano de publicação: 2016 Tipo de documento: Article