Flexibility–rigidity index for protein–nucleic acid flexibility and fluctuation analysis. Issue 14 (1st March 2016)

• Record Type: Journal Article
• Authors: Opron, Kristopher; Xia, Kelin; Burton, Zach; Wei, Guo‐Wei
• Is Part Of: Journal of computational chemistry. Volume 37:Issue 14(2016)
• Page Start: 1283
• Page End: 1295
• Publication Date: 2016-03-01
• Subjects: thermal fluctuation -- atomic flexibility -- protein–nucleic acid complex -- multiscale; Chemistry -- Data processing -- Periodicals; 542.85
• DOI: 10.1002/jcc.24320
• Languages: English
• ISSNs: 0192-8651

Abstract

Abstract : 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. © 2016 Wiley Periodicals, Inc. Abstract : The flexibility of protein–nucleic acid complexes is associated with their functions in signaling, gene regulation, transcription, translation, splicing, post‐transcriptional modification, and so on. This work introduces "flexibility–rigidity index (FRI)" as an accurate and efficient approach for the flexibility analysis of protein–nucleic acid complexes, including large ribosomes and RNA polymerases.