title: Flexibility-rigidity index for protein-nucleic acid flexibility and fluctuation analysis.
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.
authors.affiliation: Department of Biochemistry and Molecular Biology, Michigan State University, Michigan, 48824.
authors.forename: Kristopher
authors.initials: K
authors.lastname: Opron
authors.affiliation: Department of Mathematics, Michigan State University, Michigan, 48824.
authors.forename: Kelin
authors.initials: K
authors.lastname: Xia
authors.affiliation: Department of Biochemistry and Molecular Biology, Michigan State University, Michigan, 48824.
authors.forename: Zach
authors.initials: Z
authors.lastname: Burton
authors.affiliation: Mathematical Biosciences Institute, The Ohio State University, Columbus, Ohio, 43210.
authors.forename: Guo-Wei
authors.initials: GW
authors.lastname: Wei
mesh_terms: D000465:Algorithms; D009696:Nucleic Acids / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*
chemical_list: D009696:Nucleic Acids; D011506:Proteins
keywords: atomic flexibility; multiscale; protein-nucleic acid complex; thermal fluctuation