Rigidity and flexibility of protein-nucleic acid complexes

The study of protein-nucleic acid complexes is relevant for the understanding of many biological processes, including transcription, translation, replication, and recombination. The individual molecules in such complexes must be rigid enough to allow geometric matching of complementary shapes, yet sufficiently flexible to perform their functions. In this paper, we present a newly developed extension to KINARI-Web, our freely available server for biomolecular rigidity analysis, to permit the analysis of PDB files containing nucleic acids and protein-nucleic acid complexes. Previously, only the protein portion of these complexes could be analyzed by KINARI. To the best of our knowledge, no other publicly available rigidity analysis software has this capability. We demonstrate this new feature by performing in silico rigidity studies on two data sets of protein-nucleic acid complexes, both in the absence and presence of nucleic acids. We find that the inclusion of nucleic acids significantly alters the rigidity of 40% of the 506 structures we analyzed.

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