Osamu Miyashita

TL;DR: This work presents a model for global structural transformations, such as allostery, that involve large-scale motion and possible partial unfolding, illustrating the method with the conformational transition of adenylate kinase.

TL;DR: A coarse grained model is employed to explore the interplay between protein structure, folding and function which is applicable to allosteric or non-allosteric proteins and it is demonstrated that local unfolding may be due, in part, to competing intra-protein interactions.

TL;DR: Large, functionally relevant conformational changes for elongation factor G bound to the ribosome, Escherichia coli RNA polymerase and cowpea chlorotic mottle virus are elucidated as the result of the application of NMFF from high-resolution structures to cryo-electron microscopy maps.

TL;DR: It is demonstrated that refinement based on normal mode analysis provides an accurate and fast alternative for the flexible fitting of high-resolution structure into a low-resolution density map and that lower resolution (multi-scale) structural models can be used for the normal mode searching in lieu of fully atomic models with little loss of overall accuracy.

TL;DR: In this article, a molecular dynamics simulation of the intramolecular vibrational energy transfer in myoglobin at near zero temperature was performed, and the coupling coefficients had high correlation with how much the coupled modes geometrically overlapped with each other.