Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories

摘要

In cells, molecules do not arbitrarily interact with others; interact only with molecules of a particular type. This molecular recognition is a very important molecular function as one of the molecular bases on which the cells sustain their lives. Recently, it has been found that molecular recognition, which occurs not only between protein and protein but also between RNA and protein, plays important roles in the cell. Understanding of the molecular recognition at the atomic level is one of the challenging problems in the field of molecular biology and biochemistry. In this review, we address the theoretical and practical aspects of molecular dynamics simulation, which has become an important tool for studying the molecular recognition. From the theoretical viewpoint, many free energy calculation methods based on statistical mechanics have been developed. As for the practical aspects, it is important that the evolution of the computing technique not only enabled long-time simulations, but also enhanced prediction accuracy of simulations with developing new reliable force fields. By the recent development of theory and technology, the challenging tasks such as analysis and prediction of conformational distribution, structural change, and free energy of protein and/or nucleic acid systems are becoming possible.