JOURNAL OF COMPUTATIONAL CHEMISTRY 37(8) 712-723 2016年3月 [査読有り]
We develop a new method for calculating the hydration free energy (HFE) of a protein with any net charge. The polar part of the energetic component in the HFE is expressed as a linear combination of four geometric measures (GMs) of the protein str...
JOURNAL OF PHYSICAL CHEMISTRY B 119(44) 14120-14129 2015年11月 [査読有り]
The new type of molecular recognition, in which an intrinsically disordered region (IDR) of a protein binds to many different target proteins with target-dependent structure formation, is indispensable to the expression of life phenomena and also ...
JOURNAL OF CHEMICAL PHYSICS 143(12) 125102 2015年9月 [査読有り]
It is of great interest from both scientific and practical viewpoints to theoretically predict the thermal-stability changes upon mutations of a protein. However, such a prediction is an intricate task. Up to now, significantly many approaches for...
JOURNAL OF CHEMICAL PHYSICS 142(14) 145103 2015年4月 [査読有り]
In earlier works, we showed that the entropic effect originating from the translational displacement of water molecules plays the pivotal role in protein folding and denaturation. The two different solvent models, hard-sphere solvent and model wat...
JOURNAL OF PHYSICAL CHEMISTRY B 119(8) 3423-3433 2015年2月 [査読有り]
AcrB, a homotrimer, is the pivotal part of a multidrug efflux pump. A functionally rotating picture has been proposed for the drug transport by AcrB, but its mechanism remains unresolved. Here, we investigate the energetics of the whole functional...