Free-energy landscape of tRNA translocation through ribosome analysed using MD simulations and cryo-EM density maps

Ishida, Hisashi; Matsumoto, Atsushi

no journal, , 

Kinetics of hydrogen-bonding of protein hydration water and its dynamical coupling with protein dynamics

Nakagawa, Hiroshi; Kataoka, Mikio

no journal, , 

Unique physical properties of water are originated from the hydrogen bond. The hydrogen bond determines the spatial network patterns and water dynamics. Hydration water around the molecules, such as ions, polymers and bio-molecules, has quite different physical properties from bulk water. The protein hydration affects the biological function of the protein. Here, by using the molecular dynamics simulation, we show that the hydrogen bond kinetics of the protein hydration water is strongly affected by the local bonding patterns near the tagged hydrogen bond and that percolation of hydration water on the protein surface essentially determines the cooperative hydrogen bond forming and breaking dynamics. These dynamical characters of hydration water are quite different from those of the bulk water. The hydrogen bond kinetics between hydration water is correlated with the kinetics between the protein and hydration water, suggesting the dynamical coupling between them. The percolation of hydrogen bond network would contribute to the physical properties of protein hydration water. This hydration water dynamics induces the protein dynamical transition observed by neutron inelastic scattering. The dynamical coupling between hydration water and protein should be essential for protein thermal fluctuation and functionality.

Automatic similarity identification of 2D diffraction patterns with noisy background for 3D coherent X-ray diffractive imaging

Tokuhisa, Atsushi*; Jochi, Yasumasa*; Kono, Hidetoshi; Go, Nobuhiro*

no journal, , 

Dynamics of cardiomyopathy-causing mutant of troponin observed by neutron scattering

Matsuo, Tatsuhito; Natali, F.*; Zaccai, G.*; Fujiwara, Satoru

no journal, , 

Troponin is a protein that regulates the muscle contraction depending on the intracellular Ca2+ concentration. K247R mutation of TnT is known to cause the hypertrophic cardiomyopathy. In this work, neutron scattering was used to detect possible changes in dynamics of troponin caused by mutation. Elastic incoherent neutron scattering experiments were carried out on solution samples of the wild type, and K247R mutant at the IN13 spectrometer at the Institut Laue-Langevin, at temperatures between 280 K and 292 K with an interval of 3 K. From the measured scattering data, force constants (k), which reflect the resilience of the protein, were calculated. The k values for the wild type and K247R mutant were 0.077 (0.035) N/m and 0.046 (0.026) N/m (mean(s.d.)), respectively. This suggests that the disease-causing mutant is more flexible than the wild type. The large flexibility might modulate Ca2+ signal transmission mechanism, leading to the functional aberration.