Yasumasa Joti

Hydration Affects Both Harmonic and Anharmonic Nature of Protein Dynamics

To understand the effect of hydration on protein dynamics, inelastic neutron-scattering experiments were performed on staphylococcal nuclease samples at differing hydration levels: dehydrated, partially hydrated, and hydrated. At cryogenic temperatures, hydration affected the collective motions with energies lower than 5 meV, whereas the high-energy localized motions were independent of hydration. The prominent change was a shift of boson peak toward higher energy by hydration, suggesting a hardening of harmonic potential at local minima on the energy landscape. The 240 K transition was observed only for the hydrated protein. Significant quasielastic scattering at 300 K was observed only for the hydrated sample, indicating that the origin of the transition is the motion activated by hydration water. The neutron-scattering profile of the partially hydrated sample was quite similar to that of the hydrated sample at 100 K and 200 K, whereas it was close to the dehydrated sample at 300 K, indicating that partial hydration is sufficient to affect the harmonic nature of protein dynamics, and that there is a threshold hydration level to activate anharmonic motions. Thus, hydration water controls both harmonic and anharmonic protein dynamics by differing means.

Detecting coupled collective motions in protein by independent subspace analysis

Protein dynamics evolves in a high-dimensional space, comprising aharmonic, strongly correlated motional modes. Such correlation often plays an important role in analyzing protein function. In order to identify significantly correlated collective motions, here we employ independent subspace analysis based on the subspace joint approximate diagonalization of eigenmatrices algorithm for the analysis of molecular dynamics (MD) simulation trajectories. From the 100 ns MD simulation of T4 lysozyme, we extract several independent subspaces in each of which collective modes are significantly correlated, and identify the other modes as independent. This method successfully detects the modes along which long-tailed non-Gaussian probability distributions are obtained. Based on the time cross-correlation analysis, we identified a series of events among domain motions and more localized motions in the protein, indicating the connection between the functionally relevant phenomena which have been independently revealed by experiments.

Hydration Effect on Low-Frequency Protein Dynamics Observed in Simulated Neutron Scattering Spectra

Hydration effects on protein dynamics were investigated by comparing the frequency dependence of the calculated neutron scattering spectra between full and minimal hydration states at temperatures between 100 and 300 K. The protein boson peak is observed in the frequency range 1–4 meV at 100 K in both states. The peak frequency in the minimal hydration state shifts to lower than that in the full hydration state. Protein motions with a frequency higher than 4 meV were shown to undergo almost harmonic motion in both states at all temperatures simulated, whereas those with a frequency lower than 1 meV dominate the total fluctuations above 220 K and contribute to the origin of the glass-like transition. At 300 K, the boson peak becomes buried in the quasielastic contributions in the full hydration state but is still observed in the minimal hydration state. The boson peak is observed when protein dynamics are trapped within a local minimum of its energy surface. Protein motions, which contribute to the boson peak, are distributed throughout the whole protein. The fine structure of the dynamics structure factor is expected to be detected by the experiment if a high resolution instrument (<∼20 μeV) is developed in the near future.

Hydration-dependent protein dynamics revealed by molecular dynamics simulation of crystalline staphylococcal nuclease.

Molecular dynamics simulations of crystalline Staphylococcal nuclease in full and minimal hydration states were performed to study hydration effects on protein dynamics at temperatures ranging from 100 to 300 K. In a full hydration state (hydration ratio in weight, h=0.49), gaps are fully filled with water molecules, whereas only crystal waters are included in a minimal hydration state (h=0.09). The inflection of the atomic mean-square fluctuation of protein as a function of temperature, known as the glass-like transition, is observed at approximately 220 K in both cases, which is more significant in the full hydration state. By examining the temperature dependence of residual fluctuation, we found that the increase of fluctuations in the loop and terminal regions, which are exposed to water, is much greater than that in other regions in the full hydration state, but the mobilities of the corresponding regions are relatively restricted in the minimal hydration state by intermolecular contact. The atomic mean-square fluctuation of water molecules in the full hydration state at 300 K is 1 order of magnitude greater than that in the minimal hydration state. Above the transition temperature, most water molecules in the full hydration state behave like bulk water and act as a lubricant for protein dynamics. In contrast, water molecules in the minimal hydration state tend to form more hydrogen bonds with the protein, restricting the fluctuation of these water molecules to the level of the protein. Thus, intermolecular interaction and solvent mobility are important to understand the glass-like transition in proteins.

Protein-ligand complex structure from serial femtosecond crystallography using soaked thermolysin microcrystals and comparison with structures from synchrotron radiation

The applicability of the ligand-soaking method in serial femtosecond crystallography has been examined to examine the feasibility of pharmaceutical applications of X-ray free-electron lasers.

An efficient timer and sizer of protein motions reveals the time scales of functional dynamics in structured biomacromolecules

Life ticks as fast as how efficiently proteins perform their functional dynamics. Well-folded/structured biomacromolecules perform functions via large-scale intrinsic motions across multiple conformational states, which occur at timescales of nano-to milliseconds. Computationally expensive molecular dynamics (MD) simulation has been the only theoretical tool to gauge the time and sizes of these motions, though barely to their slowest ends. Here, we convert a computationally cheap elastic network model (ENM) into a molecular timer and sizer to gauge the slowest functional motions of proteins and ribosome. Quasi-harmonic analysis, fluctuation-profile matching (FPM) and the Wiener–Khintchine theorem (WKT) are used to define the “time-periods”, t, for anharmonic principal components (PCs) which are validated by NMR order parameters. The PCs with their respective “time-periods” are mapped to the eigenvalues (λENM) of the corresponding ENM modes. Thus, the power laws t(ns) = 86.9λENM-1.9 and σ2(Å2) = 46.1λENM-2.5 are established allowing the characterization of the time scales of NMR-resolved conformers, crystallographic anisotropic displacement parameters, and important ribosomal motions, as well as motional sizes of the latter. TOC Graphics

Current status and future plan of the soft x-ray beamline at SACLA (Conference Presentation)

SACLA was inaugurated in March 2012 with two beamlines: BL3 for hard X-ray FEL and BL1 for wide range spontaneous emission. To enhance the research opportunities in soft X-ray region, the SCSS test accelerator, which was a prototype linac of SACLA and decommissioned in 2013, was upgraded, relocated to the SACLA undulator hall, and connected to BL1. The commissioning of this upgraded BL1 had been started from September in 2015, and user operation was started from June 2016. Currently, SASE-FEL pulses in the photon energy range of 20 to 150 eV are available and average pulse energy is about 70 μJ at 100 eV. We are developing beam diagnostic systems such as an arrival timing diagnostics between the SXFEL and the synchronized optical laser. We have further upgrade plans of the accelerator and the beamline. In this presentation, I will report the latest status and future upgrade plans of this beamline.

Dynamic Structure of Protein to be Studied by Neutron Scattering

Proteins are molecular machines with structures that have evolved to perform various biological functions. Like all machines the link between structure and function is through dynamics. To properly understand function it is therefore necessary to understand the nature of protein dynamics. Inelastic neutron scattering is a spectroscopic technique which can be used to study protein dynamics on the timescale from 10-12 to 10-9 seconds, where functionrelevant protein motions take place. We hope that neutron scattering experiments to be performed by using high-intensity neutron source at J-PARC provide us valuable information on the protein dynamics.

Slow Protein Dynamics to be Detected in Inelastic Neutron Scattering Spectra Studied by Molecular Simulation

The dynamic structure factors were calculated by using the results of biomolecular simulations at the room and cryogenic temperatures. Three types of simulation, normal mode analysis, molecular dynamics in vacuum, and molecular dynamics in water were applied to HEW Lysozyme. At the room temperature, the shapes of the three dynamic structure factors are in good agreement in the high frequency regions (> 60 cm−1), but considerably different in the low frequency regions (< 60 cm−1). At the cryogenic temperature, the so‐called boson peak (∼ 30 cm−1) is observed only in the results of molecular dynamics in water. The slow dynamics of protein, found in these low frequency regions, are likely to play important roles to protein function.