Tokyo Institute of Technology · Biochemistry, Genetics and Molecular Biology
Professor H. Hata's research lab specializes in computational and structural biology, focusing on molecular dynamics simulations to understand protein-ligand interactions, protein complex dissociation, and the role of solvent dynamics in biomolecular recognition. The lab develops advanced simulation methods such as dPaCS-MD/MSM to calculate binding free energies and analyze complex dissociation pathways at atomic resolution. Their work spans from fundamental biophysics—such as protein folding, hydration effects under high pressure, and nucleic acid secondary structure kinetics—to applications in drug design and enzyme mechanisms. The lab also investigates cytoskeletal dynamics and post-translational regulation in cellular signaling, integrating experimental and computational approaches.
Figures are computed from collected data and may differ slightly.
The POP2 (Caf1) protein in Saccharomyces cerevisiae affects a variety of transcriptional processes and is a component of the Ccr4p complex. We have isolated five multicopy suppressor genes of a pop2 deletion mutation: CCR4, DHH1 (a putative RNA helicase), PKC1, STM1, and MPT5 (multicopy suppressor of pop two). Overexpression of either the CCR4 or DHH1 genes effectively suppressed phenotypes associated with pop2 mutant cells; overexpression of PKC1, STM1, or MPT5 genes produced only partial suppr
We recently proposed a computational procedure to simulate the dissociation of protein/ligand complexes using the dissociation Parallel Cascade Selection Molecular Dynamics simulation (dPaCS-MD) method and to analyze the generated trajectories using the Markov state model (MSM). This procedure, called dPaCS-MD/MSM, enables calculation of the dissociation free energy profile and the standard binding free energy. To examine whether this method can reproduce experimentally determined binding free e
We have prepared axonemes without outer dynein arms from sea-urchin (Pseudocentrotus depressus, Hemicentrotus pulcherrimus) sperm flagella by selective solubilization with NaCl. Electron microscopy revealed that the axonemes gradually lost their outer arms in 0.5 M NaCl during 10 min. Such axonemes retained 42.8 +/- 7.3% of their total axonemal ATPase activity and showed C, A, D and B bands in the dynein region of 4% SDS-gel, while a solubilized fraction of the outer arms consisted almost entire
Restoration of the local gauge symmetry and its connection to color confinement is investigated in non-Abelian gauge theories with covariant gauge fixing. We consider the Noether current Jaµ,ν of the local gauge transformation with transformation functions Λb(x) linear in xµ;Λb(x)=δabxν. This current is conserved only in the physical subspace of the state vector space and in perturbation theory contains a massless pole communicating to the gauge field. We define the local gauge symmetry restorat
Nucleic acid secondary structure plays an important role in nucleic acid-nucleic acid recognition/hybridization processes, and is also a vital consideration in DNA nanotechnology. Although the influence of stable secondary structures on hybridization kinetics has been characterized, unstable secondary structures, which show positive ΔG° with self-folding, can also form, and their effects have not been systematically investigated. Such thermodynamically unfavorable secondary structures should not
High pressure below 100 MPa interferes inter-molecular interactions without causing pressure denaturation of proteins. In Escherichia coli, the binding of the chemotaxis signaling protein CheY to the flagellar motor protein FliM induces reversal of the motor rotation. Using molecular dynamics (MD) simulations and parallel cascade selection MD (PaCS-MD), we show that high pressure increases the water density in the first hydration shell of CheY and considerably induces water penetration into the
1-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-3-(2-chloroethyl)-3- nitrosourea hydrochloride (ACNU), a cancer chemotherapeutic bifunctional alkylating agent, causes chloroethylation of DNA and subsequent DNA strand cross-linking through an ethylene bridge. We isolated and characterized two ACNU-sensitive mutants from mutagenized Chinese hamster ovary cells and found them to be new drug-sensitive recessive Chinese hamster mutants. Both mutants were sensitive to various monofunctional alkylating agen
The magnetic properties and the recording characteristics of multilayer CoNiCr thin film media with Cr interlayers have been examined. A great improvement in the signal-to-noise ratio is obtained by increasing the number of split layers: this improvement is due to the reduced media noise, which is accompanied by a reduction in the coercive squareness. TEM (transmission electron microscopy) observation shows that the CoNiCr grains in the multilayer media are more isolated compared with the single
A low-noise medium using double-layer CoNiCr thin films for high-density longitudinal magnetic recording has been developed. This medium consists of a Cr underlayer, a first CoNiCr layer, a Cr interlayer, and a second CoNiCr layer. In this study, the effects of Cr interlayer on the magnetic properties and read/write characteristics are investigated. Coercivity increases while remanence thickness product and coercive squareness decrease with increasing Cr interlayer thickness. The media noise is
We consider, in the covariantly gauge-fixed continuum theory of QCD formulated by the Euclidean path integral, a specific local gauge symmetry transformation which changes the boundary condition of the gauge fields. This local gauge symmetry is spontaneously broken in perturbation theory. We show that if this symmetry is restored dynamically, then the total confinement of color is realized. The restoration condition is found to coincide with the color confinement condition proposed earlier by Ku
The soft dilaton theorem is derived in covariant and light-cone gauge closed string field theories. We have to take special care of the singularity of the diagrams where the zero-momentum dilaton is attached to one of the external on-shell lines.
A 3-string vertex of open Neveu-Schwarz (NS) and Ramond (R) superstrings is constructed explicity in terms of oscillator language for the joining and splitting type interaction. Both for the 3-NS and NS-R-R cases, it is shown to satisfy theBRS invariance if the space-time dimension is 10. A bit peculiar connection conditions of the “fermionic” coordinates as well as their Neumann functions are disscussed in detail.
Diffusion of photoexcited carriers and the subsequent thermal diffusion by photoexcitation of a nanoparticulate TiO 2 thin film were observed by the heterodyne transient grating (HD-TG) method. The observed HD-TG signal showed that the photoexcited carriers were generated inhomogeneously in the depth direction and they diffused both in the depth and parallel directions of the film. The diffusion processes were analyzed using a two-dimensional diffusion model. The thermal profile generated by the
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