Shoji Takada

Allostery, the coupling between ligand binding and protein conformational change, is the heart of biological network and it has often been explained by two representative models, the induced-fit and the population-shift models. Here, we clarified for what systems one model fits better than the other by performing molecular simulations of coupled binding and conformational change. Based on the dynamic energy landscape view, we developed an implicit ligand-binding model combined with the double-ba

We propose a reduced model of proteins and simulate folding of a designed three helix bundle protein with 54 residues, the dynamics of a random heteropolymer, and the helix formation of a short peptide, up to ∼1 μs, near the estimated lower bound of folding time. The model has explicit backbone atoms, while solvent effects are taken into account via effective potentials. Interactions include two multibody terms; (1) the hydrogen bond strength reflecting the local dielectric constant that is depe

Protein folding has been a long-lived problem in biophysics. Much important progress has been made in the 90s by focusing on small single-domain proteins (1). In particular, (i) site-resolved measurement of the folding transition state ensemble, quantified as φ-values (2), made it possible to understand folding mechanisms relatively unambiguously, stimulating interaction between experimentalists and theoreticians; (ii) the energy-landscape theory (3) gave us a general framework based on statisti

Due to hierarchic nature of biomolecular systems, their computational modeling calls for multiscale approaches, in which coarse-grained (CG) simulations are used to address long-time dynamics of large systems. Here, we review recent developments and applications of CG modeling methods, focusing on our methods primarily for proteins, DNA, and their complexes. These methods have been implemented in the CG biomolecular simulator, CafeMol. Our CG model has resolution such that ∼10 non-hydrogen atoms

Tunneling energy splittings of vibrationally excited states are calculated quantum mechanically using several models of two-dimensional symmetric double well potentials. Various effects of vibrational excitation on tunneling are found to appear, depending on the topography of potential energy surface; the symmetry of the mode coupling plays an essential role. Especially, oscillation of tunneling splitting with respect to vibrational quantum number can occur and is interpreted by a clear physical

A general Wentzel–Kramers–Brillouin (WKB) theory of multidimensional tunneling is formulated and an illuminating physical picture of the effects of multidimensionality is provided. Two basic problems are solved: (i) Maslov’s semiclassical wave function in the classically accessible region is connected to the wave function in the classically inaccessible region and (ii) the latter is propagated into the deep tunneling region. It is found that there exist two distinct types of tunneling: pure tunn

While recent experiments revealed that some pioneer transcription factors (TFs) can bind to their target DNA sequences inside a nucleosome, the binding dynamics of their target recognitions are poorly understood. Here we used the latest coarse-grained models and molecular dynamics simulations to study the nucleosome-binding procedure of the two pioneer TFs, Sox2 and Oct4. In the simulations for a strongly positioning nucleosome, Sox2 selected its target DNA sequence only when the target was expo

We optimize a physical energy function for proteins with the use of the available structural database and perform three benchmark tests of the performance: (1) recognition of native structures in the background of predefined decoy sets of Levitt, (2) de novo structure prediction using fragment assembly sampling, and (3) molecular dynamics simulations. The energy parameter optimization is based on the energy landscape theory and uses a Monte Carlo search to find a set of parameters that seeks the

Nucleosomes, basic units of chromatin, are known to show spontaneous DNA unwrapping dynamics that are crucial for transcriptional activation, but its structural details are yet to be elucidated. Here, employing a coarse-grained molecular model that captures residue-level structural details up to histone tails, we simulated equilibrium fluctuations and forced unwrapping of single nucleosomes at various conditions. The equilibrium simulations showed spontaneous unwrapping from outer DNA and subseq

While nucleosome positioning on eukaryotic genome play important roles for genetic regulation, molecular mechanisms of nucleosome positioning and sliding along DNA are not well understood. Here we investigated thermally-activated spontaneous nucleosome sliding mechanisms developing and applying a coarse-grained molecular simulation method that incorporates both long-range electrostatic and short-range hydrogen-bond interactions between histone octamer and DNA. The simulations revealed two distin

Residue-level coarse-grained (CG) models have become one of the most popular tools in biomolecular simulations in the trade-off between modeling accuracy and computational efficiency. To investigate large-scale biological phenomena in molecular dynamics (MD) simulations with CG models, unified treatments of proteins and nucleic acids, as well as efficient parallel computations, are indispensable. In the GENESIS MD software, we implement several residue-level CG models, covering structure-based a

High-speed (HS) atomic force microscopy (AFM) is a prominent imaging technology that observes large-scale structural dynamics of biomolecules near the physiological condition, but the AFM data are limited to the surface shape of specimens. Rigid-body fitting methods were developed to obtain molecular structures that fit to an AFM image, without accounting for conformational changes. Here, we developed a method to fit flexibly a three-dimensional (3D) biomolecular structure into an AFM image. Fir