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Journal Articles

H3 histone tail conformation within the nucleosome and the impact of K14 acetylation studied using enhanced sampling simulation

Ikebe, Kimiyoshi; Sakuraba, Shun*; Kono, Hidetoshi

PLOS Computational Biology, 12(3), p.e1004788_1 - e1004788_13, 2016/03

 Times Cited Count:31 Percentile:91.07(Biochemical Research Methods)

Journal Articles

Dimensionality reduction and correlation of biomolecular motions

Sakuraba, Shun

Tokei Suri, 62(2), p.171 - 184, 2014/12

In this review, we explain dimensionality reduction techniques applied in the field of the biomolecular simulation. The methods based on the linear transformation are reviewed. We also investigate how these methods use correlation for reducing the dimension of biomolecules. Our review includes functional mode analysis, principal component analysis, full correlation analysis, quasi anharmonic analysis, and independent subspace analysis. We also discuss the physical interpretation and implications of the methods.

Journal Articles

Molecular binding sites are located near the interface of intrinsic dynamics domains (IDDs)

Li, H.*; Sakuraba, Shun; Chandrasekaran, A.*; Yang, L.-W.*

Journal of Chemical Information and Modeling, 54(8), p.2275 - 2285, 2014/08

 Times Cited Count:14 Percentile:70.87(Chemistry, Medicinal)

We provide evidence supporting that protein-protein and protein-ligand docking poses are functions of protein shape and intrinsic dynamics. Over sets of 68 protein-protein complexes and 240 non-homologous enzymes, we recognize common predispositions for binding sites to have minimal vibrations and angular momenta while two interacting proteins orient so as to maximize the angle between their rotation/bending axes ($$> 65^{circ}$$). The findings are then used to define quantitative criteria to filter out docking decoys less likely to be the near-native poses, hence the chances to find near-native hits can be doubled. With the novel approach to partition a protein into `domains' of robust but disparate intrinsic dynamics, 90% of catalytic residues in enzymes can be found within the first 50% of the residues closest to the interface of these dynamics domains. The results suggest an anisotropic rather than isotropic distribution of catalytic residues near the mass centers of enzymes.

Journal Articles

ERmod; Fast and versatile computation software for solvation free energy with approximate theory of solutions

Sakuraba, Shun; Matsubayashi, Nobuyuki*

Journal of Computational Chemistry, 35(21), p.1592 - 1608, 2014/08

 Times Cited Count:43 Percentile:79.55(Chemistry, Multidisciplinary)

ERmod is a software package to efficiently and approximately compute the solvation free energy using the method of energy representation. Molecular simulation is to be conducted at two condensed-phase systems of the solution of interest and the reference solvent with test-particle insertion of the solute. The subprogram $texttt{ermod}$ in ERmod then provides a set of energy distribution functions from the simulation trajectories, and another subprogram $texttt{slvfe}$ determines the solvation free energy from the distribution functions through an approximate functional. The present paper describes the design and implementation of ERmod, and illustrates its performance in solvent water for two organic solutes and two protein solutes. Actually, the free-energy computation with ERmod is not restricted to the solvation in homogeneous medium such as fluid and polymer, and can treat the binding into weakly ordered system with nano-inhomogeneity such as micelle and lipid membrane. ERmod is available on web at $texttt{http://sourceforge.net/projects/ermod}$.

Journal Articles

Adaptive lambda square dynamics simulation; An Efficient conformational sampling method for biomolecules

Ikebe, Kimiyoshi; Sakuraba, Shun; Kono, Hidetoshi

Journal of Computational Chemistry, 35(1), p.39 - 50, 2014/01

 Times Cited Count:14 Percentile:45.64(Chemistry, Multidisciplinary)

Oral presentation

Molecular dynamics simulation of Cs$$^{+}$$ - protein system

Sakuraba, Shun

no journal, , 

In the present research we report the benchmark of Cs$$^{+}$$-ion parameters used in molecular dynamics (MD) simulation. We also suggest possible improvements to it by adding the cation-$$pi$$ interaction as an extra Lennard-Jones parameter.

Oral presentation

Free energy profile for nucleosomal DNA unwrapping

Kono, Hidetoshi; Yonetani, Yoshiteru; Ikebe, Kimiyoshi; Sakuraba, Shun; Ishida, Hisashi

no journal, , 

Oral presentation

Oral presentation

Oral presentation

Conformational sampling of a histone tail with ALSD simulation

Ikebe, Kimiyoshi; Sakuraba, Shun; Kono, Hidetoshi

no journal, , 

no abstracts in English

Oral presentation

Conformational sampling simulation of an H3 histone tail by Adaptive Lambda Square Dynamics method

Ikebe, Kimiyoshi; Sakuraba, Shun; Kono, Hidetoshi

no journal, , 

no abstracts in English

Oral presentation

Free energy profile of nucleosomal DNA unwrapping

Kono, Hidetoshi; Sakuraba, Shun; Ishida, Hisashi

no journal, , 

Oral presentation

Spotting the difference in the molecular dynamics of the biomolecules

Sakuraba, Shun; Kono, Hidetoshi

no journal, , 

Upon analyzing molecular dynamics simulation, two or more simulation results are often compared - it is also the case with biomolecular simulations. Comparing the effect of the mutations, pressure change or ligand binding, is the common example of such cases, to name a few. In this presentation we will show that an existing method, called Linear Discriminant Analysis (LDA), is useful for comparing several simulations. Applications and the comparison to the existing methods will be presented.

Oral presentation

How does an acetylation on a histone tail affect the conformation

Ikebe, Kimiyoshi; Sakuraba, Shun; Kono, Hidetoshi

no journal, , 

no abstracts in English

Oral presentation

Free energy profile for nucleosomal DNA unwrapping

Kono, Hidetoshi; Sakuraba, Shun; Ishida, Hisashi

no journal, , 

Oral presentation

How does an acetylation on a histone tail affect the conformation ?

Ikebe, Kimiyoshi; Sakuraba, Shun; Kono, Hidetoshi

no journal, , 

no abstracts in English

Oral presentation

How does an acetylation affect conformation of an H3 histone tail?

Ikebe, Kimiyoshi; Sakuraba, Shun*; Kono, Hidetoshi

no journal, , 

Oral presentation

Dynamics of nucleosomes and impact of acetylation

Kono, Hidetoshi; Ikebe, Kimiyoshi; Sakuraba, Shun*; Ishida, Hisashi

no journal, , 

Oral presentation

How does an acetylation affect the conformation of H3 histone tail ?

Ikebe, Kimiyoshi; Sakuraba, Shun*; Kono, Hidetoshi

no journal, , 

25 (Records 1-20 displayed on this page)