Laboratory for Biomolecular Function Simulation

Our team develops methodologies of molecular simulation and conducts applied studies for understanding of the molecular mechanics of cell functions. We are trying to analyze entire conformational transitions of supercomplexes of proteins with huge-scale molecular simulations using a peta-flops computer. We are also trying to develop methodologies that can reconstruct celluar environments in a computer to investigate the dynamics of protein molecules in celluar environments. The prediction of protein dynamics in celluar environments can lead to the elucidatoin of molecular mechanisms of diseases and the development of new drugs.

Research Subjects

• Development of multi-scale simulation method
• Simulations uncer cellular environment
• Simulations of biomolecules related to human diseases

Publications

1. Re, S., Nishima, W., Miyashita, N., and Sugita, Y.:
   "Conformational flexibility of N-glycans in solution studied by REMD simulations"
   Bio9phys. Rev. 4 (2012) 179-187.
2. Nishima, W., Miyashita, N., Yamaguchi, Y., Sugita, Y., and Re, S.:
   "Effect of Bisecting GlcNAcand Core Fucosylation on Conformational Properties of Biantennary Complex-Type N-Glycans in Solution"
   J. Phys. Chem. B. 116 (2012) 8504-8512.
3. Feig, M., and Sugita, Y.:
   "Variable Interactions between Protein Crowders and Biomolecular Solutes are Important in Understanding Cellular Crowding."
   J. Phys. Chem. B. 116 (2012) 599-605.
4. Mori, T., Ogushi, F., and Sugita, Y.:
   "Analysis of lipid surface area in protein-membrane systems combining voronoi tessellation and monte carlo integration methods."
   J. Comput. Chem. 33 (2012) 286-293.
5. Morita, M., Mohan Katta, A.V.S.K., Ahmad, S., Mori, T., Sugita, Y., and Mizuguchi, K.:
   "Lipid recognition properties of amino acids in membrane proteins from atomic resolution data"
   BMC Biophys. 4 (2011) 21.
6. Re, S., Miyashita, N., Yamaguchi, Y., and Sugita, Y.:
   "Structural Diversity and Changes in Conformational Equilibria of Biantennary Complex-Type N-Glycans in Water Revealed by Replica-Exchange Molecular Dynamics Simulation."
   Biophys. J. 101 (2011) L44-L46.
7. Imai, T., Miyashita, N., Sugita, Y., Kovalenko, A., Hirata, F., and Kidera, A.:
   "Functionality Mapping on Internal Surfaces of Multidrug Transporter AcrB Based on Molecular Theory of Solvation: Implications for Drug Efflux Pathway"
   J. Phys. Chem. B 115 (2011) 8288-8295.
8. Re, S., Imai, T., Jung, J., Ten-no, S., and Sugita, Y.:
   "Geometrically Associative Yet Electronically Dissociative Character in the Transition State of Enzymatic Reversible Phosphorylation."
   J. Comput. Chem. 32 (2011) 260-270.