PeopleMembers

Team Leader Yuji Sugita

EDUCATION

1993 B.S. (Chemistry) Faculty of Science, Kyoto University
1995 M.A. (Chemistry) Department of Chemistry, Graduate School of Science, Kyoto University
1998 Ph.D. (Science) Department of Chemistry, Graduate School of Science, Kyoto University

RESEARCH EXPERIENCES

1998 Postdoctoral fellow, RIKEN
1998 Research Associate (Joshu), Institute for Molecular Science
2002 Lecturer, Institute of Molecular and Cellular Biosciences, the University of Tokyo
2007 Associate Chief Scientist, Theoretical Biochemistry Laboratory, RIKEN (~March, 2012)
2010 Team Leader (Concurrently), RIKEN Advanced Institute for Computational Sciences
2011 Team Leader (Concurrently), RIKEN Quantitative Biology Center
2012 Chief Scientist, Theoretical Molecular Science Laboratory, RIKEN

TEACHING EXPERIENCES

Visiting Professor, Department of Chemistry, Faculty of Science, Rikkyo University
Part-time instructor, Department of Physics, Faculty of Science, Gakushuin University
Visiting Professor, Graduate School of Frontier Biosciences, Osaka University

PROFESSIONAL AFFILIATIONS

The Physical Society of Japan, The Biophysical Society of Japan, The Molecular Simulation Society of Japan, Protein Science Society of Japan, BioSuperComputing Research Community, Biophysical Society(US), American Chemical Society(US)

AWARDS

2008 Young Scientist Award of the Physical Society of Japan (Ryoiki 12)
2009 Young Scientist Award of the Molecular Simulation Society of Japan
2009 Morino Award for Molecular Science

PUBLICATIONS

Peer review articles

  1. Andrei V. Pisliakov, Tomoya Hino, Yoshitsugu Shiro, and Yuji Sugita: “Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase”, PLoS Comp. Biol. 8 (2012) e1002674.
  2. Wataru Nishima, Naoyuki Miyashita, Yoshiki Yamaguchi, Yuji Sugita*, and Suyong Re*: “Effect of Bisecting GlcNAc and Core Fucosylation on Conformational Properties of Biantennary Complex-Type N-Glycans in Solution”, J. Phys. Chem. B 116 (2012) 8505-8512.
  3. Cheol Ho Choi, Suyong Re, Michael Feig, and Yuji Sugita: “Quantum mechanical/effective fragment potential molecular dynamics (QM/EFP-MD) study on intra-molecular proton transfer of glycine in water”, Chem. Phys. Lett. 539 (2012) 218-221.
  4. Ryuhei Harada, Yuji Sugita, and Michael Feig: “Protein crowding effects on water hydration and diffusion studied by all-atom molecular dynamics simulations”, J. Am. Chem. Soc. 134 (2012) 4842-4849.
  5. Mizuho Kajikawa, Pai-Chi Li, Eiji Goto, Naoyuki Miyashita, Masami Aoki-Kawasumi, Mari Mito-Yoshida, Mika Ikegaya, Yuji Sugita, Satoshi Ishido: “The Intertransmembrane Region of Kaposi’s Sarcoma-Associated Herpesvirus Modulator of Immune Recognition 2 Contributes to B7-2 Downregulation”, J. Virrology 86 (2012) 5288-5296.
  6. Masamichi Nagae, Suyong Re, Emiko Mihara, Terukazu Nogi, Yuji Sugita, and Junichi Takagi: “Crystal structure of alpha 5 beta 1 integrin ectodomain: Atomic details of the fibronectin receptor”, J. Cell. Biol. 197 (2012) 131-140.
  7. Masamichi Nagae, Suyong Re, Emiko Mihara, Terukazu Nogi, Yuji Sugita, and Junichi Takagi: “Crystal structure of alpha 5 beta 1 integrin ectodomain: Atomic details of the fibronectin receptor”, J. Cell. Biol. 197 (2012) 131-140.
  8. Fumiko Ogushi, Reiko Ishitsuka, Toshihide Kobayashi, and Yuji Sugita*: “Rapid flip-flop motions of cholesterol, diacylgrycerol, and ceramide in phospholipid bilayers”, Chem. Phys. Lett. 552 (2012) 96-102.
  9. Takaharu Mori, Fumiko Ogushi, and Yuji Sugita*: “Voronoi analysis of lipid surface area in protein-membrane systems”, J. Comp. Chem. 33 (2012) 286-293.
  10. Yushi Matsumoto, TakehikoTosha, Andrei V. Pisliakov, Tomoya Hino, Hiroshi Sugimoto, Singo Nagano, Yuji Sugita, and Yoshitsugu Shiro: “Crystal structure of Quinol-Dependent Nitric Oxide Reductase from Beobacillus Strearothermophilus”, Nature Struct. Mol. Biol. 19 (2012) 238-245.
  11. Mizuki Morita, A.V.S.K. M Katta, Shander Ahmad, Takaharu Mori, Yuji Sugita, and Kenji Mizuguchi: “Lipid recognition properties of amino acids in membrane proteins from atomic resolution data”, BMC Biophysics 4 (2011) 21.
  12. Suyong Re, Naoyuki Miyashita, Yoshiki Yamaguchi, and Yuji Sugita*: “Structural diversity and changes in conformational equilibria of biantennary complex-type N-glycans in water revealed by replica-exchange molecular dynamics simulation”, Biophys. J. (Letter), 101 (2011) L44-L46.
  13. Naoto Shibata, Hirofumi Sato, Shigeyoshi Sakaki, and Yuji Sugita: “Theoretical study of magnesium fluoride in aqueous solution”, J. Phys. Chem. B. 115 (2011) 10553-10559.
  14. Takashi Imai, Naoyuki Miyashita, Yuji Sugita, Andrei Kovalenko, Fumio Hirata and Akinori Kidera: “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.
  15. Satoshi Yasuda, Takashi Yoshidome, Yuichi Harano, Roland Roth, Hiraku Oshima, Koji Oda, Yuji Sugita, Mitsunori Ikeguchi, and Masahiro Kinoshita: “Free-Energy Function for Discriminating the Native Fold of a Protein from Misfolded Decoys”, Proteins: Structure, Function, and Bioinformatics 79 (2011) 2161-2171.
  16. Shander Ahmad, Yumiembam H. Singh, Yogesh Paudel, Takaharu Mori, Yuji Sugita and Kenji Mizuguchi: “Integrated prediction of one-dimensional equilibrium structural features and relationship with dynamic structure of helical membrane proteins”, BBA Bioinformatics, 11 (2010) 533.
  17. Yuji Sugita, Mitsunori Ikeguchi and Chikashi Toyoshima: “Insight into the relationship between Ca2+-affinity and shielding of bulk water in the Ca2+-pump from molecular dynamics simulations”, Proc. Natl. Acad. Sci. USA 107 (2010) 21465-21469.
  18. Takaharu Mori, Ryuichiro Ishitani, Tomoya Tsukazaki, Osamu Nureki and Yuji Sugita*: “Molecular Mechanisms Underlying the Early Stage of Protein Translocation through Sec Translocon”, Biochemistry 49 (2010) 945-950.
  19. Takashi Imai and Yuji Sugita: “Dynamic Correlation between Pressure-Induced Protein Structural Transition and Water Penetration”, J. Phys. Chem. B 114 (2010) 2281-2286.
  20. Jaewoon Jung, Yuji Sugita and Sei-ichiro Ten-no: “MP2 gradient in the generalized hybrid orbital (GHO) QM/MM method”, J. Chem. Phys. 132 (2010) 084106.
  21. Suyong Re, Jaewoon Jung, Sei-ichro Ten-no and Yuji Sugita*: “Geometrically Associative Yet Electronically Dissociative Character in the Transition State of Enzymatic Reversible Phosphorylation”, J. Comp. Chem. 32 (2011) 260-270.
  22. Takao Yoda, Yuji Sugita and Yuko Okamoto: “Hydrophobic core formation and dehydration in protein folding studied by generalized-ensemble simulations”, Biophys. J. 99 (2010) 1637-1644.
  23. Takashi Yoshidome, Koji Oda, Yuichi Harano, Roland Roth, Yuji Sugita, Mitsunori Ikeguchi and Masahiro Kinoshita: Free-energy function based on an all-atom model for proteins. PROTEINS 77 (2009) 950-961.
  24. Naoyuki Miyashita, John E. Straub, D. Thirumalai and Yuji Sugita*: “Transmembrane Structures of Amyloid Precursor Protein Dimer Predicted by Replica-Exchange Molecular Dynamics Simulations”, J. Am. Chem. Soc. (Communication) 131 (2009) 3438-3439.
  25. Suyong Re, Jaewoon Jung, Sei-ichiro Ten-no and Yuji Sugita*: “Mechanism of the phosphate ester hydrolysis catalyzed by Phosphoserine Phosphatase”, Chem. Phys. Lett. 480 (2009) 284-288.
  26. Ryuichiro Ishitani, Yuji Sugita, Naoshi Dohmae, Shuya Furuya, Motoyuki Hattori and Osamu Nureki: “Mg2+-sensing mechanism of Mg2+ transporter MgtE probed by molecular dynamics study”, Proc. Natl. Acad. Sci. USA 105 (2008) 15393-15398.
  27. Tomoya Tsukazaki, Hiroyuki Mori, Shuya Fukai, Ryuichiro Ishitani, Takaharu Mori, Naoshi Dohmae, Anna Perederina, Yuji Sugita, Dmitry G. Vassylyev, Koreaki Ito and Osamu Nureki: “Conformational transition of Sec machinery inferred from bacterial SecYE structures”, Nature 455 (2008) 988-992.
  28. Takao Yoda, Yuji Sugita and Yuko Okamoto: “Cooperative folding mechanism of a β-hairpin peptide studied by a multicanonical replica-exchange molecular dynamics simulation”, PROTEINS, 66 (2007) 846-859.
  29. Yuichi Harano, Roland Roth, Yuji Sugita, Mitsunori Ikeguchi and Masahiro Kinoshita: “Physical Basis for Characterizing Native Structures of Proteins”, Chem. Phys. Lett. 437 (2007) 112-116.
  30. Yukio Kawashima, Yuji C. Sasaki, Yuji Sugita, Takao Yoda and Yuko Okamoto: “Replica-exchange molecular dynamics simulations of diffracted X-ray tracking”, Molecular Simulation 33 (2007) 97-102.
  31. Jaewoon Jung, Cheol Ho Choi, Yuji Sugita and Sei-ichiro Ten-no: “New implementation of a combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals”, J. Chem. Phys. 127 (2007) 204102.
  32. Yuji Sugita, Naoyuki Miyashita, Takao Yoda, Mitsunori Ikeguchi and Chikashi Toyoshima: “Structural Changes of the Cytoplasmic Domain of Phospholamban by Phosphorylation at Ser16: A Molecular Dynamics Study”, Biochemistry 45 (2006) 11752-11761.
  33. Yuji Sugita, Naoyuki Miyashita, Mitsunori Ikeguchi, Akinori Kidera and Chikashi Toyoshima: “Protonation of the acidic residues in the transmembrane cation-binding sites of the Ca2+-pump”, J. Am. Chem. Soc. (Communication) 127 (2005) 6150-6151.
  34. Yuji Sugita and Yuko Okamoto: “Molecular mechanism for stabilizing a short helical peptide studied by generalized-ensemble simulations with explicit solvent”, Biophys. J. 88 (2005) 3180-3190.
  35. Katsumi Murata, Yuji Sugita and Yuko Okamoto: “Molecular dynamics simulations of DNA dimers based on replica-exchange umbrella sampling. II. Free energy analysis”, J. Theor. Comp. Chem. 4 (2005) 433-448.
  36. Katsumi Murata, Yuji Sugita and Yuko Okamoto: “Molecular dynamics simulations of DNA dimers based on replica-exchange umbrella sampling. I. Test of sampling efficiency”, J. Theor. Comp. Chem. 4 (2005) 411-432.
  37. Koji Obara, Naoyuki Miyashita, Cheng Xu, Itaru Toyoshima, Yuji Sugita, Giuseppe Inesi and Chikashi Toyoshima: “Structural role of countertransport revealed in Ca2+ pump crystal structure in the absence of Ca2+”, Proc. Natl. Acad. Sci. USA 102 (2005) 14489-14496.
  38. Yukio Kawashima, Yuji Sugita, Takao Yoda and Yuko Okamoto: “Effects of the Fixed End in Single-Molecule Imaging Techniques: A Replica Exchange Molecular Dynamics Simulation”, Chem. Phys. Lett. 414 (2005) 449-455.
  39. Masamichi Nishino, Yuji Sugita, Takao Yoda and Yuko Okamoto: “Structures of a peptide fragment of β2-microgloblin studied by replica-exchange molecular dynamics simulations: towards the understanding of the mechanism of amyloid formation”, FEBS Lett. 579 (2005) 5425-5429.
  40. Takao Yoda, Yuji Sugita and Yuko Okamoto: “Comparisons of Force Fields for Proteins by Generalized-Ensemble Simulations”, Chem. Phys. Lett. 386 (2004) 460-467.
  41. Takao Yoda, Yuji Sugita and Yuko Okamoto: “Secondary-Structure Preferences of Force Fields for Proteins Evaluated by Generalized-Ensemble Simulations”, Chem. Phys. 307 (2004) 269-283.
  42. Katsumi Murata, Yuji Sugita and Yuko Okamoto: “Free energy calculations for DNA base stacking by replica-exchange umbrella sampling”, Chem. Phys. Lett. 385 (2004) 1-7.
  43. Ayori Mitsutake, Yuji Sugita and Yuko Okamoto: “Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. II. Application to a more complex system”, J. Chem. Phys. 118 (2003) 6676-6688.
  44. Ayori Mitsutake, Yuji Sugita and Yuko Okamoto: “Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. I. Formulation and benchmark test”, J. Chem. Phys. 118 (2003) 6664-6675.
  45. Jun Funahashi, Yuji Sugita, Akio Kitao and Katsuhide Yutani: “How can free energy component analysis explain the difference in protein stability caused by amino acid substitutions? Effect of three hydrophobic mutations at the 56th residue on the stability of human lysozyme”, Protein Eng. 16 (2003) 665-671.
  46. Michio Asahi, Yuji Sugita, Kazimierz Kurzydlowski, Stella De Leon, Michihiko Tada, Chikashi Toyoshima and David H. MacLennan: “Sarcolipin regulates sarco(endo)plasmic reticulurn Ca2+-ATPase (SERCA) by binding to transmembrane helices alone or in association with phospholamban”, Proc. Nat. Acad. Sci. USA 100 (2003) 5040-5045.
  47. Chikashi Toyoshima, Michihiko Asahi, Yuji Sugita, Reena Khanna, Takao Tsuda and David H. MacLennan: “Modeling of the inhibitory interaction of phospholamban with the Ca2+-ATPase”, Proc. Nat. Acad. Sci. USA 100 (2003) 467-472.
  48. Takeshi Nagasima, Yuji Sugita, Ayori Mitsutake and Yuko Okamoto: “Generalized-ensemble simulations of spin systems and protein systems”, Comp. Phys. Comm. 146 (2002) 69-76.
  49. Yasuyuki Ishikawa, Yuji Sugita, Takeshi Nishikawa and Yuko Okamoto: “Ab initio replica-exchange Monte Carlo method for cluster studies”, Chem. Phys. Lett. 333 (2001) 199-206.
  50. Yuji Sugita and Yuko Okamoto: “Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape”, Chem. Phys. Lett. 329 (2000) 261-270.
  51. Yuji Sugita, Akio Kitao and Yuko Okamoto: “Multidimensional replica-exchange method for free-energy calculations”, J. Chem. Phys. 113 (2000) 6042-6051.
  52. Yuji Sugita and Yuko Okamoto: “Replica-exchange molecular dynamics method for protein folding”, Chem. Phys. Lett. 314 (1999) 141-151.
  53. Yuji Sugita and Akio Kitao: “Dependence of protein stability on the structure of the denatured state: Free energy calculations of I56V mutation in human lysozyme”, Biophys. J. 75 (1998) 2178-2187.
  54. Yuji Sugita, Akio Kitao and Nobuhiro Go: “Computational analysis of thermal stability: effect of Ile -> Val mutations in human lysozyme”, Fold. Des. 3 (1998) 173-181.
  55. Yuji Sugita and Akio Kitao: “Improved protein free energy calculation by more accurate treatment of nonbonded energy: Application to chymotrypsin inhibitor 2, V57A”, PROTEINS 30 (1998) 388-400.

Review articles, Proceedings, and Book Chapters

  1. Suyong Re, Naoyuki Miyashita, Wataru Nishima, Yuji Sugita*: “Conformational flexibility of N-glycan in solution revealed by REMD simulations”, Biophys. Rev. 4 (2012) 179-187.
  2. Yuji Sugita*, Naoyuki Miyashita, Pai-Chi Li, Takao Yoda, Yuko Okamoto: “Recent applications of replica-exchange molecular dynamics simulations of biomolecules”, Current Phys. Chem. In press.
  3. Yuji Sugita*: “Free-energy landscapes of proteins in solution by generalized-ensemble simulations”, Frontier in Bioscience 14 (2009) 1292-1303.
  4. Yuji Sugita, Ayori Mitsutake, Yuko Okamoto: “Generalized-ensemble algorithms for protein folding simulations”, in “Rugged Free Energy Landscapes: Common Computational Approaches in Spin Glasses, Structural Glasses and Biological Macromolecules”, W. Janke (ed.) (Springer-Verlag, Berlin) 736 (2008) 369-407.
  5. Chikashi Toyoshima and Yuji Sugita: “ER/SR Calcium Pump: Structure”, in Encyclopedia of Biological Chemistry 2 (2004) 61-65.
  6. Chikashi Toyoshima, Hiromi Nomura and Yuji Sugita: “Minireview: Structural basis of ion pumping by Ca2+-ATPase of sarcoplasmic reticulum”, FEBS Lett. 555 (2003) 106-110.
  7. Chikashi Toyoshima, Hiromi Nomura and Yuji Sugita: “Crystal structures of Ca2+-ATPase in various physiological states”, Ann. NY. Acad. Sci. 986 (2003) 1-8.
  8. Yuji Sugita and Yuko Okamoto: “Free-energy calculations in protein folding by generalized-ensemble algorithms”, in “Lecture Notes in Computational Science and Engineering”, H.H. Gan and T. Schlick (eds.) (2002) 303-331.
  9. Ayori Mitsutake, Yuji Sugita and Yuko Okamoto: “Generalized-ensemble algorithm for molecular simulations of biopolymers”. Biopolymers 60 (2001) 96-123.
  10. Yuji Sugita and Yuko Okamoto: “An analysis on protein folding problem by replica-exchange method”, Prog. Theor. Phys. Supp. 138 (2000) 402-403.
  11. Takeshi Nishikawa, Hiroshi Ohtsuka, Yuji Sugita, T. Mikami and Yuko Okamoto: “Replica-exchange Monte Carlo method for Ar fluid”, Prog. Theor. Phys. Supp. 138 (2000) 270-271.
  12. Yuji Sugita: “Computational analysis of protein thermal stability and denatured state”, in Proceedings of The 24th Taniguchi International Symposium “Old and New Views of Protein Folding”, Kisarazu, Japan, 3-7 March, 1999, K. Kuwajima and M. Arai (eds.) (Elsevier Science) (1999) 227-236.

Review articles (in Japanese)

  1. 森　貴治、杉田　有治：「膜タンパク質が触媒する物質輸送現象の分子メカニズム」シミュレーション 30, 4 December (2011) 224-230.
  2. 李　秀栄、杉田　有治：「Modeling the Transition State of Enzyme-Catalyzed Phosphoryl Transfer Reaction using QM/MM Method」薬学雑誌 131 (2011) 1171-1182.
  3. 杉田　有治：「京速コンピュータで実現する次世代の生命科学シミュレーション」日本の科学者 45, 12 December (2010) 674-679.
  4. 杉田　有治：「生体分子の構造探索の理論」化学と工業 61 (2008) 582-584.
  5. 杉田　有治：「ぞくぞくとわかってきた膜を隔てたイオン輸送装置構造」生物物理 48, 6 (2008) 330-332.
  6. 杉田　有治：「カルシウムポンプの機能制御機構」生化学 80 (2008) 917-924.
  7. 杉田　有治，池口　満徳：「膜蛋白質の分子動力学」物性研究 (2006), 86-2, 157-197.
  8. 杉田　有治，豊島　近：「カルシウムポンプの構造と機能」蛋白質・核酸・酵素 (2005) 増刊号「生命秩序を担う生体超分子」1271－1277．（表紙の絵の一部に採用）
  9. 杉田　有治：（分担執筆）「拡張アンサンブル法」Bioinformatics辞典 (2006).
  10. 杉田　有治、光武　亜代理、岡本 祐幸：「拡張アンサンブル法によるタンパク質の折れ畳みシミュレーション」日本物理学会誌 56 (2001) 591-599.
  11. 杉田　有治、北尾　彰朗：「理論計算からタンパク質の変性構造を探る」生物物理 40 (2000) 368-373.