MICHAEL LEVITT  (May 2004)

EDUCATION:

1964-1967

B.Sc. in Physics, King's College, London, UK

1967-1968

Royal Society Fellow with S. Lifson, Weizmann Institute, Israel

1968-1971

Ph.D. in Biophysics, MRC Laboratory of Molecular Biology and Cambridge University, Cambridge, UK.

PROFESSIONAL EXPERIENCE:

1972-1974

EMBO postdoctoral Fellow, Shneior Lifson Weizmann Institute of Science, Rehovot, Israel.

1974-1979

Staff Scientist, Structural Studies, MRC Laboratory Molecular Biology, Cambridge, England.

1977-1979

Visiting Scientist with Francis Crick, Salk Institute, La Jolla, California.

1979-1987

Associate & Full Professor of Chemical Physics, Department of Chemical Physics,

 

Weizmann Institute of Science, Israel. Chair from 1980-1983, Full Professor from 1984.

1987-

Professor of Structural Biology, Department of Structural Biology, Stanford University

 

School of Medicine, Stanford. Chair from July 1993.

HONORS AND AWARDS:

1986

Federation of European Biochemical Societies Anniversary Prize (work on protein folding).

1992-

Editorial Boards of Structure and Current Opinion in Structural Biology.

2001-

Editor of Journal of Molecular Biology.

1997-2002

Co-director of Program in Mathematics and Molecular Biology (PMMB).

2001-

Fellow of the Royal Society.

2002-

Member of the of the US National Academy of Science.

2002-

Member of the Editorial Board Proc. Natl. Acad. Sci. USA.

2003-2004

Blaise Pascal Professor of Research, Foundation de l'Ecole Normale Superieure, Paris, France.

FEDERAL GOVERNMENT AND INTERNATIONAL REVIEW SERVICE

1989 - 1996

Ad Hoc reviewer for NIH, NSF and DOE.

1992

Reviewer for British Medical Research Council and Swedish National Research Foundation.

1995 - 1999

Charter Member BBCA Study Section.

PUBLICATIONS-BIBLIOGRAPHY: (Selected from a total of 131)

1.

Levitt, M., and S. Lifson. Refinement of Protein Conformations Using a Macromolecular Energy Minimization Procedure. J.Mol.Biol. 46, 269-279 (1969).

9.

Levitt, M., and A. Warshel. Computer Simulation of Protein Folding. Nature 253, 694-698 (1975).

11.

Levitt, M. A Simplified Representation of Protein Conformations for Rapid Simulation of Protein Folding. J.Mol.Biol. 104, 59-107 (1976).

12.

Levitt, M., and C. Chothia. Structural Patterns in Globular Proteins. Nature 261, 552-558 (1976).

14.

Levitt, M., and J. Greer. Automatic Identification of Secondary Structure in Globular Proteins. J.Mol.Biol. 114, 181-239 (1977).

19.

Jack, A., and M. Levitt. Refinement of Large Structures by Simultaneous Minimization of Energy and R Factor. Acta Crystallogr. A34, 931-935 (1978).

33.

Levitt, M. Molecular Dynamics of Native Protein: I. Computer Simulation of Trajectories. J.Mol.Biol. 168, 595-620 (1983).

34.

Levitt, M. Molecular Dynamics of Native Protein: II. Analysis and Nature of Motion. J.Mol.Biol. 168, 595-620 (1983).

35.

Levitt, M. Protein Folding by Restrained Energy Minimization and Molecular Dynamics. J.Mol.Biol. 170, 723-764 (1983).

44.

Levitt, M. and M.F. Perutz. Aromatic Rings Act as Hydrogen Bond Acceptors. J. Mol. Biol. 201, 751-754 (1988).

45.

Levitt, M. and R. Sharon. Accurate Simulation of Protein Dynamics in Solution. Proc. Natl. Acad. Sci. USA. 85, 7557-7561 (1988).

54.

Lee, C. and M. Levitt. Accurate Prediction of the Stability and Activity Effects of Site-directed Mutagenesis of a Protein Core. Nature, 352, 448-451 (1991).

57.

Daggett, V. and M. Levitt. A Molecular Dynamics Simulation of the C-Terminal Fragment of the L7/L12 Ribosomal Protein in Solution. Chemical Phys. 158, 501-512 (1991).

58.

Narhi, L.O., Y. Stabinsky, M. Levitt, L. Miller, R. Sachdev, S. Finley, S. Park, C. Kolvenbach, T. Arakawa and M. Zukowski. Enhanced Stability of Subtilisin by Three Point Mutations. Biotechnology and Applied Biochemistry 1:12-24 (1991).

59.

Daggett, V. and M. Levitt. Molecular Dynamics Simulation of Helix Denaturation. J. Mol. Biol. 223, 1121-1138 (1992).

60.

Hinds, D.A. and M. Levitt. A Lattice Model for Protein Structure Prediction at Low Resolution. Proc. Natl. Acad. Sci. USA. 89, 2536-2540 (1992).

61.

Levitt, M. Accurate Modeling of Protein Conformation by Automatic Segment Matching. J. Mol. Biol. 226, 507-533(1992).

62.

Daggett, V. and M. Levitt. Molecular Dynamics Simulation of the Molten Globule State. Proc. Natl. Acad. Sci. USA. 89, 5142-5146 (1992).

67.

Levitt, M. and B. Park. Water: Now You See It, Now You Don't. Structure. 1 223-226 (1993).

70.

Hinds, D.A. and M. Levitt. Exploring Conformational Space with a Simple Lattice Model for Protein Structure. J. Mol. Biol. 243 668-682 (1994).

71.

Hinds, D.A. and M. Levitt. Simulation of Protein-Folding Pathways: Lost in (Conformational) Space?. Trends in Biotechnology. 13 23-27(1995).

72.

Levitt, M., M. Hirshberg, R. Sharon and V. Daggett. Potential Energy Function and Parameters for Simulations of the Molecular Dynamics of Proteins and Nucleic Acids in Solution. Computer Physics Communications, 91, 215-231 (1995).

73.

Park, B. and M. Levitt. The Complexity and Accuracy of Discrete State Models of Protein Structure. J. Mol. Biol., 249, 493-507 (1995).

75.

Huang, E.S., S. Subbiah and M. Levitt. Recognizing Native Folds by the Arrangement of Hydrophobic and Polar Residues. J. Mol. Biol., 252, 709-720 (1995).

77.

Tsai, J., M. Gerstein and M. Levitt. Keeping the Shape but Changing the Charge: A Simulation Study of Urea and its Iso-Steric Analogues. J. Chem. Phys., 104, 9417-9430 (1996).

78.

Huang, E.S., J. Tsai, S. Subbiah and M. Levitt. Using a Hydrophobic Contact Potential to Evaluate Native and Near-Native Folds Generated by Molecular Dynamics Simulations. J. Mol. Biol., 257, 716-725(1996).

79.

Hinds, D.A. and M. Levitt. From Structure to Sequence and Back Again. J. Mol. Biol., 258, 201-209 (1996).

80.

Park, B. and M. Levitt. Energy Functions that Discriminate X-ray and Near-Native Folds from Well-Constructed Decoys. J. Mol. Biol., 258, 367-392 (1996).

82.

Park, B., Huang, E. S. and M. Levitt. Factors Affecting the Ability of Energy Functions to Discriminate Correct from Incorrect Folds. J. Mol. Biol., 266, 831-846 (1997).

83.

Levitt, M., Hirshberg, M., Sharon, R., Laidig, K.E., and Daggett, V. Calibration and Testing of a Water Model for Simulation of the Molecular Dynamics of Proteins and Nucleic Acids in Solution. J. Phys. Chem. B 25:5051-5061 (1997).

84.

Hirshberg, M. and M. Levitt. Simulating the Dynamics of the DNA Double Helix in Solution. In Dynamics and the Problem of Recognition in Biological Macromolecules, ed. Jardetzky, O. and Lefevre, J. Plenum Press, New York, pp. 173-191 (1997).

86.

Gerstein, M. and M. Levitt. A Structural Census of the Current Population of Protein Sequences. Proc. Natl. Acad. Sci., 99, 11911-11916 (1997).

87.

Tsai, J., M. Gerstein, and M. Levitt. Simulating the Minimum Core for Hydrophobic Collapse in Globular Proteins. Protein Science, 6, 1-11 (1997).

90.

Gerstein, M. and M. Levitt. Comprehensive Assessment of Automatic Structural Alignment Against a Manual Standard, the SCOP Classification of Proteins Protein Science, 7, 445-456 (1998).

91.

Levitt, M and M. Gerstein. A Unified Statistical Framework for Sequence Comparison and Structure Comparison. Proc. Natl. Acad. Sci., 95, 5913-5920 (1998).

92.

Gerstein, M. and M. Levitt. Simulating Water and the Molecules of Life. Scientific American, Nov. 100-105, (1998).

96.

Brenner S.E., D. Barken, and M. Levitt M. The PRESAGE Database for Structural Genomics. Nucleic Acids Res. 27:251-3 (1999).

97.

Koehl P. and M. Levitt. A Brighter Future for Protein Structure Prediction. Nat Struct Biol. 6:108-111 (1999).

98.

Samudrala, R., Y. Xia, E.S. Huang, and M. Levitt. Bona Fide Ab Initio Protein Structure Prediction Using a Combined Hierarchical Approach. Proteins, Struct., Funct. and Gen. Suppl. 3S: 194-198 (1999).

99.

Tsai, J., M. Levitt and D. Baker. Hierarchy of Structure Loss in MD Simulations of SRC SH3 Domain Unfolding. J. Mol. Biol. 291: 215-225 (1999).

100.

Koehl P. and M. Levitt. De Novo Protein Design. I. In Search of Stability and Specificity. J. Mol. Biol. 293: 1161-1181 (1999).

101.

Koehl P. and M. Levitt. De Novo Protein Design. II. Plasticity in Sequence Space. J. Mol. Biol. 293: 1183-1193 (1999).

102.

Koehl P. and M. Levitt. Structure-Based Conformational Preferences Of Amino Acids. Proc. Natl. Acad. Sci. U S A, 96:12524-12529 (1999).

103.

Brenner S.E, Koehl, P. and M. Levitt. The Astral Compendium for Protein Structure and Sequence Analysis Nucleic Acids Res.,28:254-256 (2000).

104.

Brenner, S. E. and M. Levitt. Expectations from Structural Genomics. Protein Science, 9, 197-200 (2000).

106.

Yona, G. and M. Levitt. A Unified Sequence-Structure Classification of Protein Sequences: Combining Sequence and Structure in a Map of the Protein Space. RECOMB 2000, pp. 308-317, ACM (2000).

107.

Samudrala, R. Huang, E.S., Koehl, P. and M. Levitt. Constructing side chains on near-native main chains for ab initio protein structure prediction. Protein Eng. 3, 453-457 (2000).

108.

Xia, Y., Huang, E.S., Levitt, M. and Samudrala, R. Ab initio construction of protein tertiary structures using a hierarchical approach. J. Mol. Biol., 300, 171-185 (2000).

111.

Xia. Y. and M. Levitt. Extracting Knowledge-Based Energy Functions from Protein Structures by Error Rate Minimization: Comparison of Methods Using Lattice Model. J. Chem. Phys. 113, 9318-9330 (2000).

112.

Fain, B. and M. Levitt. A Novel Method for Sampling Alpha-helical Protein Backbones, J. Mol. Biol., 305, 191-201 (2001).

113.

Levitt, M. The Birth of Computational Structural Biology, Nature Str. Biol., 8, 392-393 (2001).

114.

Raschke, T.M., Tsai, J. and M. Levitt. Quantification of the Hydrophobic Interaction by Simulations of the Aggregation of Small Hydrophobic Solutes in Water. Proc. Natl. Acad. Sci., 98, 5965-5660 (2001).

115.

Fain, B., Y. Xia, and M. Levitt. Determination of Optimal Chebyshev-Expanded Hydrophobic Discrimination Function for Globular Proteins. IBM J. Res. Dev. 45. 525-532 (2001).

116.

Chandonia J.M., Walker N.S., Lo Conte L., Koehl P., Levitt M., and Brenner S.E. ASTRAL compendium enhancements. Nucleic Acids Res. 30: 260-263 (2002).

117.

Koehl P. and M. Levitt.  Improved Recognition of Native-Like Protein Structures Using a Family of Designed Sequences. Proc Natl. Acad. Sci U S A. 99: 691-696 (2002).

118.

Koehl P. and M. Levitt. Protein Topology and Stability Define the Space of Allowed Sequences. Proc Natl. Acad. Sci U S A. 99: 1280-1285 (2002).

119.

Yona G. and M. Levitt. Within the Twilight Zone: A Sensitive Profile-Profile Comparison Tool Based on Information Theory. J Mol Biol. 315: 1257-1275 (2002).

120.

Xia, Y and M. Levitt. Roles of Mutation and Recombination in the Evolution of Protein Thermodynamics. Proc Natl. Acad. Sci U S A. 99: 10382-10387 (2002).

121.

Fain, B., Xia, Y. and M. Levitt. Design of an Optimal Chebyshev-Expanded Discrimination Function for Globular Proteins. Protein Sci. 11: 2010-2021 (2002).

122.

Samudrala R. and M. Levitt.  A Comprehensive Analysis of 40 Blind Protein Structure Predictions. BMC Struct. Biol. 2: 3-10 (2002).

123.

Kolodny, R., Koehl, P., Guibas, L., and M. Levitt.  Small Libraries of Protein Fragments Model Native Protein Structures Accurately. J Mol Biol. 323:297-307 (2002).

124.

Koehl, P. and M. Levitt. Sequence Variations within Protein Families are Linearly Related to Structural Variations. J. Mol. Biol. 323:551-562 (2002).

125

Kolodny, R. and M. Levitt.  Protein Decoy Assembly Using Short Fragments under Geometric Constraints. Biopolymers, 68: 278-285 (2003).

126.

Tsai. J. and M. Levitt.  Evidence of Turn and Salt Bridge Contributions to β-Hairpin Stability: MD Simulations of C-terminal Fragment from the B1 Domain of Protein G. Biophys. Chem.102:187-201 (2002).

127.

Keasar, C. and M. Levitt.  A Novel Approach to Decoy Set Generation: Designing a Physical Energy Function Having Local Minima with Native Structure Characteristics. J. Mol. Biol. 329, 159-174 (2003).

128.

Fain B, and M. Levitt M.  Funnel Sculpting for in Silico Assembly of Secondary Structure Elements of Proteins. Proc Natl. Acad. Sci U S A. 100: 10700-10705 (2003).

129.

Chandonia J. M., Hon G., Walker N.S., Lo Conte L., Koehl P., Levitt M. and S.E. Brenner.  The ASTRAL Compendium in 2004. Nucleic Acids Res. 32: 189-192 (2004).

130.

Xia,Y. and M. Levitt.  Funnel-Like Organization in Sequence Space Determines the Distributions of Protein Stability and Folding Rate Preferred by Evolution. Proteins, 55: 107-114.

131.

Xia,Y. and M. Levitt.  Simulating Protein Evolution in Sequence and Structure Space.  Curr. Opin. Struct. Biol. 14: 202-207 (2004).

 

Copyright Michael Levitt. (updated May 2004)