Curriculum Vitae and Selected Scientific Publications

Jeremy M. Berg, Ph.D.

Note: This is an archived page that is not updated.

Professional Experience

11/03-7/11 Director, National Institute of General Medical Sciences
National Institutes of Health, Bethesda, MD
7/08-7/11 Senior Investigator, National Institute of Diabetes and Digestive and Kidney Diseases
Laboratory of Molecular Biology
National Institutes of Health, Bethesda, MD
7/90-10/03  Professor and Director, Department of Biophysics and Biophysical Chemistry
Johns Hopkins University School of Medicine, Baltimore, MD Director, Markey Center for Macromolecular Structure and Function
Johns Hopkins University School of Medicine, Baltimore, MD
7/92-10/03  Professor of Chemistry (Joint Appointment)
Johns Hopkins University, Baltimore, MD
4/02-10/03 Director, Institute for Basic Biomedical Sciences
Johns Hopkins University School of Medicine, Baltimore, MD
1/02-10/03 Co-Director, Keck Center for Rational Design of Biologically Active Molecules
Johns Hopkins University, Baltimore, MD
9/86-6/90  Assistant Professor, Department of Chemistry
Johns Hopkins University, Baltimore, MD
11/84-8/86 Jane Coffin Childs Memorial Fund Postdoctoral Fellow
Johns Hopkins University School of Medicine, Baltimore, MD
Carl O. Pabo, Advisor
1985 Ph.D. in Chemistry, Harvard University, Cambridge, MA Dissertation:  "The Development of a Structural, Spectroscopic, and Reactivity Model for the Active Sites of Molybdenum-Containing Enzymes"
Richard H. Holm, Advisor
9/80-8/83 National Science Foundation Predoctoral Fellow, Harvard University, Cambridge, MA
1980 M.S. in Chemistry, Stanford University, Stanford, CA
Keith O. Hodgson, Advisor
1980 B.S. in Chemistry with Honors and Distinction
Stanford University, Stanford, CA
10/79-12/79 Visiting Research Associate, Charles F. Kettering Research Laboratory, Yellow Springs, OH

Honors

  • President, American Society for Biochemistry and Molecular Biology (term begins in 2012)
  • Phi Beta Kappa, elected 1979 
  • B.S. with Honors and Distinction
  • National Science Foundation Predoctoral Fellow, 1980-1983
  • Jane Coffin Childs Memorial Fund Postdoctoral Fellow, 1984-1986
  • Camille and Henry Dreyfus Foundation Distinguished New Faculty in Chemistry Award, 1986
  • Searle Scholar, 1987-1990 
  • Alfred P. Sloan Foundation Fellow, 1988
  • Presidential Young Investigator, 1988-1993
  • Wilson Prize Lecturer, Harvard University, 1988
  • Eli Lilly Grantee in Biochemistry, 1988
  • Plenary Lecturer, Australian Biochemical Society, 1990
  • Excellence in Chemistry Award, ICI Pharmaceuticals, 1992
  • Musselman Lecturer, Gettysburg College, 1993
  • American Chemical Society Award in Pure Chemistry, 1993
  • Drew University Research Scholar, 1994
  • Lutz Lecturer, University of Virginia, 1995
  • Eli Lilly Award for Fundamental Research in Biological Chemistry, 1995
  • Maryland Outstanding Young Scientist of the Year, 1995
  • W. Barry Wood Teaching Award, Johns Hopkins University School of Medicine, 1995, 1996
  • Graduate Student Teaching Award, Johns Hopkins University School of Medicine, 1997
  • Professor's Teaching Award for the Preclinical Sciences, Johns Hopkins University School of Medicine, 1997
  • Harrison Howe Award, Rochester Section, American Chemical Society, 1997
  • Stauffer Lecturer, Stanford University, 1998
  • Five College Lecturer, University of Massachusetts, 2001
  • Grollman Lecturer, University of Maryland, Baltimore, 2004
  • Elliot S. Vessell Lecturer, Pennsylvania State College of Medicine, 2007
  • American Association for the Advancement of Science Fellow, elected 2007
  • NIH Plain Language Silver Award (two awards), 2008
  • NIH Director's Award, 2008
  • 2009 Distinguished Service Award, Biophysical Society
  • 2010 Elected, Institute of Medicine, The National Academies
  • 2011 Howard K. Schachman Public Service Award, American Society for Biochemistry and Molecular Biology
  • 2011 Public Service Award, American Chemical Society

Research Interests

Roles of metal ions in biological systems, zinc-containing DNA-binding and gene regulatory proteins, calcium-binding proteins, structure determination methods including X-ray crystallography and NMR, mirror-image proteins, protein targeting to peroxisomes and other organelles, molecular recognition, structure-based drug design, the role of zinc in immunological signal transduction pathways, bioinformatics of metalloproteins, protein structure prediction based on homology modeling.

NIH Service (Selected)

  • NIH Extramural Activities Working Group (2003-2007)
  • NIH Ethics Advisory Committee (2004-2006)
  • Co-Chair, NIH Roadmap Implementation Working Group, High-Risk Research (NIH Director's Pioneer Award Program, NIH Director's New Innovator Award Program) (2004-2011)
  • Co-Chair, NIH Roadmap Implementation Working Group, Bioinformatics and Computational Biology (National Centers for Biomedical Computing) (2004-2011)
  • Co-Chair, NIH Roadmap Implementation Working Group, Structural Biology (Membrane Proteins) (2004-2011)
  • Co-Chair, NIH Peer Review Advisory Committee (2005-2008)
  • Co-Chair, Search Committee, Director, NIH Office of Portfolio Analysis and Strategic Initiatives (OPASI) (2006)
  • NIH OPASI Working Group (2006-present; co-chair, 2007-2011)
  • Co-Chair, NIH Task Force on Minority Training Programs (2006-2011)
  • NIH Working Group on Implementation of the NIH Reform Act of 2006 (2007-2008)
  • NIH Working Group on Women in Scientific Careers (2007-2011)
  • NIH Steering Committee (2007-2011)
  • Co-Chair, NIH Steering Committee Working Group on Peer Review (2007-2008)
  • NIH Liaison to the National Science Foundation (2008-2011)
  • NIH Scientific Management Review Board (2008-2011)
  • Co-Chair, Search Committee, Director, National Human Genome Research Institute (2008-2009)
  • Co-Chair, NIH Basic Behavioral and Social Science Opportunity Network (OppNet) (2009-2011)

Scientific Publications

  1. M.A. Bobrik, E.J. Laskowski, R.W. Johnson, W.O. Gillum, J.M. Berg, K.O. Hodgson, and R.H. Holm, "Selenium Substitution in [Fe 4S 4(SR) 4] 2-:  Synthesis and Comparative Properties of [Fe 4X 4(YC 6H 5) 4] 2- (X,Y=S,Se) and the Structure of [(CH 3) 4N] 2[Fe 4Se 4(SC 6H 5) 4]," Inorg. Chem. 1978, 17, 1402-1410.
  2. T.E. Wolff, J.M. Berg, C. Warrick, K.O. Hodgson, R.H. Holm, and R.B. Frankel, "The Molybdenum-Iron-Sulfur Cluster Complex [Mo 2Fe 6S 9(SC 2H 5) 8] 3-. A Synthetic Approach to the Molybdenum Site in Nitrogenase," J.  Am. Chem. Soc. 1979, 100, 4630-4632.
  3. J.M. Berg, K.O. Hodgson, S.P. Cramer, J.L. Corbin, A. Elsberry, N. Pariyadath, and E.I. Stiefel, "Structural Results Relevant to the Molybdenum Sites in Xanthine Oxidase and Sulfite Oxidase.  Structures of MoO 2L, L=(SCH 2CH 2) 2NCH 2CH 2X with X=SCH 3, N(CH 3) 2," J. Am. Chem. Soc. 1979, 101, 2774-2776.
  4. R.E. Koeppe, II, J.M. Berg, K.O. Hodgson, and L. Stryer, "Gramicidin A Crystals Contain Two Cation Binding Sites per Channel," Nature 1979, 279, 723-725.
  5. T.E. Wolff, J.M. Berg, K.O. Hodgson, R.B. Frankel, and R.H. Holm, "Synthetic Approaches to the Molybdenum Site in Nitrogenase.  Preparation and Structural Properties of the Molybdenum-Iron-Sulfur 'Double-Cubane' Cluster Complexes Mo 2Fe 6S 8(SCH 2CH 3) 9] 3- and [Mo 2Fe 6S 9(SCH 2CH 3) 8] 3-," J. Am. Chem. Soc. 1979, 101, 4140-4150.
  6. J.M. Berg, K.O. Hodgson, and R.H. Holm, "Crystal Structure of [(C 2H 5) 4N] 3[Fe 4S 4(SCH 2Ph) 4], a Reduced Ferredoxin Site Analogue with a Nontetragonal Fe 4S 4 Core Structure in the Solid State ," J. Am. Chem. Soc. 1979, 101, 4586-4593.
  7. T.E. Wolff, J.M. Berg, P.P. Power, K.O. Hodgson, R.H. Holm, and R.B. Frankel, "Self-Assembly of Molybdenum-Iron-Sulfur Clusters as a Synthetic Approach to the Molybdenum Site in Nitrogenase.  Identification of the Major Products Formed by the System FeCl 3/MS 42-/C 2H 5SH (M=Mo,W)," J. Am. Chem. Soc. 1979, 101, 5454-5456.
  8. R.E. Ginsburg, J.M. Berg, R.K. Rothrock, J.P. Collman, K.O. Hodgson, and L.F. Dahl, "The Geometrical Influence of Solid-State Ion-Pair Interactions of Alkali Metal Ions with a Binuclear Iron Acyl Monoanion,[Fe 2(CO) 5[C(O)R](? 2-PPh 2) 2] - (where R=Ph,Me).  Structural Analysis of the [Li(THF) 3] +, [Na(THF) 2] +, and [(Ph 3P) 2N] + Salts," J. Am. Chem. Soc. 1979, 101, 7218-7231.
  9. T.D. Tullius, S.D. Conradson, J.M. Berg, and K.O. Hodgson, "Structural Chemistry of Molybdenum in Metalloenzymes as Elucidated by EXAFS," in Molybdenum Chemistry of Biological Significance, W.E. Newton and S. Otsuka, eds., Plenum Publishing Corporation, New York, 1980, pp. 139-155.
  10. E.I. Stiefel, K.F. Miller, A.E. Bruce, N. Pariyadath, J. Heinecke, J.L. Corbin, J.M. Berg, and K.O. Hodgson, "Mo(VI) Complexes of N,S Donor Ligands:  Relevance to Molybdenum Enzymes," in Molybdenum Chemistry of Biological Significance, W.E. Newton and S. Otsuka, eds., Plenum Publishing Corporation, New York, 1980, pp. 279-294.
  11. T.E. Wolff, J.M. Berg, P.P. Power, K.O. Hodgson, and R.H. Holm, "Structural Characterization of the Iron-Bridged 'Double-Cubane' Cluster Complexes [Mo 2Fe 7S 8(SC 2H 5) 12] 3- and [M 2Fe 7S 8(SCH 2C 6H 5) 12] 4-(M=Mo,W) Containing MFe 3S 4 Cores," Inorg. Chem. 1980, 19, 430-437.
  12. J.M. Berg and K.O. Hodgson, "A Redetermination of the Structure of MoO 2[S 2CN(C 2H 5) 2] 2:  Confirmation of the Usual MoO 22+ Geometry," Inorg. Chem. 1980, 19, 2180-2181.
  13. E.I. Stiefel, K.F. Miller, A.E. Bruce, J.L. Corbin, J.M. Berg, and K.O. Hodgson, "A Nonoctahedral Dioxo Molybdenum Complex with a Coordinated Partial Disulfide Bond," J. Am. Chem. Soc. 1980, 102, 3624-3626.
  14. K.S. Hagen, J.M. Berg, and R.H. Holm, "The Synthesis and Structure of Deca(Benzenethiolato)tetraferrate(II) Dianion, an Intermediate in the Assembly of [Fe 4S 4(SC 6H 5) 4] 2- from Simple Reagents," Inorg. Chim. Acta 1980, 45, L17-L18.
  15. T.E. Wolff, J.M. Berg, and R.H. Holm, "Synthesis, Structure, and Properties of the Cluster Complex [MoFe 4S 4(SC 2H 5) 3(C 6H 4O 2) 3] 3-, Containing a Single-Cubane Type MoFe 3S 4 Core," Inorg. Chem. 1981, 20, 174-180.
  16. F.W. Kutzler, R.A. Scott, J.M. Berg, K.O. Hodgson, S. Doniach, S.P. Cramer, and C.H. Chang, "Single-Crystal Polarized X-Ray Absorption Spectroscopy.  Observation and Theory for [MoO 2S 2] 2-," J. Am. Chem. Soc. 1981, 103, 6083-6088.
  17. J.M. Berg and R.H. Holm, "Structures and Reactions of Iron-Sulfur Protein Clusters and Their Synthetic Analogs," in Iron-Sulfur Proteins, T.G. Spiro, ed., Wiley-Interscience, New York , 1982, pp. 1-66.
  18. J.F. Wishart, C. Ceccarelli, R.L. Lindvedt, J.M. Berg, D.P. Foley, T. Frey, J.E. Hahn, K.O. Hodgson, and R. Weis, "Synthesis, Structure and Magnetism of a New Type of p-Molecular Complex Containing Binuclear Copper(II) Complexes and Benzene:  Bis[2,2-dimethyl-7-(phenylimino)-3,5,7-octanetrionato]dicopper(II)-Benzene and Bis[2,2-dimethyl-7-((4-nitrophenyl)imino)-3,5,7-octanetrionato]dicopper(II)-Bis(benzene)," Inorg. Chem. 1983, 22, 1667-1671.
  19. J.M. Berg and R.H. Holm, "Structure Proofs of Ligated and Polymeric Dioxomolybdenum(VI)-Tridentate Complexes: MoO 2[C 5H 3N-2,6-(CH 2S) 2](C 4H 8SO) and [MoO 2(C 5H 3N-2,6-(CH 2O) 2)] n," Inorg. Chem. 1983, 22, 1768-1771.
  20. J. Sola, Y. Do, J.M. Berg, and R.H. Holm, "Soluble Metal Sulfides:  Synthesis and Structures of [M 6S 17] 4- (M=Nb,Ta), Isocahedral-Fragment Cages Containing Four Types of Coordinated Sulfide," J. Am. Chem. Soc. 1983, 105, 7784-7786.
  21. E.J. Corey, B. De, J. Ponder, and J.M. Berg, "The Stereochemistry and Biosynthesis of Hybridalactone.  An Eicosanoid from Laurencia Hybrida," Tetrahedron Lett. 1984, 25, 1015-1018.
  22. J.M. Berg and R.H. Holm, "A Synthetic Approach to the Mononuclear Active Sites of Molybdoenzymes:  Catalytic-Oxygen Atom Transfer Reactions by Oxomolybdenum(IV,VI) Complexes with Saturation Kinetics and Without Molybdenum(V) Dimer Formation," J. Am. Chem. Soc. 1984, 106, 3035-3036.
  23. K.C. Calvo and J.M. Berg, "The Stereochemistry of the Conant-Swan Fragmentation:  The Absence of a Phenonium-Type Intermediate," J. Am. Chem. Soc. 1984, 106, 4202-4204.
  24. M.S. Reynolds, J.M. Berg, and R.H. Holm, "The Kinetics of Oxygen Atom Transfer Reactions Involving Oxomolybdenum Complexes.  A General Treatment for Reactions with Intermediate Oxo-Bridged Molybdenum(V) Dimer Formation," Inorg.Chem. 1984, 23, 3057-3062.
  25. J.M. Berg, D.J. Spira, K.O. Hodgson, A.E. Bruce, K.F. Miller, J.L. Corbin, and E.I. Stiefel, "Six-Coordinate Dioxo Molybdenum(VI) Complexes Containing a Non-Octahedral Structure with a Short Sulfur-Sulfur Contact," Inorg. Chem. 1984, 23, 3412-3418.
  26. R.H. Holm and J.M. Berg, "Molecular Active Sites of Molybdoenzymes:  Chemical Approaches to Structure and Reactivity," Pure Appl. Chem. 1984, 56, 1645-1657.
  27. J.M. Berg, K.O. Hodgson, A.E. Bruce, J.L. Corbin, N. Pariyadath, and E.I. Stiefel, "The Crystal and Molecular Structures of Dioxo Mo(VI) Complexes with Tripodal, Tetradentate N,S Donor Ligands," Inorg. Chim. Acta 1984, 90, 25-33.
  28. J.M. Berg, D.J. Spira, K. Woo, E. McCord, R. Lye, M.-S. Co, J. Belmont, C. Barnes, K. Kosydar, S. Raybuck, K.O. Hodgson, A.E. Bruce, J.L. Corbin, and E.I. Stiefel, "Structural Comparison of Octahedral MoO 22+ Complexes of Bidentate and Linear Tetradentate N,S-Donor Ligands," Inorg. Chim. Acta 1984, 90, 35-39.
  29. E.J. Corey, T.A. Engler, and J.M. Berg, "rel-Methyl (3R,-3aR,4aS,5S,7R,8R,8aS,9aS)- 5-bromododecahydro-3-isopropyl-8,9a-dimethyl-10-oxo-4a,8-(epoxymethano)-4aH- benz[f]indane-7-carboxylate (1) and rel-Methyl(3R,3aS,4aS,5S,7R,8R,8aS,9aS)-bromo- dodecahydro-3-isopropyl-8,9a-dimethyl-10-oxo-4a,8-(epoxymethano)-4aH-benz[f]indene-7-carboxylate(2)," Acta Cryst. 1985, C41, 289-292.
  30. J.M. Berg and R.H. Holm, "A Model for the Active Sites of Molybdoenzymes:  Synthesis, Structures, and Properties," J. Am. Chem. Soc. 1985, 107, 917-925.
  31. J.M. Berg and R.H. Holm, "A Model for the Active Sites of Molybdoenzymes:  Reactivity, Kinetics, and Catalysis," J. Am. Chem. Soc. 1985, 107, 925-932.
  32. J. Sola, Y. Do, J.M. Berg, and R.H. Holm, "Soluble Sulfides of Niobium(IV) and Tantalum(V):  Synthesis, Structures, and Properties of the Five-Fold Symmetric Cages [M 6S 17] 4-," Inorg. Chem. 1985, 24, 1706-1713.
  33. S.R. Jordan, T.V. Whitcombe, J.M. Berg, and C.O. Pabo, "Systematic Variation in DNA Length Yields Highly Ordered Repressor-Operator Cocrystals," Science 1985, 230, 1383-1385.
  34. J.M. Berg, "Nucleic Acid-Binding Proteins--More Metal-Binding Fingers," Nature 1986, 319, 264-265.
  35. J.M. Berg, "Potential Metal-Binding Domains in Nucleic Acid Binding Proteins," Science 1986, 232, 485-487.
  36. J.M. Berg and K.O. Hodgson, "A Binuclear Copper(II) Complex with a Bridging Thioether Ligand.  The Crystal and Molecular Structure of Dicopper(Thiobis- (ethylenenitrile)tetracetate) Pentahydrate," Inorg. Chem. 1986, 25, 1800-1823.
  37. E.W. Harlan, J.M. Berg, and R.H. Holm, "Thermodynamic Fitness of Molybdenum(IV,VI) Complexes for Oxygen Atom Transfer Reactions, Including Those with Enzymatic Substrates," J. Am. Chem. Soc. 1986, 108, 6992-7000.
  38. R.H. Holm and J.M. Berg, "Toward Functional Models of Metalloenzyme Active Sites:  Analogue Reaction Systems of the Molybdenum Oxo-Transferases," Acc. Chem. Res. 1986, 19, 363-370.
  39. J.M. Berg, "Histones and Metal-Binding Domains--Response to Raul A. Saavedra," Science 1986, 234, 1589.
  40. J.M. Berg, S.R. Jordan, and C.O. Pabo, "The Structure and Function of the Lambda Repressor," in DNA-Protein Interactions and Gene Regulation, E.B. Thompson and J. Papaconstinou, eds., University of Texas Press, Austin, Texas, 1987, pp. 3-12.
  41. A.D. Frankel, J.M. Berg, and C.O. Pabo, "Metal-Dependent Folding of a Single Zinc Finger from Transcription Factor IIIA," Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 4841-4845.
  42. J.M. Berg, "Metal Ions in Proteins:  Structural and Functional Roles," ColdSpringHarborSymp. Quant. Biol. 1987, 52, 579-585.
  43. J.M. Berg, "Book Review of URFS and ORFS - A Primer on How to Analyze Derived Amino Acid Sequences by Russell F. Doolittle," Bio/Technology 1987, 5, 1162-1165.
  44. J.M. Berg, "A Proposed Structure for the Zinc Binding Domains from Transcription Factor IIIA and Related Proteins," Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 99-102.
  45. J.M. Berg, "Zinc Fingers:  The Role of Zinc(II) in Transcription Factor IIIA and Related Proteins," Met. Ions in Biol. Sys. 1989, 25, 235-254.
  46. J.M. Berg, "Metal-Binding Domains in Nucleic Acid-Binding and Gene-Regulatory Proteins," Prog. Inorg. Chem. 1989, 37, 143-185.
  47. J.M. Berg, "Searching for Metal Binding Domains" in Transition Metal-DNA Interactions, T.D. Tullius, ed., American Chemical Society Symposium Series, 1989, 90-96.
  48. J.M. Berg and D.L. Merkle, "On the Metal Ion Specificity of "Zinc Finger" Proteins," J. Am. Chem. Soc. 1989, 111, 3759-3761.
  49. L.M. Green and J.M. Berg, "A Retroviral Cys-X 2-Cys-X 4-His-X 4-Cys Peptide Binds Metal Ions:  Spectroscopic Studies and a Proposed Three-Dimensional Structure," Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 4047-4051.
  50. J.M. Berg, "DNA Binding Specificity of Steroid Receptors," Cell 1989, 57, 1065-1068.
  51. J.M. Berg, "Zinc Finger" in McGraw-Hill Yearbook of Science and Technology, McGraw-Hill, New York , 1989, pp. 362-363.
  52. J.M. Berg, "Zinc Finger Domains:  Hypotheses and Current Knowledge," Ann. Rev. Biophys. Biophys. Chem. 1990, 19, 405-420.
  53. J.M. Berg, "Zinc Fingers and Other Metal Binding Domains:  Elements for Interactions Between Macromolecules," J. Biol. Chem. 1990, 265, 6513-6516.
  54. L.M. Green and J.M. Berg, "Retroviral Nucleocapsid Protein-Metal Ion Interactions:  Folding and Sequence Variants," Proc. Natl. Acad. Sci. U.S.A. 1990, 87, 6403-6407.
  55. G.R. Pellegrino and J.M. Berg, "Identification and Characterization of "Zinc Finger" Domains by the Polymerase Chain Reaction," Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 671-675.
  56. B.A.  Krizek, B.T. Amann, V.J. Kilfoil, D.L. Merkle, and J.M. Berg, "A Consensus Zinc Finger Peptide:  Design, High Affinity Metal Binding, pH Dependent Structure, and a His to Cys Sequence Variant," J. Am. Chem. Soc. 1991, 113, 4518-4523.
  57. D.L. Merkle, M.H. Schmidt, and J.M. Berg, "Design and Characterization of a Ligand-Binding Metallopeptide,"  J. Am. Chem. Soc. 1991, 113, 5450-5451.
  58. D.L. Merkle and J.M. Berg, "Characterization of Metal Requirements for Nucleic Acid Binding Proteins," Methods in Enzymology 1991, 208, 46-54.
  59. M.H. Schmidt and J.M. Berg, "Predictions of the Occurrence and Structure of Metal Binding Domains in Gene Regulatory Proteins" in Transcriptional Control Mechanisms, S. McKnight and K. Yamamoto, eds., Cold Spring Harbor, 1992, 599-613.
  60. J.R. Desjarlais and J.M. Berg, "Redesigning the DNA-binding Specificity of a Zinc Finger Protein:  A Data Base Guided Approach," Proteins:  Structure, Function, and Genetics 1992, 12, 101-104.  Erratum, Proteins:  Structure, Function, and Genetics 1992, 13, 272.
  61. S.F. Michael, V.J. Kilfoil, M.H. Schmidt, B.T. Amann, and J.M. Berg, "Metal Binding and Folding Properties of a Minimalist Cys 2His 2 Zinc Finger Peptide,"  Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 4796-4800.
  62. J.R. Desjarlais and J.M. Berg, "Toward Rules Relating Zinc Finger Protein Sequences and DNA Binding Site Preferences," Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 7345-7349.
  63. L.E. Zawadzke and J.M. Berg, "A Racemic Protein," J. Am. Chem. Soc. 1992, 114, 4002-4003.
  64. B.A. Krizek and J.M. Berg, "Complexes of Zinc Finger Peptides with Ni 2+ and Fe 2+," Inorg. Chem. 1992, 31, 2984-2986.
  65. J.M. Berg, "Sp1 and the Subfamily of Zinc Finger Proteins with Guanine-Rich Binding Sites," Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 11109-11110.
  66. J.M. Berg, "Zinc-finger Proteins," Current Opinion in Structural Biology 1993, 3, 11-16.
  67. C.A. Kim and J.M. Berg. "Thermodynamic ß-Sheet Propensities Measured Using a Zinc Finger Peptide," Nature 1993, 362, 267-270.
  68. J.R. Desjarlais and J.M. Berg, "Use of a Zinc Finger Consensus Framework and Specificity Rules to Design Specific DNA Binding Proteins," Proc. Natl. Acad. Sci. USA 1993, 90, 2256-2260.
  69. B.A. Krizek, D.L. Merkle, and J.M. Berg, "Ligand Variation and Metal Binding Specificity in Zinc Finger Peptides," Inorg. Chem. 1993, 32, 937-940.
  70. Y. Shi, R. Beger, and J.M. Berg, "Metal Binding Properties of Single Amino Acid Deletion Mutants of Zinc Finger Peptides:  Studies Using Cobalt(II) as a Spectroscopic Probe," Biophys. J. 1993, 64, 749-753.
  71. L.V. Harper, B.T. Amann, V.J. Kilfoil, and J. M. Berg, "NMR Studies of a Cobalt-Substituted Zinc Finger Peptide," J. Am. Chem. Soc. 1993, 115, 2577-2580.
  72. L.E. Zawadzke and J.M. Berg, "The Structure of a Centrosymmetric Protein Crystal, " Proteins:  Structure, Function, and Genetics 1993, 16, 301-305.
  73. H.M. Dintzis, D.E. Symer, R.Z. Dintzis, L.E. Zawadzke, and J.M. Berg, "A Comparison of the Immunogenicity of Protein Enantiomers," Proteins:  Structure, Function, and Genetics 1993, 16, 306-308.
  74. B.A. Krizek, L.E. Zawadzke, and J.M. Berg, " Independence of Metal Binding Between Tandem Cys 2His 2 Zinc Finger Domains," Protein Science 1993,  2, 1313-1319.
  75. J.M. Berg, "Metalloprotein Design," Current Opinion in Structural Biology 1993, 3, 585-588.
  76. J.M. Berg and L.E. Zawadzke, "Racemic Macromolecules for Use in X-ray Crystallography," Current Opinion in Biotechnology 1994, 5, 343-345.
  77. J.R. Desjarlais and J.M. Berg, "Length-encoded Multiplex Binding Site Determination:  Application to Zinc Finger Proteins," Proc. Natl. Acad. Sci. USA 1994, 91, 11099-11103.
  78. S. Mori, M.O. Johnson, J.M. Berg, and P.C.M. van Zijl, "Water Exchange Filter (WEX Filter) for Nuclear Magnetic Resonance Studies of Macromolecules," J. Am. Chem. Soc. 1994, 116, 11982-11984.
  79. J.M. Berg, "Zinc Finger Domains: From Predictions to Design," Acc. Chem. Res. 1995, 28, 14-19.
  80. Y. Shi and J.M. Berg, "A Direct Comparison of the Properties of Natural and Designed Zinc Finger Proteins," Chemistry and Biology 1995, 2, 83-89.
  81. Y.-S. Wu, V.L.H. Bevilacqua, and J.M. Berg, "Fibrillin Domain Folding and Calcium Binding:  Significance to Marfan Syndrome," Chemistry and Biology 1995, 2, 91-97.
  82. Y. Shi and J.M. Berg, "Specific DNA-RNA Hybrid Binding by Zinc Finger Proteins," Science 1995, 268, 282-284.
  83. J. Thornton and J.M. Berg, "Protein Engineering-Editorial Overview," Current Opinion in Biotechnology 1995, 6, 367-369.
  84. C.A. Kim and J.M. Berg, "Serine at Position 2 in the DNA Recognition Helix of a Cys 2His 2 Zinc Finger Peptide is Not, in General, Responsible for Base Recognition," J. Mol. Biol. 1995, 252, 1-5.
  85. J.E. Kalish, C. Theda, J.C. Morrell, J.M. Berg, and S.J. Gould, "Formation of the Peroxisome Lumen is Abolished by Loss of Pichia pastoris Pas7p, a Zinc-Binding Integral Membrane Protein of the Peroxisome," Mol. Cell. Biol. 1995, 15, 6406-6419.
  86. A.S. Woods, J.C. Buchsbaum, T.A. Worrall, J.M. Berg, and R.J. Cotter, "Matrix-Assisted Laser Desorption/Ionization of Noncovalently Bound Compounds," Analytical Chemistry 1995, 67, 4462-4465.
  87. S. Mori, J.M. Berg, and P.C.M. van Zijl, "Separation of Intramolecular NOE and Exchange Peaks in Water Exchange Spectroscopy Using Spin-Echo Filters," Journal of Biomolecular NMR 1996, 7, 77-82.
  88. S. Mori, C. Abeygunawardana, P.C.M. van Zijl, and J.M. Berg, "Water Exchange Filter with Improved Sensitivity (WEX II) to Study Solvent-Exchangable Protons.  Application to the Consensus Zinc Finger Peptide CP-1," Journal of Magnetic Resonance Ser. B 1996, 110, 96-101.
  89. Y. Shi and J.M. Berg, "DNA Unwinding Induced by Zinc Finger Protein Binding," Biochemistry 1996, 35, 3845-3848.
  90. J.M. Berg and Y. Shi, "The Galvanization of Biology:  A Growing Appreciation for the Roles of Zinc," Science 1996, 271, 1081-1085.
  91. H.A. Godwin and J.M. Berg, "A Fluorescent Zinc Probe Based on Metal-Induced Peptide Folding," J. Am. Chem. Soc. 1996, 118, 6514-6515.
  92. C. Kim and J.M. Berg, "A 2.2 Å Resolution Crystal Structure of a Designed Zinc Finger Protein Bound to DNA," Nature Structural Biology 1996, 3, 940-945.
  93. M.T. Worthington, B.T. Amann, D. Nathans, and J.M. Berg, "Metal Binding Properties and Secondary Structure of the Zinc-Binding Domain of Nup475," Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 13754-13759.
  94. J.M. Berg and N.W. Goffeney, "Centrosymmetric Crystals of Biomolecules:  The Racemate Method," Methods in Enzymology 1997, 276, 619-627.
  95. J.M. Berg and H.A. Godwin, "Lessons from Zinc Binding Peptides," Ann. Rev. Biophys. Biomol. Struc. 1997, 26, 357-371.
  96. J.M. Berg, "Lorentzian Lineshapes are Intrinsic to Autoradiographic Detection," Appendix for "Quantitative Analysis of Electrophoresis Data:  Novel Curve Fitting Methodology and its Application to the Determination of a Protein-DNA Binding Constant" by S.E. Shadle, D.F. Allen, H. Guo, W.K. Pogozelski, J.S. Bashkin, and T.D. Tullius, Nucleic Acids Research 1997, 25, 860.
  97. C.A. Blasie and J.M. Berg, "Electrostatic Interactions Across a Beta Sheet," Biochemistry 1997, 36, 6218-6222.
  98. J.M. Berg, "Letting Your Fingers Do The Walking," Nature Biotechnology 1997, 15, 323.
  99. P.C. Roehm and J.M. Berg, "Sequential Metal Binding by the RING Finger Domain of BRCA1," Biochemistry 1997, 36, 10240-10245.
  100. S. Mori, C. Abeygunawardana, J.M. Berg, and P.C.M. van Zijl, "NMR Study of Rapidly Exchanging Backbone Amide Proteins in Staphylococcal Nuclease and the Correlation with Structural and Dynamic Properties," J. Amer. Chem. Soc. 1997, 119, 6844-6852.
  101. Y.-G. Kim, Y. Shi, J.M. Berg, and S. Chandrasegaran, "Site-Specific Cleavage of DNA-RNA Hybrids by Zinc Finger-FokI Cleavage Domain Fusions," Gene 1997, 203, 43-49.
  102. N.D. Clarke and J.M.Berg, "Zinc Fingers in Caenorhabditis elegans:  Finding Families and Probing Pathways," Science 1998, 282, 2018-2022.
  103. P.C. Roehm and J.M. Berg, "Selectivity of Methylation of Metal-Bound Cysteinates and its Consequences," J. Amer. Chem. Soc. 1998, 120, 13083-1308.
  104. J. Smith, J.M. Berg, and S. Chandrasegaran, "A Detailed Study of the Substrate Specificity of a Chimeric Restriction Enzyme," Nucleic Acids Research 1999, 27, 674-681.
  105. H.J. Berkovits and J.M. Berg, "Metal and DNA Binding Properties of a Two-Domain Fragment of Neural Zinc Finger Factor 1, a CCHC-type Zinc Finger Protein," Biochemistry 1999, 38, 16926-16830.
  106. C.A. Blasie and J.M. Berg, "Toward Ligand Identification with a CCHHC Zinc-Binding Domain from the NZF/MyT1 Family," Inorg. Chem. 2000, 39, 348-351.
  107. G.J. Gatto, Jr., B.V. Geisbrecht, S.J. Gould, and J.M. Berg, "A Proposed Model for the PEX5-Peroxisomal Targeting Signal-1 Recognition Complex," Proteins:  Structure, Function, and Genetics 2000, 38, 241-246.
  108. J.C. Buchsbaum and J.M. Berg, "Kinetics of Metal Binding by a Zinc Finger Peptide," Inorganica Chimica Acta 2000, 297, 217-219.
  109. G.J. Gatto, Jr., B.V. Geisbrecht, S.J. Gould, and J.M. Berg, "Peroxisomal Targeting Signal-1 Recognition by the TPR Domains of Human PEX5," Nature Structural Biology 2000, 7, 1091-1095.
  110. J.M. Berg and J.R. Lorsch, "Mechanism of Ribosomal Peptide Bond Formation," Science 2001, 291, 203.
  111. D. Jantz and J.M. Berg, "Binding Assays Get Into the Groove," Nature Biotechnology 2002, 20, 126-127.
  112. S.L.J. Michel and J.M. Berg, "Building a Metal Binding Domain, One Half at a Time," Chem. Biol. 2002, 9, 667-668.
  113. C.A. Blasie and J.M. Berg, "Structure-Based Thermodynamic Analysis of a Coupled Metal Binding-Protein Folding Reaction Involving a Zinc Finger Peptide," Biochemistry 2002, 41, 15068-15073.
  114. B.T. Amann, M.T. Worthington, and J.M. Berg, "A Cys 3His Zinc-Binding Domain from Nup475/Tristetraprolin: A Novel Fold with a Disklike Structure," Biochemistry 2003, 42, 217-221.
  115. C.C. Harper, J.M. Berg, and S.J. Gould, "PEX5 binds the PTS1 independently of Hsp70 and the peroxin PEX12," J. Biol. Chem. 2003, 278, 7897-7901.
  116. G.J. Gatto, Jr., E.L. Maynard, A.L. Guerrerio, B.V. Geisbrecht, S.J. Gould,  and J.M. Berg, "Correlating Structure and Affinity for PEX5:PTS1 Complexes," Biochemistry 2003, 42, 1660-1666.
  117. G.J. Gatto, Jr. and J.M. Berg, "Nonrandom tripeptide sequence distributions at protein carboxyl termini," Genome Research 2003, 13, 617-623.
  118. D. Jantz and J.M. Berg, "Expanding the DNA-Recognition Repertoire for Zinc Finger Proteins Beyond, 20 Amino Acids," J. Amer. Chem. Soc. 2003, 125, 4960-4961.
  119. S.L.J. Michel, A.L. Guerrerio, and J.M. Berg, "Selective RNA-Binding by a Single CCCH Zinc-Binding Domain from Nup475/Tristetraprolin," Biochemistry 2003, 42, 4626-4630.
  120. C.A. Blasie and J.M. Berg, "Kinetics and Thermodynamics of Copper(II) Binding to Apoazurin," J. Amer. Chem. Soc. 2003, 125, 6866-6867.
  121. J.M. Berg, "Fingering nucleic acids:  The RNA did it," Nature Structural Biology 2003, 10, 986-987.
  122. H.J. Berkovits-Cymet, B.T. Amann, and J.M. Berg, "Solution Structure of a CCHHC Domain of Neural Zinc Finger Factor-1 and its Implications for DNA Binding," Biochemistry 2004, 43, 898-903.
  123. D. Jantz, B.T. Amann, G.J. Gatto, Jr., and J.M. Berg, "The Design of Functional DNA-Binding Proteins Based on Zinc Finger Domains," Chemical Reviews 2004,  104, 789-799.
  124. A.L. Guerrerio and J.M. Berg, "Metal Ion Affinities of the Zinc Finger Domains of the Metal Responsive Element-Binding Transcription Factor-1 (MTF1),"  Biochemistry 2004, 43, 5437-5444. 
  125. D. Jantz and J.M. Berg, "Reduction in DNA-Binding Affinity of Cys 2His 2 Zinc Finger Proteins by linker phosphorylation. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 7589-7593.  
  126. E.L. Maynard, G.J. Gatto, Jr., and J.M. Berg, "Pex5p Binding Affinities for Canonical and Non-Canonical PTS1 Peptides," Proteins: Structure, Function, and Genetics 2004, 55, 856-861.
  127. C. A. Blasie and J.M. Berg, "Entropy-Enthalpy Compensation in Ionic Interactions Probed in a Zinc Finger Peptide,"  Biochemistry 2004, 43, 10600-10604.
  128. K.R. Thickman, A. Davis, and J.M. Berg, "Site Selection in Tandem Arrays of Metal-Binding Domains," Inorg. Chem. 2004,  43, 7897-7901.
  129. M. Mani, J. Smith, K. Kandavelou, J.M. Berg, and S. Chandrasegaren, "Binding of Two Zinc Finger Nuclease Monomers is Required for Effective Double-Strand DNA Cleavage," Biochem. Biophys. Res. Comm. 2005, 334, 1191-1197.
  130. E.L. Maynard and J.M. Berg, "Quantitative Analysis of Peroxisomal Targeting Signal Type-1 Binding to Wild-type and Pathogenic Mutants of Pex5p Supports an Affinity Threshold for Peroxisomal Protein Targeting," J. Mol. Biol. 2007, 368, 1259-1266.
  131. G.G. Martin, H.A. Hostetler, A.L. McIntosh, S.E. Tichy, B.J. Williams, D.H. Russell, J.M. Berg, T.A. Spencer, J. Bell, A.B. Kier, and F. Schroeder, "Structure and Function of the Sterol Carrier Protein-2 (SCP-2) N-Terminal Pre-Sequence," Biochemistry 2008, 47, 5915-5934 (PMCID 2474712).
  132. A.M. Davis and J.M. Berg, "Homodimerization and Heterodimerization of Minimal Zn(II)-Binding Domain Peptides of T-cell Proteins CD4, CD8 a, and Lck," J. Amer. Chem. Soc. 2009, 131, 11492-11497 (PMCID 2769085).
  133. D. Jantz and J.M. Berg, "Probing the DNA-Binding Affinity and Specificity of Designed Zinc Finger Proteins," Biophys. J. 2009, in press.

Selected Other Publications

  1. J.M. Berg, "Policy Forum: The Problems of Bonus Pay," Science, 2004, 304, 824.
  2. J. Norvell and J.M. Berg, "The Protein Structure Initiative, Five Years Later," The Scientist, 2005, 19, 30-31.
  3. D.F. Alexander, B.M. Alving, J.F. Battey, J.M. Berg, F.S. Collins, A.S. Fauci, J.I. Gallin, P.A. Grady, R.J. Hodes, S.H. Hrynkow, T.R. Insel, J.F. Jones, S.I. Katz, S.C. Landis, T.K. Li, D.A. Lindberg, E.G. Nabel, J.E. Niederhuber, R.I. Pettigrew, G.P. Rodgers, J. Ruffin, A. Scarpa, D.A. Schwartz, P.A. Sieving, S.E. Straus, L.A. Tabak, N.D. Volkow, Response to: "Rescuing the NIH before it is too late," J. Clin. Invest., 2006, 116, 1462-1463.
  4. J.M. Berg, "Opportunities for Chemical Biologists: A View from the National Institutes of Health," ACS Chemical Biology, 2006, 1, 547-548.
  5. J.M. Berg, "Nurturing Nobel Winners," Time, November 12, 2007, 13.
  6. J.C. Norvell and J.M. Berg, "Update on the Protein Structure Initiative," Structure 2007, 15, 1519-1522.

Books

S.J. Lippard and J.M. Berg, Principles of Bioinorganic Chemistry, 1994, University Science Books, Mill Valley, CA. (Translated into German, Japanese, French, Polish, and Chinese.)

J.M. Berg, J.L. Tymoczko, and L. Stryer, Biochemistry 2001, 2001, W.H. Freeman, New York, NY.

J.M. Berg, J.L. Tymoczko, and L. Stryer, Biochemistry (5 th edition), 2002, W.H. Freeman, New York, NY. (Translated into French, German, Spanish, Italian, Korean, Japanese, Portugese, Chinese, Greek, and Polish.)

K. Saltsman, J. Berg, and G. Tomaselli, A Clinical Companion to Accompany Biochemistry, 2002, W.H. Freeman, New York, NY.

J.M. Berg, J.L. Tymoczko, and L. Stryer, Biochemistry (6 th edition), 2006, W.H. Freeman, New York, NY. (Translated into German, Spanish, Italian, Portugese, Chinese, Korean, Japanese, and French.)