Timothy J. Richmond - List of Publication #

1. T. A. Steitz, T. J. Richmond, D. Wise and D. Engelman (1974). "The lac repressor protein: molecular shape, subunit structure, and proposed model for operator interaction based on structural studies of microcrystals", Proc Natl Acad Sci USA 71, 593-7.

2. T. J. Richmond and T. A. Steitz (1976). "Protein-DNA interaction investigated by binding Escherichia coli lac repressor protein to poly[d(A.U-HgX)]", J Mol Biol 103, 25-38.

3. F. M. Richards and T. J. Richmond (1978). "Sovents, interfaces and protein structure", in Molecular Interactions and Activity in Proteins, Vol. Ciba Foundataion Symposium 60, pp. 23-45, Excerpta Medica, Amsterdam.

4. T. J. Richmond and F. M. Richards (1978). "Packing of alpha-helices: Geometrical constraints and contact areas", J Mol Biol 119, 537-55.

5. F. E. Cohen, T. J. Richmond and F. M. Richards (1979). "Protein folding: evaluation of some simple rules for the assembly of helices into tertiary structures with myoglobin as an example", J Mol Biol 132, 275-88.

6. F. M. Richards, T. J. Richmond, M. J. E. Sternberg and F. E. Cohen (1980). "Formation and fluctuations of tertiary structure - the association of alpha helices", in Protein Folding (R. Jaenicke, Ed.), pp. 117-29, Elsevier/North-Holland Biomedical Press.

7. J. T. Finch, R. S. Brown, D. Rhodes, T. J. Richmond, B. Rushton, L. C. Lutter and A. Klug (1981). "X-ray diffraction study of a new crystal form of the nucleosome core showing higher resolution", J Mol Biol 145, 757-69.

8. T. J. Richmond, A. Klug, J. T. Finch and L. C. Lutter (1981). "The organization of DNA in the nucleosome core particle", in Proceedings of the 2nd SUNYA Conversation in the Discipline Biomol. Stereodynamics (R. H. Sarma, Ed.), Vol. II, pp. 109-23.

9. T. J. Richmond, J. T. Finch and A. Klug (1983). "Studies of nucleosome structure", in Cold Spring Harb Symp Quant Biol, Vol. 47, pp. 493-501.

10. T. J. Richmond (1984). "Solvent accessible surface area and excluded volume in proteins: Analytical equations for overlapping spheres and implications for the hydrophobic effect", J Mol Biol 178, 63-89.

11. T. J. Richmond, J. T. Finch, B. Rushton, D. Rhodes and A. Klug (1984). "Structure of the nucleosome core particle at 7 Å resolution", Nature 311, 532-7.

12. A. Klug, J. T. Finch and T. J. Richmond (1985). "The crystallographic structure of the octamer histone core of the nucleosome", Science 229, 1109-10.

13. T. V. O'Halloran, S. J. Lippard, T. J. Richmond and A. Klug (1987). "Multiple heavy-atom reagents for macromolecular X-ray structure determination. Application to the nucleosome core particle", J Mol Biol 194, 705-12.

14. T. J. Richmond (1987). "Another folding problem?", Nature 326, 18-9.

15. T. J. Richmond (1987). "Partial peak scan measurement and profile analysis: application to diffractometry using 0, 1, & 2-dimensional detectors.", in Computational Aspects of Protein Crystal Structure Analysis, DLSCI- R25P (J. Helliwell, P. Machin, and M. Papiz, Eds.), pp. 171-8, Daresbury Laboratory.

16. T. J. Richmond (1988). "X-ray crystallography of protein-DNA interactions", in Proceedings of the Yakult International Symposium, Yakult Honsha, Tokyo.

17. T. J. Richmond, M. A. Searles and R. T. Simpson (1988). "Crystals of a nucleosome core particle containing defined sequence DNA", J Mol Biol 199, 161-70.

18. S. Tan, G. Ammerer and T. J. Richmond (1988). "Interactions of purified transcription factors: binding of yeast MATalpha1 and MCM1 to cell type-specific, upstream activation Sequences", EMBO J 7, 4255-64.

19. T. Schnyder, D. F. Sargent, T. J. Richmond, H. M. Eppenberger and T. Wallimann (1990). "Crystallization and preliminary X-ray analysis of two different forms of mitochondrial creatine kinase from chicken cardiac muscle", J Mol Biol 216, 809-12.

20. S. Tan and T. J. Richmond (1990). "DNA binding-induced conformational change of the yeast transcriptional activator MCM1", Cell 62, 367-77.

21. M. M. Struck, A. Klug and T. J. Richmond (1992). "Comparison of X-ray structures of the nucleosome core particle in two different hydration states", J Mol Biol 224, 253-64.

22. M. R. Bavand, R. Wagner and T. J. Richmond (1993). "HIV-1 reverse transcriptase: polymerization properties of the p51 homodimer compared to the p66/p51 heterodimer", Biochemistry 32, 10543-52.

23. B. Ganter, S. Tan and T. J. Richmond (1993). "Genomic footprinting of the promoter regions of STE2 and STE3 genes in the yeast Saccharomyces cerevisiae", J Mol Biol 234, 975-87.

24. P. Koenig and T. J. Richmond (1993). "The X-ray structure of the GCN4-bZIP bound to ATF/CREB site DNA shows the complex depends on DNA flexibility", J Mol Biol 233, 139-54.

25. T. J. Richmond, T. J. Rechsteiner and K. Luger (1993). "Studies of nucleosome structure", in Cold Spring Harb Symp Quant Biol, Vol. 58, pp. 265-72.

26. B. von Freyberg, T. J. Richmond and W. Braun (1993). "Surface area included in energy refinement of proteins. A comparative study on atomic solvation parameters", J Mol Biol 233, 275-92.

27. W. Keller, P. Koenig and T. J. Richmond (1995). "Crystal structure of a bZIP/DNA complex at 2.2 A: determinants of DNA specific recognition", J Mol Biol 254, 657-67.

28. L. Pellegrini, S. Tan and T. J. Richmond (1995). "Structure of serum response factor core bound to DNA", Nature 376, 490-8.

29. T. J. Richmond and F. Thoma (1995). "Chromatin assembly and structure", in Molecular Biology and Biotechnology: A Comprehensive Desk Reference (R. Meyers, Ed.), pp. 175-9, VCH, Weinheim.

30. A. J. Flaus, K. Luger, S. Tan and T. J. Richmond (1996). "Mapping nucleosome position at single base-pair resolution by using site-directed hydroxyl radicals", Proc Natl Acad Sci USA 93, 1370-5.

31. T. J. Richmond and F. Thoma (1996). "Chromatin assembly and structure", in Encyclopedia of Molecular Biology (R. Meyers, Ed.), pp. 360-70, VCH, Weinheim.

32. S. Tan, Y. Hunziker, D. F. Sargent and T. J. Richmond (1996). "Crystal structure of a yeast TFIIA/TBP/DNA complex", Nature 381, 127-34.

33. K. Luger, A. W. Maeder, R. K. Richmond, D. F. Sargent and T. J. Richmond (1997). "Crystal structure of the nucleosome core particle at 2.8 Å resolution", Nature 389, 251-60.

34. K. Luger, T. Rechsteiner, A. Flaus, M. M. Waye and T. J. Richmond (1997). "Characterization of nucleosome core particles containing histone proteins made in bacteria", J Mol Biol 272, 301-11.

35. A. Flaus and T. J. Richmond (1998). "Positioning and stability of nucleosomes on MMTV 3'LTR sequences", J Mol Biol 275, 427-41.

36. K. Luger and T. J. Richmond (1998). "DNA binding within the nucleosome core", Curr Opin Struct Biol 8, 33-40.

37. K. Luger and T. J. Richmond (1998). "The histone tails of the nucleosome", Curr Opin Genet Dev 8, 140-6.

38. G. Panetta, M. Buttinelli, A. Flaus, T. J. Richmond and D. Rhodes (1998). "Differential nucleosome positioning on xenopus oocyte and somatic 5 S RNA genes determines both TFIIIA and H1 binding: A mechanism for selective H1 repression", J Mol Biol 282, 683-97.

39. T. J. Richmond and T. A. Steitz (1998). "Protein-nucleic acid interactions", Curr Opin Struct Biol 8, 11-3.

40. C. Spangenberg, K. Eisfeld, W. Stunkel, K. Luger, A. Flaus, T. J. Richmond, M. Truss and M. Beato (1998). "The mouse mammary tumour virus promoter positioned on a tetramer of histones H3 and H4 binds nuclear factor 1 and OTF1", J Mol Biol 278, 725-39.

41. S. Tan and T. J. Richmond (1998). "Crystal structure of the yeast MATalpha2/MCM1/DNA ternary complex", Nature 391, 660-6.

42. S. Tan and T. J. Richmond (1998). "Eukaryotic transcription factors", Curr Opin Struct Biol 8, 41-8. 43. A. Flaus and T. J. Richmond (1999). "Base-pair resolution mapping of nucleosome positions using sitedirected hydroxy radicals", Methods Enzymol 304, 251-63.

44. A. Flaus and T. J. Richmond (1999). "Base-pair resolution mapping of nucleosomes in vitro", Methods Mol Biol 119, 45-60.

45. M. Goldberg, A. Harel, M. Brandeis, T. J. Rechsteiner, T. J. Richmond, A. M. Weiss and Y. Gruenbaum (1999). "The tail domain of lamin Dm0 binds histones H2A and H2B", Proc Natl Acad Sci USA 96, 2852-7.

46. K. Luger, A. W. Maeder and T. J. Richmond (1999). "The nucleosome core structure at 2.0 Å resolution", in Human FrontierWorkshop VII: Transcription Regulation in Eukaryotes (P. Chambon, T. Fukasawa, R. D. Kornberg, and C. C. Coath, Eds.), pp. 28-35, Human Frontier Science Program,, Strasbourg.

47. K. Luger, T. J. Rechsteiner and T. J. Richmond (1999). "Expression and purification of recombinant histones and nucleosome reconstitution", Methods Mol Biol 119, 1-16.

48. K. Luger, T. J. Rechsteiner and T. J. Richmond (1999). "Preparation of nucleosome core particle from recombinant histones", Methods Enzymol 304, 3-19.

49. F. Gaiser, S. Tan and T. J. Richmond (2000). "Novel dimerization fold of RAP30/RAP74 in human TFIIF at 1.7 A resolution", J Mol Biol 302, 1119-27.

50. K. Luger, A. W. Maeder, R. K. Richmond, D. F. Sargent and T. J. Richmond (2000). "The atomic structure of the nucleosome core particle.", in Biomolecular Stereodynamics (R. H. Sarma, Ed.), Vol. Vol. 11, pp. 190- 200, Adenine Press, New York.

51. T. J. Richmond and J. Widom (2000). "Nucleosome and chromatin structure", in Chromatin Structure and Gene Expression (S. C. R. Elgin, and J. L. Workman, Eds.), pp. 1-23, Oxford University Press, Oxford.

52. E. Santelli and T. J. Richmond (2000). "Crystal Structure of MEF2A Core Bound to DNA at 1.5 A Resolution", J Mol Biol 297, 437-49.

53. S. Tan, Y. Hunziker, L. Pellegrini and T. J. Richmond (2000). "Crystallization of the yeast MATalpha2/MCM1/DNA ternary complex: general methods and principles for protein/DNA cocrystallization", J Mol Biol 297, 947-59.

54. G. Capitani, R. Rossmann, D. F. Sargent, M. G. Gruetter, T. J. Richmond and H. Hennecke (2001). "Structure of the soluble domain of a membrane-anchored thioredoxin-like protein from Bradyrhizobium japonicum reveals unusual properties", J Mol Biol 311, 1037-48.

55. M. E. Gelbart, T. J. Rechsteiner, T. J. Richmond and T. Tsukiyama (2001). "Interactions of ISW2 chromatin remodeling complex with nucleosomal arrays: analyses using recombinant yeast histones and immobilized templates", Mol Cell Biol 21, 2098-106.

56. M. Hassler and T. J. Richmond (2001). "The B-box dominates SAP-1-SRF interactions in the structure of the ternary complex", EMBO J 20, 3018-28.

57. T. J. Richmond (2001). "The structural basis of gene regulation for DNA organized as chromatin", Chimia 55, 487-92.

58. C. A. Davey and T. J. Richmond (2002). "DNA-dependent divalent cation binding in the nucleosome core particle", Proc Natl Acad Sci USA 99, 11169-74.

59. C. A. Davey, D. F. Sargent, K. Luger, A. W. Maeder and T. J. Richmond (2002). "Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution", J Mol Biol 319, 1097-113.

60. E. Eichhorn, C. A. Davey, D. F. Sargent, T. Leisinger and T. J. Richmond (2002). "Crystal structure of Escherichia coli alkanesulfonate monooxygenase SsuD", J Mol Biol 324, 457-68.

61. P. R. Mittl, G. Fritz, D. F. Sargent, T. J. Richmond, C. W. Heizmann and M. G. Gruetter (2002). "Metal-free MIRAS phasing: structure of apo-S100A3", Acta Crystallogr D Biol Crystallogr 58, 1255-61.

62. I. Berger, C. Bieniossek, C. Schaffitzel, M. Hassler, E. Santelli and T. J. Richmond (2003). "Direct interaction of Ca2+/calmodulin inhibits histone deacetylase 5 repressor core binding to myocyte enhancer factor 2", J Biol Chem 278, 17625-35.

63. M. Bleichenbacher, S. Tan and T. J. Richmond (2003). "Novel Interactions between the components of human and yeast TFIIA/TBP/DNA complexes", J Mol Biol 332, 783-93.

64. B. Dorigo, T. Schalch, K. Bystricky and T. J. Richmond (2003). "Chromatin fiber folding: requirement for the histone H4 N-terminal tail", J Mol Biol 327, 85-96.

65. H. Gaillard, D. J. Fitzgerald, C. L. Smith, C. L. Peterson, T. J. Richmond and F. Thoma (2003). "Chromatin Remodeling Activities Act on UV-damaged Nucleosomes and Modulate DNA Damage Accessibility to Photolyase", J Biol Chem 278, 17655-63.

66. T. J. Richmond (2003). "The lure of DNA in chromatin.", in The Secret of Life (M. Balaban, Ed.), pp. 86-97, Faircount, London.

67. T. J. Richmond and C. A. Davey (2003). "The structure of DNA in the nucleosome core", Nature 423, 145- 50.

68. I. Berger, D. J. Fitzgerald and T. J. Richmond (2004). "Baculovirus expression system for heterologous multiprotein complexes", Nat Biotechnol 22, 1583-7.

69. B. Dorigo, T. Schalch, A. Kulangara, S. Duda, R. R. Schroeder and T. J. Richmond (2004). "Nucleosome arrays reveal the two-start organization of the chromatin fiber", Science 306, 1571-3.

70. D. J. Fitzgerald, C. DeLuca, I. Berger, H. Gaillard, R. Sigrist, K. Schimmele and T. J. Richmond (2004). "Reaction cycle of the yeast Isw2 chromatin remodeling complex", EMBO J 23, 3836-43.

71. D. F. Sargent and T. J. Richmond (2004). "Comment on flash-cooling of macromolecular crystals to overcome increased mosaicity by Yao, Yasutake & Tanaka (2004)", Acta Crystallogr D Biol Crystallogr 60, 616.

72. T. Schalch, S. Duda, D. F. Sargent and T. J. Richmond (2005). "X-ray structure of a tetranucleosome and its implications for the chromatin fibre", Nature 436, 138-41.

73. D. J. Fitzgerald, I. Berger, C. Schaffitzel, K. Yamada, T. J. Richmond and I. Berger (2006). "Protein complex expression by using multigene baculoviral vectors", Nat Meth 3, 1021-32.

74. T. J. Richmond (2006). "Genomics: predictable packaging", Nature 442, 750-2.

75. D. J. Fitzgerald, C. Schaffitzel, P. Berger, R. Wellinger, C. Bieniossek, T. J. Richmond and I. Berger (2007). "Multiprotein expression strategy for structural biology of eukaryotic complexes", Structure 15, 275-9.

76. M. S. Ong, T. J. Richmond and C. A. Davey (2007). "DNA stretching and extreme kinking in the nucleosome core", J Mol Biol 368, 1067-74.

77. C. Bieniossek, T. J. Richmond and I. Berger (2008). "MultiBac: multigene baculovirus-based eukaryotic protein complex production", in Current Protocols in Protein Science, pp. 5.20.1-6, John Wiley & Sons, Inc.

78. V. Galius, C. Leontiou, T. J. Richmond and G. Wider (2008). "Projected [H-1,N-15]-HMQC-[H-1,H-1]- NOESY for large molecular systems: application to a 121 kDa protein-DNA complex", Journal of Biomolecular NMR 40, 175-81.

79. C. Bieniossek, Y. Nie, D. Frey, N. Olieric, C. Schaffitzel, I. Collinson, C. Romier, P. Berger, T. J. Richmond, M. O. Steinmetz and I. Berger (2009). "Automated unrestricted multigene recombineering for multiprotein complex production", Nat Meth 6, 447-50.