Publications

Search Pub Med - Fairly Comprehensive Listing of Doniach group biophysical papers

Sebastian Doniach: Publications 1995-2005

1. S. Doniach, J. Bascle, T. Garel, H. Orland. "Partially folded states of proteins: characterization by x-ray scattering." J. Mol. Biol. 254: 960-967 (1995).

2. N. Manini, Erio Tosatti and S. Doniach. "Enhanced electron pairing in a lattice of Berry phase molecules." Phys. Rev. B 51: 3731-3742 (1995).

3. Castor Fu and S. Doniach. "Model for FeSi, a strongly correlated insulator." Phys. Rev. B 15: 17439-17445 (1995).

4. S. Doniach. "Antibody-antigen binding: Structure-function relationships viewed at atomic scale resolution." In: Handbook on Experimental Immunology, 5th Edition. L. Herzenberg, ed. (Blackwell Science, Inc. Oxford, 1997).

5. M. Pellegrini and S. Doniach. "Modeling solvation contributions to conformational free energy changes of biomolecules using a potential of mean force expansion." J. Chem. Phys. 103: 2696-2702 (1995).

6. S. Doniach. "Reflections on the superconductor-insulator transition." J. Phys. and Chem. of Solids 56: 1601-1603 (1996), *Corrected Version 57 page 506: I-III (1996).

7. T. Onogi and S. Doniach. "Simulation of quantum melting of the vortex lattice and of fractional quantum Hall-like states of the quantum vortex liquid in 2D superconductors." Solid State Communications 98: 1-5 (1996).

8. D. Eliezer, P. Wright, S. Doniach, K. Hodgson, H. Tsuruta, P. Jennings. "Time-resolved small angle x-ray scattering establishes that an apomyoglobin kinetic folding intermediate is compact." Science 270: 487-88 (1995).

9. M. Pellegrini, N. Gronbech-Jensen and S. Doniach. "Potentials of mean force for biomolecular simulations: theory and test on alanine dipeptide." J. Chem. Phys. 104 (21): 8639-8648 (1996).

10. S. Doniach, T. Garel, H. Orland. "Phase diagram of a semiflexible polymer chain in a solvent: Application to protein folding." J. Chem. Phys. 105 (4): 1601-8 (1996).

11. S. Doniach, J. Bascle, T. Garel, H. Orland. "Partially folded states of proteins: Characterization by x-ray scattering." J. Mol. Biol. 254: 960-67 (1995).

12. L. Chen, K. Hodgson, S. Doniach. "A lysozyme folding intermediate revealed by solution x-ray scattering." J. Mol. Biol. 261 (5): 658-671 (1996).

13. S. Doniach. "Studies of the structure of matter with photons from an x-ray free electron laser." J. Synchrotron Radiation 3: 260-267 (1996).

14. S. Ryu, A. Kapitulnik, S. Doniach. "Field-driven topological glass transition in a model flux line lattice." Phys. Rev. Lett. 77: 2300-3 (1996).

15. S. Ryu, M. Hellerqvist, S. Doniach, A. Kapitulnik, D. Stroud. "Dynamical phase transition in a driven disordered vortex lattice." Phys. Rev. Lett. 77: 5114-17 (1996).

16. M. Pellegrini, N. Gronbech-Jensen, S. Doniach. "Simulations of the thermodynamic properties of a short polyalanine peptide using potentials of mean force." Physica A 239: 244-54 (May 1997).

17. P. Eastman and S. Doniach. "Multiple time step diffusive Langevin dynamics for proteins." Proteins: Structure, Function, and Genetics 30: 215-227 (1998).

18. H. Watanabe and S. Doniach. "Metal-insulator transition of the two-band Hubbard model in infinite dimension and its relevance to a strongly correlated electron system: NiS2-xSex." Phys. Rev. B 57: 3829-3837 (1998).

19. A.Y. Matsuura, H. Watanabe, C. Kim, Z-X. Shen, S. Doniach, T. Thio, J.W. Bennett. "The metal-insulator transition in NiS2-xSex and the local impurity self-consistent approximation model." Phys. Rev. B-Condensed Matter 58: 3690-3696 (1998).

20. Lingling Chen, Gudrun Wildegger, Thomas Kiefhaber, Keith Hodgson, Sebastian Doniach. "Kinetics of lysozyme refolding: Structural characterization of a non-specifically collapsed state using time-resolved x-ray scattering." J. Mol. Biol. 276 (1): 225-237 (1998).

21. V. Uversky, Dan Segel, S. Doniach, A. Fink. "Association-induced folding of globular proteins." Proc. Natl. Acad. Sci. 95 (10): 5480-5483 (1998).

22. Daniel J. Segel, Anthony L. Fink, Keith O. Hodgson, Sebastian Doniach. "Protein denaturation: A small angle x-ray scattering study of the ensemble of unfolded states of cytochrome c." Biochemistry 37: 12443-12451 (1998).

23. D. Das and S. Doniach. "Weakly localized bosons." Phys. Rev. B 57: 14440-14443 (1998).

24. Andreas Kraemer and S. Doniach. "Superinsulator Phase of two-dimensional superconductors." Phys. Rev. Lett. 81: 3523-3526 (1998).

25. S. Doniach, K. Hodgson, I. Lindau, P. Pianetta, H. Winick. "Early work with synchrotron radiation at Stanford." Synchrotron Radiation 4: 380-395 (1997).

26. S. Doniach and E.H. Sondheimer. Green's Function for Solid State Physicists. Reprint edition with new material on the physics of correlated electron systems, Imperial College Press (distributed by World Scientific), Summer 1998

27. Peter Eastman, Matteo Pellegrini and Sebastian Doniach. "Protein flexibility in solution and crystals." J. Chem. Phys. 110: 10141-10152 (May 1999).

28. D. Das and S. Doniach. "Existence of a Bose metal at T=0." Phys. Rev. B. 60: 1261-1275 (July 1999).

29. Kramer and S. Doniach. "Superinsulator phase of two-dimensional superconductors." Phys. Rev. Lett. 81: 3523-3526 (1998).

30. Vladimir Uversky, Anton Karnoup, Daniel Segel, Sangita Seshadri, Sebastian Doniach, Anthony Fink. "Anion-induced folding of staphylococcal nuclease: Characterization of multiple equilibrium partially folded intermediates." J. Mol. Biol. 278: 879-894 (1998).

31. D. Segel, A. Bachmann, J. Hofrichter, K. Hodgson, S. Doniach and T. Kiefhaber. "Characterization of transient intermediates in lysozyme folding with time-resolved SAXS." J. Mol. Biol. 288: 489-499 (May 1999).

32. P. Eastman and S. Doniach. "Protein dynamics simulations from nanoseconds to microseconds." Current Opinion in Structural Biology 9 (2): 157-163 (April 1999).

33. K.W. Plaxco, I.S. Millett, D.J. Segel, S. Doniach, D. Baker. "Chain collapse can occur concomitantly with the rate-limiting step in protein folding." Nature Structural Biology 6 (6): 554-556 (June 1999).

34. V.N. Uversky, A.S. Karnoup, R. Kurana, D.J. Segel, S. Doniach, A.L. Fink. "Association of partially-folded intermediates of staphylococcal nuclease induces structure and stability." Protein Science 8: 161-173 (January 1999).

35. D. Segel, D. Eliezer, V. Uversky, A. Fink, K. Hodgson, S. Doniach. "Transient dimer in the refolding kinetics of cytochrome c characterized by small-angle x-ray scattering." Biochemistry 38 (46): 15352-15359 (November 1999).

36. V. Uversky, J. Gillespie, I. Millett, A. Vasiliev, A. Khodyakova, R. Vasilenko, I. Rodionov, G. Kozlovskaya, D. Dolgikh, V. Abramov, A. Vartapetian, A. Fink, S. Doniach, E. Permyakov. "Zn2+-mediated structure formation and compaction of the "natively unfolded" human prothymosin ?." Biochemical and Biophysical Research Communications 267: 663-668 (Jan. 19, 2000).

37. S. Doniach. "Fourth-generation x-ray sources: Some possible applications to biology." J. of Synchrotron Radiation 7 (3): 116-120 (May 2000).

38. D. Walther, F. Cohen and S. Doniach. "Reconstruction of low resolution three-dimensional density maps from one-dimensional small angle x-ray scattering data for biomolecules." J. of Applied Crystallography 33 (2): 350-363 (April 2000).

39. P. Eastman, N. Gronbech-Jensen, S. Doniach. "Simulation of protein folding by reaction path annealing." J. Chemical Physics 114: 3823-3841 (February 2001).

40. M. Bada, D. Walther, B. Arcangioli, M. Goldberg, S. Doniach, M. Delarue. "Solution structural studies and low resolution model of the S. pombe SAP1 protein." J. Mol. Biol. 300: 563-574 (July 2000).

41. R. Russell, Ian S. Millett, S. Doniach, D. Herschlag. "Small angle x-ray scattering reveals a compact intermediate in folding of the tetrahymena group I RNA enzyme." Nature, Structural Biology 7 (5): 367-370 (May 2000).

42. V. Uversky, J. Gillespie, I. Millett, A. Khodyakova, A. Vasiliev, T. Chernovskaya, R. Vasilenko, G. Kozovskaya, D. Dolgikh, A. Fink, S. Doniach, V. Abramov. "Natively unfolded human prothymosin alpha adopts partially folded collapsed conformation at acidic pH." Biochemistry 38: 15009-15016 (November 1999).

43. S. Doniach. "Changes in biomolecular conformation seen by small-angle x-ray scattering." Chemical Reviews 101 (6): 1763-1778 (June 2001).

44. R. Russell, X. Zhuang, H. Babcock, I. Millett, S. Doniach, S. Chu, D. Herschlag. "Channels in the folding landscape." Proc. Nat. Acad. Sci. (U.S.A.) 99 (1): 155-160 (January 2002).

45. D. Das and S. Doniach. "The Bose metal: gauge field fluctuations and scaling for field tuned quantum phase transitions." Phys. Rev. B 64 (13): 4511 (October 2001).

46. I.S. Millett, L.E. Townsley, F. Chiti, S. Doniach, K.W. Plaxco. "Equilibrium collapse and the kinetic 'foldability' of proteins." Biochemistry 41 (1): 321-325 (January 2002).

47. H. Wille, M.D. Michelitsch, V. Guenebaut, S. Supattapone, D.J. Segel, D. Walther, H. Serban, S. Doniach, F.E. Cohen, D.A. Agard, S.B. Prusiner. "Structural studies of the scrapie prion protein by electron crystallography." Biophysical Journal 82 (1), pt.2: 169A-169A (January 2002).

48. R. Russell, X.W. Zhuang, H.P. Babcock, I.S. Millett, S. Doniach, S. Chu, D. Herschlag. "Exploring the folding landscape of a structured RNA." Proc. Nat. Acad. Sci. (U.S.A.) 99 (1): 155-160 (January 8, 2002).

49. Wenjun Zheng and Sebastian Doniach. "Protein structure prediction constrained by solution X-ray scattering data and structural homology identification." J. of Mol. Biol. 316 (1): 173-187 (February 8, 2002).

50. Wing-Yiu Choy, Frans A. A. Mulder, Karin A. Crowhurst, D.R. Muhandiram, Ian S. Millett, Sebastian Doniach, Julie D. Forman-Kay, Lewis E. Kay. "Distribution of molecular size within an unfolded state ensemble using small-angle X-ray scattering and pulse field gradient NMR techniques." J. of Mol. Biol. 316 (1): 101-112 (February 2002).

51. P.O. Souillac, V.N. Uversky, I.S. Millett, R. Khurana, S. Doniach, A.L. Fink. "Effect of association state and conformational stability on the kinetics of immunoglobulin light chain amyloid fibril formation at physiological pH." J. of Biol. Chemistry 277 (15): 12657-12665 (April 2002).

52. P.O. Souillac, V.N. Uversky, I.S. Millett, R. Khurana, S. Doniach, A.L. Fink. "Elucidation of the molecular mechanism during the early events in immunoglobulin light chain amyloid fibrillation: evidence of an off-pathway oligomer at acidic pH." J. of Biol. Chemistry 277 (15): 12666-12679 (April 2002).

53. V.N. Uversky, J. Li, P. Souillac, I.S. Millett, S. Doniach, R. Jakes, M. Goedert, A.L. Fink. "Biophysical Properties of the synucleins and their propensities to fibrillate: inhibition of apha-synuclein assembly by beta- and gamma- synucleins." J. of Biol. Chemistry 277 (14): 11970-11978 (April 2002).

54. R. Russell, I.S. Millett, M.W. Tate, L.W. Kwok, B. Nakatani, S.M. Gruner, S.G.J. Mochrie, V. Pande, S. Doniach, D. Herschlag, L. Pollack, "Rapid compaction during RNA folding." Proc. Nat. Acad. Sci. (U.S.A.) 99 (7): 4266-4271 (April 2002).

55. I.S. Millet, S. Doniach, K. Plaxco. "Toward a taxonomy of the denatured state: Small angle scattering studies of unfolded proteins." Unfolded Proteins 62: 241-262 (2002).

56. D.F. Schroeter, S. Doniach. "Three-dimensional flux states as a model for the pseudogap phase of transition metal oxides." Phys. Rev. B 66 (7): 075120-5120 (August 15, 2002).

57. H. Watanabe, S. Doniach. "A dynamical mean-field theory approach to superconductivity and antiferromagnetism in a strongly correlated electron system." Condensed Matter, abstract cond-mat/0205086 (May 2002).lanl.arXiv.org

58. A.S. Meyer, J.R. Gillespie, D. Walther, I.S. Millet, S. Doniach, J. Frydman. "Closing the folding chamber of the eukaryotic chaperonin requires the transition state of ATP hydrolysis." Cell 113 (3): 369-381 (May 2, 2003).

59. V.N. Uversky, L.N. Garriques, I.S. Millett, S. Frokjaer, J. Brange, S. Doniach, A.L. Fink. "Prediction of the association state of insulin using spectral parameters." J. Of Pharmaceutical Sciences 92 (4): 847-858 (April 2003).

60. R. Das, T.T. Mills, L.W. Kwok, G.S. Maskel, I.S. Millett, S. Doniach, K.D. Finkelstein, D. Herschlag, L Pollack. "Counterion distribution around DNA probed by solution X-ray scattering." Phys. Rev. Lett. 90 (18): 188103 (May 9, 2003).

61. J. Goers, A.B. Manning-Bog, A.L. McCormack, I.S. Millett, S. Doniach, D.A. Di Monte, V.N. Uversky, A.L. Fink. "Nuclear localization of alpha-synuclein and its interaction with histones." Biochemistry 42 (28): 8465-8471 (July 22, 2003).

62. Ahmad, I.S. Millett, S. Doniach, V.N. Uversky, A.L. Fink. "Partially folded intermediates in insulin fibrillation." Biochemistry 42 (39): 11404-11416 (Oct 7, 2003).

63. Rhiju Das, Lisa W. Kwok, Ian S. Millett, Yu Bai, Thalia T. Mills, Jaby Jacob, Gregory S. Maskel, Soenke Seifert, Simon G. J. Mochrie, P. Thiyagarajan, Sebastian Doniach, Lois Pollack and Daniel Herschlag "The fastest global events in RNA folding: Electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme." J. of Mol. Biol. 332 (2): 311-319 (12 September, 2003).

64. S.E. Permyakov, I.S. Millett, S. Doniach, E.A. Permyakov, V.N. Uversky. "Natively unfolded C-terminal domain of caldesmon remains substantially unstructured after the effective binding to calmodulin." Proteins 53 (4): 855-862 (December 1, 2003).

65. S. Doniach, R. Das. "The Bose metal: a commentary." Brazilian Journal of Physics 33 (4): 740-3 (Dec. 2003). Conference: U-Super - International Workshop on Unconventional Superconductors, 20-24 May 2003, Campinas, Brazil.

66. V.N. Uversky, L.N. Garriques, I.S. Millett, S. Frokjaer, J. Brange, S. Doniach, A.L. Fink. "Prediction of the association state of insulin using spectral parameters." Journal of Pharmaceutical Sciences 92 (4): 847-858 (April 2003)

67. W.J. Zheng, S. Doniach. "A comparative study of motor-protein motions by using a simple elastic-network model." Proc. Nat. Acad. Sci. (U.S.A.) 100 (23): 13253-13258 (November 11, 2003).

68. Ahmad, I.S. Millett, S. Doniach, V.N. Uversky, A.L. Fink. "Stimulation of Insulin Fibrillation by Urea-induced Intermediates." J. of Biol. Chemistry 279 (15): 14999-15013 (Apr 9 2004).

69. J.E. Kohn, I.S. Millett, J. Jacob, B. Zagrovic, T.M. Dillon, N. Cingel, R.S. Dothager, S. Seifert, P. Thiyagarajan, T.R. Sosnick, et. al. "Random-coil behavior and the dimensions of chemically unfolded proteins." Proc. Nat. Acad. Sci. (U.S.A.) 101 (34): 12491-12496 (August 24, 2004).

70. J. Lipfert, F. Wu, J. Franklin, S. Doniach. "Protein misfolding and aggregation in a 7 residue peptide from the yeast prion protein Sup35: Simulation by reaction path annealing." Biophysical Journal 86 (1): 416a (January 2004). Conference: 48th Annual Meeting of the Biophysical Society; February 14-18, 2004; Baltimore, MD, USA.

71. D.F. Schroeter, S. Doniach. "Orbital antiferromagnetism in coupled planar systems." Phys. Rev. B 69 (9): 094407 (March 2004).

72. Ahmad, I.S. Millett, S. Doniach, V.N. Uversky, A.L. Fink. "Stimulation of Insulin Fibrillation by Urea-induced Intermediates" J. of Biol. Chemistry 279 (15): 14999-15013 (April 9, 2004).

73. K. Takamoto, R. Das, W. He, S. Doniach, M. Brenowitz, D. Herschlag, M.R. Chance. "Principles of RNA compaction: Insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations" J. of Mol. Biol. 343 (5): 1195-1206 (November 5, 2004).

74. J. Lipfert, S. Doniach. "Unzipping the polar zipper: Molecular dynamics simulation of force induced beta-amyloid disassembly and implications for future experiments" Biophysical Journal, 88 (1), pt.2, suppl. S, 401A-401A (January 2005).

75. Y. Bai, R. Das, D. Herschlag, S. Doniach. "Probing Counterion Modulated Repulsion and Attraction Between Nucleic Acid Duplexes in Solution." Proc. Nat. Acad. Sci. U.S.A. 102 (4): 1035-1040 (January 25, 2005).

76. V.N. Uversky, G. Yamin, L.A. Munishkina, M.A. Karymov, I.S. Millett, S. Doniach, Y.L. Lyubchenko, A.L Fink. "Effects of nitration on the structure and aggregation of alpha-synuclein" Molecular Brain Research; 134 (1), 84-102 (March 24, 2005).

77. W.J. Zheng, B.R. Brooks, S. Doniach, D. Thirumalai. "Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved" Structure (Cambridge); 13 (4), 565-577 (April 2005).

78. W.J. Zheng, S. Doniach. "Fold recognition aided by constraints from small angle X-ray scattering data" Protein Engineering, Design and Selection; 18 (5), 209-219 (May 2005).

79. J. Lipfert, J. Franklin, F. Wu, S. Doniach. "Protein misfolding and amyloid formation for the peptide GNNQQNY from yeast prion protein Sup35: Simulation by reaction path Annealing" J. of Mol. Biol.; 349 (3), 648-658 (June 10, 2005).

80. B. Zagrovic, J. Lipfert, E.J. Sorin, I.S. Millett, W.F. van Gunsteren, S. Doniach, V.S. Pande. "Unusual compactness of a polyproline type II structure" Proc. Nat. Acad. Sci.; (USA) 102 (33), 11698-703 (16 August 2005).

81. J. Franklin, S. Doniach. "Adaptive time stepping in biomolecular dynamics" J. of Chem. Physics; 123 (12), 124909-1-11 (22 September 2005).

82. J. E. Kohn, I. S. Millett, J. Jacob, B. Zagrovic, T.M. Dillon, N. Cingel, R.S. Dothager, S. Seifert, P. Thiyagarajan, T.R. Sosnick, M.Z. Hasan, V.S. Pande, I. Ruczinski, S. Doniach, K.W. Plaxco. "Random-coil behavior and the dimensions of chemically unfolded proteins" Proc. Nat. Acad. Sci. (USA); 101 (40): 12491 (2004) 102 (40): 14475 Correction; Errata (October 4, 2005).

83. B. Zagrovic, G. Jayachandran, I.S. Millett, S. Doniach, V.S. Pande. "How large is an alpha-helix? Studies of the radii of gyration of helical peptides by small-angle X-ray scattering and molecular dynamics" J. of Mol. Biol.; 353 (2), 232-241 (October 21, 2005).