CTBP Current Publications:

89. Acetylcholinesterase: Pivotal Roles of its Long Omega Loop (Cys69-Cys96) in Regulating Binding, J.M. Bui and J.A. McCammon, Chem.-Biol. Interact. in press (2005).

88. Relative Contributions of Desolvation, Inter- and Intramolecular Interactions to Binding Affinity in Protein Kinase Systems,

P.A. Sims, C.F. Wong, D. Vuga, J.A. McCammon, and B.M. Sefton, J. Comp. Chem. in press (2005).

87. Tetrameric Mouse Acetylcholinesterase: Continuum Diffusion Rate Calculations by Solving the Steady-State Smoluchowski Equation Using Finite Element Methods,  D. Zhang, J. Suen, Y. Zhang, Y. Song, Z. Radic, P. Taylor, M.J. Holst, C. Bajaj, N.A. Baker, and J.A. McCammon, Biophys. J. in press (2005).

86. Agorist-mediated conformational changes in ACh-binding protein revealed by simulation and intrinsic tryptophan fluorescence,

F. Gao, N. Bren, T.P. Burghardt, S. Hansen, R.H. Henchman, P. Taylor, J.A. McCammon, and S.M. Sine, J. Biol. Chem. in press (2005).

85. Ligand induced conformational change in the alpha7 nicotinic receptor, R. H. Henchman, H.L. Wang, S.M. Sine, P. Taylor, and J.A. McCammon, Biophys. J. in press (2005).

84. How does the cAMP-Dependent Protein Kinase Catalyze the Phosphorylation Reaction: an ab initio QM/MM Study, Y. Cheng, Y. Zhang, and J.A. McCammon, J. Amer. Chem. Soc. in press (2005).

83. Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-propline motifs:Accelerated molecular dynamics analysis, D. Hamelberg, T. Shen, and J.A. McCammon, J. Amer. Chem. Soc. in press (2005).

82. Release of ADP from the catalytic suburit of protein kinase A: A molecular dynamics simulationstudy, B. Lu, C.F. Wong,and J.A. McCammon, Protein Sci. 14, 159-168 (2005).

81. Theory and Applications of Computational Chemistry, J.A. McCammon, C. Dykstra, G. Frenking, K. Kim, and G. Scuseria, Eds. Elsevier, Amsterdam, in press (2005).

80. Simple Energy Landscape Model for the Kinetics of Functional Transitions in Proteins, O. Miyashita, P. G. Wolynes, J. N. Onuchic, accepted to J. Phys.Chem.    [ download .pdf ]

79. Probing the Kinetics of Single Molecule Protein Folding,  V.B.P. Leite, J.N. Onuchic, G. Stell, and J. Wang, accepted to Biophys. J., (2004).    [ download .pdf ]

78. Transition state and encounter complex for fast association of cytochrome c2 with bacterial reaction center,   O. Miyashita, J.N. Onuchic and M. Y. Okamura, Proc. Natl. Acad. Sci 101, 1617416179 (2004).    [ download .pdf ]

77. Fluctuation-regularized Front Propagation Dynamics, E. Cohen, D.A. Kessler and H. Levine, Phys. Rev. Lett,  submitted.

76. NMR structure refinement by replica exchange, J. Chen, W. Im, and C.L. Brooks III, J. Amer. Chem. Soc., in press.

75. Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling, J. Chen, H-S Won, W. Im, H.J. Dyson & C.L. Brooks III, J Biomolec NMR, in press.

74. The self-regulating gene: an exact solution, J.E.M. Hornos, D. Schultz, G.C.P. Innocentini, J. Wang, J.N. Onuchic and P.G. Wolynes, Phys. Rev. Let. (to be submitted).

73. Protein structural flexibility: molecular motions, R.H. Henchman and J.A. McCammon, Nature Encyclopedia of Life Sciences, Nature Publishing Group, Macmillan Publishers, in press.

72. Finite concentration effects on diffusion-controlled reactions, S. Senapati, C.F. Wong, and J.A. McCammon, J. Chem. Phys. 121, 7896-7900 (2004).    [ download .pdf ]

71. Charge Optimization of the Interface between Protein Kinases and their Ligands, P.A. Sims, C.F. Wong, and J.A. McCammon, J. Comp. Chem. 25, 1416-1429 (2004).    [ download .pdf ]

70. Acetylcholinesterase: Enhanced Fluctuations and Alternative Routes to the Active Site in the Complex with Fasciculin-2, J.M. Bui, K. Tai, and J.A. McCammon, J. Amer. Chem. Soc. 126, 7198-7205 (2004).    [ download .pdf ]

69. PDB2PQR: An Automated Pipeline for the Setup, Execution, and Analysis of Poisson-Boltzmann Electrostatics Calculations, T.J. Dolinsky, J.E. Nielsen, J.A. McCammon, and N.A. Baker, Nucl. Acid Res. 32, W665-W669 (2004).    [ download .pdf ]

68. Discovery of a Novel Binding Trench in HIV Integrase, J. Schames, R.H. Henchman, J.S. Siegel, C.A. Sotriffer, H. Ni, and J.A. McCammon, J. Med. Chem. 47, 1879-1881 (2004).    [ download .pdf ]

67. Substantial regional variation in substitution rates in the human genome: importance of GC content, gene density and telomere-specific effects, P.F. Arndt, D.A. Petrov, and T. Hwa, Genome Res. submitted    [ download .pdf ]

66.  Electrostatic Interaction between RNA and Protein Capsid in CCMV Simulated by a Coarse-grain RNA model and a Monte Carlo Approach, D. Zhang, R. Konecny, N.A. Baker, J.A. McCammon, Biopolymers, 75 (4), 325-337 (2004).    [ download .pdf ]

65.  Bacterial Linguistic Communication and Social Intelligence, E. Ben-Jacob, I. Becker, Y. Shapira, and H. Levine, Trends in Microbiology, 12, 366-372 (2004).    [ download .pdf ]

64.  Physical Schemata underlying Biological Pattern Formation - Examples, Issues and Strategies, H. Levine and E. Ben-Jacob, Phys. Biol., 1, 14-22 (2004).    [ download .pdf ]

63. Dynamic instabilities of fracture under biaxial strain using a phase field mode, H. Henry and H. Levine, Phys. Rev. Lett. 93, 105504, (2004).    [ download .pdf ]

62. Interactive Essential Dynamics, J. Mongan, Journal of Computer Aided Molecular Design. submitted    [ download .pdf ]

61. Constant pH Molecular Dynamics in Generalized Born Implicit Solvent, J. Mongan, D.A. Case and J. A. McCammon, J. Comp. Comp. Chem. 25, 2038-48 (2004).    [ download .pdf ]

60.  Domain swapping is a consequence of minimal frustration, S. Yang, S. Cho, Y. Levy, M.S. Cheung, H. Levine, P.G. Wolynes and J. N. Onuchic, PNAS, 101, 13786 (2004).    [ download .pdf ]

59.  Positive feedback in a brainstem sensorimotor loop, Q. -T. Nguyen and D. Kleinfeld, in press.    [ download .pdf ]

58. Modeling Polyglutamine Structure Using a Host-Guest Method Combining Landscape Theory with Experimental Constraints, J. M. Finke, M. S. Cheung, and J. N. Onuchic, Biophys. J., 87, 1900-1918 (2004).    [ download .pdf ]

57. The functional energy landscape for interleukin-1beta.  Modulation of the population ensemble through native-state topology, M. Roy, L. L. Chavez, D. K. Heidary, J. N. Onuchic, and P. A. Jennings, J. Mol. Bio., submitted.    

56. Using nanopores to learn RNA structures, U. Gerland, R. Bundschuh, T. Hwa, Biophys. J. submitted    [ download .pdf ]

55. Quantifying the roughness on the Free Energy Landscape: Entropic bottlenecks and protein folding rates, L. L. Chavez, J. N. Onuchic and C. Clementi, J. Am. Chem. Soc., 126, 8426-8432 (2004).    [ download .pdf ]

54. Gatekeepers in the Ribosomal Protein S6: Thermodynamics, Kinetics, and Folding Pathways

Revealed by a Minimalist Protein Model, A. D. Stoycheva, C. L. Brooks III, and J. N. Onuchic, J. Mol. Bio., 340, 571-585 (2004).    [ download .pdf ]

53. Standard Free Energy of Releasing a Localized Water Molecule from the Binding Pockets of Proteins: Double-Decoupling Method, D. Hamelberg, and J.A. McCammon, J. Amer. Chem. Soc., 126, 7683-7689 (2004).    [ download .pdf ]

52.  Accelerated Molecular Dynamics: A promising and efficient simulation method for biomolecules, D. Hamelberg, J. Mongan and J.A. McCammon, Journal of Chemical Physics 120, 11919-11929 (2004).    [ download .pdf ]

51. A Single Residue Provides A Dynamic Link Between the SH2 Domain and Active Site of the COOH Terminal Src Kinase, Csk, L. Wong, S. Lieser, B. Chie-Leon, O. Miyashita, B. Aubol, J. Shaffer, J.N. Onuchic, P.A. Jennings, V.L. Woods, Jr. and J.A. Adams, J. Mol. Biol. , 341, 93-106 (2004).    [ download .pdf ]

50. Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM, F. Tama, O. Miyashita, and C.L. Brooks, J. Struct. Biol., 147 (3), 315-26, (2004).    [ download .pdf ]

49.  Ribosome Motions Modulate Electrostatic Properties, J. Trylska, R. Konecny, F. Tama, C.L. Brooks, and J.A. McCammon, Biopolymers. 74, 423-431 (2004).    [ download .pdf ]

48.  Goal-directed whisking behavior increases phase-locking between vibrissa movement and electrical activity in primary sensory cortex in rat, K. Ganguly and D. Kleinfeld, PNAS 101, 12348-53 (2004).    [ download .pdf ]

47.  Ultrashort pulsed laser light:  A cool tool for ultraprecise cutting of tissue and cells, P.S. Tsai, J. A. Squier and D. Kleinfeld, Optics and Photonics News 15, 24-29 (2004).    [ download .pdf ]

46. Dynamics of Electron Transfer Pathways in Cytochrome c Oxidase, M.-L. Tan, I. Balabin and J.N. Onuchic.  Biophys. J., 86, 1813-1819 (2004).    [ download .pdf ]