Older Publications at Madison (2001-08)

2008

108. Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. Parameterization, Y. Yang, H. Yu, D. York, M. Elstner* and Q. Cui*, J. Chem. Theo. Comp., 4, 2067-2084 (2008)

107. Computational Molecular Biomechanics: A Hierarchical Multiscale Framework with Applications to Gating of Mechanosensitive Channels of Large Conductance, X. Chen* & Q. Cui*, Book Chapter in Advances in Computational NanoMechanics, In press (2008) Invited Book Chapter

106. Mechanosensitive Channels: Insights from Continuum-Based Simulations, Y. Tang, J. Yoo, A. Yethiraj, Q. Cui* and X. Chen*, Cell Biochem. & Biophys., 52, 1-18 (2008) Invited Review

105. Amino acids with an intermolecular proton bond as the proton storage site in bacteriorhodopsin, P. Phatak&, N. Ghosh&, H. Yu, Q. Cui* and M. Elstner*, Proc. Natl. Acad. Sci. USA, 105, 19672-19677 (2008) [&These authors contributed equally]

104. Extensive conformational changes are required to turn on ATP hydrolysis in myosin, Y. Yang, H. Yu and Q. Cui*, J. Mol. Biol., 381, 1407-1420 (2008)

103. pKa of residue 66 in Staphylococal nuclease: insights from QM/MM simulations with conventional sampling, N. Ghosh, Q. Cui*, J. Phys. Chem. B, 112, 8387-8397 (2008) (Cover)

102. Gating Mechanisms of Mechanosensitive Channels of Large Conductance Part II: Systematic Study of Conformational Transitions, Y. Tang, J. Yoo, A. Yethiraj, Q. Cui and X. Chen*, Biophys. J. 95, 581-596 (2008) (Cover)

101. Gating Mechanisms of Mechanosensitive Channels of Large Conductance Part I: A Continuum Mechanics-Based Hierarchical Framework, X. Chen*, Q. Cui, Y. Tang, J. Yoo and A. Yethiraj, Biophys. J. 95, 563-580 (2008)

100. QM/MM and multi-scale methods for the simulation of biochemical processes in complex environments, Q. Cui and M. Elstner, in Solvation effects on molecules and biomolecules: Computational methods and applications, Ed. S. Canuto, Springer Series: Challenges and Advances in Computational Chemistry and Physics, In press (2008) Invited Book Chapter

99. ``Multi-scale" QM/MM methods with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) Method, Q. Cui and M. Elstner, in Multi-scale Quantum Models for Biocatalysis, Eds. D. York, T. Lee, In press (2008) Invited Book Chapter

98. Does Arg remain protonated in the lipid membrane? Insights from microscopic pKa calculations, J. Yoo and Q. Cui*, Biophys. J. Lett, L61-L63 (2008)

97. Functional Motions in Biomolecules: Insights from Computational Studies at Multiple Scales, A. W. van Wynsberghe, L. Ma, X. Chen and Q. Cui*, in "Computational Structural Biology", Eds. T. Schwede, M. Peitsch, pp253-298 World Scientific (2008)

96. Proton transfer in Carbonic Anhydrase is controlled by electrostatics rather than the orientation of the acceptor group, D. Riccardi, P. Koenig, H. Guo and Q. Cui*, Biochem., 47, 2369-2378 (2008)

95. Allostery and Cooperativity Revisited, Q. Cui, M. Karplus, Protein Sci., 17, 1295-1307 (2008)

94. Establishing effective simulation protocols for $\beta$ and $\alpha/\beta$ mixed peptides. II. Molecular Mechanical (MM) model for Cyclic $\beta$-residue, X. Zhu, A. Yethiraj and Q. Cui, J. Phys. Chem. B, 112, 5439-5448(2008)

93. Discovery and mechanistic study of Al-III-catalyzed transamidation of tertiary amides, J. M. Hoerter, K. M. Otte, S. H. Gellman, Q. Cui and S. S. Stahl, J. Am. Chem. Soc., 130, 647-654 (2008)

2007

92. The vibrational spectra of protonated water clusters: A benchmark for SCC-DFTB, H. Yu and Q. Cui*, J. Chem. Phys., 127, 234504 (2007)

91. Antibiotic deactivation by a dizinc $\beta$-Lactamase: Mechanistic insights from QM/MM and DFT studies, D. Xu, H. Guo* and Q. Cui, J. Am. Chem. Soc., 129, 10814-10822 (2007)

90. Numerical simulations of patch clamp and nanoindentation experiments on mechanosensitive channels of large conductance, Y. Tang, X. Chen*, J. Yoo and A. Yethiraj, Q. Cui, J. Exp. Mech. 49, 35-46 (2009) [Published on line: 3 Jul 2007]

89. The activation mechanism of a signaling protein at atomic resolution from advanced computations, L. Ma, Q. Cui, J. Am. Chem. Soc., 129, 10261-10268 (2007)

88. Application of the computationally efficient self-consistent-charge density-functional-tight-binding method to Magnesium-containing molecules, Z. Cai, P. Lopez, J. R. Reimers, Q. Cui and M. Elstner, J. Phys. Chem. A (DFTB Symposium issue), 111, 5743-5750 (2007)

87. Extension of the Self-Consistent-Charge Tight-Binding-Density-Functional (SCC-DFTB) method: third order expansion of the DFT total energy and introduction of a modified effective Coulomb interaction, Y. Yang, H. Yu, D. York, Q. Cui and M. Elstner, J. Phys. Chem. A 111, 10861-10873 (2007)

86. Interactions between phosphate and water in solution: a Natural Bond Orbital based analysis in a QM/MM framework, Y. Yang, Q. Cui, J. Phys. Chem. B Lett., 111, 3999-4002 (2007)

85. pKa analysis for the zinc-bound water in Human Carbonic Anhydrase II: benchmark for "multi-scale" QM/MM simulations and mechanistic implications, D. Riccardi, Q. Cui, J. Phys. Chem. A, Special Issue in SCC-DFTB, 111, 5703-5711 (2007) PDF

84. Antibiotic binding to metallo-beta-lactamase L1 from Stenotrophomonas maltophilia: SCC-DFTB/CHARMM and DFT studies, D. Xu, H. Guo and Q. Cui, J. Phys. Chem. A, Special Issue in SCC-DFTB, 111, 5630-5636 (2007)

83. Establishing effective simulation protocols for $\beta$ and mixed $\alpha/\beta$ peptides, 1. QM and QM/MM models, X. Zhu, A. Yethiraj and Q. Cui, J. Chem. Theo. Comp., 3, 1538-1549 (2007)

82. Mechanochemical coupling in myosin motor domain, II. Analysis of critical residues, H. Yu, L. Ma, Y. Yang and Q. Cui, PLoS Comp. Biol. 3, 0214 (2007) PDF

81. Mechanochemical coupling in myosin motor domain, I. Equilibrium active site simulations, H. Yu, L. Ma, Y. Yang and Q. Cui, PLoS Comp. Biol. 3, 0199 (2007) PDF

80. TiIV-mediated reactions between primary amines and secondary carboxamides: Amidine formation versus transamidation, D. A. Kissounko, J. M. Hoerter, I. A. Guzei, Q. Cui, S. H. Gellman, S. S. Stahl, J. Am. Chem. Soc., 129, 1776-1783 (2007) PDF

79. Protein structural variation in computational models and crystallographic data, D. A. Kondrashov, A. W. Van Wynsberghe, R. M. Bannen, Q. Cui and G. N. Phillips, Jr., Structure, 15, 169-177 (2007) PDF

78. A specific reaction parameterization for the AM1/d Hamiltonian for transphosphorylation reactions, K. Nam, Q. Cui, J. Gao, D. M. York, J. Theo. Comp. Chem., 3, 486-504 (2007) PDF

2006

77. "Proton holes" in long-range proton transfers in solution and enzymes, D. Riccardi, P. Konig, H. Yu, X. Prat-Resina, M. Elstner, T. Frauenheim, Q. Cui, J. Am. Chem. Soc., 128, 16302-16311 (2006) PDF

76. Interpreting correlated motions using normal mode analysis, A. W. Van Wynsberghe, Q. Cui, Structure, 14, 1647-1653 (2006) PDF

75. Temperature dependence of salt-protein association is sequence specific, L. Ma, Q. Cui, Biochem. 45, 14466-14472 (2006) PDF

74. Optimization and evaluation of a coarse-grained model of protein motion using X-ray crystal data, D. A. Kondrashov, Q. Cui and G. N. Phillips, Jr., Biophys. J. 91, 2760-2767 (2006) PDF

73. A finite element framework for studying mechanical response of macromolecules: Application to the gating of the mechanosensitive channel, MscL, Y. Tang, G. Cao, X. Chen, J. Yoo, A. Yethiraj, Q. Cui, Biophys. J. 91, 1248-1263 (2006) PDF version (Cover)

72. Effects of Temperature and Salt Concentration on the Structural Stability of Human Lymphotactin: Insights from Molecular Simulations, M. Formaneck, L. Ma, Q. Cui, J. Am. Chem. Soc. 128, 9506-9517 (2006) PDF version

71. The use of a generalized Born model for the analysis of protein conformational transitions. A comparative study with explicit solvent simulations for chemotaxis Y Protein (CheY), M. Formaneck, Q. Cui, J. Comput. Chem. 27, 1923-1943 (2006) PDF version

70. Development of effective QM/MM methods for complex biophysical processes, D. Riccardi, et al.,Q. Cui, J. Phys. Chem. B Feature Article, J. Phys. Chem. B 110, 6458-6469 (2006) PDF version (Cover)

69. Reconciling the "old" and "new" views of protein allostery. A molecular simulation study of chemotaxis Y protein (CheY) M. Formaneck, L. Ma, Q. Cui, Proteins, 63, 846-867 (2006) PDF version

2005

68. Hydrogenation of Imines by Hydroxycyclopentadienyl Ruthenium Hydride: Intramolecular Trapping Evidence for Hydride and Proton Transfer Outside the Coordination Sphere of the Metal, C. P. Casey, G. A. Bikzhanova, Q. Cui, and I. A. Guzei, J. Am. Chem. Soc., 127, 14062-14071 (2005) PDF version

67. Towards theoretical analysis of long-range proton transfer kinetics in biomolecular pumps, P. Koenig, N. Ghosh, M. Hoffman, M. Elstner, Th. Frauenheim, Q. Cui, J. Phys. Chem. A (Truhlar Issue), 110, 548-563 (2006) PDF version

66. Comparisons of mode analyses at different resolutions applied to nucleic acid systems, A. Van Wynsberghe, Q. Cui, Biophys. J., 89, 2939-2949 (2005) (Cover) PDF version

65. Theoretical analysis of mechanochemical coupling in myosin, Q. Cui, Special Issue in Royal Society Chemistry, p66-75 (2006) PDF version

64. Benchmark calculations of proton affinities and gas phase basicities of molecules important in the study of biological phosphoryl transfer, K. Range, D. Riccardi, Q. Cui, M. Elstner and D. M. York, PhysChemChemPhys, 7, 3070-3079 (2005)

63. Theoretical and computational studies of vectorial processes in biomolecules, Q. Cui, Special Issue on "New Perspectives in Theoretical Chemistry" in Theoretical Chemistry Accounts, 116, 51-59 (2006) PDF version

62. pKa calculations in solution and proteins using free energy perturbations and hybrid QM/MM simulations, D. Riccardi, P. Schaefer, Q. Cui, J. Phys. Chem. B, 109, 17715-17733 (2005) (Cover) PDF version

61. Reliable treatment of long-range electrostatics in combined QM/MM simulation of macromolecules, P. Schaefer, D. Riccardi, Q. Cui, J. Chem. Phys. 123, 014905 (2005) PDF version

60. Direct determination of reaction path and saddle points on the potential of mean force surface, G. Li, Q. Cui, J. Mol. Graphics & Modelling, Special Issue for Prof. I. Hillier, 24, 82-93 (2005) PDF version

59. A critical evaluation of different QM/MM frontier treatments using SCC-DFTB as the QM method, P. Koenig, M. Hoffman, Th. Frauenheim, Q. Cui, J. Phys. Chem. B, 109, 9082-9095 (2005) PDF version

58. Normal mode analysis of macromolecules: from enzyme active site to molecular machines, G. Li, A. van Wynsberghe, O. N. A. Demerdash, Q. Cui, In Normal mode analysis in chemistry and biology: algorithms and applications, Eds. Q. Cui, I. Bahar, CRC Press, 2005

57. Hydrogen elimination from a hydroxycyclopentadienyl Ruthenium (II) hydride: study of hydrogen activation in a ligand-metal bifunctional hydrogenation catalyst, C. P. Casey, J. B. Johnson, S. W. Singer and Q. Cui, J. Am. Chem. Soc. 127, 3100-3109 (2005) PDF version

2004

56. QM/MM Studies of Enzyme Catalyzed Dechlorination of 4-Chlorobenzoyl-CoA and Their Implications to Kinetic Model, D. Xu, Y. Wei, J. Wu, D. Dunaway-Mariano and H. Guo, Q. Cui, J. Gao, J. Am. Chem. Soc. 126, 13649-13658 (2004) PDF version

55. Normal mode analysis suggests protein flexibility modulation throughout RNA polymerase's functional cycle, A. Van Wynsberghe, G. Li, Q. Cui, Biochem. 43, 13083-13096 (2004) PDF version

54. The importance of van der Waals interactions in QM/MM simulations, D. Riccardi, G. Li, Q. Cui, J. Phys. Chem. B 108, 6467-6478 (2004) PDF version

53. A QM/MM study of a nucleophilic aromatic substitution reaction catalyzed by 4-Chlorobenzoyl-CoA dehalogenase, D. Xu, H. Guo, J. Gao and Q. Cui, Chem. Comm. 7, 892-893 (2004) PDF version

52. A normal mode analysis of structural plasticity in the biomolecular motor F1-ATPase, Q. Cui, G. Li, J. Ma, M. Karplus, J. Mol. Biol. 340, 345-372 (2004) PDF version

51. Mechanochemical coupling in myosin. A theoretical analysis of ATP hydrolysis with molecular dynamics and combined QM/MM reaction path calculations, G. Li, Q. Cui, J. Phys. Chem. B 108, 3342-3357 (2004) PDF version

50. Analysis of functional motions in "Brownian molecular machines" with an efficient block normal mode approach. Myosin-II and Ca2+-ATPase, G. Li, Q. Cui, Biophys. J. 86, 743-763 (2004) PDF version

2003

49. What is so special about Arg 55 in the catalysis of cyclophilin A? Insights from hybrid QM/MM simulations, G. Li, Q. Cui, J. Am. Chem. Soc. 125, 15028-15038(2003) PDF version

48. pKa calculations with combined QM/MM free energy perturbations, G. Li, Q. Cui, J. Phys. Chem. B 107, 14521-14528 (2003) PDF version

47. Catalysis and specificity in enzymes: A study of triosephosphate isomerase (TIM) and comparison with methylglyoxal synthase (MGS), Q. Cui, M. Karplus, Adv. Prot. Chem. (Review) 66, 315-372 (2003) PDF version

46. Free energy perturbation calculations with combined QM/MM potentials. Complications, simplifications and application to redox potential calculations, G. Li, X. Zhang, Q. Cui, J. Phys. Chem. B, 107, 8643-8653 (2003) PDF version

45. The missing link between thermodynamics and structure in F1-ATPase, W. Yang, Y. Q. Gao, Q. Cui, J. Ma, M. Karplus, Proc. Natl. Acad. Sci. USA, 100, 874-879 (2003) PDF version

44. Kinetic isotope effects for concerted multiple proton transfer: A direct dynamics study of an active site model of carbonic anhydrase II, Z. Smedarchina, W. Siebrand, A. Fernandez-Ramos, Q. Cui, J. Am. Chem. Soc. 125, 243-251 (2003) PDF version

2002

43. The functional specificities of Methylglyoxal Synthase (MGS) and Triosephosphate Isomerase (TIM) are not due to stereoelectronic effects: A combined QM/MM analysis, X. Zhang, D. H. T. Harrison, Q. Cui, J. Am. Chem. Soc. 124, 14871-14878 (2002) PDF version

42. Combining implicit solvent models with hybrid QM/MM methods - A critical test with glycine, Q. Cui, J. Chem. Phys. 117, 4720-4728 (2002) PDF version

41. A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca2+-ATPase, G. Li, Q. Cui, Biophys. J, 83, 2457-2474 (2002) PDF version

40. Calculating accurate redox potentials in enzymes with a combined QM/MM free energy perturbation approach, M. S. Formaneck, G. Li, X. Zhang, Q. Cui, J. Theo. Comput. Chem. (Invited article), 1, 53 (2002) PDF version