All Faculty and Research Staff Publications

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2008
Cui Q, Karplus M. Allostery and cooperativity revisited. Protein Science. 2008 ;17:1295-1307.
Phatak P, Ghosh N, Yu HB, Cui Q, Elstner M. Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin. Proceedings of the National Academy of Sciences of the United States of America. 2008 ;105:19672-19677.
Yang Y, Yu HB, York D, Elstner M, Cui Q. Description of Phosphate Hydrolysis Reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) Theory. 1. Parameterization. Journal of Chemical Theory and Computation. 2008 ;4:2067-2084.
Hoerter JM, Otte KM, Gellman SH, Cui Q, Stahl SS. Discovery and mechanistic study of Al-III-catalyzed transamidation of tertiary amides. Journal of the American Chemical Society. 2008 ;130:647-654.
Yoo J, Cui Q. Does arginine remain protonated in the lipid membrane? Insights from microscopic pK(a) calculations. Biophysical Journal. 2008 ;94:L61-L63.
Zhu X, Koenig P, Gellman SH, Yethiraj A, Cui Q. Establishing Effective Simulation Protocols for β- and α/β-Peptides. II. Molecular Mechanical (MM) Model for a Cyclic β-Residue. Journal of Physical Chemistry B. 2008 ;112:5439-5448.
Yang Y, Yu H, Cui Q. Extensive conformational transitions are required to turn on ATP hydrolysis in myosin. Journal of Molecular Biology. 2008 ;381:1407-1420.
Chen X, Cui Q, Tang Y, Yoo J, Yethiraj A. Gating mechanisms of mechanosensitive channels of large conductance, I: A continuum mechanics-based hierarchical framework. Biophysical Journal. 2008 ;95:563-580.
Tang Y, Yoo J, Yethiraj A, Cui Q, Chen X. Gating mechanisms of mechanosensitive channels of large conductance, II: Systematic study of conformational transitions. Biophysical Journal. 2008 ;95:581-596.
Tang YY, Yoo J, Yethiraj A, Cui Q, Chen X. Mechanosensitive channels: Insights from continuum-based simulations. Cell Biochemistry and Biophysics. 2008 ;52:1-18.
Ghosh N, Cui Q. pK(a) of residue 66 in Staphylococal nuclease. I. Insights from QM/MM simulations with conventional sampling. Journal of Physical Chemistry B. 2008 ;112:8387-8397.
Riccardi D, Koenig P, Guo H, Cui Q. Proton transfer in carbonic anhydrase is controlled by electrostatics rather than the orientation of the acceptor. Biochemistry. 2008 ;47:2369-2378.
2007
Ma L, Cui Q. Activation mechanism of a signaling protein at atomic resolution from advanced computations. Journal of the American Chemical Society. 2007 ;129:10261-10268.
Xu D, Guo H, Cui Q. Antibiotic binding to dizinc beta-lactamase L1 from Stenotrophomonas maltophilia: SCC-DFTB/CHARMM and DFT Studies. Journal of Physical Chemistry A. 2007 ;111:5630-5636.
Cai Z-L, Lopez P, Reimers JR, Cui Q, Elstner M. Application of the computationally efficient self-consistent-charge density-functional tight-binding method to magnesium-containing molecules. Journal of Physical Chemistry A. 2007 ;111:5743-5750.
Zhu X, Yethiraj A, Cui Q. Establishing effective simulation protocols for beta- and alpha/beta-mixed peptides. I. QM and QM/MM models. Journal of Chemical Theory and Computation. 2007 ;3:1538-1549.
Yang Y, Yu H, York D, Cui Q, Elstner M. Extension of the self-consistent-charge density-functional tight-binding method: Third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction. Journal of Physical Chemistry A. 2007 ;111:10861-10873.
Yang Y, Cui Q. Interactions between phosphate and water in solution: A natural bond orbital based analysis in a QM/MM framework. Journal of Physical Chemistry B. 2007 ;111:3999-4002.
Yu H, Ma L, Yang Y, Cui Q. Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations. Plos Computational Biology. 2007 ;3:199-213.
Yu H, Ma L, Yang Y, Cui Q. Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues. Plos Computational Biology. 2007 ;3:214-230.
Riccardi D, Cui Q. pK(a) analysis for the zinc-bound water in human carbonic anhydrase II: Benchmark for "Multiscale" QM/MM simulations and mechanistic implications. Journal of Physical Chemistry A. 2007 ;111:5703-5711.
Kondrashov DA, Van Wynsberghe AW, Bannen RM, Cui Q, Phillips, Jr. GN. Protein structural variation in computational models and crystallographic data. Structure. 2007 ;15:169-177.
Kondrashov DA, Van Wynsberghe AW, Bannen RM, Cui Q, Phillips, Jr. GN. Protein structural variation in computational models and crystallographic data (vol 15, pg 169, 2007). Structure. 2007 ;15:637-637.
Nam K, Cui Q, Gao J, York DM. Specific reaction parametrization of the AM1/d Hamiltonian for phosphoryl transfer reactions: H, O, and P atoms. Journal of Chemical Theory and Computation. 2007 ;3:486-504.
Kissounko DA, Hoerter JM, Guzei IA, Cui Q, Gellman SH, Stahl SS. Ti-IV-mediated reactions between primary amines and secondary carboxamides: Amidine formation versus transamidation. Journal of the American Chemical Society. 2007 ;129:1776-1783.
Yu H, Cui Q. The vibrational spectra of protonated water clusters: A benchmark for self-consistent-charge density-functional tight binding. Journal of Chemical Physics. 2007 ;127.
2006
Riccardi D, Schaefer P, Yang Y, Yu H, Ghosh N, Prat-Resina X, Koenig P, Li G, Xu D, Guo H, et al. Development of Effective Quantum Mechanical/Molecular Mechanical (QM/MM) Methods for Complex Biological Processes. Journal of Physical Chemistry B. 2006 ;110:6458-6469.
Formaneck MS, Ma L, Cui Q. Effects of temperature and salt concentration on the structural stability of human lymphotactin: Insights from molecular simulations. Journal of the American Chemical Society. 2006 ;128:9506.
Van Wynsberghe AW, Cui Q. Interpreting correlated motions using normal mode analysis. Structure. 2006 ;14:1647.
Li G, Van Wynsberghe A, Demerdash ONA, Cui Q. Normal mode analysis of macromolecules: from enzyme active sites to molecular machines. Normal Mode Analysis. 2006 :65-89, 4 plates.
Kondrashov DA, Cui Q, Phillips GN. Optimization and evaluation of a coarse-grained model of protein motion using X-ray crystal data. Biophysical Journal. 2006 ;91:2760-2767.
Riccardi D, Koenig P, Prat-Resina X, Yu H, Elstner M, Frauenheim T, Cui Q. "Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis. Journal of the American Chemical Society. 2006 ;128:16302-16311.
Cui Q, Thorgersen MP, Westler WM, Markley JL, Downs DM. Solution structure of YggX: A prokaryotic protein involved in Fe(II) trafficking. Proteins Structure Function & Bioinformatics. 2006 ;62:578-586.
Ma L, Cui Q. The temperature dependence of salt-protein association is sequence specific. Biochemistry. 2006 ;45:14466.
Cui Q. Theoretical analysis of mechanochemical coupling in the biomolecular motor myosin. Modelling Molecular Structure and Reactivity in Biological Systems. 2006 :66-75.
Cui Q. Theoretical and computational studies of vectorial processes in biomolecular systems. Theoretical Chemistry Accounts. 2006 ;116:51.
Konig PH, Ghosh N, Hoffmann M, Elstner M, Tajkhorshid E, Frauenheim T, Cui Q. Toward theoretical analyis of long-range proton transfer kinetics in biomolecular pumps [Review]. Journal of Physical Chemistry A. 2006 ;110:548-563.
Formaneck MS, Cui Q. 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). Journal of Computational Chemistry. 2006 ;27:1923.
2005
Range K, Riccardi D, Cui Q, Elstner M, York DM. Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer. Physical Chemistry Chemical Physics. 2005 ;7:3070-3079.
Van Wynsberghe AW, Cui Q. Comparison of mode analyses at different resolutions applied to nucleic acid systems. Biophysical Journal. 2005 ;89:2939-2949.
Konig PH, Hoffmann M, Frauenheim T, Cui Q. A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method [Review]. Journal of Physical Chemistry B. 2005 ;109:9082-9095.
Li GH, Cui Q. Direct determination of reaction paths and stationary points on potential of mean force surfaces. Journal of Molecular Graphics and Modelling. 2005 ;24:82-93.
Casey CP, Johnson JB, Singer SW, Cui Q. Hydrogen elimination from a hydroxycyclopentadienyl ruthenium(II) hydride: Study of hydrogen activation in a ligand-metal bifunctional hydrogenation catalyst. Journal of the American Chemical Society. 2005 ;127:3100-3109.
Guo H, Lipscomb WN, Cui Q, Karplus M. Molecular dynamics simulations of yeast chorismate mutase: substrate conformational transitions and enzymatic catalysis. NATO Sci. Ser., Ser. I. 2005 ;364:63-74.
Riccardi D, Schaefer P, Cui Q. pK(a) calculations in solution and proteins with QM/MM free energy perturbation simulations: A quantitative test of QM/MM protocols [Review]. Journal of Physical Chemistry B. 2005 ;109:17715-17733.
Casey CP, Bikzhanova GA, Cui Q, Guzei IA. Reduction of Imines by hydroxycyclopentadienyl ruthenium hydride: Intramolecular trapping evidence for hydride and proton transfer outside the coordination sphere of the metal. Journal of the American Chemical Society. 2005 ;127:14062-14071.
Schaefer P, Riccardi D, Cui Q. Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules - art. no. 014905. Journal of Chemical Physics. 2005 ;123:14905.

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