All Faculty and Research Staff Publications

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Yoo J, Cui Q. Chemical versus Mechanical Perturbations on the Protonation State of Arginine in Complex Lipid Membranes: Insights from Microscopic pK(a) Calculations. Biophysical Journal. 2010 ;99:1529-1538.
Van Wynsberghe AW, Cui Q. Conservation and Variation of Structural Flexibility in Protein Families. Structure. 2010 ;18:281-283.
Rao L, Cui Q, Xu X. Electronic Properties and Desolvation Penalties of Metal Ions Plus Protein Electrostatics Dictate the Metal Binding Affinity and Selectivity in the Copper Efflux Regulator. Journal of the American Chemical Society. 2010 ;132:18092-18102.
Zhu X, Koenig P, Hoffmann M, Yethiraj A, Cui Q. Establishing Effective Simulation Protocols for beta- and alpha/beta-Peptides. III. Molecular Mechanical Model for Acyclic beta-Amino Acids. Journal of Computational Chemistry. 2010 ;31:2063-2077.
Riccardi D, Cui Q, Phillips, Jr. GN. Evaluating Elastic Network Models of Crystalline Biological Molecules with Temperature Factors, Correlated Motions, and Diffuse X-Ray Scattering. Biophysical Journal. 2010 ;99:2616-2625.
Hou GH, Zhu XA, Cui Q. An Implicit Solvent Model for SCC-DFTB with Charge-Dependent Radii. Journal of Chemical Theory and Computation. 2010 ;6:2303-2314.
Yi CQ, Jia GF, Hou GH, Dai Q, Zhang W, Zheng GQ, Jian X, Yang CG, Cui Q, He CA. Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase. Nature. 2010 ;468:330-U223.
Daily MD, Phillips GN, Cui Q. Many Local Motions Cooperate to Produce the Adenylate Kinase Conformational Transition. Journal of Molecular Biology. 2010 ;400:618-631.
Wu Z, Cui Q, Yethiraj A. A New Coarse-Grained Model for Water: The Importance of Electrostatic Interactions. Journal of Physical Chemistry B. 2010 ;114:10524-10529.
Ma L, Pegram L, Record MT, Cui Q. Preferential Interactions between Small Solutes and the Protein Backbone: A Computational Analysis. Biochemistry. 2010 ;49:1954-1962.
Riccardi D, Yang S, Cui Q. Proton transfer function of carbonic anhydrase: Insights from QM/MM simulations. Biochimica Et Biophysica Acta-Proteins and Proteomics. 2010 ;1804:342-351.
Mondal J, Zhu X, Cui Q, Yethiraj A. Self-Assembly of beta-Peptides: Insight from the Pair and Many-Body Free Energy of Association. Journal of Physical Chemistry C. 2010 ;114:13551-13556.
Mondal J, Zhu X, Cui Q, Yethiraj A. Sequence-Dependent Interaction of beta-Peptides with Membranes. Journal of Physical Chemistry B. 2010 ;114:13585-13592.
Goyal P, Elstner M, Cui Q. Application of the SCC-DFTB Method to Neutral and Protonated Water Clusters and Bulk Water. Journal of Physical Chemistry B. 2011 ;115:6790-6805.
Gaus M, Cui Q, Elstner M. DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB). Journal of Chemical Theory and Computation. 2011 ;7:931-948.
Ma L, Sundlass NK, Raines RT, Cui Q. Disruption and Formation of Surface Salt Bridges Are Coupled to DNA Binding by the Integration Host Factor: A Computational Analysis. Biochemistry. 2011 ;50:266-275.
Wu Z, Cui Q, Yethiraj A. Driving Force for the Association of Hydrophobic Peptides: The Importance of Electrostatic Interactions in Coarse-Grained Water Models. Journal of Physical Chemistry Letters. 2011 ;2:1794-1798.
Yang S, Cui Q. Glu-286 Rotation and Water Wire Reorientation Are Unlikely the Gating Elements for Proton Pumping in Cytochrome c Oxidase. Biophysical Journal. 2011 ;101:61-69.
Daily MD, Phillips, Jr. GN, Cui Q. Interconversion of Functional Motions between Mesophilic and Thermophilic Adenylate Kinases. Plos Computational Biology. 2011 ;7.
Wu Z, Cui Q, Yethiraj A. A New Coarse-Grained Force Field for Membrane-Peptide Simulations. Journal of Chemical Theory and Computation. 2011 ;7:3793-3802.
Wu Y, Ma L, Cheley S, Bayley H, Cui Q, Chapman ER. Permeation of Styryl Dyes through Nanometer-Scale Pores in Membranes. Biochemistry. 2011 ;50:7493-7502.
Goyal P, Ghosh N, Phatak P, Clemens M, Gaus M, Elstner M, Cui Q. Proton Storage Site in Bacteriorhodopsin: New Insights from Quantum Mechanics/Molecular Mechanics Simulations of Microscopic pK(a) and Infrared Spectra. Journal of the American Chemical Society. 2011 ;133:14981-14997.
Clemens M, Phatak P, Cui Q, Bondar A-N, Elstner M. Role of Arg82 in the Early Steps of the Bacteriorhodopsin Proton-Pumping Cycle. Journal of Physical Chemistry B. 2011 ;115:7129-7135.
Xia F, Rudack T, Cui Q, Kotting C, Gerwert K. Detailed Structure of the H2PO4--Guanosine Diphosphate Intermediate in Ras-GAP Decoded from FTIR Experiments by Biomolecular Simulations. Journal of the American Chemical Society. 2012 ;134:20041-20044.
Xing YN, Nukaya M, Satyshur KA, Jiang L, Stanevich V, Korkmaz EN, Burdette L, Kennedy GD, Cui Q, Bradfield CA. Identification of the Ah-Receptor Structural Determinants for Ligand Preferences. Toxicological Sciences. 2012 ;129:86-97.
Zienau J, Cui Q. Implementation of the Solvent Macromolecule Boundary Potential and Application to Model and Realistic Enzyme Systems. Journal of Physical Chemistry B. 2012 ;116:12522-12534.
Daily MD, Makowski L, Phillips GN, Cui Q. Large-scale motions in the adenylate kinase solution ensemble: Coarse-grained simulations and comparison with solution X-ray scattering. Chemical Physics. 2012 ;396:84-91.
Hou GH, Zhu X, Elstner M, Cui Q. A Modified QM/MM Hamiltonian with the Self-Consistent-Charge Density-Functional-Tight-Binding Theory for Highly Charged QM Regions. Journal of Chemical Theory and Computation. 2012 ;8:4293-4304.
Meuwly M, Cui Q. Protein functional dynamics: From femtoseconds to milliseconds Preface. Chemical Physics. 2012 ;396:1-2.
Mondal J, Zhu X, Cui Q, Yethiraj A. Sequence-Dependent pK(a) Shift Induced by Molecular Self-Assembly: Insights from Computer Simulation. Journal of Physical Chemistry B. 2012 ;116:491-495.
Riccardi D, Zhu X, Goyal P, Yang S, Hou GH, Cui Q. Toward molecular models of proton pumping: Challenges, methods and relevant applications. Science China-Chemistry. 2012 ;55:3-18.
Daily MD, Yu HB, Phillips GN, Cui Q. Allosteric Activation Transitions in Enzymes and Biomolecular Motors: Insights from Atomistic and Coarse-Grained Simulations. In: Klinman J, Hammes-Schiffer S Vol. 337. Berlin: Springer-Verlag Berlin; 2013. pp. 139-164.
Goyal P, Lu JX, Yang S, Gunner MR, Cui Q. Changing hydration level in an internal cavity modulates the proton affinity of a key glutamate in cytochrome c oxidase. Proceedings of the National Academy of Sciences of the United States of America. 2013 ;110:18886-18891.
Lu XY, Cui Q. Charging Free Energy Calculations Using the Generalized Solvent Boundary Potential (GSBP) and Periodic Boundary Condition: A Comparative Analysis Using Ion Solvation and Oxidation Free Energy in Proteins. Journal of Physical Chemistry B. 2013 ;117:2005-2018.
Yoo J, Jackson MB, Cui Q. A Comparison of Coarse-Grained and Continuum Models for Membrane Bending in Lipid Bilayer Fusion Pores. Biophysical Journal. 2013 ;104:841-852.
Ruther RE, Cui Q, Hamers RJ. Conformational Disorder Enhances Electron Transfer Through Alkyl Monolayers: Ferrocene on Conductive Diamond. Journal of the American Chemical Society. 2013 ;135:5751-5761.
Sundlass NK, Eller CH, Cui Q, Raines RT. Contribution of Electrostatics to the Binding of Pancreatic-Type Ribonucleases to Membranes. Biochemistry. 2013 ;52:6304-6312.
Mori T, Hamers RJ, Pedersen JA, Cui Q. An Explicit Consideration of Desolvation is Critical to Binding Free Energy Calculations of Charged Molecules at Ionic Surfaces. Journal of Chemical Theory and Computation. 2013 ;9:5059-5069.
Fu Y, Jia GF, Pang XQ, Wang RN, Wang X, Li CJ, Smemo S, Dai Q, Bailey KA, Nobrega MA, et al. FTO-mediated formation of N-6-hydroxymethyladenosine and N-6-formyladenosine in mammalian RNA. Nature Communications. 2013 ;4.
Cui Q, Zhang LL, Wu Z, Yethiraj A. Generation and sensing of membrane curvature: Where materials science and biophysics meet. Current Opinion in Solid State & Materials Science. 2013 ;17:164-174.
Yoo J, Cui Q. Membrane-Mediated Protein-Protein Interactions and Connection to Elastic Models: A Coarse-Grained Simulation Analysis of Gramicidin A Association. Biophysical Journal. 2013 ;104:128-138.
Pang XQ, Han KL, Cui Q. A simple but effective modeling strategy for structural properties of non-heme Fe(II) sites in proteins: Test of force field models and application to proteins in the AlkB family. Journal of Computational Chemistry. 2013 ;34:1620-1635.
Hou GH, Cui Q. Stabilization of Different Types of Transition States in a Single Enzyme Active Site: QM/MM Analysis of Enzymes in the Alkaline Phosphatase Superfamily. Journal of the American Chemical Society. 2013 ;135:10457-10469.
Jarecki BW, Zheng SQ, Zhang LL, Li XX, Zhou X, Cui Q, Tang WP, Chanda B. Tethered Spectroscopic Probes Estimate Dynamic Distances with Subnanometer Resolution in Voltage-Dependent Potassium Channels. Biophysical Journal. 2013 ;105:2724-2732.
Yoo J, Cui Q. Three-Dimensional Stress Field around a Membrane Protein: Atomistic and Coarse-Grained Simulation Analysis of Gramicidin A. Biophysical Journal. 2013 ;104:117-127.
Wu Z, Cui Q, Yethiraj A. Why Do Arginine and Lysine Organize Lipids Differently? Insights from Coarse-Grained and Atomistic Simulations. Journal of Physical Chemistry B. 2013 ;117:12145-12156.