All Faculty and Research Staff Publications

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2016
Pham GH, Rana A, Korkmaz EN, Trang VH, Cui Q, Strieter ER. Comparison of native and non-native ubiquitin oligomers reveals analogous structures and reactivities. Protein Science. 2016 ;25:456-471.
Jin HY, Goyal P, Das AK, Gaus M, Meuwly M, Cui Q. Copper Oxidation/Reduction in Water and Protein: Studies with DFTB3/MM and VALBOND Molecular Dynamics Simulations. Journal of Physical Chemistry B. 2016 ;120:1894-1910.
Bai H, Xue RH, Bao H, Zhang LL, Yethiraj A, Cui Q, Chapman ER. Different states of synaptotagmin regulate evoked versus spontaneous release. Nature Communications. 2016 ;7.
Son CY, McDaniel JG, Schmidt JR, Cui Q, Yethiraj A. First-Principles United Atom Force Field for the Ionic Liquid BMIM+BF4-: An Alternative to Charge Scaling. Journal of Physical Chemistry B. 2016 ;120:3560-3568.
Zhu LL, Wu JZ, Liu L, Liu YL, Yan Y, Cui Q, Chen X. Gating mechanism of mechanosensitive channel of large conductance: a coupled continuum mechanical-continuum solvation approach. Biomechanics and Modeling in Mechanobiology. 2016 ;15:1557-1576.
Zhang LL, Rajendram M, Weibel DB, Yethiraj A, Cui Q. Ionic Hydrogen Bonds and Lipid Packing Defects Determine the Binding Orientation and Insertion Depth of RecA on Multicomponent Lipid Bilayers. Journal of Physical Chemistry B. 2016 ;120:8424-8437.
Cui Q. Perspective: Quantum mechanical methods in biochemistry and biophysics. Journal of Chemical Physics. 2016 ;145.
Zhao WL, Xu ZJ, Cui Q, Sahai N. Predicting the Structure-Activity Relationship of Hydroxyapatite-Binding Peptides by Enhanced-Sampling Molecular Simulation. Langmuir. 2016 ;32:7009-7022.
Roston D, Cui Q. QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes. In: Voth GA Vol. 577. San Diego: Elsevier Academic Press Inc; 2016. pp. 213-250.
Lu XY, Fang D, Ito S, Okamoto Y, Ovchinnikov V, Cui Q. QM/MM free energy simulations: recent progress and challenges. Molecular Simulation. 2016 ;42:1056-1078.
Christensen AS, Kubar T, Cui Q, Elstner M. Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications. Chemical Reviews. 2016 ;116:5301-5337.
Goldschen-Ohm MP, Klenchin VA, White DS, Cowgill JB, Cui Q, Goldsmith RH, Chanda B. Structure and dynamics underlying elementary ligand binding events in human pacemaking channels. eLife. 2016 ;5:e20797.
Roston D, Cui Q. Substrate and Transition State Binding in Alkaline Phosphatase Analyzed by Computation of Oxygen Isotope Effects. Journal of the American Chemical Society. 2016 ;138:11946-11957.
Cui Q, Hernandez R, Mason SE, Frauenheim T, Pedersen JA, Geiger F. Sustainable Nanotechnology: Opportunities and Challenges for Theoretical/Computational Studies. Journal of Physical Chemistry B. 2016 ;120:7297-7306.
Kromann JC, Christensen AS, Cui Q, Jensen JH. Towards a barrier height benchmark set for biologically relevant systems. Peerj. 2016 ;4.
2015
Rajendram M, Zhang LL, Reynolds BJ, Auer GK, Tuson HH, Ngo KV, Cox MM, Yethiraj A, Cui Q, Weibel DB. Anionic Phospholipids Stabilize RecA Filament Bundles in Escherichia coli. Molecular Cell. 2015 ;60:374-384.
Gaus M, Jin HY, Demapan D, Christensen AS, Goyal P, Elstner M, Cui Q. DFTB3 Parametrization for Copper: The Importance of Orbital Angular Momentum Dependence of Hubbard Parameters. Journal of Chemical Theory and Computation. 2015 ;11:4205-4219.
Zheng YQ, Cui Q. The histone H3 N-terminal tail: a computational analysis of the free energy landscape and kinetics. Physical Chemistry Chemical Physics. 2015 ;17:13689-13698.
Christensen AS, Elstner M, Cui Q. Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization. Journal of Chemical Physics. 2015 ;143.
Korkmaz EN, Volkman BF, Cui Q. Interplay of Electrostatics and Hydrophobic Effects in the Metamorphic Protein Human Lymphotactin. Journal of Physical Chemistry B. 2015 ;119:9547-9558.
Goyal P, Yang S, Cui Q. Microscopic basis for kinetic gating in cytochrome c oxidase: insights from QM/MM analysis. Chemical Science. 2015 ;6:826-841.
Xu ZJ, Yang Y, Zhao WL, Wang ZQ, Landis WJ, Cui Q, Sahai N. Molecular mechanisms for intrafibrillar collagen mineralization in skeletal tissues. Biomaterials. 2015 ;39:59-66.
Ngo V, da Silva MC, Kubillus M, Li H, Roux B, Elstner M, Cui Q, Salahub DR, Noskov SY. Quantum Effects in Cation Interactions with First and Second Coordination Shell Ligands in Metalloproteins. Journal of Chemical Theory and Computation. 2015 ;11:4992-5001.
Taylor KC, Buvoli M, Korkmaz EN, Buvoli A, Zheng YQ, Heinze NT, Cui Q, Leinwand LA, Rayment I. Skip residues modulate the structural properties of the myosin rod and guide thick filament assembly. Proceedings of the National Academy of Sciences of the United States of America. 2015 ;112:E3806-E3815.
Hu LL, Lu JY, Cheng JD, Rao QH, Li Z, Hou HF, Lou ZY, Zhang L, Li W, Gong W, et al. Structural insight into substrate preference for TET- mediated oxidation. Nature. 2015 ;527:118-122.
2014
Gaus M, Cui Q, Elstner M. Density functional tight binding: application to organic and biological molecules. Wiley Interdisciplinary Reviews-Computational Molecular Science. 2014 ;4:49-61.
Cui Q, Elstner M. Density functional tight binding: values of semi-empirical methods in an ab initio era. Physical Chemistry Chemical Physics. 2014 ;16:14368-14377.
Zhang LL, Yethiraj A, Cui Q. Free Energy Calculations for the Peripheral Binding of Proteins/Peptides to an Anionic Membrane. 1. Implicit Membrane Models. Journal of Chemical Theory and Computation. 2014 ;10:2845-2859.
Jia CX, Wu Z, Lietz CB, Liang ZD, Cui Q, Li LJ. Gas-Phase Ion Isomer Analysis Reveals the Mechanism of Peptide Sequence Scrambling. Analytical Chemistry. 2014 ;86:2917-2924.
Wolf S, Freier E, Cui Q, Gerwert K. Infrared spectral marker bands characterizing a transient water wire inside a hydrophobic membrane protein. Journal of Chemical Physics. 2014 ;141.
Mori T, Hamers RJ, Pedersen JA, Cui Q. Integrated Hamiltonian Sampling: A Simple and Versatile Method for Free Energy Simulations and Conformational Sampling. Journal of Physical Chemistry B. 2014 ;118:8210-8220.
Cui Q, Nussinov R. Making Biomolecular Simulations Accessible in the Post-Nobel Prize Era. Plos Computational Biology. 2014 ;10.
Qian HJ, Irle S, Lu XY, Roston D, Mori T, Elstner M, Cui Q. Molecular Simulation of Water and Hydration Effects in Different Environments: Challenges and Developments for DFTB Based Models AU Goyal, P Qian, HJ Irle, S Lu, XY Roston, D Mori, T Elstner, M Cui, Q. Journal of Physical Chemistry B. 2014 ;118:11007-11027.
Gaus M, Lu XY, Elstner M, Cui Q. Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications. Journal of Chemical Theory and Computation. 2014 ;10:1518-1537.
Xu DG, Cui Q, Guo H. Quantum mechanical/molecular mechanical studies of zinc hydrolases. International Reviews in Physical Chemistry. 2014 ;33:1-41.
Xu ZJ, Yang Y, Wang ZQ, Mkhonto D, Shang C, Liu ZP, Cui Q, Sahai N. Small Molecule-Mediated Control of Hydroxyapatite Growth: Free Energy Calculations Benchmarked to Density Functional Theory. Journal of Computational Chemistry. 2014 ;35:70-81.
Shen QT, Schuh AL, Zheng YQ, Quinney K, Wang L, Hanna M, Mitchell JC, Otegui MS, Ahlquist P, Cui Q, et al. Structural analysis and modeling reveals new mechanisms governing ESCRT-III spiral filament assembly. Journal of Cell Biology. 2014 ;206:763-777.
Odoh SO, Bondarevsky GD, Karpus J, Cui Q, He C, Spezia R, Gagliardi L. UO22+ Uptake by Proteins: Understanding the Binding Features of the Super Uranyl Binding Protein and Design of a Protein with Higher Affinity. Journal of the American Chemical Society. 2014 ;136:17484-17494.
2013
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.

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