Published 2009-2012

154. Detailed structure of the H₂PO₄^–-GDP intermediate in Ras-GAP decoded from FTIR experiments by biomolecular simulations, F. Xia, T. Rudack, Q. Cui, C. Kotting and K. Gerwert, J. Am. Chem. Soc. 134, 20041-20044 (2012)

153. Implementation of the Solvent Macromolecule Boundary Potential and Application to Model and Realistic Enzyme Systems, J. Zienau and Q. Cui*, J. Phys. Chem. B 116, 12522-12534 (2012)

152. A modified QM/MM Hamiltonian with the Self-Consistent-Charge Density-Functional-Tight-Binding Theory for highly charged QM regions, G. Hou, X. Zhu, M. Elstner and Q. Cui*, J. Chem. Theo. Comp. 8, 4293-4304 (2012)

151. Identification of the Ah-receptor structural determinants for ligand preferences, Y. N. Xing*, M. Nukaya, K. Satyshur, L. Jiang, V. Stanevich, E. N. Korkmaz, L. Burdette, G. Kennedy, Q. Cui, C. A. Bradfield, Toxicol. Sci., 129, 86-97 (2012)

150. Large-scale motions in the adenylate kinase solution ensemble: coarse-grained simulations and comparison with solution X-ray scattering, M. Daily, L. Makowski, G. N. Phillips, Jr. and Q. Cui*, Special Issue on ”Functional dynamics of proteins”, Chem. Phys. 396, 84-91 (2012)

149. Protein Functional Dynamics: From Femtoseconds to Milliseconds, M. Meuwly and Q. Cui, Editorial, Special Issue on ”Functional dynamics of proteins”, Chem. Phys., 396, 1-2 (2012)

148. Catalysis induced by molecular self-assembly: insights from computer simulation, J. Mondal, X. Zhu, Q. Cui and A. Yethiraj*, J. Phys. Chem. B 116, 491-495 (2012)

147. QM/MM analysis suggests that Alkaline Phosphatase (AP) and Nucleotide pyrophosphatase phosphodiesterase slightly tighten the transition state for phosphate diester hydrolysis relative to solution: implication for catalytic promiscuity in the AP superfamily, G. Hou and Q. Cui*, J. Am. Chem. Soc. 134, 229-246 (2012)

146. Toward molecular models of proton pumping: challenges, methods and relevant applications, D. Riccardi, X. Zhu, P. Goyal, S. Yang, G. Hou and Q. Cui*, Invited Review, Special Issue of Science China, Chemistry, 55, 3-18 (2012)

145. The driving force for the association of hydrophobic peptides: The importance of electrostatic interactions in coarse-grained water models, Z. Wu, Q. Cui* and A. Yethiraj*, J. Phys. Chem. Lett. 2, 1794-1798 (2011)

144. A new coarse-grained force field for membrane-peptide simulations, Z. Wu, Q. Cui* and A. Yethiraj*, J. Chem. Theo. Comp. 11, 3793-3802 (2011)

143. Permeation of styryl dyes through nm-scale pores in membranes, Y. Wu, L. Ma, S. Cheley, H. P. Bayley, Q. Cui and E. Chapman*, Biochem. 50, 7493-7502 (2011)

142. Interconversion of Functional Motions between Mesophilic and Thermophilic Adenylate Kinases, M. Daily, G. N. Phillips, Jr., Q. Cui*, PLos Comp. Biol. 7, e1002103 (2011)

141. Glu286 rotation and water wire reorientation are unlikely the gating elements for proton pumping in Cytochrome c oxidase, S. Yang and Q. Cui*, Biophys. J., 101, 61-69 (2011)

140. Proton storage site in bacteriorhodopsin: new insights from QM/MM simulations of microscopic pK_a and infrared spectra, P. Goyal, N. Ghosh, P. Phatak, M. Clemens, M. Gauss, M. Elstner* and Q. Cui*, J. Am. Chem. Soc. 133, 14981-14997 (2011)

139. Application of the SCC-DFTB method to neutral and protonated water clusters and bulk water, P. Goyal, M. Elstner and Q. Cui*, J. Phys. Chem. B 115, 6790-6805 (2011)

138. Role of Arg82 in the early steps of the bacteriorhodopsin proton-pumping cycle, M. Clemens, P. Phatak, Q. Cui, A. N. Bondar, M. Elstner*, J. Phys. Chem. B 115, 7129-7135 (2011)

137. DFTB-3^rd: Extension of the self-consistent-charge density-functional tight-binding method SCC-DFTB, M. Gaus, Q. Cui and M. Elstner*, J. Chem. Theo. Comp., 7, 931-948 (2011)

136. Theoretical Study of Bone Sialoprotein in Bone Biomineralization, Y. Yang, Q. Cui and N. Sahai, Cells, Tissues, Organs, 194, 182-187 (2011)

135. Disruption and formation of surface salt bridges are coupled to DNA binding in integration host factor: a computational analysis, L. Ma, N. Sundlass, R. T. Raines and Q. Cui*, Biochem., 50, 266-275 (2011)

134. Computational Studies of Enzyme Motions, Q. Cui*, Encyclopedia of Biophysics, Springer Invited Review (2010)

133. Chemical vs. mechanical perturbations on the protonation state of Arginine in complex lipid membranes: insights from microscopic pKa calculations, J. Yoo and Q. Cui*, Biophys. J. 99, 1529-1538 (2010)

132. Metal binding selectivity of CueR metalloregulatory protein: A theoretical analysis, L. Rao, Q. Cui* and X. Xu*, J. Am. Chem. Soc. 132, 18092-18102 (2010)

131. Self-assembly of beta-peptides: insight from the pair and many-body free energy of association, J. Mondal, X. Zhu, Q. Cui and A. Yethiraj*, J. Phys. Chem. C, 114, 13551-13556 (2010)

130. Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Monooxygenase, C. Yi, G. Jia, G. Hou, Q. Dai, G. Zheng, X. Jian, C. G. Yang, Q. Cui, and C. He*, Nature, 468, 330-333 (2010)

129. An implicit solvent model for SCC-DFTB with Charge-Dependent Radii, G. Hou, X. Zhu and Q. Cui*, J. Chem. Theo. Comp., 6, 2303-2314 (2010)

128. Elastic Network Models of Proteins in Crystals, D. Riccardi*, Q. Cui and G. N. Phillips, Jr.* Biophys. J., 99, 2616-2625 (2010)

127. Sequence-dependent interaction of beta-peptides with membranes, J. Mondal, X. Zhu, Q. Cui and A. Yethiraj*, J. Phys. Chem. B, 14, 13585-13592 (2010)

126. QM/MM Alchemical free energy simulations: Challenges and Recent Developments, W. Yang*, Q. Cui, D. Min and H. Li, Annual Reports in Comput. Chem.6, 51-62 Invited Review (2010)

125. A new coarse-grained model for water: The importance of electrostatic interactions, Z. Wu, Q. Cui* and A. Yethiraj*, J. Phys. Chem. B 114, 10524-10529 (2010)

124. How does bone sialoprotein promote the nucleation of hydroxyapatite? A molecular dynamics study using model peptides of different conformations, Y. Yang, Q. Cui, and N. Sahai*, Langmuir, 26, 9848-9859 (2010)

123. Many low-barrier local motions cooperate to produce the adenylate kinase conformational transition, M. Daily, G. N. Phillips, Jr. and Q. Cui*, J. Mol. Biol., 400, 618-631 (2010)

122. Conservation and Variation of Structural Flexibility in Protein Families, A. W. Van Wynsberghe*, Q. Cui*, Structure, 18, 281-283 (2010) Invited Commentary

121. Preferential interactions between small solutes and the protein backbone: A computational analysis, L. Ma, L. Pegram, M. T. Record, Jr., Q. Cui*, Biochem., 49, 1954-1962 (2010)

120. Establishing effective simulation protocols for beta- and alpha/beta-peptides. III. Molecular Mechanical (MM) model for a non-cyclic beta-residue, X. Zhu, P. Koenig, M. Hoffman, A. Yethiraj* and Q. Cui*, J. Comp. Chem., 31, 2063-2077 (2010)

119. Proton Transfer Function of Carbonic Anhydrase: Insights from QM/MM simulations, D. Riccardi, S. Yang and Q. Cui*, BBA-Prot. & Proteomics, Invited special issue on “Carbonic Anhydrase and Superoxide Dismutase”, 1804, 342-351 (2010)

118. Curvature Generation and Pressure Profile in Membrane with lysolipids: Insights from coarse-grained simulations, J. Yoo and Q. Cui, Biophys. J. 97, 2267-2276 (2009)

117. The hydrolysis activity of Adenosine triphosphate in myosin: a theoretical analysis of anomeric effects and the nature of transition state, Y. Yang and Q. Cui, J. Phys. Chem. A (R. M. Pitzer Festschrift), 113, 12439-12446 (2009)

116. CHARMM: The biomolecular simulation program, B. R. Brooks, et al., Q. Cui, et al., M. Karplus, J. Comp. Chem. 30, 1545-1614 (2009)

115. Multi-scale methods for the description of chemical events in biological systems, M. Elstner and Q. Cui, in NIC (John von Neumann Institut fur Computing) series. In press (2009) Invited Book Chapter

114. Does water relayed proton transfer play a role in phosphoryl transfer reactions? A theoretical analysis of uridine 3′-m-nitrobenzyl phosphate isomerization in water and tert-butanol, Y. Yang and Q. Cui, J. Phys. Chem. B 113, 4930-4939 (2009)

113. Microscopic pKa analysis of Glu 286 in Cytochrome c Oxidase ( Rhodobacter sphaeroids): towards a consistent molecular model, N. Ghosh, X. Prat-Resina, M. Gunner and Q. Cui*, Biochem. 48, 2468-2485 (2009)

112. A computational framework for mechanical response of macromolecules: application to the salt concentration dependence of DNA bendability, L. Ma, A. Yethiraj, X. Chen* and Q. Cui*, Biophys. J. 96, 3543-3554 (2009)

111. Application of elastic network models to proteins in the crystalline state, D. Riccardi, Q. Cui and G. Phillips, Jr.* Biophys. J. 96, 464-475 (2009)

110. Mechanochemical coupling in molecular motors: insights from molecular simulations of the myosin motor domain, H. Yu, Y. Yang, L. Ma and Q. Cui*, Book Chapter in Energy Flows in Proteins, Eds. D. Leitner and J. E. Straub, CRC Press In press (2009) Invited Book Chapter