{"id":158,"date":"2018-02-06T14:36:40","date_gmt":"2018-02-06T19:36:40","guid":{"rendered":"https:\/\/sites.bu.edu\/cui-group\/?page_id=158"},"modified":"2018-07-05T14:45:06","modified_gmt":"2018-07-05T18:45:06","slug":"past","status":"publish","type":"page","link":"https:\/\/sites.bu.edu\/cui-group\/papers\/past\/","title":{"rendered":"Published 2009-2012"},"content":{"rendered":"

<\/a>154. Detailed structure of the H2<\/sub>PO4<\/sub>–<\/sup>-GDP intermediate in Ras-GAP decoded from FTIR experiments by biomolecular simulations, F. Xia, T. Rudack, Q. Cui, C. Kotting and K. Gerwert,\u00a0<\/span>J. Am. Chem. Soc.<\/i>\u00a0<\/span>134, 20041-20044 (2012)<\/p>\n

<\/a><\/a>153. Implementation of the Solvent Macromolecule Boundary Potential and Application to Model and Realistic Enzyme Systems, J. Zienau and Q. Cui*,\u00a0<\/span>J. Phys. Chem. B\u00a0<\/span><\/i>116, 12522-12534 (2012)<\/p>\n

<\/a><\/a>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*,\u00a0<\/span>J. Chem. Theo. Comp.<\/i>\u00a0<\/span>8, 4293-4304 (2012)<\/p>\n

<\/a><\/a>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,\u00a0<\/span>Toxicol. Sci.<\/i>, 129, 86-97 (2012)<\/p>\n

<\/a><\/a>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*,\u00a0<\/span>Special Issue on ”Functional dynamics of proteins”, Chem. Phys.<\/i>\u00a0<\/span>396, 84-91 (2012)<\/p>\n

<\/a><\/a>149. Protein Functional Dynamics: From Femtoseconds to Milliseconds, M. Meuwly and Q. Cui, Editorial,\u00a0<\/span>Special Issue on ”Functional dynamics of proteins”, Chem. Phys.<\/i>, 396, 1-2 (2012)<\/p>\n

<\/a><\/a>148. Catalysis induced by molecular self-assembly: insights from computer simulation, J. Mondal, X. Zhu, Q. Cui and A. Yethiraj*,\u00a0<\/span>J. Phys. Chem. B\u00a0<\/span><\/i>116, 491-495 (2012)<\/p>\n

<\/a><\/a>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*,\u00a0<\/span>J. Am. Chem. Soc.\u00a0<\/span><\/i>134, 229-246 (2012)<\/p>\n

<\/a><\/a>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*,\u00a0<\/span>Invited Review, Special Issue of Science China, Chemistry<\/i>, 55, 3-18 (2012)<\/p>\n

<\/a><\/a>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*,\u00a0<\/span>J. Phys. Chem. Lett.\u00a0<\/span><\/i>2, 1794-1798 (2011)<\/p>\n

<\/a><\/a>144. A new coarse-grained force field for membrane-peptide simulations, Z. Wu, Q. Cui* and A. Yethiraj*,\u00a0<\/span>J. Chem. Theo. Comp.\u00a0<\/span><\/i>11, 3793-3802 (2011)<\/p>\n

<\/a><\/a>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*,\u00a0<\/span>Biochem.<\/i>\u00a0<\/span>50, 7493-7502 (2011)<\/p>\n

<\/a><\/a>142. Interconversion of Functional Motions between Mesophilic and Thermophilic Adenylate Kinases, M. Daily, G. N. Phillips, Jr., Q. Cui*,\u00a0<\/span>PLos Comp. Biol.<\/i>\u00a0<\/span>7, e1002103 (2011)<\/p>\n

<\/a><\/a>141. Glu286 rotation and water wire reorientation are unlikely the gating elements for proton pumping in Cytochrome c oxidase, S. Yang and Q. Cui*,\u00a0<\/span>Biophys. J.<\/i>, 101, 61-69 (2011)<\/p>\n

<\/a><\/a>140. Proton storage site in bacteriorhodopsin: new insights from QM\/MM simulations of microscopic pKa<\/sub>\u00a0<\/span>and infrared spectra, P. Goyal, N. Ghosh, P. Phatak, M. Clemens, M. Gauss, M. Elstner* and Q. Cui*,\u00a0<\/span>J. Am. Chem. Soc.<\/i>\u00a0<\/span>133, 14981-14997 (2011)<\/p>\n

<\/a>139. Application of the SCC-DFTB method to neutral and protonated water clusters and bulk water, P. Goyal, M. Elstner and Q. Cui*,\u00a0<\/span>J. Phys. Chem. B\u00a0<\/span><\/i>115, 6790-6805 (2011)<\/p>\n

<\/a>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*,\u00a0<\/span>J. Phys. Chem. B<\/i>\u00a0<\/span>115, 7129-7135 (2011)<\/p>\n

<\/a>137. DFTB-3rd<\/sup>: Extension of the self-consistent-charge density-functional tight-binding method SCC-DFTB, M. Gaus, Q. Cui and M. Elstner*,\u00a0<\/span>J. Chem. Theo. Comp.<\/i>, 7, 931-948 (2011)<\/p>\n

<\/a><\/a>136. Theoretical Study of Bone Sialoprotein in Bone Biomineralization, Y. Yang, Q. Cui and N. Sahai,\u00a0<\/span>Cells, Tissues, Organs<\/i>, 194, 182-187 (2011)<\/p>\n

<\/a>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*,\u00a0<\/span>Biochem.<\/i>, 50, 266-275 (2011)<\/p>\n

<\/a>134. Computational Studies of Enzyme Motions, Q. Cui*,\u00a0<\/span>Encyclopedia of Biophysics<\/i>, Springer\u00a0<\/span>Invited Review<\/b>\u00a0<\/span>(2010)<\/p>\n

<\/a>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*,\u00a0<\/span>Biophys. J.<\/i>\u00a0<\/span>99, 1529-1538 (2010)<\/p>\n

<\/a>132. Metal binding selectivity of CueR metalloregulatory protein: A theoretical analysis, L. Rao, Q. Cui* and X. Xu*,\u00a0<\/span>J. Am. Chem. Soc.\u00a0<\/span><\/i>132, 18092-18102 (2010)<\/p>\n

<\/a>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*,\u00a0<\/span>J. Phys. Chem. C<\/i>, 114, 13551-13556 (2010)<\/p>\n

<\/a>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*,\u00a0<\/span>Nature<\/i>, 468, 330-333 (2010)<\/p>\n

<\/a>129. An implicit solvent model for SCC-DFTB with Charge-Dependent Radii, G. Hou, X. Zhu and Q. Cui*,\u00a0<\/span>J. Chem. Theo. Comp.<\/i>, 6, 2303-2314 (2010)<\/p>\n

<\/a>128. Elastic Network Models of Proteins in Crystals, D. Riccardi*, Q. Cui and G. N. Phillips, Jr.*\u00a0<\/span>Biophys. J.<\/i>, 99, 2616-2625 (2010)<\/p>\n

<\/a>127. Sequence-dependent interaction of beta-peptides with membranes, J. Mondal, X. Zhu, Q. Cui and A. Yethiraj*,\u00a0<\/span>J. Phys. Chem. B<\/i>, 14, 13585-13592 (2010)<\/p>\n

<\/a>126. QM\/MM Alchemical free energy simulations: Challenges and Recent Developments, W. Yang*, Q. Cui, D. Min and H. Li,\u00a0<\/span>Annual Reports in Comput. Chem.<\/i>6, 51-62\u00a0<\/span>Invited Review<\/b>\u00a0<\/span>(2010)<\/p>\n

<\/a>125. A new coarse-grained model for water: The importance of electrostatic interactions, Z. Wu, Q. Cui* and A. Yethiraj*,\u00a0<\/span>J. Phys. Chem. B<\/i>\u00a0<\/span>114, 10524-10529 (2010)<\/p>\n

<\/a>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*,\u00a0<\/span>Langmuir<\/i>, 26, 9848-9859 (2010)<\/p>\n

<\/a>123. Many low-barrier local motions cooperate to produce the adenylate kinase conformational transition, M. Daily, G. N. Phillips, Jr. and Q. Cui*,\u00a0<\/span>J. Mol. Biol.<\/i>, 400, 618-631 (2010)<\/p>\n

<\/a>122. Conservation and Variation of Structural Flexibility in Protein Families, A. W. Van Wynsberghe*, Q. Cui*,\u00a0<\/span>Structure<\/i>, 18, 281-283 (2010)\u00a0<\/span>Invited Commentary<\/b><\/p>\n

<\/a>121. Preferential interactions between small solutes and the protein backbone: A computational analysis, L. Ma, L. Pegram, M. T. Record, Jr., Q. Cui*,\u00a0<\/span>Biochem.<\/i>, 49, 1954-1962 (2010)<\/p>\n

<\/a>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*,\u00a0<\/span>J. Comp. Chem.<\/i>, 31, 2063-2077 (2010)<\/p>\n

<\/a>119. Proton Transfer Function of Carbonic Anhydrase: Insights from QM\/MM simulations, D. Riccardi, S. Yang and Q. Cui*,\u00a0<\/span>BBA-Prot. & Proteomics, Invited special issue on “Carbonic Anhydrase and Superoxide Dismutase”<\/i>, 1804, 342-351 (2010)<\/p>\n

<\/a><\/a>118. Curvature Generation and Pressure Profile in Membrane with lysolipids: Insights from coarse-grained simulations, J. Yoo and Q. Cui,\u00a0<\/span>Biophys. J.\u00a0<\/span><\/i>97, 2267-2276 (2009)<\/p>\n

<\/a>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,\u00a0<\/span>J. Phys. Chem. A (R. M. Pitzer Festschrift)<\/i>, 113, 12439-12446 (2009)<\/p>\n

<\/a>116. CHARMM: The biomolecular simulation program, B. R. Brooks, et al., Q. Cui, et al., M. Karplus,\u00a0<\/span>J. Comp. Chem.\u00a0<\/span><\/i>30, 1545-1614 (2009)<\/p>\n

<\/a>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.\u00a0<\/span>In press<\/i>\u00a0<\/span>(2009)\u00a0<\/span>Invited Book Chapter<\/b><\/p>\n

<\/a>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\u00a0<\/span>tert<\/i>-butanol, Y. Yang and Q. Cui,\u00a0<\/span>J. Phys. Chem. B\u00a0<\/span><\/i>113, 4930-4939 (2009)<\/p>\n

<\/a>113. Microscopic pKa analysis of Glu 286 in Cytochrome c Oxidase (\u00a0<\/span>Rhodobacter sphaeroids<\/i>): towards a consistent molecular model, N. Ghosh, X. Prat-Resina, M. Gunner and Q. Cui*,\u00a0<\/span>Biochem.\u00a0<\/span><\/i>48, 2468-2485 (2009)<\/p>\n

<\/a>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*,\u00a0<\/span>Biophys. J.<\/i>\u00a0<\/span>96, 3543-3554 (2009)<\/p>\n

<\/a>111. Application of elastic network models to proteins in the crystalline state, D. Riccardi, Q. Cui and G. Phillips, Jr.*\u00a0<\/span>Biophys. J.\u00a0<\/span><\/i>96, 464-475 (2009)<\/p>\n

<\/a>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\u00a0<\/span>Energy Flows in Proteins<\/i>, Eds. D. Leitner and J. E. Straub, CRC Press\u00a0<\/span>In press<\/i>\u00a0<\/span>(2009)\u00a0<\/span>Invited Book Chapter<\/b><\/p>\n","protected":false},"excerpt":{"rendered":"

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,\u00a0J. Am. Chem. Soc.\u00a0134, 20041-20044 (2012) 153. Implementation of the Solvent Macromolecule Boundary Potential and Application to Model and Realistic Enzyme Systems, J. Zienau and Q. Cui*,\u00a0J. Phys. Chem. […]<\/p>\n","protected":false},"author":10766,"featured_media":0,"parent":153,"menu_order":2,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/sites.bu.edu\/cui-group\/wp-json\/wp\/v2\/pages\/158"}],"collection":[{"href":"https:\/\/sites.bu.edu\/cui-group\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.bu.edu\/cui-group\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.bu.edu\/cui-group\/wp-json\/wp\/v2\/users\/10766"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.bu.edu\/cui-group\/wp-json\/wp\/v2\/comments?post=158"}],"version-history":[{"count":4,"href":"https:\/\/sites.bu.edu\/cui-group\/wp-json\/wp\/v2\/pages\/158\/revisions"}],"predecessor-version":[{"id":376,"href":"https:\/\/sites.bu.edu\/cui-group\/wp-json\/wp\/v2\/pages\/158\/revisions\/376"}],"up":[{"embeddable":true,"href":"https:\/\/sites.bu.edu\/cui-group\/wp-json\/wp\/v2\/pages\/153"}],"wp:attachment":[{"href":"https:\/\/sites.bu.edu\/cui-group\/wp-json\/wp\/v2\/media?parent=158"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}