Zhou Group Publications

2013

    193. H.-X. Zhou and P. A. Bates (2013). Modeling protein association mechanisms and kinetics. Curr. Op. Struct. Biol. (submitted).

    192. S. R. Leonard, A. R. Cormier, X. Pang, M. I. Zimmerman, H.-X. Zhou, and A. K. Paravastu (2013). Solid-state NMR evidence for β-hairpin structure within MAX8 designer peptide nanofibers. Biophys. J. (submitted).

    191. H. Dong, M. Yi, T.A. Cross, and H.-X. Zhou (2013). Ab initio calculations and validation of the pH-dependent structures of the His37-Trp41 quartet, the heart of acid activation and proton conductance in the M2 protein of Influenza A virus. Chem. Sci. (in press).pdf  Supplementary Material

    190. J. Dai and H.-X. Zhou (2013). An NMDA receptor gating mechanism developed from MD simulations reveals molecular details underlying subunit-specific contributions. Biophys. J. (in press).

    189. H.-X. Zhou and T. A. Cross (2013). Modeling the membrane environment has implications for membrane protein structure and function: Influenza A M2 protein. Protein Sci. 22, 381-394.pdf

    188. H.-X. Zhou (2013). Influences of crowded cellular environments on protein folding, binding, and oligomerization: biological consequences and potentials of atomistic modeling. FEBS. Lett. 587, 1053-1061.pdf

    187. S. Qin, J. Mittal, and H.-X. Zhou (2013). Folding free energy surfaces of three small proteins under crowding: validation of the postprocessing method by direct simulation. Phys. Biol. (in press).

    186. H.-X. Zhou (2013). Polymer crowders and protein crowders act similarly on protein folding stability. FEBS. Lett. 587, 394-397.pdf

    185. H.-X. Zhou and S. Qin (2013). Simulation and modeling of crowding effects on the thermodynamic and kinetic properties of proteins with atomic details. Biophys. Rev. 5, 207-215.pdf

    184. H.-X. Zhou and T. A. Cross (2013). Influences of membrane mimetic environments on membrane protein structures. Annu. Rev. Biophys. 42, 361-392.pdf  Supplemental Material

    183. S. Qin and H.-X. Zhou (2013). A suite of web servers for predictions ranging from protein structure to binding kinetics. Biophys. Rev. 5, 41-46.pdf

    182. X. Pang and H.-X. Zhou (2013). Poisson-Boltzmann calculations: van der Waals or molecular surface? Commun. Comput. Phys. 13, 1-12.pdf

2012

    181. S. Qin, L. Cai, and H.-X. Zhou (2012). A method for computing association rate constants of atomistically represented proteins under macromolecular crowding. Phys. Biol. 9, 066008.pdf

    180. N. Greives and H.-X. Zhou (2012). BDflex: a method for efficient treatment of molecular flexibility in calculating protein-ligand binding rate constants from Brownian dynamics simulations. J. Chem. Phys. 137, 135105.pdf

    179. C. K. P. Long, H.-X. Zhou, and P. B. Chase (2012). Familial hypertrophic cardiomyopathy related E180G mutation increases flexibility of human cardiac α-tropomyosin. FEBS Lett. 586, 3503-3507.pdf

    178. Y. Phillip, M. Harel, R. Khait, S. Qin, H.-X. Zhou, and G. Schreiber (2012). Contrasting factors on the kinetic path to protein complex formation nullify the effects of crowding agents. Biophys. J. 103, 1011-1019.pdf

    177. X. Pang, K. H. Zhou, S. Qin, and H.-X. Zhou (2012). Prediction and dissection of widely-varying association rate constants of actin-binding proteins. PLoS Comput. Biol. 8, e1002696.pdf

    176. H.-X. Zhou, X. Pang, and L. Cai (2012). Rate constants and mechanisms of intrinsically disordered proteins binding to structured targets. Phys. Chem. Chem. Phys. 14, 10466-10476.pdf  Faculty of 1000 Evaluation

    175. J. Du, T. A. Cross, and H.-X. Zhou (2012). Recent progress in structure-based anti-influenza drug design. Drug Discov. Today 17, 1111-1120.pdf

    174. J. Du, H. Dong, and H.-X. Zhou (2012). Size matters in activation/inhibition of ligand-gated ion channels. Trends Pharmacol. Sci. 33, 482-493.pdf

    173. C. K. P. Long, H.-X. Zhou, and P. B. Chase (2012). Persistence length of human cardiac α-tropomyosin measured by single molecule direct probe microscopy. PLoS ONE 7, e39676.pdf

    172. H. Dong, M. Sharma, H.-X. Zhou, and T. A. Cross (2012). Glycines: role in α-helical membrane protein structures and a potential indicator for native conformation. Biochemistry 51, 4779-4789.pdf  Supporting Information

    171. J. Du, H. Dong, and H.-X. Zhou (2012). Gating mechanism of a P2X4 receptor developed from normal mode analysis and molecular dynamics simulations. Proc. Natl. Acad. Sci. USA. 109, 4140-4145.pdf

    170. X. Pang and H.-X. Zhou (2012). A common model for cytokine receptor activation: combined scissor-like rotation and self-rotation of receptor dimer induced by class I cytokine. PLoS Comput. Biol. 8, e1002427.pdf

    169. T. A. Cross, H. Dong, M. Sharma, D. D. Busath, and H.-X. Zhou (2012). M2 protein from influenza A: from multiple structures to biophysical and functional insights. Curr. Opin. Virol. 2, 128-133.pdf

    168. A. Szabo and H.-X. Zhou (2012). Role of diffusion in the kinetics of reversible enzyme-catalyzed reactions. Bull. Korean Chem. Soc. 33, 925-928.pdf

    167. H.-X. Zhou (2012). Intrinsic disorder: signaling via highly specific but short-lived association. Trends Biochem. Sci. 37, 43-48.pdf

2011

    166. S. Qin, X. Pang, and H.-X. Zhou (2011). Automated prediction of protein association rate constants. Structure 19, 1744-1751.pdf  Supplementary Information

    165. H.-X. Zhou (2011). Mechanistic insight into the H₂O/D₂O isotope effect in the proton transport of the influenza virus M2 protein. J. Membr. Biol. 244:93-96.pdf

    164. J. L. Barreda and H.-X. Zhou (2011). Theory and simulation of diffusion-influenced, stochastically gated ligand binding to buried sites. J. Chem. Phys. 135, 145101.pdf  JCP

    163. S. J. Fleishman, T. A. Whitehead, E.-M. Strauch, J. E. Corn, S. Qin, H.-X. Zhou, J. C. Mitchell, O. N. Demerdash, M. Takeda-Shitaka, G. Terashi, I. H. Moal, X. Li, P. A. Bates, M. Zacharias, H. Park, J. Ko, H. Lee, C. Seok, T. Bourquard, J. Bernauer, A. Poupon, J. Aze, S. Soner, S. K. Ovali, P. Ozbek, N. Ben Tal, T. Haliloglu, H. Hwang, T. Vreven, B. G. Pierce, Z. Weng, L. Perez-Cano, C. Pons, J. Fernadez-Recio, F. Jiang, F. Yang, X. Gong, L. Cao, X. Xu, B. Liu, P. Wang, C. Li, C. Wang, C. H. Robert, M. Guharoy, S. Liu, Y. Huang, L. Li , D. Guo, Y. Chen, Y. Xiao, N. London, Z. Itzhaki, O. Schueler-Furman, Y. Inbar, V. Patapov, M. Cohen, G. Schreiber, Y. Tsuchiya, E. Kanamori, D. M. Standley, H. Nakamura, K. Kinoshita, C. M. Driggers, R. G. Hall, J. L. Morgan, V. L. Hsu, J. Zhan, Y. Yang, Y. Zhou, P. L. Kastritis, A. M. J. J. Bonvin, W. Zhang, C. J. Camacho, K. P. Kilambi, A. Sircar, J. J. Gray, M, Ohue, N. Uchikoga, Y. Matsuzaki, T. Ishida, Y. Akiyama, R. Khashan, S. Bush, D. Fouches, A. Tropsha, J. Esquivel-Rodrigez, D. Kihara, P. B. Stranges, R. Jacak, B. Kuhlman, S. Huang, X. Zou, S. J. Wodak, J. Janin, and D. Baker (2011). Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J. Mol. Biol. 414, 289-302.pdf

    162. A. M. Berezhkovskii, A. Szabo, and H.-X. Zhou (2011). Diffusion-influenced ligand binding to buried sites in macromolecules and transmembrane channels. J. Chem. Phys. 135, 075103.pdf

    161. X. Pang, S. Qin, and H.-X. Zhou (2011). Rationalizing 5,000-fold differences in receptor-binding rate constants of four cytokines. Biophys. J. 101, 1175-1183.pdf

    160. H. Dong and H.-X. Zhou (2011). Atomistic mechanism for the activation and desensitization of an AMPA-subtype glutamate receptor. Nat. Commun. 2, 354.pdf

    159. H.-X. Zhou (2011). Rapid search for specific sites on DNA through conformational switch of nonspecifically bound proteins. Proc. Natl. Acad. Sci. USA. 108, 8651-8656.pdf  Supporting Text  Faculty of 1000 Evaluation

    158. H.-X. Zhou (2011). Equivalence of two approaches for modeling ion permeation through a transmembrane channel with an internal binding site. J. Chem. Phys. 134, 135101.pdf  JCP

    157. H.-X. Zhou (2011). Q&A: What is biophysics? BMC Biology 9, 13.pdf

    156. J. L. Barreda and H.-X. Zhou (2011). A solvable model for the diffusion and reaction of neurotransmitters in a synaptic junction. BMC Biophys. 4, 5.pdf

    155. L. Cai and H.-X. Zhou (2011). Theory and simulation on the kinetics of protein-ligand binding coupled to conformational change. J. Chem. Phys. 134, 105101.pdf

    154. H.-X. Zhou (2011). A theory for the proton transport of the influenza virus M2 protein: extensive test against conductance data. Biophys. J. 100, 912-921.pdf

    153. S. Qin and H.-X. Zhou (2011). Structural models of protein-DNA complexes based on interface prediction and docking. Curr. Protein Pept. Sci. 12, 531-539.pdf

    152. T. A. Cross, M. Sharma, M. Yi, and H.-X. Zhou (2011). Influence of solubilizing environments on membrane protein structures. Trends Biochem. Sci. 36, 117-125.pdf

    151. M. Sharma, C. Li, D. D Busath, H.-X. Zhou, and T. A. Cross (2011). Drug sensitivity, drug-resistant mutations, and structures of the conductance domains of three viral porins. BBA-Biomembranes 1808, 538-546.pdf

2010

    150. W. Lee, X. Zeng, H.-X. Zhou, V. Bennett, W. Yang, and P. E. Marszalek (2010). Full reconstruction of a vectorial protein folding pathway by atomic force microscopy and molecular dynamics simulations. J. Biol. Chem. 285, 38167-38172.pdf

    149. M. Sharma, M. Yi, H. Dong, H. Qin, E. Peterson, D. D. Busath, H.-X. Zhou, and T. A. Cross (2010). Insight into the mechanism of the influenza A proton channel from a structure in a lipid bilayer. Science 330, 509-512.pdf

    148. H.-X. Zhou (2010). Speeding up in a crowd. Physics 3, 77.pdf.

    147. H.-X. Zhou (2010). Diffusion-influenced transport of ions across a transmembrane channel with an internal binding site. J. Phys. Chem. Lett. 1, 1973-1976.pdf

    146. H. Dong, S. Qin, and H.-X. Zhou (2010). Effects of macromolecular crowding on protein conformational changes. PLoS Comput. Biol. 6, e1000833.pdf

    145. S. Qin and H.-X. Zhou (2010). Selection of near-native poses in CAPRI rounds 13-19. Proteins 78, 3166-3173.pdf

    144. H.-X. Zhou (2010). Rate theories for biologists. Q. Rev. Biophys. 43, 219-293.pdf

    143. H. Tjong and H.-X. Zhou (2010). The folding transition-state ensemble of a four-helix bundle protein: helix propensity as a determinant and macromolecular crowding as a probe. Biophys. J. 98, 2273-2280.pdf

    142. S. Qin and H.-X. Zhou (2010). Generalized fundamental measure theory for atomistic modeling of macromolecular crowding. Phys. Rev. E 81, 031919.pdf  Supplementary Information

    141. H.-X. Zhou (2010). From induced fit to conformational selection: a continuum of binding mechanism controlled by the timescale of conformational transitions. Biophys. J. 98, L15-L17.pdf  Supporting Material

    140. S. Qin, D. D. L. Minh, J. A. McCammon, and H.-X. Zhou (2010). Method to predict crowding effects by postprocessing molecular dynamics trajectories: application to the flap dynamics of HIV-1 protease. J. Phys. Chem. Lett. 1, 107-110.pdf  Faculty of 1000 Evaluation

    139. H.-X. Zhou and J. A. McCammon (2010). The gates of ion channels and enzymes. Trends Biochem. Sci. 35, 179-185.pdf

    138. X. Zeng, H. Hu, H.-X. Zhou, P. E. Marszalek, and W. Yang (2010). Equilibrium sampling for biomolecules under mechanical tension. Biophys. J. 98, 733-740.pdf

    137. A. Bazavov, B. A. Berg, and H.-X. Zhou (2010). Application of biased metropolis algorithms: from protons to proteins. Math. Comput. Simul. 80, 1056-1067.pdf

2009

    136. A. W. Maniccia, W. Yang, J. A. Johnson, S. Li, H. Tjong, H.-X. Zhou, L. A. Shaket, and J. J. Yang (2009). Inverse tuning of metal binding affinity and protein stability by altering charged coordination residues in designed calcium binding proteins. PMC Biophysics 2:11.pdf

    135. M. Yi, T. A. Cross, and H.-X. Zhou (2009). Conformational heterogeneity of the M2 proton channel and a structural model for channel activation. Proc. Natl. Acad. Sci. USA 106, 13311-13316.pdf  Supporting Figures  Supporting Text.

    134. J. Batra, K. Xu, S. Qin, and H.-X. Zhou (2009). Effect of macromolecular crowding on protein binding stability: modest stabilization and significant biological consequences. Biophys. J. 97, 906-911.pdf

    133. S. Qin and H.-X. Zhou (2009). Atomistic modeling of macromolecular crowding predicts modest increases in protein folding and binding stability. Biophys. J. 97, 12-19.pdf  Faculty of 1000 Evaluation

    132. S. Qin and H.-X. Zhou (2009). Dissection of the high rate constant for the binding of a ribotoxin to the ribosome. Proc. Natl. Acad. Sci. USA 106, 6974-7979.pdf  Supporting Information  Commentary

    131. H.-X. Zhou and M. K. Gilson (2009). Theory of free energy and entropy in noncovalent binding. Chem. Rev. 109, 4092-4107.pdf  Supporting Information

    130. J. Batra, K. Xu, and H.-X. Zhou (2009). Nonaddtive effects of mixed crowding on protein stability. Proteins 77, 133-138.pdf

    129. H.-X. Zhou (2009). Crowding effects of membrane proteins. J. Phys. Chem. B 113, 7995-8005.pdf

    128. G. Schreiber, G. Haran, and H.-X. Zhou (2009). Fundamental aspects of protein-protein association kinetics. Chem. Rev. 109, 839-860.pdf

    127. G.-C. Dong, P.-H. Chuang, K.-c. Chang, P.-s. Jan, P.-I. Hwang, H.-B. Wu, M. Yi, H.-X. Zhou, and H. M. Chen (2009). Blocking effect of an immuno-suppressive agent, cynarin, on CD28 of T-Cell receptor. Pharm. Res. 26, 375-381.pdf

2008

    126. J.-M. Yuan, C.-L. Chyan, H.-X. Zhou, T.-Y. Chung, H. Peng, G. Ping, and G. Yang (2008). The effects of macromolecular crowding on the mechanical stability of protein molecules. Protein Sci. 17, 2156-2166.pdf

    125. S. Li, W. Yang, A. W. Maniccia, D. Barrow Jr., H. Tjong, H.-X. Zhou, and J. J. Yang (2008). Rational design of a conformation switchable Ca2+ and Tb3+ binding protein without using multiple coupled metal binding sites. FEBS J. 275, 5048-5061.pdf

    124. H.-X. Zhou (2008). The debut of PMC Biophysics. PMC Biophysics 1, 1.pdf

    123. H. Tjong and H.-X. Zhou (2008). Accurate calculations of binding, folding, and transfer free energies by a scaled generalized Born method. J. Chem. Theory Comput. 4, 1733-1744.pdf

    122. M. Yi, H. Nymeyer, and H.-X. Zhou (2008). Test of the Gouy-Chapman theory for a charged lipid membrane against explicit-solvent molecular dynamics simulations. Phys. Rev. Lett. 101, 038103.pdf  Faculty of 1000 Evaluation

    121. M. Yi, T. A. Cross, and H.-X. Zhou (2008). A secondary gate as a mechanism for inhibition of the M2 proton channel by amantadine. J. Phys. Chem. B 112, 7977-7979.pdf

    120. H.-X. Zhou (2008). A minimum-reaction-flux solution to master-equation models of protein folding. J. Chem. Phys. 128, 195104.pdf

    119. H.-X. Zhou, S. Qin, and H. Tjong (2008). Modeling protein-protein and protein-nucleic acid interactions: structure, thermodynamics, and kinetics. Annu. Report Comput. Chem. 4, 67-87.pdf

    118. H.-X. Zhou (2008). Effect of mixed macromolecular crowding agents on protein folding. Proteins 72, 1109-1113.pdf

    117. M. Yi, H. Tjong, and H.-X. Zhou (2008). Spontaneous conformational change and toxin binding in α7 nicotinic acetylcholine receptor: insight into channel activation and inhibition. Proc. Natl. Acad. Sci. 105, 8280-8285.pdf

    116. H. Tjong and H.-X. Zhou (2008). Prediction of protein solubility from calculation of transfer free energy. Biophys. J. 95, 2601-2609.pdf.

    115. R. Alsallaq and H.-X. Zhou (2008). Protein association with circular DNA: rate enhancement by nonspecific binding. J. Chem. Phys. 128, 115108.pdf

    114. H. Tjong and H.-X. Zhou (2008). On the dielectric boundary in Poisson-Boltzmann calculations. J. Chem. Theory Comput. 4, 507-514.pdf

    113. H.-X. Zhou, G. Rivas, and A. P. Minton (2008). Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences. Annu. Rev. Biophys. 37, 375-397.pdf

    112. H.-X. Zhou (2008). Calculation of free-energy differences and potentials of mean force by a multi-energy gap method. J. Chem. Phys. 128, 114104.pdf

    111. C. Li, M. Yi, J. Hu, H.-X. Zhou, and T. A. Cross (2008). Solid-state NMR and MD simulations of the anti-viral drug amantadine solubilized in DMPC bilayers. Biophys. J. 94, 1295-1302.pdf

    110. H. Nymeyer and H.-X. Zhou (2008). A Method to determine dielectric constants in non-homogeneous systems: application to biological membranes. Biophys. J. 94, 1185-1193.pdf

    109. W. Yang, H. Nymeyer, H.-X. Zhou, B. A. Berg, and R. Bruschweiler (2008). Quantitative computer simulations of biomolecules: a snapshot. J. Comput. Chem. 29, 668-672.pdf

    108. R. Alsallaq and H.-X. Zhou (2008). Electrostatic rate enhancement and transient complex of protein-protein association. Proteins 71, 320-335.pdf

    107. S. Qin and H.-X. Zhou (2008). Prediction of salt and mutational effects on the association rate of U1A protein and U1 small nuclear RNA stem/loop II. J. Phys. Chem. B 112, 5955-5960.pdf

    106. H.-X. Zhou (2008). Protein folding in confined and crowded environments. Arch. Biochem. Biophys., 469, 76-82.pdf

2007

    105. H.-X. Zhou (2007). Helix formation inside a nanotube: possible influence of backbone-water hydrogen bonding by the confining surface through modulation of water activity. J. Chem. Phys. 127, 245101.pdf

    104. N. Bhattacharya, M. Yi, H.-X. Zhou, and T. Logan (2007). Backbone dynamics in an intramolecular prolylpeptide-SH3 complex from the diphtheria toxin repressor, DtxR. J. Mol. Biol. 374, 977-992.

    103. S. Qin and H.-X. Zhou (2007). A holistic approach to protein docking. Proteins 69, 743-749.pdf

    102. S. Qin and H.-X. Zhou (2007). meta-PPISP: a meta web server for protein-protein interaction site prediction. Bioinformaticss 23, 3386-3387.pdf

    101. H.-X. Zhou and S. Qin (2007). Interaction-site prediction for protein complexes: a critical assessment. Bioinformatics 23, 2203-2209.pdf

    100. H. Tjong and H.-X. Zhou (2007). GBr⁶NL: a generalized Born method for accurately reproducing solvation energy of the nonlinear Poisson-Boltzmann equation. J. Chem. Phys. 126, 195102.pdf

    99. H. Tjong, S. Qin, and H.-X. Zhou (2007). PI²PE: protein interface/interior prediction engine. Nucl. Acids Res. 35, W357-W362.pdf

    98. S. Qin and H.-X. Zhou (2007). Do electrostatic interactions destabilize protein-nucleic acid binding? Biopolymers 86, 112-118.pdf  InThisIssue

    97. H. Tjong and H.-X. Zhou (2007). GBr⁶: a parameterization-free, accurate, analytical generalized Born method. J. Phys. Chem. B 111, 3055-3061.pdf

    96. R. Alsallaq and H.-X. Zhou (2007). Prediction of protein-protein association rates from a transition-state theory. Structure 15, 215-224.pdf

    95. H. Tjong and H.-X. Zhou (2007). DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Nucl. Acids Res. 35, 1465-1477.pdf

    94. M. K. Gilson and H.-X. Zhou (2007). Calculation of protein-ligand binding affinities. Annu. Rev. Biophys. Biomol. Struct. 36, 21-42.E-print

    93. R. Alsallaq and H.-X. Zhou (2007). Energy landscape and transition state of protein-protein association. Biophys. J. 92, 1486-1502.pdf

2006

    92. H. Tjong and H.-X. Zhou (2006). The dependence of electrostatic solvation energy on dielectric constants in Poisson-Boltzmann calculations. J. Chem. Phys. 125, 206101.pdf

    91. H.-X. Zhou (2006). Quantitative relation between intermolecular and intramolecular binding of Pro-rich peptides to SH3 domains. Biophys. J. 91, 3170-3181.pdf

    90. X. Huang and H.-X. Zhou (2006). Similarity and difference in the unfolding of thermophilic and mesophilic cold shock proteins studied by molecular dynamics simulations. Biophys. J. 91, 2451-2463.pdf

    89. F. Dong and H.-X. Zhou (2006). Electrostatic contribution to the binding stability of protein-protein complexes. Proteins 65, 87-102.pdf

    88. J. Hu, R. Fu, K. Nishimura, L. Zhang, H.-X. Zhou, D. D. Busath, V. Vijayvergiya, and T. A. Cross (2006). Histidines, heart of the hydrogen ion channel from influenza A virus: toward an understanding of conductance and proton selectivity. Proc. Natl. Acad. Sci. USA 103, 6865-6870.pdf

2005

    87. H.-X. Zhou (2005). How do biomolecular systems speed up and regulate rates? Phys. Biol. 2, R1-R25.Physical Biology  pdf

    86. B. A. Berg and H.-X. Zhou (2005). Rugged Metropolis sampling with simultaneous updating of two dynamical variables. Phys. Rev. E 72, 016712.pdf

    85. H. Chen and H.-X. Zhou (2005). Prediction of solvent accessibility and sites of deleterious mutations from protein sequence. Nucl. Acids Res. 33, 3193-3199.pdf

    84. D. S. Spencer, K. Xu, T. M. Logan, and H.-X. Zhou (2005). Effects of pH, salt, and macromolecular crowding on the stability of FK506-binding protein: an integrated experimental and theoretical study. J. Mol. Biol. 351, 219-232.

    83. H. Chen and H.-X. Zhou (2005). Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data. Proteins 61, 21-35.pdf

    82. H.-X. Zhou (2005). Interactions of macromolecules with salt ions: an electrostatic theory for the Hofmeister effect. Proteins 61, 69-78.pdf

    81. A. D. J. van Dijk , S. J. de Vries, C. Dominguez, H. Chen, H.-X. Zhou, and A. M. J. J. Bonvin (2005). Data-driven docking: HADDOCK's adventures in CAPRI. Proteins 60, 232-238.pdf

    80. X. Huang, F. Dong, and H.-X. Zhou (2005). Electrostatic recognition and induced fit in the k-PVIIA toxin binding to Shaker potassium channel. J. Am. Chem. Soc 127, 6836-6849.pdf

    79. H.-X. Zhou (2005). A model for the mediation of processivity of DNA-targeting proteins by nonspecific binding: dependence on DNA length and presence of obstacles. Biophys. J. 88, 1608-1615.pdf

2004

    78. H.-X. Zhou and A. Szabo (2004). Enhancement of association rates by nonspecific binding to DNA and cell membranes. Phys. Rev. Lett. 93, 178101.pdf

    77. H.-X. Zhou (2004). Polymer models of protein stability, folding, and interactions. Biochemistry 43, 2141-2154.pdf

    76. H.-X. Zhou (2004). Loops, linkages, rings, catenanes, cages, and crowders: entropy-based strategies for stabilizing proteins. Acc. Chem. Res. 37, 123-130.pdf

    75. H.-X. Zhou (2004). Protein folding and binding in confined spaces and in crowded solutions. J. Mol. Recog. 17, 368-375.pdf

    74. H.-X. Zhou (2004). Improving the understanding of human genetic diseases through predictions of protein structures and protein-protein interaction sites. Curr. Med. Chem. 11, 539-549.

2003

    73. H.-X. Zhou (2003). How often does the myristoylated N-terminal latch of c-Abl come off? FEBS Lett. 552, 160-162.pdf

    72. H.-X. Zhou (2003). Effect of backbone cyclization on protein folding stability: chain entropies of both the unfolded and the folded states are restricted. J. Mol. Biol. 332, 257-264.reprint

    71. H.-X. Zhou (2003). Association and dissociation kinetics of colicin E3 and immunity protein 3: convergence of theory and experiment. Protein Sci. 12, 2379-2382.pdf

    70. H.-X. Zhou (2003). Effect of catenation on protein folding stability. J. Am. Chem. Soc. 125, 9280-9281.pdf  Faculty of 1000 Evaluation

    69. H.-X. Zhou (2003). Quantitative account of the enhanced affinity of two linked scFvs specific for different epitopes on the same antigen. J. Mol. Biol. 329, 1-8.reprint

    68. F. Dong, M. Vijayakumar, and H.-X. Zhou (2003). Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar. Biophys. J. 85, 49-60.pdf

    67. H.-X. Zhou (2003). Direct test of the Gaussian-chain model for treating residual charge-charge interactions in the unfolded state of proteins. J. Am. Chem. Soc. 125, 2060-2061.pdf

    66. H.-X. Zhou and F. Dong (2003). Electrostatic contributions to the stability of a thermophilic cold shock protein. Biophys. J. 84, 2216-2222.pdf

    65. H.-X. Zhou (2003). Theory for the rate of contact formation in a polymer chain with local conformational transitions. J. Chem. Phys. 118, 2010-2015.pdf

2002

    64. H.-X. Zhou (2002). Toward the physical basis of thermophilic proteins: linking of enriched polar interactions and reduced heat capacity of unfolding. Biophys. J. 83, 3126-3133.pdf

    63. H.-X. Zhou (2002). Residual charge interactions in unfolded staphylococcal nuclease can be explained by the Gaussian-chain model. Biophys. J. 83, 2981-2986.pdf

    62. F. Dong and H.-X. Zhou (2002). Electrostatic contributions to T4 lysozyme stability: solvent-exposed charges versus semi-buried salt bridges. Biophys. J. 83, 1341-1347.pdf

    61. H.-X. Zhou (2002). Residual electrostatic effects in the unfolded state of the N-terminal domain of L9 can be attributed to non-specific non-local charge-charge interactions. Biochemistry 41, 6533-6538.pdf

    60. H.-X. Zhou (2002). Dimensions of denatured proteins chains from hydrodynamic data. J. Phys. Chem. B 106, 5769-5775.pdf

    59. H.-X. Zhou (2002). A Gaussian-chain model for treating residual charge-charge interactions in the unfolded state of proteins. Proc. Natl. Acad. Sci. USA 99, 3569-3574.pdf  Faculty of 1000 Evaluation

    58. H.-X. Zhou and R. Zwanzig (2002). Barrier crossing coupled to a small set of oscillators. J. Phys. Chem. A 106, 7562-7564.pdf

    57. A. H. Boschitsch, M. O. Fenley, and H.-X. Zhou (2002). Fast boundary element method for the linear Poisson-Boltzmann equation. J. Phys. Chem. B 202, 2741-2754.pdf

    56. H.-X. Zhou (2002). A model for the binding of the inactivation N-terminal to the ion pore of Shaker potassium channel: both electrostatic attraction and covalent linkage are required for rapid inactivation. J. Phys. Chem. B 106, 2393-2397.pdf

2001

    55. H.-X. Zhou (2001). The affinity-enhancing roles of flexible linkers in two-domain DNA-binding proteins. Biochemistry 40, 15069-15073.pdf  Faculty of 1000 Evaluation

    54. H.-X. Zhou and K. A. Dill (2001). Stabilization of proteins in confined spaces. Biochemistry 40, 11289-11293.pdf  Faculty of 1000 Evaluation

    53. M. Vijayakumar and H.-X. Zhou (2001). Salt bridges stabilize the folded structure of barnase. J. Phys. Chem. B 105, 7334-7340.pdf

    52. H.-X. Zhou (2001). Single-chain versus dimeric protein folding: thermodynamic and kinetic consequences of covalent linkage. J. Am. Chem. Soc. 123, 6730-6731.pdf

    51. H.-X. Zhou (2001). Loops in proteins can be modeled as worm-like chains. J. Phys. Chem. B 105, 6763-6766.pdf

    50. H.-X. Zhou and Y. Shan (2001). Prediction of protein interaction sites from sequence profiles and residue neighbor list. Proteins 44, 336-343.pdf

    49. H.-X. Zhou (2001). Disparate ionic-strength dependence of on and off rates in protein- protein association. Biopolymers 59, 427-433.pdf  Faculty of 1000 Evaluation

    48. H.-X. Zhou and G. Wang (2001). Predicted structures of two proteins involved in human diseases. Cell Biochem. Biophys. 35, 35-47.pdf

    47. H.-X. Zhou (2001). A unified picture of protein hydration: prediction of hydrodynamic properties from known structures. Biophys. Chem. 93, 171-179.pdf

    46. Y. Shan, G. Wang, and H.-X. Zhou (2001). Fold recognition and accurate query-template alignment by a combination of PSI-BLAST and threading. Proteins 42, 23-37.pdf

1989-2000

    45. M. Vijayakumar and H.-X. Zhou (2000). Prediction of residue-residue pair frequencies in proteins. J. Phys. Chem. B 104, 9755-9764.pdf

    44. Y. Shan and H.-X. Zhou (2000). Correspondence of potentials of mean force in proteins and in liquids. J. Chem. Phys. 113, 4794-4798.pdf

    43. A. M. Berezhkovskii, A. Szabo, G. H. Weiss, and H.-X. Zhou (1999). Reaction dynamics on a thermally fluctuating potential. J. Chem. Phys. 111, 9952-9957.

    42. M. Vijayakumar, H. Qian, and H.-X. Zhou (1999). Hydrogen bonds between short polar side chains and peptide backbone: prevalence in proteins and effects on helix-forming propensities. Proteins 34, 497-507.

    41. H.-X. Zhou, S. T. Wlodek, and J. A. McCammon (1998). Conformation gating as a mechanism for enzyme specificity. Proc. Natl. Acad. Sci. USA 95, 9280-9283.pdf

    40. M. Vijayakumar, K.-Y. Wong, G. Schreiber, A. R. Fersht, A. Szabo, and H.-X. Zhou (1998). Electrostatic enhancement of diffusion-controlled protein-protein association: comparison of theory and experiment on barnase and barstar. J. Mol. Biol. 278, 1015-1024.pdf

    39. H.-X. Zhou (1998). Theory of the diffusion-influenced substrate binding rate to a buried and gated active site. J. Chem. Phys.108, 8146-8154.

    38. H.-X. Zhou (1998). Comparison of three Brownian-dynamics algorithms for calculating rate constants of diffusion-influenced reactions. J. Chem. Phys.108, 8139-8145.

    37. H.-X. Zhou, J. M. Briggs, S. Tara, and J. A. McCammon (1998). Correlation between rate of enzyme-substrate diffusional encounter and average Boltzmann factor around active site. Biopolymers 45, 355-360.

    36. H.-X. Zhou (1997). Enhancement of protein-protein association rate by interaction potential: accuracy of prediction based on local Boltzmann factor. Biophys. J. 73, 2441-2445.

    35. H.-X. Zhou, K.-Y. Wong, and M. Vijayakumar (1997). Design of fast enzymes by optimizing interaction potential in active site. Proc. Natl. Acad. Sci. USA 94, 12372-12377.

    34. H.-X. Zhou (1997). Theory and simulation of the influence of diffusion in enzyme-catalyzed reactions. J. Phys. Chem. B 101, 6642-6651.

    33. H.-X. Zhou and M. Vijayakumar (1997). Modeling of protein conformational fluctuations in pKa predictions. J. Mol. Biol. 267, 1002-1011.

    32. H.-X. Zhou (1997). Control of reduction potential by protein matrix: lesson from a spherical protein model. J. Biol. Inorg. Chem. 2, 109-113.

    31. H.-X. Zhou, J. M. Briggs, and J. A. McCammon (1996). A 240-fold electrostatic rate-enhancement for acetylcholinesterase-substrate binding can be predicted by the potential within the active site. J. Am. Chem. Soc. 118, 13069-13070.

    30. H.-X. Zhou (1996). Effect of interaction potentials in diffusion-influenced reactions with small reactive regions. J. Chem. Phys. 105, 7235-7237.

    29. H.-X. Zhou and A. Szabo (1996). Theory and simulation of the time-dependent rate coefficients of diffusion-influenced reactions. Biophys. J. 71, 2440-2457.

    28. H.-X. Zhou (1996). Dielectric continuum model for calculating reorganization free energies of electron transfer in proteins. J. Chem. Phys. 105, 3726-3733.

    27. H.-X. Zhou and Y. Chen (1996). Chemically driven motility of Brownian particles. Phys. Rev. Lett. 77, 194-197.

    26. M. J. Potter, B. Luty, H.-X. Zhou, and J. A. McCammon (1996). Time-dependent rate coefficients from Brownian dynamics simulations. J. Phys. Chem. 100, 5149-5154.

    25. H.-X. Zhou and A. Szabo (1996). Theory and simulation of stochastically-gated diffusion-influenced reactions. J. Phys. Chem. 100, 2597-2604.

    24. J. A. Ernst, R. T. Clubb, H.-X. Zhou, A. M. Gronenborn, and G. M. Clore (1995). Use of NMR to detect water within nonpolar protein cavities. Science 270, 1848-1849.

    23. H.-X. Zhou (1995). Calculation of translational friction and intrinsic viscosity. II. Application to globular proteins. Biophys. J. 69, 2298-2303.

    22. H.-X. Zhou (1995). Calculation of translational friction and intrinsic viscosity. I. General formulation for arbitrarily shaped particles. Biophys. J. 69, 2286-2297.

    21. H.-X. Zhou and A. Szabo (1995). Microscopic formulation of Marcus' theory of electron transfer. J. Chem. Phys. 103, 3481-3494.

    20. J. A. Ernst, R. T. Clubb, H.-X. Zhou, A. M. Gronenborn, and G. M. Clore (1995). Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR. Science 267, 1813-1817.

    19. H.-X. Zhou (1995). Continuum-model studies of redox reactions, complex formation, and electron transfer: the paradigm of cytochrome c and cytochrome c peroxidase. in A. Pullman, J. Jortner, and B. Pullman (Eds.), "Modelling of Biomolecular Structures and Mechanisms", 381-398. Kluwer Academic Publishers, Dordrecht.

    18. H.-X. Zhou (1994). Effects of mutations and complex formation on the redox potentials of cytochrome c and cytochrome c peroxidase. J. Am. Chem. Soc. 116, 10362-10375.

    17. J. F. Douglas, H.-X. Zhou, and J. B. Hubbard (1994). Hydrodynamic friction and the electrostatic capacitance of an arbitrarily-shaped objects. Phys. Rev. E 49, 5319-5331.

    16. H.-X. Zhou, A. Szabo, J. F. Douglas, and J. B. Hubbard (1994). A Brownian dynamics algorithm for calculating the hydrodynamic friction and the electrostatic capacitance of an arbitrarily-shaped object. J. Chem. Phys. 100, 3821-3826.

    15. H.-X. Zhou (1994). Macromolecular electrostatic energy within the nonlinear Poisson-Boltzmann equation. J. Chem. Phys. 100, 3152-3162.

    14. O. Schaad, H.-X. Zhou, A. Szabo, W. A. Eaton, and E. R. Henry (1993). Simulation of the kinetics of ligand binding to a protein by molecular dynamics: geminate rebinding of nitric oxide to myoglobin. Proc. Natl. Acad. Sci. USA 90, 9547-9551.

    13. H.-X. Zhou (1993). Boundary element solution of macromolecular electrostatics: interaction energy between two proteins. Biophys. J. 65, 955-963.

    12. H.-X. Zhou (1993). Brownian dynamics study of the influences of electrostatic interaction and diffusion on protein-protein association kinetics. Biophys. J. 64, 1711-1726.

    11. H.-X. Zhou (1993). Dynamic spherical model for solvation in a dipolar lattice. J. Phys. Chem. 97, 4216-4223.

    10. H.-X. Zhou, B. Bagchi, A. Papazyan, and M. Maroncelli (1992). Solvation dynamics in a Brownian dipole lattice: a comparison between theory and computer simulation. J. Chem. Phys. 97, 9311-9320.

    9. B. A. Luty, J. A. McCammon, and H.-X. Zhou (1992). Diffusive reaction rates from Brownian dynamics simulations: replacing the outer cut-off surface by an analytical treatment. J. Chem. Phys. 97, 5682-5686.

    8. H.-X. Zhou and B. Bagchi (1992). Dielectric and orientational relaxation in a Brownian dipolar lattice. J. Chem. Phys. 97, 3610-3620.

    7. H.-X. Zhou and A. Szabo (1991). Comparison between molecular dynamics simulations and the Smoluchowski theory of reactions in a hard sphere liquid. J. Chem. Phys. 95, 5948-5952.

    6. H.-X. Zhou and R. Zwanzig (1991). A rate process with an entropy barrier. J. Chem. Phys. 94, 6147-6152.

    5. H.-X. Zhou (1990). Kinetics of diffusion-influenced reactions studied by Brownian dynamics. J. Phys. Chem. 94, 8794-8800.

    4. H.-X. Zhou and F. A. Ferrone (1990). Theoretical description of the spatial dependence of sickle hemoglobin polymerization. Biophys. J. 58, 695-703.

    3. H.-X. Zhou and A. Szabo (1990). Mean field theory of transient fluorescence quenching in the frequency domain. J. Chem. Phys. 92, 3874-3880.

    2. H.-X. Zhou (1990). On the calculation of diffusive reaction rates using Brownian dynamics simulations. J. Chem. Phys. 92, 3092-3095.

    1. H.-X. Zhou (1989). The exponential nature of barrier crossings studied by Langevin dynamics. Chem. Phys. Lett. 164, 285-290.