Research Topics
| Huan Xiang ZhouSummaryAffiliation: Florida State University Country: USA Publications
| Collaborators
|
Detail Information
Publications
Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstarFeng Dong
Department of Physics, Florida State University, Tallahassee, Florida 32306, USA
Biophys J 85:49-60. 2003..This study calls for further scrutiny of the different Poisson-Boltzmann protocols and demonstrates potential danger in drawing conclusions on electrostatic contributions based on a particular calculation protocol...
Interaction-site prediction for protein complexes: a critical assessmentHuan Xiang Zhou
Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
Bioinformatics 23:2203-9. 2007..Future developments will be directed at tackling problems such as building structural models for multi-component structural complexes...- Protein folding and binding in confined spaces and in crowded solutionsHuan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
J Mol Recognit 17:368-75. 2004..Crowding will shift the binding equilibrium of proteins toward the bound state. The significant slowing down in protein diffusion by crowding, perhaps beneficial for chaperonin action, could result in a decrease in protein binding rates... - A model for the mediation of processivity of DNA-targeting proteins by nonspecific binding: dependence on DNA length and presence of obstaclesHuan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
Biophys J 88:1608-15. 2005.... - Protein folding in confined and crowded environmentsHuan Xiang Zhou
Department of Physics and Institute of Biophysics and School of Computational Science, Florida State University, Tallahassee, FL 32306, USA
Arch Biochem Biophys 469:76-82. 2008..Concerted theoretical modeling and test-tube and in vivo experiments promise to elucidate the complexity of protein folding in cellular environments... - Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequencesHuan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, Florida 32306, USA
Annu Rev Biophys 37:375-97. 2008..Theoretical and experimental approaches to the characterization of crowding- and confinement-induced effects in systems approaching the complexity of living organisms are suggested... - Interactions of macromolecules with salt ions: an electrostatic theory for the Hofmeister effectHuan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee 32306, USA
Proteins 61:69-78. 2005..The theory yields a direct link between the salting-out effect and surface tension and is able to provide rationalizations for the effects of salt on the folding stability of several proteins... - How do biomolecular systems speed up and regulate rates?Huan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, FL 32306, USA
Phys Biol 2:R1-25. 2005..Simple physical models are presented here to illustrate these processes and provide a unifying framework for understanding speed attainment and regulation in biomolecular systems... - Effect of mixed macromolecular crowding agents on protein foldingHuan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, FL 32306, USA
Proteins 72:1109-13. 2008..We further predict that, for any crowding agent, the stabilizing effect can be optimized both by varying the molecular weight and the mixing ratio of two species with different molecular weights... - A minimum-reaction-flux solution to master-equation models of protein foldingHuan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, Florida 32306, USA
J Chem Phys 128:195104. 2008..The approach presented here significantly simplifies the solution of master-equation models and, at the same time, directly yields insight into folding mechanisms... 
Calculation of free-energy differences and potentials of mean force by a multi-energy gap methodHuan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, FL 32306, USA
J Chem Phys 128:114104. 2008..Applications to model systems confirm the expected increase in accuracy of calculated free-energy differences and potentials of mean force...- Quantitative relation between intermolecular and intramolecular binding of pro-rich peptides to SH3 domainsHuan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, USA
Biophys J 91:3170-81. 2006..These and other examples suggest that flexible linkers and sequence motifs tethered to them, like folded protein domains, are also subject to tight control during evolution... - Helix formation inside a nanotube: possible influence of backbone-water hydrogen bonding by the confining surface through modulation of water activityHuan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahasse, Florida 32306, USA
J Chem Phys 127:245101. 2007..With physically reasonable parameters, the dependence of the helical content on the diameter of the nanotube obtained in the simulations is well reproduced... - Polymer models of protein stability, folding, and interactionsHuan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
Biochemistry 43:2141-54. 2004..In future developments, more realistic models may emerge from molecular dynamics simulations, and these models will guide experiments to advance our understanding of the unfolded state and flexible linkers... - How often does the myristoylated N-terminal latch of c-Abl come off?Huan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
FEBS Lett 552:160-2. 2003..5%... - Toward the physical basis of thermophilic proteins: linking of enriched polar interactions and reduced heat capacity of unfoldingHuan Xiang Zhou
Institute of Molecular Biophysics and Department of Physics, Florida State University, Tallahassee, FL 32306, USA
Biophys J 83:3126-33. 2002..A reduced DeltaC(p) might serve as an indicator for the contribution of polar interactions to folding stability... - Association and dissociation kinetics of colicin E3 and immunity protein 3: convergence of theory and experimentHuan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
Protein Sci 12:2379-82. 2003..This outcome is just what was anticipated by a theory for the binding of two linked domains to a protein. The E3/Im3 system thus provides a powerful paradigm for the interplay of theory and experiment... - The affinity-enhancing roles of flexible linkers in two-domain DNA-binding proteinsH X Zhou
Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
Biochemistry 40:15069-73. 2001..However, there is room for improvement in many of the recently designed proteins. The theoretical limits presented should provide a useful guide for current efforts of designing DNA-binding proteins... - A Gaussian-chain model for treating residual charge-charge interactions in the unfolded state of proteinsHuan Xiang Zhou
Department of Physics, Drexel University, Philadelphia, PA 19104, USA
Proc Natl Acad Sci U S A 99:3569-74. 2002.... - Residual electrostatic effects in the unfolded state of the N-terminal domain of L9 can be attributed to nonspecific nonlocal charge-charge interactionsHuan Xiang Zhou
Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
Biochemistry 41:6533-8. 2002..This indicates that the residual electrostatic effects in the unfolded state of NTL9 can be attributed to nonspecific nonlocal charge-charge interactions... - Residual charge interactions in unfolded staphylococcal nuclease can be explained by the Gaussian-chain modelHuan Xiang Zhou
Department of Physics, Drexel University, Philadelphia, PA 19104, USA
Biophys J 83:2981-6. 2002..The dominance of nonspecific local interactions appears to be supported by some experimental evidence... - Insight into the mechanism of the influenza A proton channel from a structure in a lipid bilayerMukesh Sharma
Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
Science 330:509-12. 2010..This mechanism explains the main observations on M2 proton conductance... - PI2PE: protein interface/interior prediction engineHarianto Tjong
Institute of Molecular Biophysics and School of Computational Science and Department of Physics, Florida State University, Tallahassee, FL 32306, USA
Nucleic Acids Res 35:W357-62. 2007..scs.fsu.edu. To illustrate the utility of these web servers, cons-PPISP and DISPLAR predictions are used to construct a structural model for a multicomponent protein-DNA complex... - Effects of pH, salt, and macromolecular crowding on the stability of FK506-binding protein: an integrated experimental and theoretical studyDaniel S Spencer
Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
J Mol Biol 351:219-32. 2005..For any environmental variable, it is the balance of its effects on the folded and unfolded states that determines the outcome on the folding stability... - GBr6NL: a generalized Born method for accurately reproducing solvation energy of the nonlinear Poisson-Boltzmann equationHarianto Tjong
Department of Physics and Institute of Molecular Biophysics, and School of Computational Science, Florida State University, Tallahassee, Florida 32306, USA
J Chem Phys 126:195102. 2007..GBr(6)NL predictions for the salts effects on the electrostatic interaction energies of two protein:RNA complexes are very promising... - A holistic approach to protein dockingSanbo Qin
Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
Proteins 69:743-9. 2007..Our Model 7 is rated number one among all submissions according to L_rmsd. Six of our other submissions are rated acceptable. As scorer, eight of our submissions are rated acceptable... - Effect of macromolecular crowding on protein binding stability: modest stabilization and significant biological consequencesJyotica Batra
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA
Biophys J 97:906-11. 2009.... - Solid-state NMR and MD simulations of the antiviral drug amantadine solubilized in DMPC bilayersConggang Li
Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32310, USA
Biophys J 94:1295-302. 2008..The lipid headgroup orientation changes on drug binding as characterized by the anisotropy of (31)P chemical shielding and (14)N quadrupolar interactions and by the MD simulation... - Electrostatic contributions to the stability of a thermophilic cold shock proteinHuan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
Biophys J 84:2216-22. 2003..These results should provide insight for understanding the thermostability of other thermophilic proteins... - Atomistic modeling of macromolecular crowding predicts modest increases in protein folding and binding stabilitySanbo Qin
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA
Biophys J 97:12-9. 2009..The stabilization of crowding on the binding stability of barnase and barstar, based on atomistic modeling of the proteins, was similarly modest. These findings have profound implications for macromolecular crowding inside cells... - Rugged Metropolis sampling with simultaneous updating of two dynamical variablesBernd A Berg
Department of Physics, Florida State University, Tallahassee, Florida 32306-4350, USA
Phys Rev E Stat Nonlin Soft Matter Phys 72:016712. 2005..Correlations between three or more dihedral angles appear to prevent larger improvements at low temperatures. We also investigate a multihit Metropolis scheme, which spends more CPU time on variables with large autocorrelation times... - The folding transition-state ensemble of a four-helix bundle protein: helix propensity as a determinant and macromolecular crowding as a probeHarianto Tjong
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA
Biophys J 98:2273-80. 2010..This study shows that molecular dynamics simulations combined with calculation of crowding effects provide an avenue for characterize the transition-state ensemble in atomic details... - A method to determine dielectric constants in nonhomogeneous systems: application to biological membranesHugh Nymeyer
Department of Chemistry and Biochemistry, School of Computational Science, Florida State University, Tallahassee, Florida 32306, USA
Biophys J 94:1185-93. 2008..These results have implications for the design of implicit membrane models and our understanding of protein-membrane interactions... - Quantitative account of the enhanced affinity of two linked scFvs specific for different epitopes on the same antigenHuan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
J Mol Biol 329:1-8. 2003..3 and HyHEL-10. The wide applicability of the theory is demonstrated by diverse examples of protein-protein interactions constrained by flexible linkers... - meta-PPISP: a meta web server for protein-protein interaction site predictionSanbo Qin
Institute of Molecular Biophysics, School of Computational Science, Florida State University, Tallahassee, Florida 32306, USA
Bioinformatics 23:3386-7. 2007..8 to 18.2 percentage points. Similar improvements in accuracy are also seen on CAPRI and other targets. AVAILABILITY: meta-PPISP can be accessed at http://pipe.scs.fsu.edu/meta-ppisp.html.. - Structural models of protein-DNA complexes based on interface prediction and dockingSanbo Qin
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
Curr Protein Pept Sci 12:531-9. 2011..Evaluations of both the DNA binding sites for 20 proteins and the structural models of the two protein-DNA complexes against experimental results demonstrate the significant promise of our model-building approach... - Automated prediction of protein association rate constantsSanbo Qin
Department of Physics and Institute of Molecular Biophysics, Tallahassee, FL 32306, USA
Structure 19:1744-51. 2011..We expect this server to be a valuable tool for systems biology applications and for kinetic characterization of protein-protein and protein-nucleic acid association in general... - Mechanistic insight into the h(2)o/d (2)o isotope effect in the proton transport of the influenza virus m2 proteinHuan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, USA
J Membr Biol 244:93-6. 2011..This putatively essential role of the His37 tetrad in the functional mechanism of the M2 channel makes it a promising target for designing mutation-tolerant drugs... - Electrostatic rate enhancement and transient complex of protein-protein associationRamzi Alsallaq
Department of Physics, Florida State University, Tallahassee, Florida 32306, USA
Proteins 71:320-35. 2008..Together these results demonstrate that the transient-complex theory is predictive of electrostatic rate enhancement and can help parameterize PB calculations... - Prediction of protein solubility from calculation of transfer free energyHarianto Tjong
Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, Florida 32306, USA
Biophys J 95:2601-9. 2008..This study provides valuable insights into the physical basis of protein solubility... - Influence of solubilizing environments on membrane protein structuresTimothy A Cross
Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
Trends Biochem Sci 36:117-25. 2011..Structures determined in detergents and detergent micelles can have notable differences from those determined in lipid bilayers. These differences make it imperative to validate membrane protein structures... - Do electrostatic interactions destabilize protein-nucleic acid binding?Sanbo Qin
Institute of Molecular Biophysics, School of Computational Science, Florida State University, Tallahassee, FL 32306, USA
Biopolymers 86:112-8. 2007..Effects of charge mutations differentiated the two calculation protocols; PB calculations with the vdW surface had smaller deviations overall from experimental data... - Prediction of protein-protein association rates from a transition-state theoryRamzi Alsallaq
Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, FL 32306, USA
Structure 15:215-24. 2007..The predictions for the wild-type complexes and 23 mutants are found to agree closely with experimental data over wide ranges of ionic strength... - DISPLAR: an accurate method for predicting DNA-binding sites on protein surfacesHarianto Tjong
Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, FL 32306, USA
Nucleic Acids Res 35:1465-77. 2007..Its application to the prion protein yielded a DNA-binding site that is consistent with recent NMR chemical shift perturbation data, suggesting that it can complement experimental techniques in characterizing protein-DNA interfaces... - Electrostatic contributions to T4 lysozyme stability: solvent-exposed charges versus semi-buried salt bridgesFeng Dong
Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
Biophys J 83:1341-7. 2002.... - A method for computing association rate constants of atomistically represented proteins under macromolecular crowdingSanbo Qin
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
Phys Biol 9:066008. 2012..Applications demonstrate that this computational method allows for realistic modeling of protein association kinetics under crowding... - M2 protein from influenza A: from multiple structures to biophysical and functional insightsTimothy A Cross
Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, United States
Curr Opin Virol 2:128-33. 2012..High-resolution structural results in lipid bilayers have provided novel insights into the functional mechanism of the unique HxxxW cluster in the M2 proton channel... - A common model for cytokine receptor activation: combined scissor-like rotation and self-rotation of receptor dimer induced by class I cytokineXiaodong Pang
Department of Physics, Florida State University, Tallahassee, Florida, United States of America
PLoS Comput Biol 8:e1002427. 2012..The transient-complex based approach presented here may provide a strategy for designing antagonists and prove useful for elucidating activation mechanisms of other receptors... - Theory and simulation of diffusion-influenced, stochastically gated ligand binding to buried sitesJorge L Barreda
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
J Chem Phys 135:145101. 2011..Induced switch, whereby the conformation of the protein adapts to the incoming ligand, leads to considerable rate enhancement... - A secondary gate as a mechanism for inhibition of the M2 proton channel by amantadineMyunggi Yi
Department of Physics, Institute of Molecular Biophysics, School of Computational Science, Florida State University, Tallahassee, FL 32306, USA
J Phys Chem B 112:7977-9. 2008..Our study suggests a novel role for Val27 in the inhibition of the M2 proton channel by amantadine... - Protein association with circular DNA: rate enhancement by nonspecific bindingRamzi Alsallaq
Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, FL 32306, USA
J Chem Phys 128:115108. 2008..The higher rate of the linear DNA is possibly due to its more open shape, which affords it a higher ability to draw the protein from the bulk to its surface. The analytical solution is verified by Brownian dynamics simulations... - Direct test of the Gaussian-chain model for treating residual charge-charge interactions in the unfolded state of proteinsHuan Xiang Zhou
Department of Physics, Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
J Am Chem Soc 125:2060-1. 2003..Predicted pK(a)'s were in good agreement with experiment. The clustering of Asp and Glu residues along the sequence was suggested to limit pK(a) shifts and contribute to the folding stability by destabilizing the unfolded state... - Effect of backbone cyclization on protein folding stability: chain entropies of both the unfolded and the folded states are restrictedHuan Xiang Zhou
Department of Physics, Florida State University, Tallahassee, FL 32306, USA
J Mol Biol 332:257-64. 2003..Calculations of deltadeltaG(cycl) for a broad selection of circular proteins suggest that the stabilizing effect of backbone cyclization is modest, reflecting entropy reductions in both the unfolded and the folded states... - Loops, linkages, rings, catenanes, cages, and crowders: entropy-based strategies for stabilizing proteinsHuan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
Acc Chem Res 37:123-30. 2004..Theoretical analyses demonstrate the importance of accounting for consequences on the folded as well as the unfolded state and provide guidance for further exploitation of these stabilization strategies... - Familial hypertrophic cardiomyopathy related E180G mutation increases flexibility of human cardiac α-tropomyosinCampion K P Loong
Department of Biological Science, The Florida State University, Tallahassee, FL 32306 4370, USA
FEBS Lett 586:3503-7. 2012..This marked increase in flexibility can significantly impact systolic and possibly diastolic phases of cardiac contraction, ultimately leading to hypertrophy... - Conformational heterogeneity of the M2 proton channel and a structural model for channel activationMyunggi Yi
Department of Physics, Florida State University, Tallahassee, FL 32306, USA
Proc Natl Acad Sci U S A 106:13311-6. 2009.... - Quantitative computer simulations of biomolecules: a snapshotWei Yang
School of Computational Science, Florida State University, Tallahassee, Florida 32306, USA
J Comput Chem 29:668-72. 2008..Substantial progress in all these areas was reported... - Generalized fundamental measure theory for atomistic modeling of macromolecular crowdingSanbo Qin
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
Phys Rev E Stat Nonlin Soft Matter Phys 81:031919. 2010..The method makes it possible to achieve exhaustive conformational sampling in modeling crowding effects and to tackle challenges posed by large protein oligomers and by complex mixtures of crowders... - Rapid search for specific sites on DNA through conformational switch of nonspecifically bound proteinsHuan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
Proc Natl Acad Sci U S A 108:8651-6. 2011..This induced-switch mechanism provides robust speedup of protein-DNA binding rates, and appears to be adopted by many transcription factors and DNA-modifying enzymes... - Effects of macromolecular crowding on protein conformational changesHao Dong
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, United States of America
PLoS Comput Biol 6:e1000833. 2010..These quantitative results and qualitative trends will serve as valuable guides for expected crowding effects on protein conformation changes inside cells... - Test of the Gouy-Chapman theory for a charged lipid membrane against explicit-solvent molecular dynamics simulationsMyunggi Yi
Department of Physics, Florida State University, Tallahassee, Florida 32306, USA
Phys Rev Lett 101:038103. 2008..We demonstrate that the ion distributions from the simulations agree remarkably well with GC predictions when information on the adsorption of counterions to the bilayer is incorporated... - Backbone dynamics in an intramolecular prolylpeptide-SH3 complex from the diphtheria toxin repressor, DtxRNilakshee Bhattacharya
Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
J Mol Biol 374:977-92. 2007..The results here provide new insights into the nature of the intramolecular complex and provide a better understanding of the biological role of the SH3 domain in regulating DtxR activity... - Selection of near-native poses in CAPRI rounds 13-19Sanbo Qin
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
Proteins 78:3166-73. 2010..Our strategy of mixing predicted and known interface information appears to be widely applicable for the selection of near-native poses... - Similarity and difference in the unfolding of thermophilic and mesophilic cold shock proteins studied by molecular dynamics simulationsXiaoqin Huang
Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, Florida 32306, USA
Biophys J 91:2451-63. 2006..Thus electrostatic interactions appear to play similar roles in the difference in folding stability and kinetics between the pair of proteins... - Atomistic mechanism for the activation and desensitization of an AMPA-subtype glutamate receptorHao Dong
Department of Physics, Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
Nat Commun 2:354. 2011..The detailed mechanism of channel activation and desensitization suggested by the simulations here is consistent with existing data and may serve as a guide for new experiments and for the design of pharmacological agents... - Drug sensitivity, drug-resistant mutations, and structures of three conductance domains of viral porinsMukesh Sharma
Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32310, USA
Biochim Biophys Acta 1808:538-46. 2011..Indeed, drug binding and drug resistance in these viral porins appears to result from a complex set of factors... - From induced fit to conformational selection: a continuum of binding mechanism controlled by the timescale of conformational transitionsHuan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA
Biophys J 98:L15-7. 2010..The timescale of conformational transitions thus plays a crucial role in controlling binding mechanisms... - A theory for the proton transport of the influenza virus M2 protein: extensive test against conductance dataHuan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA
Biophys J 100:912-21. 2011..This study demonstrates that the conductance function of the M2 proton channel can now be quantitatively rationalized by the structure and dynamics of the protein... - Effect of catenation on protein folding stabilityHuan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
J Am Chem Soc 125:9280-1. 2003..This dramatic stabilization derives from the dual effects of backbone cyclization and constrained relative motion between the subunits afforded by the catenane topology... - Rationalizing 5000-fold differences in receptor-binding rate constants of four cytokinesXiaodong Pang
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA
Biophys J 101:1175-83. 2011..Together these results suggest that protein charges can be manipulated to tune k(a) and control biological function... - The effects of macromolecular crowding on the mechanical stability of protein moleculesJian Min Yuan
Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
Protein Sci 17:2156-66. 2008..The experimental results and interpretation presented could have wide implications for the many proteins that experience mechanical stresses and perform mechanical functions in the crowded environment of the cell... - The gates of ion channels and enzymesHuan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
Trends Biochem Sci 35:179-85. 2010..In particular, aromatic residues often appear to serve as gates, probably because of their ability, through side chain rotation, to effect large changes in cross section... - Prediction of salt and mutational effects on the association rate of U1A protein and U1 small nuclear RNA stem/loop IISanbo Qin
Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, Florida 32306, USA
J Phys Chem B 112:5955-60. 2008..These observations are rationalized. Moreover, predicted effects of salt and charge mutations are found to be in quantitative agreement with experimental results... - Energy landscape and transition state of protein-protein associationRamzi Alsallaq
Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, Florida, USA
Biophys J 92:1486-502. 2007..This formalism of protein-protein association is applied to the barnase-barstar complex, reproducing the experimental results for the association rate over a wide range of ionic strength... - Electrostatic recognition and induced fit in the kappa-PVIIA toxin binding to Shaker potassium channelXiaoqin Huang
Institute of Molecular Biophysics and School of Computational Science, Department of Physics, Florida State University, Tallahassee, FL 32306, USA
J Am Chem Soc 127:6836-49. 2005.... - Electrostatic contribution to the binding stability of protein-protein complexesFeng Dong
Department of Physics, Drexel University, Philadelphia, Pennsylvania, USA
Proteins 65:87-102. 2006..The results presented here will serve as a guide for future refinement in electrostatic calculation and inclusion of nonelectrostatic effects... - Dissection of the high rate constant for the binding of a ribotoxin to the ribosomeSanbo Qin
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
Proc Natl Acad Sci U S A 106:6974-9. 2009..Our calculations rationalize a host of experimental observations and identify a strategy for designing proteins that bind their targets with high speed... - Spontaneous conformational change and toxin binding in alpha7 acetylcholine receptor: insight into channel activation and inhibitionMyunggi Yi
Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, FL 32306, USA
Proc Natl Acad Sci U S A 105:8280-5. 2008..The open state has high affinity for agonists, leading to channel activation, whereas the closed state upon distortion has high affinity for antagonists, leading to inhibition... - Rate theories for biologistsHuan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
Q Rev Biophys 43:219-93. 2010.... - Equivalence of two approaches for modeling ion permeation through a transmembrane channel with an internal binding siteHuan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics, Tallahassee, Florida 32306, USA
J Chem Phys 134:135101. 2011..That work provided the foundation for bridging the two approaches. Here we show that, by representing a binding site as an energy well, the two approaches indeed give the same result for the rate of ion transport... - Crowding effects of membrane proteinsHuan Xiang Zhou
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
J Phys Chem B 113:7995-8005. 2009..It is hoped that the article will encourage quantitative analyses in future experiments and spur systematic investigation of membrane crowding effects... - A solvable model for the diffusion and reaction of neurotransmitters in a synaptic junctionJorge L Barreda
Department of Physics and Institute of Molecular Biophysics, Tallahassee, Florida 32306, USA
BMC Biophys 4:5. 2011..abstract:.. - Improving the understanding of human genetic diseases through predictions of protein structures and protein-protein interaction sitesHuan-Xiang Zhou
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
Curr Med Chem 11:539-49. 2004..This initial study illustrates the value of the predicted structure models and may serve as an example for expanded studies of other disease proteins... - Enhancement of association rates by nonspecific binding to DNA and cell membranesHuan-Xiang Zhou
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
Phys Rev Lett 93:178101. 2004..The presence of a surface potential around the target enhances the rate of specific association and for reversible reactions leads to deviations from single exponential relaxation... - GBr(6): a parameterization-free, accurate, analytical generalized born methodHarianto Tjong
Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, Florida 32306, USA
J Phys Chem B 111:3055-61. 2007..The dependencies of the electrostatic solvation free energy on solute and solvent dielectric constants and on salt concentration are fully accounted for in our method... - Prediction of solvent accessibility and sites of deleterious mutations from protein sequenceHuiling Chen
Department of Physics, Drexel University Philadelphia, PA 19104, USA
Nucleic Acids Res 33:3193-9. 2005..Of the total of 130 residues predicted as sites of deleterious mutations, 104 (or 80%) were correct... - Nonadditive effects of mixed crowding on protein stabilityJyotica Batra
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
Proteins 77:133-8. 2009.... - Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR dataHuiling Chen
Department of Physics, Drexel University, Philadelphia, Pennsylvania, USA
Proteins 61:21-35. 2005..cons-PPISP predicted 174 interface residues with 69% accuracy and 47% coverage and promises to complement experimental techniques in characterizing protein-protein interfaces. ... - Histidines, heart of the hydrogen ion channel from influenza A virus: toward an understanding of conductance and proton selectivityJun Hu
Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32310, USA
Proc Natl Acad Sci U S A 103:6865-70. 2006..Furthermore, electrophysiological measurements of multichannel and single-channel experiments confirm that these protein constructs are functional... - Calculation of protein-ligand binding affinitiesMichael K Gilson
Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA
Annu Rev Biophys Biomol Struct 36:21-42. 2007..Ultimately, major improvements in modeling accuracy will likely require advances on multiple fronts, as well as continued validation against experiment...