Huan Xiang Zhou

Summary

Affiliation: Florida State University
Country: USA

Publications

  1. pmc Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar
    Feng Dong
    Department of Physics, Florida State University, Tallahassee, Florida 32306, USA
    Biophys J 85:49-60. 2003
  2. pmc PI2PE: protein interface/interior prediction engine
    Harianto 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
  3. pmc DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces
    Harianto 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
  4. pmc Prediction of solvent accessibility and sites of deleterious mutations from protein sequence
    Huiling Chen
    Department of Physics, Drexel University Philadelphia, PA 19104, USA
    Nucleic Acids Res 33:3193-9. 2005
  5. ncbi request reprint The affinity-enhancing roles of flexible linkers in two-domain DNA-binding proteins
    H X Zhou
    Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
    Biochemistry 40:15069-73. 2001
  6. ncbi request reprint Protein folding and binding in confined spaces and in crowded solutions
    Huan Xiang Zhou
    Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
    J Mol Recognit 17:368-75. 2004
  7. pmc Effect of mixed macromolecular crowding agents on protein folding
    Huan 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
  8. pmc A model for the mediation of processivity of DNA-targeting proteins by nonspecific binding: dependence on DNA length and presence of obstacles
    Huan Xiang Zhou
    Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
    Biophys J 88:1608-15. 2005
  9. pmc A minimum-reaction-flux solution to master-equation models of protein folding
    Huan 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
  10. ncbi request reprint Interactions of macromolecules with salt ions: an electrostatic theory for the Hofmeister effect
    Huan 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

Collaborators

Detail Information

Publications94

  1. pmc Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar
    Feng 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...
  2. pmc PI2PE: protein interface/interior prediction engine
    Harianto 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...
  3. pmc DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces
    Harianto 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...
  4. pmc Prediction of solvent accessibility and sites of deleterious mutations from protein sequence
    Huiling 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...
  5. ncbi request reprint The affinity-enhancing roles of flexible linkers in two-domain DNA-binding proteins
    H 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...
  6. ncbi request reprint Protein folding and binding in confined spaces and in crowded solutions
    Huan 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...
  7. pmc Effect of mixed macromolecular crowding agents on protein folding
    Huan 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...
  8. pmc A model for the mediation of processivity of DNA-targeting proteins by nonspecific binding: dependence on DNA length and presence of obstacles
    Huan Xiang Zhou
    Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
    Biophys J 88:1608-15. 2005
    ....
  9. pmc A minimum-reaction-flux solution to master-equation models of protein folding
    Huan 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...
  10. ncbi request reprint Interactions of macromolecules with salt ions: an electrostatic theory for the Hofmeister effect
    Huan 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...
  11. doi request reprint Calculation of free-energy differences and potentials of mean force by a multi-energy gap method
    Huan 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...
  12. ncbi request reprint 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...
  13. doi request reprint Helix formation inside a nanotube: possible influence of backbone-water hydrogen bonding by the confining surface through modulation of water activity
    Huan 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...
  14. pmc Quantitative relation between intermolecular and intramolecular binding of pro-rich peptides to SH3 domains
    Huan 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...
  15. pmc Protein folding in confined and crowded environments
    Huan 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...
  16. ncbi request reprint Interaction-site prediction for protein complexes: a critical assessment
    Huan Xiang Zhou
    Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
    Bioinformatics 23:2203-9. 2007
    ..A review that presents the current status of interface prediction and an overview of its applications and project future developments is in order...
  17. pmc Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences
    Huan 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...
  18. ncbi request reprint Polymer models of protein stability, folding, and interactions
    Huan 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...
  19. pmc Toward the physical basis of thermophilic proteins: linking of enriched polar interactions and reduced heat capacity of unfolding
    Huan 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...
  20. pmc Residual charge interactions in unfolded staphylococcal nuclease can be explained by the Gaussian-chain model
    Huan 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...
  21. ncbi request reprint Residual electrostatic effects in the unfolded state of the N-terminal domain of L9 can be attributed to nonspecific nonlocal charge-charge interactions
    Huan 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...
  22. pmc A Gaussian-chain model for treating residual charge-charge interactions in the unfolded state of proteins
    Huan Xiang Zhou
    Department of Physics, Drexel University, Philadelphia, PA 19104, USA
    Proc Natl Acad Sci U S A 99:3569-74. 2002
    ....
  23. pmc Association and dissociation kinetics of colicin E3 and immunity protein 3: convergence of theory and experiment
    Huan 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...
  24. ncbi request reprint 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%...
  25. pmc Insight into the mechanism of the influenza A proton channel from a structure in a lipid bilayer
    Mukesh 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...
  26. ncbi request reprint A holistic approach to protein docking
    Sanbo 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...
  27. pmc Electrostatic contributions to the stability of a thermophilic cold shock protein
    Huan 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...
  28. ncbi request reprint Rugged Metropolis sampling with simultaneous updating of two dynamical variables
    Bernd 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...
  29. pmc Solid-state NMR and MD simulations of the antiviral drug amantadine solubilized in DMPC bilayers
    Conggang 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...
  30. pmc Histidines, heart of the hydrogen ion channel from influenza A virus: toward an understanding of conductance and proton selectivity
    Jun 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...
  31. ncbi request reprint Effects of pH, salt, and macromolecular crowding on the stability of FK506-binding protein: an integrated experimental and theoretical study
    Daniel 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...
  32. ncbi request reprint GBr6NL: a generalized Born method for accurately reproducing solvation energy of the nonlinear Poisson-Boltzmann equation
    Harianto 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...
  33. pmc Effect of macromolecular crowding on protein binding stability: modest stabilization and significant biological consequences
    Jyotica Batra
    Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA
    Biophys J 97:906-11. 2009
    ....
  34. pmc Atomistic modeling of macromolecular crowding predicts modest increases in protein folding and binding stability
    Sanbo 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...
  35. pmc Electrostatic contributions to T4 lysozyme stability: solvent-exposed charges versus semi-buried salt bridges
    Feng Dong
    Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
    Biophys J 83:1341-7. 2002
    ....
  36. ncbi request reprint Electrostatic recognition and induced fit in the kappa-PVIIA toxin binding to Shaker potassium channel
    Xiaoqin 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
    ....
  37. pmc The folding transition-state ensemble of a four-helix bundle protein: helix propensity as a determinant and macromolecular crowding as a probe
    Harianto 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...
  38. ncbi request reprint meta-PPISP: a meta web server for protein-protein interaction site prediction
    Sanbo Qin
    Institute of Molecular Biophysics, School of Computational Science, Florida State University, Tallahassee, Florida 32306, USA
    Bioinformatics 23:3386-7. 2007
    ..At coverages identical to those of the individual methods, the accuracy of meta-PPISP is higher by 4.8 to 18.2 percentage points. Similar improvements in accuracy are also seen on CAPRI and other targets...
  39. pmc A method to determine dielectric constants in nonhomogeneous systems: application to biological membranes
    Hugh 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...
  40. ncbi request reprint Electrostatic contribution to the binding stability of protein-protein complexes
    Feng 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...
  41. pmc Prediction of protein solubility from calculation of transfer free energy
    Harianto 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...
  42. pmc Binding of MgtR, a Salmonella transmembrane regulatory peptide, to MgtC, a Mycobacterium tuberculosis virulence factor: a structural study
    Frantz L Jean-Francois
    National High Magnetic Field Laboratory, Tallahassee, FL 32306, USA Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
    J Mol Biol 426:436-46. 2014
    ..Based on the experimental restraints, a structural model of this heterodimer was developed using computational techniques. The result is that MgtR appears to be ideally situated in the membrane to influence the functionality of MgtC. ..
  43. ncbi request reprint Enhancement of association rates by nonspecific binding to DNA and cell membranes
    Huan 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...
  44. ncbi request reprint Quantitative account of the enhanced affinity of two linked scFvs specific for different epitopes on the same antigen
    Huan 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...
  45. pmc Prediction and dissection of widely-varying association rate constants of actin-binding proteins
    Xiaodong Pang
    Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, United States of America
    PLoS Comput Biol 8:e1002696. 2012
    ..This study demonstrates the various ways that actin-binding proteins use physical properties to tune their association mechanisms and rate constants to suit distinct regulatory functions...
  46. pmc Structural models of protein-DNA complexes based on interface prediction and docking
    Sanbo 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...
  47. pmc Automated prediction of protein association rate constants
    Sanbo 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...
  48. pmc Mechanistic insight into the h(2)o/d (2)o isotope effect in the proton transport of the influenza virus m2 protein
    Huan 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...
  49. pmc Influence of solubilizing environments on membrane protein structures
    Timothy 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...
  50. pmc Using the concept of transient complex for affinity predictions in CAPRI rounds 20-27 and beyond
    Sanbo Qin
    Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, 32306
    Proteins 81:2229-36. 2013
    ..We conclude that the interaction energy landscape and the transient complex in particular will complement existing features in leading to better prediction of binding affinities...
  51. pmc Conformational heterogeneity of the M2 proton channel and a structural model for channel activation
    Myunggi Yi
    Department of Physics, Florida State University, Tallahassee, FL 32306, USA
    Proc Natl Acad Sci U S A 106:13311-6. 2009
    ....
  52. ncbi request reprint 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...
  53. ncbi request reprint Prediction of protein-protein association rates from a transition-state theory
    Ramzi 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...
  54. pmc Similarity and difference in the unfolding of thermophilic and mesophilic cold shock proteins studied by molecular dynamics simulations
    Xiaoqin 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...
  55. pmc Electrostatic rate enhancement and transient complex of protein-protein association
    Ramzi 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...
  56. pmc Modeling the membrane environment has implications for membrane protein structure and function: influenza A M2 protein
    Huan Xiang Zhou
    Department of Physics, Florida State University, Tallahassee, Florida 32306, USA
    Protein Sci 22:381-94. 2013
    ..Integration with computation has provided detailed understanding of the functional mechanism for proton selectivity, conductance and gating of this important drug target...
  57. pmc A method for computing association rate constants of atomistically represented proteins under macromolecular crowding
    Sanbo 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...
  58. pmc M2 protein from influenza A: from multiple structures to biophysical and functional insights
    Timothy 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...
  59. pmc A common model for cytokine receptor activation: combined scissor-like rotation and self-rotation of receptor dimer induced by class I cytokine
    Xiaodong 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...
  60. pmc Theory and simulation of diffusion-influenced, stochastically gated ligand binding to buried sites
    Jorge 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...
  61. ncbi request reprint Loops, linkages, rings, catenanes, cages, and crowders: entropy-based strategies for stabilizing proteins
    Huan 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...
  62. ncbi request reprint Direct test of the Gaussian-chain model for treating residual charge-charge interactions in the unfolded state of proteins
    Huan 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...
  63. ncbi request reprint Improving the understanding of human genetic diseases through predictions of protein structures and protein-protein interaction sites
    Huan 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...
  64. ncbi request reprint Effect of backbone cyclization on protein folding stability: chain entropies of both the unfolded and the folded states are restricted
    Huan 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...
  65. pmc A secondary gate as a mechanism for inhibition of the M2 proton channel by amantadine
    Myunggi 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...
  66. doi request reprint Protein association with circular DNA: rate enhancement by nonspecific binding
    Ramzi 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...
  67. pmc Familial hypertrophic cardiomyopathy related E180G mutation increases flexibility of human cardiac α-tropomyosin
    Campion 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...
  68. pmc Effects of macromolecular crowding on protein conformational changes
    Hao 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...
  69. pmc Selection of near-native poses in CAPRI rounds 13-19
    Sanbo 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...
  70. pmc Rapid search for specific sites on DNA through conformational switch of nonspecifically bound proteins
    Huan 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...
  71. pmc Generalized fundamental measure theory for atomistic modeling of macromolecular crowding
    Sanbo 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...
  72. ncbi request reprint Quantitative computer simulations of biomolecules: a snapshot
    Wei 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...
  73. pmc Backbone dynamics in an intramolecular prolylpeptide-SH3 complex from the diphtheria toxin repressor, DtxR
    Nilakshee 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...
  74. pmc Test of the Gouy-Chapman theory for a charged lipid membrane against explicit-solvent molecular dynamics simulations
    Myunggi 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...
  75. ncbi request reprint Effect of catenation on protein folding stability
    Huan 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...
  76. pmc Energy landscape and transition state of protein-protein association
    Ramzi 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...
  77. pmc Prediction of salt and mutational effects on the association rate of U1A protein and U1 small nuclear RNA stem/loop II
    Sanbo 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...
  78. pmc The effects of macromolecular crowding on the mechanical stability of protein molecules
    Jian 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...
  79. pmc Atomistic mechanism for the activation and desensitization of an AMPA-subtype glutamate receptor
    Hao 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...
  80. pmc Rationalizing 5000-fold differences in receptor-binding rate constants of four cytokines
    Xiaodong 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...
  81. pmc From induced fit to conformational selection: a continuum of binding mechanism controlled by the timescale of conformational transitions
    Huan 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...
  82. pmc Drug sensitivity, drug-resistant mutations, and structures of three conductance domains of viral porins
    Mukesh 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...
  83. pmc The gates of ion channels and enzymes
    Huan 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...
  84. pmc A theory for the proton transport of the influenza virus M2 protein: extensive test against conductance data
    Huan 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...
  85. pmc Spontaneous conformational change and toxin binding in alpha7 acetylcholine receptor: insight into channel activation and inhibition
    Myunggi 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...
  86. pmc Dissection of the high rate constant for the binding of a ribotoxin to the ribosome
    Sanbo 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...
  87. pmc Rate theories for biologists
    Huan Xiang Zhou
    Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
    Q Rev Biophys 43:219-93. 2010
    ....
  88. pmc Crowding effects of membrane proteins
    Huan 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...
  89. pmc A solvable model for the diffusion and reaction of neurotransmitters in a synaptic junction
    Jorge L Barreda
    Department of Physics and Institute of Molecular Biophysics, Tallahassee, Florida 32306, USA
    BMC Biophys 4:5. 2011
    ..abstract:..
  90. pmc Equivalence of two approaches for modeling ion permeation through a transmembrane channel with an internal binding site
    Huan 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...
  91. ncbi request reprint GBr(6): a parameterization-free, accurate, analytical generalized born method
    Harianto 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...
  92. doi request reprint Nonadditive effects of mixed crowding on protein stability
    Jyotica Batra
    Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
    Proteins 77:133-8. 2009
    ....
  93. ncbi request reprint Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data
    Huiling 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. ...
  94. ncbi request reprint Calculation of protein-ligand binding affinities
    Michael 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...