Hao Hu

Summary

Affiliation: Duke University Medical Center
Country: USA

Publications

  1. pmc Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods
    Hao Hu
    Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
    Annu Rev Phys Chem 59:573-601. 2008
  2. pmc Mechanism of OMP decarboxylation in orotidine 5'-monophosphate decarboxylase
    Hao Hu
    Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
    J Am Chem Soc 130:14493-503. 2008
  3. pmc Simulating water with the self-consistent-charge density functional tight binding method: from molecular clusters to the liquid state
    Hao Hu
    Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
    J Phys Chem A 111:5685-91. 2007
  4. pmc Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method
    Xiancheng Zeng
    Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
    J Chem Phys 130:164111. 2009
  5. doi request reprint Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface
    Hao Hu
    Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
    J Chem Phys 128:034105. 2008
  6. pmc Mechanism of Cdc25B phosphatase with the small molecule substrate p-nitrophenyl phosphate from QM/MM-MFEP calculations
    Jerry M Parks
    Department of Chemistry, Duke University, 124 Science Drive, 5301 French Science Center, Durham, North Carolina 27708 0346, USA
    J Phys Chem B 113:5217-24. 2009
  7. doi request reprint Liquid water simulations with the density fragment interaction approach
    Xiangqian Hu
    Department of Chemistry, Duke University, Durham, NC 27708, USA
    Phys Chem Chem Phys 14:7700-9. 2012
  8. pmc A pseudobond parametrization for improved electrostatics in quantum mechanical/molecular mechanical simulations of enzymes
    Jerry M Parks
    Department of Chemistry, Duke University, 124 Science Drive, 5301 French Science Center, Durham, North Carolina 27708 0346, USA
    J Chem Phys 129:154106. 2008
  9. pmc Equilibrium sampling for biomolecules under mechanical tension
    Xiancheng Zeng
    Department of Chemistry, Duke University, Durham, North Carolina, USA
    Biophys J 98:733-40. 2010
  10. pmc Catalytic mechanism of 4-oxalocrotonate tautomerase: significances of protein-protein interactions on proton transfer pathways
    Pan Wu
    Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
    J Phys Chem B 116:6889-97. 2012

Collaborators

Detail Information

Publications20

  1. pmc Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods
    Hao Hu
    Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
    Annu Rev Phys Chem 59:573-601. 2008
    ..This review features recent developments overcoming these challenges and enabling accurate free-energy determination for reaction processes in solution and in enzymes, along with applications...
  2. pmc Mechanism of OMP decarboxylation in orotidine 5'-monophosphate decarboxylase
    Hao Hu
    Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
    J Am Chem Soc 130:14493-503. 2008
    ..Our simulation results support the direct decarboxylation mechanism and highlight the importance of proper recognition of protein bound water molecules in the protein-ligand binding and the enzyme catalysis...
  3. pmc Simulating water with the self-consistent-charge density functional tight binding method: from molecular clusters to the liquid state
    Hao Hu
    Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
    J Phys Chem A 111:5685-91. 2007
    ....
  4. pmc Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method
    Xiancheng Zeng
    Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
    J Chem Phys 130:164111. 2009
    ..The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions...
  5. doi request reprint Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface
    Hao Hu
    Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
    J Chem Phys 128:034105. 2008
    ....
  6. pmc Mechanism of Cdc25B phosphatase with the small molecule substrate p-nitrophenyl phosphate from QM/MM-MFEP calculations
    Jerry M Parks
    Department of Chemistry, Duke University, 124 Science Drive, 5301 French Science Center, Durham, North Carolina 27708 0346, USA
    J Phys Chem B 113:5217-24. 2009
    ..Thus, Cdc25 may employ a unique dephosphorylation mechanism among protein tyrosine phosphatases, at least in the case of the small molecule substrate p-nitrophenyl phosphate...
  7. doi request reprint Liquid water simulations with the density fragment interaction approach
    Xiangqian Hu
    Department of Chemistry, Duke University, Durham, NC 27708, USA
    Phys Chem Chem Phys 14:7700-9. 2012
    ..With this approach, large-scale quantum mechanical simulations for water and other liquids become feasible...
  8. pmc A pseudobond parametrization for improved electrostatics in quantum mechanical/molecular mechanical simulations of enzymes
    Jerry M Parks
    Department of Chemistry, Duke University, 124 Science Drive, 5301 French Science Center, Durham, North Carolina 27708 0346, USA
    J Chem Phys 129:154106. 2008
    ..Such an approach may enable higher accuracy than general purpose parameters for specific QM/MM applications...
  9. pmc Equilibrium sampling for biomolecules under mechanical tension
    Xiancheng Zeng
    Department of Chemistry, Duke University, Durham, North Carolina, USA
    Biophys J 98:733-40. 2010
    ..REM-US may provide a robust approach to modeling of mechanical stretching on polysaccharides and even nucleic acids...
  10. pmc Catalytic mechanism of 4-oxalocrotonate tautomerase: significances of protein-protein interactions on proton transfer pathways
    Pan Wu
    Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
    J Phys Chem B 116:6889-97. 2012
    ..We further explained that the docking process of 2o4hex can influence the specific reactant conformations and an alternative substrate (2-hydroxymuconate) may serve as reactant under a different reaction mechanism than 2o4hex...
  11. pmc Direct detection of the formation of V-amylose helix by single molecule force spectroscopy
    Qingmin Zhang
    Center for Biologically Inspired Materials and Material Systems and Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
    J Am Chem Soc 128:9387-93. 2006
    ....
  12. pmc Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: fractional electron approach
    Xiancheng Zeng
    Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
    J Chem Phys 128:124510. 2008
    ....
  13. doi request reprint Hepatitis C virus NS5B polymerase: QM/MM calculations show the important role of the internal energy in ligand binding
    Jerry M Parks
    Department of Chemistry, Duke University, 124 Science Drive, 5301 French Science Center, Durham, NC 27708 0346, USA
    J Phys Chem B 112:3168-76. 2008
    ..We show that the most important energetic component contributing to binding for this particular protein-ligand system is the conformational (i.e., QM internal) energy...
  14. pmc Autocatalytic intramolecular isopeptide bond formation in gram-positive bacterial pili: a QM/MM simulation
    Xiangqian Hu
    Department of Chemistry, Duke University, Durham, North Carolina 27708, United States of America
    J Am Chem Soc 133:478-85. 2011
    ..Our results may hopefully shed light on the molecular mechanisms of pilin biogenesis in gram-positive bacteria...
  15. pmc Simulating force-induced conformational transitions in polysaccharides with the SMD replica exchange method
    Zhenyu Lu
    Department of Chemistry, Duke University, Durham, NC 27708, USA
    Biophys J 91:L57-9. 2006
    ....
  16. doi request reprint A gradient-directed Monte Carlo approach for protein design
    Xiangqian Hu
    Department of Chemistry, French Family Science Center, Duke University, Durham, North Carolina 27708 0346, USA
    J Comput Chem 31:2164-8. 2010
    ..As such, GDMC sampling enhances the efficiency of protein design...
  17. ncbi request reprint Dual-topology/dual-coordinate free-energy simulation using QM/MM force field
    Hao Hu
    Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
    J Chem Phys 123:041102. 2005
    ..The method has been tested in computing the solvation free-energy differences of several molecular pairs and shows close agreement with experimental results...
  18. ncbi request reprint Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution
    Hao Hu
    Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599 7260, USA
    Proteins 50:451-63. 2003
    ..For both solutes, the distribution from the QM/MM simulation shows greater similarity with the distribution in high-resolution protein structures than is the case for any of the MM simulations...
  19. ncbi request reprint Increased rigidity of eglin c at acidic pH: evidence from NMR spin relaxation and MD simulations
    Hao Hu
    Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
    Biochemistry 42:13856-68. 2003
    ..As these findings show, the stability of a molecular structure is distinct from its conformational rigidity, and the two can even change in opposite directions, against naïve expectation...
  20. ncbi request reprint Relating side-chain mobility in proteins to rotameric transitions: insights from molecular dynamics simulations and NMR
    Hao Hu
    Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, NC 27599 7360, USA
    J Biomol NMR 32:151-62. 2005
    ....