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Abstract
The specific electric field generated by a protease at its active site is considered as an important source of the catalytic power. Accurate calculation of electric field at the active site of an enzyme has both fundamental and practical importance. Measuring site-specific changes of electric field at internal sites of proteins due to, eg, mutation, has been realized by using molecular probes with CO or CN groups in the context of vibrational Stark effect. However, theoretical prediction of change in electric field inside a protein based on a conventional force field, such as AMBER or OPLS, is often inadequate. For such calculation, quantum chemical approach or quantum-based polarizable or polarized force field is highly preferable. Compared with the result from conventional force field, significant improvement is found in predicting experimentally measured mutation-induced electric field change using quantum-based methods, indicating that quantum effect such as polarization plays an important role in accurate description of electric field inside proteins. In comparison, the best theoretical prediction comes from fully quantum mechanical calculation in which both polarization and inter-residue charge transfer effects are included for accurate prediction of electrostatics in proteins.
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Affiliation(s)
- X Wang
- Center for Optics & Optoelectronics Research, College of Science, Zhejiang University of Technology, Hangzhou, Zhejiang, China; School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - X He
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China; NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China.
| | - J Z H Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China; NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China; New York University, New York, NY, United States.
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2
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Abstract
A local linear least square (LLLS) method to fit multidimensional potential energy surface for quantum dynamics calculation is presented. The method uses only energy data points within a local area in multidimentional space. The potential is fit using a linear least square method with singular value decomposition. The method is tested in quantum dynamical calculation for three-dimensional H + H2 reaction. The result indicates that the local linear least square fitting is accurate and computationally efficient.
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Affiliation(s)
- Da W. Zhang
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Yi M. Li
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - J. Z. H. Zhang
- Department of Chemistry, New York University, New York, NY 10003, USA
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
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3
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Abstract
The peroxisome proliferator-activated receptor (PPAR-gamma) is a ligand-dependent transcription factor that is important in adipocyte differentiation and glucose homeostasis. This paper presents a detailed dynamics study of PPAR-gamma and its binding to the agonist rosiglitazone using both polarized and unpolarized force fields. The numerical result revealed the critical role of protein polarization in stabilizing the activation function-2 (AF-2) in ligand binding to PPAR-gamma and a helix structure (helix-2'). Specifically when nonpolarized force field is used, a critical H-bond in PPAR-gamma binding is broken, which caused AF-2 to adopt random structures. In addition, helix-2' is partially denatured during the MD simulation, due to the breaking of a backbone hydrogen bond. In contrast, when polarized force field is employed in MD simulation, the PPAR-gamma ligand binding structure is stabilized and the local structure of helix-2' remains folded, both being in excellent agreement with experimental observations. The current result demonstrates the importance of electronic polarization of protein in stabilizing hydrogen bonding, which is critical to preserving the native structure of local helices and protein-ligand binding in PPAR-gamma.
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Affiliation(s)
- C G Ji
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
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4
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Bao J, Zhang DW, Zhang JZH, Huang PL, Huang PL, Lee-Huang S. Computational study of bindings of olive leaf extract (OLE) to HIV-1 fusion protein gp41. FEBS Lett 2007; 581:2737-42. [PMID: 17537437 DOI: 10.1016/j.febslet.2007.05.029] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Revised: 05/03/2007] [Accepted: 05/09/2007] [Indexed: 10/23/2022]
Abstract
Recent experimental study found that OLE (olive leaf extract) has anti-HIV activity by blocking the HIV virus entry to host cells [Lee-Huang, S., Zhang, L., Huang, P.L., Chang, Y. and Huang, P.L. (2003) Anti-HIV activity of olive leaf extract (OLE) and modulation of host cell gene expression by HIV-1 infection and OLE treatment. Biochem. Biophys. Res. Commun. 307, 1029; Lee-Huang, S., Huang, P.L., Zhang, D., Lee, J.W., Bao, J., Sun, Y., Chang, Y.-Tae, Zhang, J.Z.H. and Huang, P.L. (2007) Discovery of small-molecule HIV-1 fusion and integrase inhibitors oleuropein and hydroxytyrosol. Biochem. Biophys. Res. Commun. 354, 872-878, 879-884]. As part of a joint experimental and theoretical effort, we report here computational study to help identify and characterize the binding complexes of several main compounds of OLE (olive leaf extract) to HIV-1 envelop protein gp41. A number of possible binding modes are found by docking oleuropein and its metabolites, aglycone, elenolic acid and hydroxytyrosol, onto the hydrophobic pocket on gp41. Detailed OLE-gp41 binding interactions and free energies of binding are obtained through molecular dynamics simulation and MM-PBSA calculation. Specific molecular interactions in our predicted OLE/gp41 complexes are identified and hydroxytyrosol is identified to be the main moiety for binding to gp41. This computational study complements the corresponding experimental investigation and helps establish a good starting point for further refinement of OLE-based gp41 inhibitors.
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Affiliation(s)
- J Bao
- Department of Chemistry, New York University, New York, NY 10003, USA
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5
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Varandas AJC, Caridade PJSB, Zhang JZH, Cui Q, Han KL. Dynamics of X+CH4 (X=H,O,Cl) reactions: How reliable is transition state theory for fine-tuning potential energy surfaces? J Chem Phys 2006; 125:64312. [PMID: 16942291 DOI: 10.1063/1.2217953] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Trajectory calculations run on global potential energy surfaces have shown that the topology of the entrance channel has strong implications on the dynamics of the title reactions. This may explain why huge differences are observed between the rate constants calculated from global dynamical methods and those obtained from local methods that employ the same potential energy surfaces but ignore such topological details. Local dynamics approaches such as transition state-based theories should then be used with caution for fine-tuning potential energy surfaces, especially for fast reactions with polyatomic species since the key statistical assumptions of the theory may not be valid for all degrees of freedom.
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Affiliation(s)
- A J C Varandas
- Departamento de Química, Universidade de Coimbra, 3004-535 Coimbra, Portugal.
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6
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Chen XH, Zhang JZH. Molecular fractionation with conjugated caps density matrix with pairwise interaction correction for protein energy calculation. J Chem Phys 2006; 125:44903. [PMID: 16942188 DOI: 10.1063/1.2218341] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Pairwise interaction correction (PIC) is introduced to account for electron density polarization due to short-range interactions such as hydrogen bonding and close contact between molecular fragments in the molecular fractionation with conjugated caps density matrix (MFCC-DM) approach for energy calculation of protein and other polymers [Chen et al., J. Chem. Phys. 122, 184105 (2005)]. With this PIC, the accuracy of the calculated protein energy and other electronic properties are improved, and the MFCC approach can be applied to study real proteins with short-range structural complexity. In the present MFCC-DM-PIC approach, the short-range interresidual interactions are represented by a pair of small molecules (interacting units) which are made from the two residues that fall within a certain distance criterion. The density matrices of fragments, concaps, interacting units and pairs are calculated by conventional Hartree-Fock or density functional theory methods and are combined to construct the full density matrix which is finally employed to calculate the total energy, electron density, electrostatic potential, dipole moment, etc., of the protein. Numerical tests on seven conformationally varied peptides are presented to demonstrate the accuracy of the MFCC-DM-PIC method.
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Affiliation(s)
- X H Chen
- Department of Chemistry, New York University, New York, New York 10003, USA
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7
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Abstract
Full quantum mechanical computational study has been carried out to study binding of efavirenz (EFZ), a second generation FDA approved nonnucleoside inhibitor, to HIV-1 reverse transcriptase (RT) and its K103N and Y181C mutants using the MFCC (molecular fractionation with conjugate caps) method. The binding interaction energies between EFZ and each protein fragment are calculated using a combination of HF/3-21G, B3LYP/6-31G* and MP2/6-31G* ab initio levels. The present computation shows that Efavirenz binds to HIV-1 RT predominantly through strong electrostatic interaction with the Lys101 residue. The small loss of binding to K103N mutant by Efavirenz can be attributed to a slightly weakened attractive interaction between the drug and Lys101 due to a conformational change of mutation. The small loss of binding to Y181C mutant by efavirenz can be attributed to the Glu698 residue moving closer to EFZ due to conformational change, which results in an increase of repulsive energy relative to the wild type (WT). The binding of efavirenz-derived DPC961 to HIV-1 RT is enhanced by an additional attractive interaction to residue Hid235 and reduced repulsion to Glu698, resulting in an increase of binding energy by about 4 kcal/mol.
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Affiliation(s)
- Ye Mei
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, College of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
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8
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Abstract
A new scheme for direct linear-scaling quantum mechanical calculation of electron density of protein systems is developed. The new scheme gives much improved accuracy of electron density for proteins than the original MFCC (molecular fractionation with conjugate caps) approach in efficient linear-scaling calculation for protein systems. In this new approach, the error associated with each cut in the MFCC approach is estimated by computing the two neighboring amino acids in both cut and uncut calculations and is corrected. Numerical tests are performed on six oligopeptide taken from PDB (protein data bank), and the results show that the new scheme is efficient and accurate.
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9
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Abstract
We present a systematic study of numerical accuracy of various forms of molecular caps that are employed in a recently developed molecular fractionation scheme for full quantum mechanical computation of protein-molecule interaction energy. A previously studied pentapeptide (Gly-Ser-Ala-Asp-Val) or P5 interacting with a water molecule is used as a benchmark system for numerical testing. One-dimensional potential energy curves are generated for a number of peptide-water interaction pathways. Our study shows that various forms of caps all give consistently accurate energies compared to the corresponding full system calculation with only small deviations. We also tested the accuracy of cutting peptide backbone at different positions and comparisons of results are presented.
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Affiliation(s)
- D W Zhang
- Department of Chemistry, New York University, New York, New York 10003, USA
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10
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Chen XH, Zhang DW, Zhang JZH. Fractionation of peptide with disulfide bond for quantum mechanical calculation of interaction energy with molecules. J Chem Phys 2004; 120:839-44. [PMID: 15267920 DOI: 10.1063/1.1630964] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a computational study of a recently developed molecular fractionation with conjugated caps (MFCC) method for application to peptide/protein that has disulfide bonds. Specifically, we employ the MFCC approach to generate peptide fragments in which a disulfide bond is cut and a pair of conjugated caps are inserted. The method is tested on two peptides interacting with a water molecule. The first is a dipeptide consisting of two cysteines (Cys-Cys) connected by a disulfide bond and the second is a seven amino acid peptide consisting of Gly-Cys-Gly-Gly-Gly-Cys-Gly with a disulfide cross link. One-dimensional peptide-water potential curves are computed using the MFCC method at various ab initio levels for a number of interaction geometries. The calculated interaction energies are found to be in excellent agreement with the results obtained from the corresponding full system ab initio calculations for both peptide/water systems. The current study provides further numerical support for the accuracy of the MFCC method in full quantum mechanical calculation of protein/peptide that contains disulfide bonds.
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Affiliation(s)
- X H Chen
- Department of Chemistry, New York University, New York, New York 10003, USA
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12
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Cui Q, He X, Wang ML, Zhang JZH. Comparison of quantum and mixed quantum–classical semirigid vibrating rotor target studies for isotopic reactions H(D,T)+CH4→HH(D,T)+CH3. J Chem Phys 2003. [DOI: 10.1063/1.1615514] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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13
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Zhang DW, Zhang JZH. Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein–molecule interaction energy. J Chem Phys 2003. [DOI: 10.1063/1.1591727] [Citation(s) in RCA: 437] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15
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Zhang DW, Wang ML, Zhang JZH. Quantum Dynamics Study of Torsional Excitation of Glycine in Collision with Hydrogen Atom on ab Initio Potential Energy Surface. J Phys Chem A 2003. [DOI: 10.1021/jp0300290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Da W. Zhang
- Department of Chemistry, New York University, New York, New York 10003
| | - Ming L. Wang
- Department of Chemistry, New York University, New York, New York 10003
| | - J. Z. H. Zhang
- Department of Chemistry, New York University, New York, New York 10003
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Zhang DW, Wang ML, Zhang JZH. Ab initio quantum dynamics study of rotationally inelastic scattering of glycine by hydrogen atom. J Chem Phys 2003. [DOI: 10.1063/1.1535892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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17
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Wang ML, Zhang JZH. Erratum: “Stereodynamics and rovibrational effect for H+CH4(v,j,K,n)→H2+CH3 reaction” [J. Chem. Phys. 116, 6497 (2002)]. J Chem Phys 2002. [DOI: 10.1063/1.1519004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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Wang ML, Zhang JZH. Erratum: “Generalized semirigid vibrating rotor target model for atom–poly reaction: Inclusion of umbrella mode for H+CH4 reaction” [J. Chem. Phys. 117, 3081 (2002)]. J Chem Phys 2002. [DOI: 10.1063/1.1519003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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19
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Wang ML, Zhang JZH. Generalized semirigid vibrating rotor target model for atom–poly reaction: Inclusion of umbrella mode for H+CH4 reaction. J Chem Phys 2002. [DOI: 10.1063/1.1494782] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Zhang DH, Zhang JZH. The semirigid vibrating rotor target model for atom-polyatom reaction: Application to H+H2O→H2+OH. J Chem Phys 2000. [DOI: 10.1063/1.480551] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Bačić Z, Zhang JZH. High‐lying rovibrational states of floppy X3 triatomics by a new D3h symmetry adapted method: Application to the H+3 molecule. J Chem Phys 1992. [DOI: 10.1063/1.461925] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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