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Theoretical characterization of the shikimate 5-dehydrogenase reaction from Mycobacterium tuberculosis by hybrid QC/MM simulations and quantum chemical descriptors. J Mol Model 2020; 26:297. [PMID: 33030705 DOI: 10.1007/s00894-020-04536-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/07/2020] [Indexed: 11/27/2022]
Abstract
In this study, we have investigated the enzyme shikimate 5-dehydrogenase from the causative agent of tuberculosis, Mycobacterium tuberculosis. We have employed a mixture of computational techniques, including molecular dynamics, hybrid quantum chemical/molecular mechanical potentials, relaxed surface scans, quantum chemical descriptors and free-energy simulations, to elucidate the enzyme's reaction pathway. Overall, we find a two-step mechanism, with a single transition state, that proceeds by an energetically uphill hydride transfer, followed by an energetically downhill proton transfer. Our mechanism and calculated free energy barrier for the reaction, 64.9 kJ mol- 1, are in good agreement with those predicted from experiment. An analysis of quantum chemical descriptors along the reaction pathway indicated a possibly important, yet currently unreported, role of the active site threonine residue, Thr65.
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Sirirak J, Lawan N, Van der Kamp MW, Harvey JN, Mulholland AJ. Benchmarking quantum mechanical methods for calculating reaction energies of reactions catalyzed by enzymes. PEERJ PHYSICAL CHEMISTRY 2020. [DOI: 10.7717/peerj-pchem.8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
To assess the accuracy of different quantum mechanical methods for biochemical modeling, the reaction energies of 20 small model reactions (chosen to represent chemical steps catalyzed by commonly studied enzymes) were calculated. The methods tested included several popular Density Functional Theory (DFT) functionals, second-order Møller Plesset perturbation theory (MP2) and its spin-component scaled variant (SCS-MP2), and coupled cluster singles and doubles and perturbative triples (CCSD(T)). Different basis sets were tested. CCSD(T)/aug-cc-pVTZ results for all 20 reactions were used to benchmark the other methods. It was found that MP2 and SCS-MP2 reaction energy calculation results are similar in quality to CCSD(T) (mean absolute error (MAE) of 1.2 and 1.3 kcal mol−1, respectively). MP2 calculations gave a large error in one case, and are more subject to basis set effects, so in general SCS-MP2 calculations are a good choice when CCSD(T) calculations are not feasible. Results with different DFT functionals were of reasonably good quality (MAEs of 2.5–5.1 kcal mol−1), whereas popular semi-empirical methods (AM1, PM3, SCC-DFTB) gave much larger errors (MAEs of 11.6–14.6 kcal mol−1). These results should be useful in guiding methodological choices and assessing the accuracy of QM/MM calculations on enzyme-catalyzed reactions.
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Affiliation(s)
- Jitnapa Sirirak
- Department of Chemistry, Faculty of Science, Silpakorn University, Nakhon Pathom, Thailand
| | - Narin Lawan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | | | | | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
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Nam K, Cui Q, Gao J, York DM. Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions: H, O, and P Atoms. J Chem Theory Comput 2015; 3:486-504. [PMID: 26637030 DOI: 10.1021/ct6002466] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A semiempirical AM1/d Hamiltonian is developed to model phosphoryl transfer reactions catalyzed by enzymes and ribozymes for use in linear-scaling calculations and combined quantum mechanical/molecular mechanical simulations. The model, designated AM1/d-PhoT, is parametrized for H, O, and P atoms to reproduce high-level density-functional results from a recently constructed database of quantum calculations for RNA catalysis ( http://theory.chem.umn.edu/Database/QCRNA ), including geometries and relative energies of minima, transition states and reactive intermediates, dipole moments, proton affinities, and other relevant properties. The model is tested in the gas phase and in solution using a QM/MM potential. The results indicate that the method provides significantly higher accuracy than MNDO/d, AM1, and PM3 methods and, for the transphosphorylation reactions, is in close agreement with the density-functional calculations at the B3LYP/6-311++G(3df,2p) level with a reduction in computational cost of 3-4 orders of magnitude. The model is expected to have considerable impact on the application of semiempirical QM/MM methods to transphosphorylation reactions in solution, enzymes, and ribozymes and to ultimately facilitate the design of improved next-generation multiscale quantum models.
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Affiliation(s)
- Kwangho Nam
- Department of Chemistry and Supercomputing Institute and the Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706
| | - Qiang Cui
- Department of Chemistry and Supercomputing Institute and the Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute and the Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706
| | - Darrin M York
- Department of Chemistry and Supercomputing Institute and the Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706
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4
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Ohwaki T, Otani M, Ozaki T. A method of orbital analysis for large-scale first-principles simulations. J Chem Phys 2014; 140:244105. [DOI: 10.1063/1.4884119] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Abstract
Techniques for modelling enzyme-catalyzed reaction mechanisms are making increasingly important contributions to biochemistry. They can address fundamental questions in enzyme catalysis and have the potential to contribute to practical applications such as drug development.
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Shravani M, Balaiah S, Srinivas K, Bhanuprakash K, Huc I. Unusual Regioselective Electrophilic Substitutions in Quinoline Foldamers: Conceptual DFT and Frontier Molecular Orbital Analysis Reveal the Crucial Role of Folding and Substituents. Chemphyschem 2012; 13:3526-34. [PMID: 22887893 DOI: 10.1002/cphc.201200397] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Indexed: 11/06/2022]
Affiliation(s)
- Madishetti Shravani
- National Institute of Pharmaceutical Education and Research, Hyderabad, Balanagar, India
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7
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Divide-and-Conquer Approaches to Quantum Chemistry: Theory and Implementation. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2011. [DOI: 10.1007/978-90-481-2853-2_5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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8
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9
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Anisimov VM, Bugaenko VL. QM/QM docking method based on the variational finite localized molecular orbital approximation. J Comput Chem 2009; 30:784-98. [DOI: 10.1002/jcc.21100] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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10
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van der Kamp MW, Shaw KE, Woods CJ, Mulholland AJ. Biomolecular simulation and modelling: status, progress and prospects. J R Soc Interface 2008; 5 Suppl 3:S173-90. [PMID: 18611844 PMCID: PMC2706107 DOI: 10.1098/rsif.2008.0105.focus] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Revised: 06/05/2008] [Accepted: 06/06/2008] [Indexed: 11/12/2022] Open
Abstract
Molecular simulation is increasingly demonstrating its practical value in the investigation of biological systems. Computational modelling of biomolecular systems is an exciting and rapidly developing area, which is expanding significantly in scope. A range of simulation methods has been developed that can be applied to study a wide variety of problems in structural biology and at the interfaces between physics, chemistry and biology. Here, we give an overview of methods and some recent developments in atomistic biomolecular simulation. Some recent applications and theoretical developments are highlighted.
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Affiliation(s)
| | | | | | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of BristolBristol BS8 1TS, UK
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11
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Chang DT, Schenter GK, Garrett BC. Self-consistent polarization neglect of diatomic differential overlap: application to water clusters. J Chem Phys 2008; 128:164111. [PMID: 18447425 DOI: 10.1063/1.2905230] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Semiempirical self-consistent field (SCF) methods based on the neglect of diatomic differential overlap (NDDO) formalism have the ability to treat the formation and breaking of chemical bonds but have been found to poorly describe hydrogen bonding and weak electrostatic complexes. In contrast, most empirical potentials are not able to describe bond breaking and formation but have the ability to add missing elements of hydrogen bonding by using classical electrostatic interactions. We present a new method which combines aspects of both NDDO-based SCF techniques and classical descriptions of polarization to describe the diffuse nature of the electronic wavefunction in a self-consistent manner. We develop the "self-consistent polarization neglect of diatomic differential overlap" (SCP-NDDO) theory with the additional description of molecular dispersion developed as a second-order perturbation theory expression. The current study seeks to model water-water interactions as a test case. To this end, we have parametrized the method to accurate ab initio complete basis set limit estimates of small water cluster binding energies of Xantheas and co-workers [J. Chem. Phys. 116, 1493 (2002); 120, 823 (2004)]. Overall agreement with the ab initio binding energies (n=2-6, and 8) is achieved with a rms error of 0.19 kcal/mol. We achieve noticeable improvements in the structure, vibrational frequencies, and energetic predictions of water clusters (n< or =21) relative to standard NDDO-based methods.
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Affiliation(s)
- Daniel T Chang
- Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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Lee JG, Lee YS, Roland C. Structural determination of large molecules through the reassembly of optimized fragments. J Mol Graph Model 2008; 27:364-75. [PMID: 18644742 DOI: 10.1016/j.jmgm.2008.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2008] [Revised: 06/09/2008] [Accepted: 06/13/2008] [Indexed: 11/12/2022]
Abstract
The accurate determination of the optimized structures of large molecules is, computationally quite expensive. As an alternate to the conventional approaches to structural optimization, we have explored the accuracy and speed-up obtained when variants of the fragmentation optimization and recombination method (FORM) are used. Specifically, the method was applied to eight prototypical molecules -n-decane, hexa-alanine, a long conjugate hydrocarbon molecule, a large polar conjugated molecule, large (5,5) armchair single-walled carbon nanotubes, a salen-aluminum complex and a multiply H-bonded system (two conformers of vancomycin aglycon with Di-N-acetyl-l-Lys-d-Ala-d-Ala - without optimizing the structure of the whole molecules. We find that FORM can predict the structure of these molecules with an acceptable accuracy, all at a computational cost that is 2-11 times less than conventional quantum mechanical methods at the Hartree-Fock (HF), density functional theory (DFT) and MP2 level of accuracy. FORM may therefore represent a viable approach for the fast structural predictions of large molecules.
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Affiliation(s)
- Jung-Goo Lee
- Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, NC 27695, USA.
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13
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Yang Y, Yu H, York D, Cui Q, Elstner M. Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method: Third-Order Expansion of the Density Functional Theory Total Energy and Introduction of a Modified Effective Coulomb Interaction. J Phys Chem A 2007; 111:10861-73. [PMID: 17914769 DOI: 10.1021/jp074167r] [Citation(s) in RCA: 213] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The standard self-consistent-charge density-functional-tight-binding (SCC-DFTB) method (Phys. Rev. B 1998, 58, 7260) is derived by a second-order expansion of the density functional theory total energy expression, followed by an approximation of the charge density fluctuations by charge monopoles and an effective damped Coulomb interaction between the atomic net charges. The central assumptions behind this effective charge-charge interaction are the inverse relation of atomic size and chemical hardness and the use of a fixed chemical hardness parameter independent of the atomic charge state. While these approximations seem to be unproblematic for many covalently bound systems, they are quantitatively insufficient for hydrogen-bonding interactions and (anionic) molecules with localized net charges. Here, we present an extension of the SCC-DFTB method to incorporate third-order terms in the charge density fluctuations, leading to chemical hardness parameters that are dependent on the atomic charge state and a modification of the Coulomb scaling to improve the electrostatic treatment within the second-order terms. These modifications lead to a significant improvement in the description of hydrogen-bonding interactions and proton affinities of biologically relevant molecules.
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Affiliation(s)
- Yang Yang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
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14
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Giese TJ, York DM. Improvement of semiempirical response properties with charge-dependent response density. J Chem Phys 2007; 123:164108. [PMID: 16268682 DOI: 10.1063/1.2080007] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The present work outlines a new method for treatment of charge-dependent polarizability in semiempirical quantum models for use in combined quantum-mechanical/molecular mechanical simulations of biological reactions. The method addresses a major shortcoming in the performance of conventional semiempirical models for these simulations that is tied to the use of a localized minimal atomic-orbital basis set. The present approach has the advantages that it uses a density basis that retains a set of linear-response equations, does not increase the atomic-orbital basis, and avoids the problem of artificial charge transfer and scaling of the polarizability seen in related models that allow atomic charges to fluctuate. The model introduces four new atom-based parameters and has been tested with the modified neglect of differential overlap d-orbital Hamiltonian against 1132 molecules and ions and shown to decrease the dipole moment and polarizability errors by factors of 2 and 10, respectively, with respect to density-functional results. The method performs impressively for a variety of charge states (from 2+ to 2-), and offers a potentially powerful extension in the design of next generation semiempirical quantum models for accurate simulations of highly charged biological reactions.
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Affiliation(s)
- Timothy J Giese
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
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15
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Range K, López CS, Moser A, York DM. Multilevel and density functional electronic structure calculations of proton affinities and gas-phase basicities involved in biological phosphoryl transfer. J Phys Chem A 2007; 110:791-7. [PMID: 16405355 DOI: 10.1021/jp054360q] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Five multilevel model chemistries (CBS-QB3, G3B3, G3MP2B3, MCG3/3, and MC-QCISD/3) and seven hybrid density functional methods (PBE0, B1B95, B3LYP, MPW1KCIS, PBE1KCIS, and MPW1B95) have been applied to the calculation of gas-phase basicity and proton affinity values for a series of 17 molecules relevant to the study of biological phosphoryl transfer. In addition, W1 calculations were performed on a subset of molecules. The accuracy of the methods was assessed and the nature of systematic errors was explored, leading to the introduction of a set of effective bond enthalpy and entropy correction terms. The multicoefficient correlation methods (MCG3/3 and MC-QCISD), with inclusion of specific zero-point scale factors, slightly outperform the other multilevel methods tested (CBS-QB3, G3B3, and G3MP2B3), with significantly less computational cost, and in the case of MC-QCISD, slightly less severe scaling. Four density functional methods, PBE1KCIS, MPW1B95, PBE0, and B1B95 perform nearly as well as the multilevel methods. These results provide an important set of benchmarks relevant to biological phosphoryl transfer reactions.
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Affiliation(s)
- Kevin Range
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, USA
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16
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Khandogin J, Gregersen BA, Thiel W, York DM. Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 1. Implementation. J Phys Chem B 2007; 109:9799-809. [PMID: 16852180 DOI: 10.1021/jp044062d] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The present paper describes the extension of a recently developed smooth conductor-like screening model for solvation to a d-orbital semiempirical framework (MNDO/d-SCOSMO) with analytic gradients that can be used for geometry optimizations, transition state searches, and molecular dynamics simulations. The methodology is tested on the potential energy surfaces for separating ions and the dissociative phosphoryl transfer mechanism of methyl phosphate. The convergence behavior of the smooth COSMO method with respect to discretization level is examined and the numerical stability of the energy and gradient are compared to that from conventional COSMO calculations. The present method is further tested in applications to energy minimum and transition state geometry optimizations of neutral and charged metaphosphates, phosphates, and phosphoranes that are models for stationary points in transphosphorylation reaction pathways of enzymes and ribozymes. The results indicate that the smooth COSMO method greatly enhances the stability of quantum mechanical geometry optimization and transition state search calculations that would routinely fail with conventional solvation methods. The present MNDO/d-SCOSMO method has considerable computational advantages over hybrid quantum mechanical/molecular mechanical methods with explicit solvation, and represents a potentially useful tool in the arsenal of multi-scale quantum models used to study biochemical reactions.
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Affiliation(s)
- Jana Khandogin
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
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17
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Matsui T, Kodera Y, Endoh H, Miyauchi E, Komatsu H, Sato K, Tanaka T, Kohno T, Maeda T. RNA recognition mechanism of the minimal active domain of the human immunodeficiency virus type-2 nucleocapsid protein. J Biochem 2007; 141:269-77. [PMID: 17202191 DOI: 10.1093/jb/mvm037] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
NCp8 of HIV-2 contains two CCHC-type zinc fingers connected by a linker, and is involved in many critical steps of the virus life cycle. It was previously shown that the first zinc finger flanked by the linker is the minimal active domain for specific binding to viral RNA. In our previous study, we determined the three-dimensional structure of NCp8-f1, including the minimal active domain, and found that a hydrogen bond between Asn(11) N(delta)H and Arg(27) O stabilized the conformation of the linker in the vicinity of the zinc finger [Kodera et al. (1998) Biochemistry 37, 17704-17713]. In this study, RNA binding activities of NCp8-f1 and three types of its mutant peptides were analysed by native PAGE assay. The activity and three-dimensional structure of NCp8-f1/N11A, in which alanine is substituted for Asn(11) thereby affecting the conformation of the linker, was analyzed and compared with those of NCp8-f1. We demonstrated that the existence of Arg(4) and/or Lys(5) and Arg(26) and/or Arg(27) were necessary for binding RNA. Furthermore, the linker's flexible orientation, which is controlled by the hydrogen bond between Asn(11) N(delta)H and Arg(27) O, appears to be a structural basis for NCp8 existing as a multi-functional protein.
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Affiliation(s)
- Takashi Matsui
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 228-8555, Japan
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Affiliation(s)
- Andrew M L Lever
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
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Jenkins LMM, Durell SR, Maynard AT, Stahl SJ, Inman JK, Appella E, Legault P, Omichinski JG. Comparison of the Specificity of Interaction of Cellular and Viral Zinc-Binding Domains with 2-Mercaptobenzamide Thioesters. J Am Chem Soc 2006; 128:11964-76. [PMID: 16953638 DOI: 10.1021/ja063329e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interactions of two 2-mercaptobenzamide thioester compounds with six diverse zinc-binding domains (ZBDs) have been analyzed by UV/visible spectroscopy, NMR spectroscopy, and nucleic acid binding assays. These thioester compounds serve as useful tools for probing the intrinsic chemical stability of ZBDs that exist within a variety of cellular and viral proteins. In our studies, the classical (Cys(2)His(2)) zinc finger ZBDs, the interleaved RING like ZBDs of protein kinase C delta (Cys(2)HisCys and HisCys(3)), and the carboxyl-terminal (Cys(2)HisCys) ZBD of Mouse Mammary Tumor Virus nucleocapsid protein (MMTV NCp10) were resistant to reaction with the thioester compounds. In contrast, the thioester compounds were able to efficiently eject zinc from the amino-terminal (Cys(2)HisCys) ZBD of MMTV NCp10, a Cys(2)HisCys ZBD from Friend of GATA-1 (FOG-1), and from both Cys(4) ZBDs of GATA-1. In all cases, zinc ejection led to a loss of protein structure. Interestingly, GATA-1 was resistant to reaction with the thioester compounds when bound to its target DNA sequence. The electronic and steric screening was calculated for select ZBDs to further explore their reactivity. Based on these results, it appears that both first and second zinc-coordination shell interactions within ZBDs, as well as nucleic acid binding, play important roles in determining the chemical stability and reactivity of ZBDs. These studies not only provide information regarding the relative reactivity of cysteine residues within structural ZBDs but also are crucial for the design of future therapeutic agents that selectively target ZBDs, such as those that occur in the HIV-1 nucleocapsid protein.
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Affiliation(s)
- Lisa M Miller Jenkins
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, 30602, USA
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Giese TJ, Gregersen BA, Liu Y, Nam K, Mayaan E, Moser A, Range K, Faza ON, Lopez CS, de Lera AR, Schaftenaar G, Lopez X, Lee TS, Karypis G, York DM. QCRNA 1.0: a database of quantum calculations for RNA catalysis. J Mol Graph Model 2006; 25:423-33. [PMID: 16580853 DOI: 10.1016/j.jmgm.2006.02.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2005] [Revised: 02/21/2006] [Accepted: 02/25/2006] [Indexed: 10/24/2022]
Abstract
This work outlines a new on-line database of quantum calculations for RNA catalysis (QCRNA) available via the worldwide web at http://theory.chem.umn.edu/QCRNA. The database contains high-level density functional calculations for a large range of molecules, complexes and chemical mechanisms important to phosphoryl transfer reactions and RNA catalysis. Calculations are performed using a strict, consistent protocol such that a wealth of cross-comparisons can be made to elucidate meaningful trends in biological phosphate reactivity. Currently, around 2000 molecules have been collected in varying charge states in the gas phase and in solution. Solvation was treated with both the PCM and COSMO continuum solvation models. The data can be used to study important trends in reactivity of biological phosphates, or used as benchmark data for the design of new semiempirical quantum models for hybrid quantum mechanical/molecular mechanical simulations.
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Affiliation(s)
- Timothy J Giese
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455-0431, USA
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Levin JG, Guo J, Rouzina I, Musier-Forsyth K. Nucleic acid chaperone activity of HIV-1 nucleocapsid protein: critical role in reverse transcription and molecular mechanism. ACTA ACUST UNITED AC 2006; 80:217-86. [PMID: 16164976 DOI: 10.1016/s0079-6603(05)80006-6] [Citation(s) in RCA: 285] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Judith G Levin
- Laboratory of Molecular Genetics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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22
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Giese TJ, Sherer EC, Cramer CJ, York DM. A Semiempirical Quantum Model for Hydrogen-Bonded Nucleic Acid Base Pairs. J Chem Theory Comput 2005; 1:1275-85. [DOI: 10.1021/ct050102l] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
Modern modelling methods can now give uniquely detailed understanding of enzyme-catalyzed reactions, including the analysis of mechanisms and the identification of determinants of specificity and catalytic efficiency. A new field of computational enzymology has emerged that has the potential to contribute significantly to structure-based design and to develop predictive models of drug metabolism and, for example, of the effects of genetic polymorphisms. This review outlines important techniques in this area, including quantum-chemical model studies and combined quantum-mechanics and molecular-mechanics (QM/MM) methods. Some recent applications to enzymes of pharmacological interest are also covered, showing the types of problems that can be tackled and the insight they can give.
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Affiliation(s)
- Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
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Kuznetsov ML, Nazarov AA, Pombeiro AJL. Protic Conversion of Nitrile into Azavinylidene Complexes of Rhenium, a Mechanistic Theoretical Study. J Phys Chem A 2005; 109:8187-98. [PMID: 16834205 DOI: 10.1021/jp0527913] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mechanism of the protonation of the rhenium nitrile chloro-complexes [ReCl(NCCH3)(PH3)4] (2), taken as models of the real systems [ReCl(NCR)(dppe)(2)] (dppe = Ph2PCH2CH2PPh2), leading to the azavinylidene products [ReCl(NC(H)CH3)(PH3)4]+ (3) was investigated by theoretical methods at the B3LYP level of theory. Electrostatic and molecular orbital arguments and thermodynamic, kinetic, and steric factors are analyzed and indicate that the chlorine atom is the most probable site of the initial proton attack, although the direct protonation of the nitrile carbon atom is also possible as a concurrent process. For the cis-isomer of 2, the initially formed chloro-protonated species cis-[Re(ClH)(NCCH3)(PH3)4]+ further converts to the azavinylidene cis-3 via either an acid-independent 1,4-proton shift or an acid-base catalyzed pathway involving a second protonation of the nitrile carbon atom to give cis-[Re(ClH)(NC(H)CH3)(PH3)4]2+ followed by elimination of the proton from the chlorine atom.
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Affiliation(s)
- Maxim L Kuznetsov
- Centro de Química Estrutural, Complexo I, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
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Mark-Danieli M, Laham N, Kenan-Eichler M, Castiel A, Melamed D, Landau M, Bouvier NM, Evans MJ, Bacharach E. Single point mutations in the zinc finger motifs of the human immunodeficiency virus type 1 nucleocapsid alter RNA binding specificities of the gag protein and enhance packaging and infectivity. J Virol 2005; 79:7756-67. [PMID: 15919928 PMCID: PMC1143677 DOI: 10.1128/jvi.79.12.7756-7767.2005] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A specific interaction between the nucleocapsid (NC) domain of the Gag polyprotein and the RNA encapsidation signal (Psi) is required for preferential incorporation of the retroviral genomic RNA into the assembled virion. Using the yeast three-hybrid system, we developed a genetic screen to detect human immunodeficiency virus type 1 (HIV-1) Gag mutants with altered RNA binding specificities. Specifically, we randomly mutated full-length HIV-1 Gag or its NC portion and screened the mutants for an increase in affinity for the Harvey murine sarcoma virus encapsidation signal. These screens identified several NC zinc finger mutants with altered RNA binding specificities. Furthermore, additional zinc finger mutants that also demonstrated this phenotype were made by site-directed mutagenesis. The majority of these mutants were able to produce normal virion-like particles; however, when tested in a single-cycle infection assay, some of the mutants demonstrated higher transduction efficiencies than that of wild-type Gag. In particular, the N17K mutant showed a seven- to ninefold increase in transduction, which correlated with enhanced vector RNA packaging. This mutant also packaged larger amounts of foreign RNA. Our results emphasize the importance of the NC zinc fingers, and not other Gag sequences, in achieving specificity in the genome encapsidation process. In addition, the described mutations may contribute to our understanding of HIV diversity resulting from recombination events between copackaged viral genomes and foreign RNA.
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Affiliation(s)
- Michal Mark-Danieli
- Department of Cell Research and Immunology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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Range K, Mayaan E, Maher LJ, York DM. The contribution of phosphate-phosphate repulsions to the free energy of DNA bending. Nucleic Acids Res 2005; 33:1257-68. [PMID: 15741179 PMCID: PMC552960 DOI: 10.1093/nar/gki272] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
DNA bending is important for the packaging of genetic material, regulation of gene expression and interaction of nucleic acids with proteins. Consequently, it is of considerable interest to quantify the energetic factors that must be overcome to induce bending of DNA, such as base stacking and phosphate–phosphate repulsions. In the present work, the electrostatic contribution of phosphate–phosphate repulsions to the free energy of bending DNA is examined for 71 bp linear and bent-form model structures. The bent DNA model was based on the crystallographic structure of a full turn of DNA in a nucleosome core particle. A Green's function approach based on a linear-scaling smooth conductor-like screening model was applied to ascertain the contribution of individual phosphate–phosphate repulsions and overall electrostatic stabilization in aqueous solution. The effect of charge neutralization by site-bound ions was considered using Monte Carlo simulation to characterize the distribution of ion occupations and contribution of phosphate repulsions to the free energy of bending as a function of counterion load. The calculations predict that the phosphate–phosphate repulsions account for ∼30% of the total free energy required to bend DNA from canonical linear B-form into the conformation found in the nucleosome core particle.
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Affiliation(s)
| | | | - L. J. Maher
- Department of Biochemistry and Molecular Biology. Mayo Clinic College of MedicineRochester, MN 55905, USA
| | - Darrin M. York
- To whom correspondence should be addressed. Tel: +1 612 624 8042; Fax: +1 612 626 7541;
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Morcock DR, Thomas JA, Gagliardi TD, Gorelick RJ, Roser JD, Chertova EN, Bess JW, Ott DE, Sattentau QJ, Frank I, Pope M, Lifson JD, Henderson LE, Crise BJ. Elimination of retroviral infectivity by N-ethylmaleimide with preservation of functional envelope glycoproteins. J Virol 2005; 79:1533-42. [PMID: 15650179 PMCID: PMC544125 DOI: 10.1128/jvi.79.3.1533-1542.2005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The zinc finger motifs in retroviral nucleocapsid (NC) proteins are essential for viral replication. Disruption of these Cys-X2-Cys-X4-His-X4-Cys zinc-binding structures eliminates infectivity. To determine if N-ethylmaleimide (NEM) can inactivate human immunodeficiency virus type 1 (HIV-1) or simian immunodeficiency virus (SIV) preparations by alkylating cysteines of NC zinc fingers, we treated infectious virus with NEM and evaluated inactivation of infectivity in cell-based assays. Inactivation was rapid and proportional to the NEM concentration. NEM treatment of HIV-1 or SIV resulted in extensive covalent modification of NC and other internal virion proteins. In contrast, viral envelope glycoproteins, in which the cysteines are disulfide bonded, remained intact and functional, as assayed by high-performance liquid chromatography, fusion-from-without analyses, and dendritic cell capture. Quantitative PCR assays for reverse transcription intermediates showed that NEM and 2,2'-dipyridyl disulfide (aldrithiol-2), a reagent which inactivates retroviruses through oxidation of cysteines in internal virion proteins such as NC, blocked HIV-1 reverse transcription prior to the formation of minus-strand strong-stop products. However, the reverse transcriptase from NEM-treated virions remained active in exogenous template assays, consistent with a role for NC in reverse transcription. Since disruption of NC zinc finger structures by NEM blocks early postentry steps in the retroviral infection cycle, virus preparations with modified NC proteins may be useful as vaccine immunogens and probes of the role of NC in viral replication.
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Affiliation(s)
- David R Morcock
- AIDS Vaccine Program, SAIC Frederick, NCI-Frederick, Building 535, 5th Floor, PO Box B, Frederick, MD 21702, USA
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Khandogin J, York DM. Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods. Proteins 2004; 56:724-37. [PMID: 15281126 DOI: 10.1002/prot.20171] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The characterization of electrostatic and chemical properties at the surface of biological macromolecules is of interest in elucidating the fundamental biological structure-function relationships as well as in problems of rational drug design. This paper presents a set of macromolecular quantum descriptors for the characterization of biological macromolecules in solution that can be obtained with modest computational cost from linear-scaling semi-empirical quantum/solvation methods. The descriptors discussed include: solvent-polarized electrostatic surface potential maps, equilibrated atomic charges, Fukui reactivity indices, approximate local hardness maps, and relative proton potentials. These properties are applied to study the conformational dependence of the electrostatic surface potential of the solvated phosphate-binding protein mutant (T141D), the regioselectivity of the zinc finger domains of HIV-1 nucleocapsid (NC) protein, and the order of pKa values of acidic residues in turkey ovomucoid third domain (OMTKY3) and of the zinc-binding residues in the carboxyl terminal zinc finger of NC. In all cases, insight beyond that obtainable from purely classical models is gained and can be used to rationalize the experimental observations. The macromolecular quantum descriptors presented here greatly extend the arsenal of tools for macromolecular characterization and offer promise in applications to modern structure-based drug design.
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Affiliation(s)
- Jana Khandogin
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
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