101
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Affiliation(s)
- Julie Grouleff
- Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
| | - Frank Jensen
- Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
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102
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Wang J, Cieplak P, Li J, Wang J, Cai Q, Hsieh M, Lei H, Luo R, Duan Y. Development of polarizable models for molecular mechanical calculations II: induced dipole models significantly improve accuracy of intermolecular interaction energies. J Phys Chem B 2011; 115:3100-11. [PMID: 21391583 PMCID: PMC3082585 DOI: 10.1021/jp1121382] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the companion paper, we presented a set of induced dipole interaction models using four types of screening functions, which include the Applequist (no screening), the Thole linear, the Thole exponential model, and the Thole Tinker-like (another form of exponential screening function) functions. In this work, we evaluate the performance of polarizability models using a large set of amino acid analog pairs in conformations that are frequently observed in protein structures as a benchmark. For each amino acid pair, we calculated quantum mechanical interaction energies at the MP2/aug-cc-pVTZ//MP2/6-311++G(d,p) level with the basis set superposition error (BSSE) correction and compared them with molecular mechanics results. Encouragingly, all polarizable models significantly outperform the additive F94 and F03 models (mimicking AMBER ff94/ff99 and ff03 force fields, respectively) in reproducing the BSSE-corrected quantum mechanical interaction energies. In particular, the root-mean-square errors (RMSEs) for three Thole models in Set A (where the 1-2 and 1-3 interactions are turned off and all 1-4 interactions are included) are 1.456, 1.417, and 1.406 kcal/mol for model AL (Thole Linear), model AE (Thole exponential), and model AT (Thole Tinker-like), respectively. In contrast, the RMSEs are 3.729 and 3.433 kcal/mol for F94 and F03 models, respectively. A similar trend was observed for the average unsigned errors (AUEs), which are 1.057, 1.025, 1.011, 2.219, and 2.070 kcal/mol for AL, AE, AT, F94/ff99, and F03, respectively. Analyses based on the trend line slopes indicate that the two fixed charge models substantially underestimate the relative strengths of noncharge-charge interactions by 24 (F03) and 35% (F94), respectively, whereas the four polarizable models overestimate the relative strengths by 5 (AT), 3 (AL, AE), and 13% (AA), respectively. Agreement was further improved by adjusting the van der Waals parameters. Judging from the notably improved accuracy in comparison with the fixed charge models, the polarizable models are expected to form the foundation for the development of high quality polarizable force fields for protein and nucleic acid simulations.
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Affiliation(s)
- Junmei Wang
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9050, USA
| | - Piotr Cieplak
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Jie Li
- University of California at Davis Genome Center and Department of Applied Science, One Shields Avenue, Davis, CA 95616, USA
| | - Jun Wang
- University of California at Irvine, Molecular Biology and Biochemistry 3144 Natural Sciences I, Irvine, CA, USA 92697-3900
| | - Qin Cai
- University of California at Irvine, Molecular Biology and Biochemistry 3144 Natural Sciences I, Irvine, CA, USA 92697-3900
| | - MengJuei Hsieh
- University of California at Irvine, Molecular Biology and Biochemistry 3144 Natural Sciences I, Irvine, CA, USA 92697-3900
| | - Hongxing Lei
- University of California at Davis Genome Center and Department of Applied Science, One Shields Avenue, Davis, CA 95616, USA
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Ray Luo
- University of California at Irvine, Molecular Biology and Biochemistry 3144 Natural Sciences I, Irvine, CA, USA 92697-3900
| | - Yong Duan
- University of California at Davis Genome Center and Department of Applied Science, One Shields Avenue, Davis, CA 95616, USA
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103
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Wang J, Cieplak P, Li J, Hou T, Luo R, Duan Y. Development of polarizable models for molecular mechanical calculations I: parameterization of atomic polarizability. J Phys Chem B 2011; 115:3091-9. [PMID: 21391553 DOI: 10.1021/jp112133g] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
In this work, four types of polarizable models have been developed for calculating interactions between atomic charges and induced point dipoles. These include the Applequist, Thole linear, Thole exponential model, and the Thole Tinker-like. The polarizability models have been optimized to reproduce the experimental static molecular polarizabilities obtained from the molecular refraction measurements on a set of 420 molecules reported by Bosque and Sales. We grouped the models into five sets depending on the interaction types, that is, whether the interactions of two atoms that form the bond, bond angle, and dihedral angle are turned off or scaled down. When 1-2 (bonded) and 1-3 (separated by two bonds) interactions are turned off, 1-4 (separated by three bonds) interactions are scaled down, or both, all models including the Applequist model achieved similar performance: the average percentage error (APE) ranges from 1.15 to 1.23%, and the average unsigned error (AUE) ranges from 0.143 to 0.158 Å(3). When the short-range 1-2, 1-3, and full 1-4 terms are taken into account (set D models), the APE ranges from 1.30 to 1.58% for the three Thole models, whereas the Applequist model (DA) has a significantly larger APE (3.82%). The AUE ranges from 0.166 to 0.196 Å(3) for the three Thole models, compared with 0.446 Å(3) for the Applequist model. Further assessment using the 70-molecule van Duijnen and Swart data set clearly showed that the developed models are both accurate and highly transferable and are in fact have smaller errors than the models developed using this particular data set (set E models). The fact that A, B, and C model sets are notably more accurate than both D and E model sets strongly suggests that the inclusion of 1-2 and 1-3 interactions reduces the transferability and accuracy.
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Affiliation(s)
- Junmei Wang
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA
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104
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Liu Y, Tao L, Lu J, Xu S, Ma Q, Duan Q. A novel force field parameter optimization method based on LSSVR for ECEPP. FEBS Lett 2011; 585:888-92. [PMID: 21349275 DOI: 10.1016/j.febslet.2011.02.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Revised: 02/13/2011] [Accepted: 02/16/2011] [Indexed: 11/27/2022]
Abstract
In this paper, we propose a novel force field parameter optimization method based on LSSVR and optimize the torsion energy parameters of ECEPP force field. In this method force field parameter optimization problem is turned into a support vector regression problem. Protein samples for regression model training are chosen from Protein Data Bank. The experiments show that the optimized force-field parameters make both α-helix and β-hairpin structures more consistent with the experimental implications than the original parameters.
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Affiliation(s)
- Yunling Liu
- College of Information and Electrical Engineering, China Agricultural University, Beijing, China
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105
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Voityuk AA, Siriwong K, Berlin YA. Effects of various halogen anions and cations of alkali metals on energetics of excess charge recombination in stilbene donor–acceptor capped DNA hairpins. Phys Chem Chem Phys 2011; 13:16028-32. [DOI: 10.1039/c1cp21056d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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106
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Zhou Y, Duan Y, Yang Y, Faraggi E, Lei H. Trends in template/fragment-free protein structure prediction. Theor Chem Acc 2011; 128:3-16. [PMID: 21423322 PMCID: PMC3030773 DOI: 10.1007/s00214-010-0799-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 08/15/2010] [Indexed: 12/13/2022]
Abstract
Predicting the structure of a protein from its amino acid sequence is a long-standing unsolved problem in computational biology. Its solution would be of both fundamental and practical importance as the gap between the number of known sequences and the number of experimentally solved structures widens rapidly. Currently, the most successful approaches are based on fragment/template reassembly. Lacking progress in template-free structure prediction calls for novel ideas and approaches. This article reviews trends in the development of physical and specific knowledge-based energy functions as well as sampling techniques for fragment-free structure prediction. Recent physical- and knowledge-based studies demonstrated that it is possible to sample and predict highly accurate protein structures without borrowing native fragments from known protein structures. These emerging approaches with fully flexible sampling have the potential to move the field forward.
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Affiliation(s)
- Yaoqi Zhou
- School of Informatics, Indiana Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indiana University Purdue University, 719 Indiana Ave #319, Walker Plaza Building, Indianapolis, IN 46202 USA
| | - Yong Duan
- UC Davis Genome Center and Department of Applied Science, University of California, One Shields Avenue, Davis, CA USA
- College of Physics, Huazhong University of Science and Technology, 1037 Luoyu Road, 430074 Wuhan, China
| | - Yuedong Yang
- School of Informatics, Indiana Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indiana University Purdue University, 719 Indiana Ave #319, Walker Plaza Building, Indianapolis, IN 46202 USA
| | - Eshel Faraggi
- School of Informatics, Indiana Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indiana University Purdue University, 719 Indiana Ave #319, Walker Plaza Building, Indianapolis, IN 46202 USA
| | - Hongxing Lei
- UC Davis Genome Center and Department of Applied Science, University of California, One Shields Avenue, Davis, CA USA
- Beijing Institute of Genomics, Chinese Academy of Sciences, 100029 Beijing, China
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107
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Baker CM, Anisimov VM, MacKerell AD. Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model. J Phys Chem B 2010; 115:580-96. [PMID: 21166469 DOI: 10.1021/jp1092338] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A polarizable force field for nucleic acid bases based on the classical Drude oscillator model is presented. Parameter optimization was performed to reproduce crystallographic geometries, crystal unit cell parameters, heats of sublimation, vibrational frequencies and assignments, dipole moments, molecular polarizabilities and quantum mechanical base-base and base-water interaction energies. The training and validation data included crystals of unsubstituted and alkyl-substituted adenine, guanine, cytosine, uracil, and thymine bases, hydrated crystals, and hydrogen bonded base pairs. Across all compounds, the RMSD in the calculated heats of sublimation is 4.1%. This equates to an improvement of more than 2.5 kcal/mol in accuracy compared to the nonpolarizable CHARMM27 force field. However, the level of agreement with experimental molecular volume decreased from 1.7% to 2.1% upon moving from the nonpolarizable to the polarizable model. The representation of dipole moments is significantly improved with the Drude polarizable force field. Unlike in additive force fields, there is no requirement for the gas-phase dipole moments to be overestimated, illustrating the ability of the Drude polarizable force field to treat accurately differently dielectric environments and indicating the improvements in the electrostatic model. Validation of the model was performed on the basis of the calculation of the gas-phase binding enthalpies of base pairs obtained via potential of mean force calculations; the additive and polarizable models both performed satisfactorily with average differences of 0.2 and 0.9 kcal/mol, respectively, and rms differences of 1.3 and 1.7 kcal/mol, respectively. Overall, considering the number of significant improvements versus the additive CHARMM force field, the incorporation of explicit polarizability into the force field for nucleic acid bases represents an additional step toward accurate computational modeling of biological systems.
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Affiliation(s)
- Christopher M Baker
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, 20 Penn Street, Baltimore, Maryland 21201, USA
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108
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Zuo Z, Gandhi NS, Mancera RL. Calculations of the Free Energy of Interaction of the c-Fos−c-Jun Coiled Coil: Effects of the Solvation Model and the Inclusion of Polarization Effects. J Chem Inf Model 2010; 50:2201-12. [DOI: 10.1021/ci100321h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhili Zuo
- Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, School of Biomedical Sciences and School of Pharmacy, Curtin University, GPO Box U1987, Perth WA 6845, Australia
| | - Neha S. Gandhi
- Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, School of Biomedical Sciences and School of Pharmacy, Curtin University, GPO Box U1987, Perth WA 6845, Australia
| | - Ricardo L. Mancera
- Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, School of Biomedical Sciences and School of Pharmacy, Curtin University, GPO Box U1987, Perth WA 6845, Australia
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109
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Han W, Wan CK, Jiang F, Wu YD. PACE Force Field for Protein Simulations. 1. Full Parameterization of Version 1 and Verification. J Chem Theory Comput 2010; 6:3373-89. [DOI: 10.1021/ct1003127] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Wei Han
- Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China, School of Chemical Biology and Biotechnology, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China, and College of Chemistry, Peking University, Beijing, China
| | - Cheuk-Kin Wan
- Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China, School of Chemical Biology and Biotechnology, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China, and College of Chemistry, Peking University, Beijing, China
| | - Fan Jiang
- Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China, School of Chemical Biology and Biotechnology, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China, and College of Chemistry, Peking University, Beijing, China
| | - Yun-Dong Wu
- Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China, School of Chemical Biology and Biotechnology, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China, and College of Chemistry, Peking University, Beijing, China
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110
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Simulations of water at the interface with hydrophilic self-assembled monolayers. Biointerphases 2010; 3:FC13-22. [PMID: 20408690 DOI: 10.1116/1.2977751] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Simulations of water at hydrophilic self-assembled monolayer (SAM) surfaces are especially relevant for biological interfaces. Well-defined, atomically smooth surfaces that can be continuously varied are possible with SAMs. These characteristics enable more accurate measurements than many other surfaces with the added advantage of tailoring the surface to treat specific chemical groups. A fundamental question is how solid surfaces affect the structure and dynamics of water. Measurements of the structure and dynamics of water at solid surfaces have improved significantly, but there remain differences among the experiments. In this article, the authors review simulations of water at the interface with hydrophilic SAMs. These simulations find that while the interfacial water molecules are slower than the bulk water molecules, the interfacial dynamics remains that of a liquid. A major biological application of SAMs is for making coatings resistant to protein adsorption. SAMs terminated with ethylene glycol monomers have proven to be excellent at resisting protein adsorption. Understanding the mechanisms behind this resistance remains an unresolved issue. Recent simulations suggest a new perspective of the role of interfacial water and the inseparable interplay between the SAM and the water.
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111
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Ponder JW, Wu C, Ren P, Pande VS, Chodera JD, Schnieders MJ, Haque I, Mobley DL, Lambrecht DS, DiStasio RA, Head-Gordon M, Clark GNI, Johnson ME, Head-Gordon T. Current status of the AMOEBA polarizable force field. J Phys Chem B 2010; 114:2549-64. [PMID: 20136072 PMCID: PMC2918242 DOI: 10.1021/jp910674d] [Citation(s) in RCA: 945] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular force fields have been approaching a generational transition over the past several years, moving away from well-established and well-tuned, but intrinsically limited, fixed point charge models toward more intricate and expensive polarizable models that should allow more accurate description of molecular properties. The recently introduced AMOEBA force field is a leading publicly available example of this next generation of theoretical model, but to date, it has only received relatively limited validation, which we address here. We show that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions. State of the art electronic structure calculations reveal generally very good agreement with AMOEBA for demanding problems such as relative conformational energies of the alanine tetrapeptide and isomers of water sulfate complexes. AMOEBA is shown to be especially successful on protein-ligand binding and computational X-ray crystallography where polarization and accurate electrostatics are critical.
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Affiliation(s)
- Jay W Ponder
- Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, Missouri 63110, USA
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112
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Jiang J, Wu Y, Wang ZX, Wu C. Assessing the Performance of Popular Quantum Mechanics and Molecular Mechanics Methods and Revealing the Sequence-Dependent Energetic Features Using 100 Tetrapeptide Models. J Chem Theory Comput 2010. [DOI: 10.1021/ct100008q] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jinliang Jiang
- College of Chemistry and Chemical Engineering, Graduate University of Chinese Academy of Sciences, Beijing, 100049, China, and Department of Chemistry and Biochemistry, University of California—Santa Barbara, Santa Barbara, California 93106
| | - Yanbo Wu
- College of Chemistry and Chemical Engineering, Graduate University of Chinese Academy of Sciences, Beijing, 100049, China, and Department of Chemistry and Biochemistry, University of California—Santa Barbara, Santa Barbara, California 93106
| | - Zhi-Xiang Wang
- College of Chemistry and Chemical Engineering, Graduate University of Chinese Academy of Sciences, Beijing, 100049, China, and Department of Chemistry and Biochemistry, University of California—Santa Barbara, Santa Barbara, California 93106
| | - Chun Wu
- College of Chemistry and Chemical Engineering, Graduate University of Chinese Academy of Sciences, Beijing, 100049, China, and Department of Chemistry and Biochemistry, University of California—Santa Barbara, Santa Barbara, California 93106
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113
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Ranaghan KE, Mulholland AJ. Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods. INT REV PHYS CHEM 2010. [DOI: 10.1080/01442350903495417] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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114
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Doshi U, Hamelberg D. Reoptimization of the AMBER Force Field Parameters for Peptide Bond (Omega) Torsions Using Accelerated Molecular Dynamics. J Phys Chem B 2009; 113:16590-5. [DOI: 10.1021/jp907388m] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Urmi Doshi
- Department of Chemistry and The Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098
| | - Donald Hamelberg
- Department of Chemistry and The Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098
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115
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Isegawa M, Kato S. Polarizable Force Field for Protein with Charge Response Kernel. J Chem Theory Comput 2009; 5:2809-21. [PMID: 26631793 DOI: 10.1021/ct900295u] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We present a molecular mechanical force field for polypeptides and proteins involving the electronic polarization effect described with the charge response kernel. All of the electrostatic parameters for 20 amino acids are obtained by ab initio electronic structure calculations and combined with the AMBER99 force field. The refittings of dihedral angle parameters in the torsional potentials are performed so as to reproduce the ab initio optimized geometries and relative energies for the conformers of dipeptides. The present force field is applied to molecular dynamics simulation calculations of the extended alanine tetra and cyclic pentapeptides in aqueous solution. The infrared spectra are calculated in order to analyze the charge polarization effect on the spectral profiles.
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Affiliation(s)
- Miho Isegawa
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shigeki Kato
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
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116
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Wang FF, Gong LD, Zhao DX. Studies on the torsions of nucleic acids using ABEEMσπ/MM method. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.05.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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117
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Lopes PEM, Roux B, MacKerell AD. Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications. Theor Chem Acc 2009; 124:11-28. [PMID: 20577578 PMCID: PMC2888514 DOI: 10.1007/s00214-009-0617-x] [Citation(s) in RCA: 265] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A current emphasis in empirical force fields is on the development of potential functions that explicitly treat electronic polarizability. In the present article, the commonly used methodologies for modelling electronic polarization are presented along with an overview of selected application studies. Models presented include induced point-dipoles, classical Drude oscillators, and fluctuating charge methods. The theoretical background of each method is followed by an introduction to extended Langrangian integrators required for computationally tractable molecular dynamics simulations using polarizable force fields. The remainder of the review focuses on application studies using these methods. Emphasis is placed on water models, for which numerous examples exist, with a more thorough discussion presented on the recently published models associated with the Drude-based CHARMM and the AMOEBA force fields. The utility of polarizable models for the study of ion solvation is then presented followed by an overview of studies of small molecules (e.g. CCl(4), alkanes, etc) and macromolecule (proteins, nucleic acids and lipid bilayers) application studies. The review is written with the goal of providing a general overview of the current status of the field and to facilitate future application and developments.
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Affiliation(s)
- Pedro E. M. Lopes
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21230, USA
| | - Benoit Roux
- Institute of Molecular Pediatric Sciences, Gordon Center for Integrative Science, University of Chicago 929 E. 57th St. Chicago, IL 60637
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21230, USA
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118
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Cieplak P, Dupradeau FY, Duan Y, Wang J. Polarization effects in molecular mechanical force fields. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:333102. [PMID: 21828594 PMCID: PMC4020598 DOI: 10.1088/0953-8984/21/33/333102] [Citation(s) in RCA: 199] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The focus here is on incorporating electronic polarization into classical molecular mechanical force fields used for macromolecular simulations. First, we briefly examine currently used molecular mechanical force fields and the current status of intermolecular forces as viewed by quantum mechanical approaches. Next, we demonstrate how some components of quantum mechanical energy are effectively incorporated into classical molecular mechanical force fields. Finally, we assess the modeling methods of one such energy component-polarization energy-and present an overview of polarizable force fields and their current applications. Incorporating polarization effects into current force fields paves the way to developing potentially more accurate, though more complex, parameterizations that can be used for more realistic molecular simulations.
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Affiliation(s)
- Piotr Cieplak
- Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92120, USA
| | - François-Yves Dupradeau
- UMR CNRS 6219—Faculté de Pharmacie, Université de Picardie Jules Verne, 1 rue des Louvels, F-80037 Amiens, France
| | - Yong Duan
- Genome Center and Department of Applied Science, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Junmei Wang
- Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Boulevard, ND9.136, Dallas, TX 75390-9050, USA
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119
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Verstraelen T, Van Speybroeck V, Waroquier M. The electronegativity equalization method and the split charge equilibration applied to organic systems: Parametrization, validation, and comparison. J Chem Phys 2009; 131:044127. [DOI: 10.1063/1.3187034] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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120
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Best RB, Hummer G. Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides. J Phys Chem B 2009; 113:9004-15. [PMID: 19514729 PMCID: PMC3115786 DOI: 10.1021/jp901540t] [Citation(s) in RCA: 649] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Obtaining the correct balance of secondary structure propensities is a central priority in protein force-field development. Given that current force fields differ significantly in their alpha-helical propensities, a correction to match experimental results would be highly desirable. We have determined simple backbone energy corrections for two force fields to reproduce the fraction of helix measured in short peptides at 300 K. As validation, we show that the optimized force fields produce results in excellent agreement with nuclear magnetic resonance experiments for folded proteins and short peptides not used in the optimization. However, despite the agreement at ambient conditions, the dependence of the helix content on temperature is too weak, a problem shared with other force fields. A fit of the Lifson-Roig helix-coil theory shows that both the enthalpy and entropy of helix formation are too small: the helix extension parameter w agrees well with experiment, but its entropic and enthalpic components are both only about half the respective experimental estimates. Our structural and thermodynamic analyses point toward the physical origins of these shortcomings in current force fields, and suggest ways to address them in future force-field development.
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Affiliation(s)
- Robert B Best
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
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121
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Illingworth CJ, Domene C. Many-body effects and simulations of potassium channels. Proc Math Phys Eng Sci 2009. [DOI: 10.1098/rspa.2009.0014] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The electronic polarizability of an ion or a molecule is a measure of the relative tendency of its electron cloud to be distorted from its normal shape by an electric field. On the molecular scale, in a condensed phase, any species sits in an electric field due to its neighbours, and the resulting polarization is an important contribution to the total interaction energy. Electrostatic interactions are crucial for determining the majority of chemical–physical properties of the system and electronic polarization is a fundamental component of these interactions. Thus, polarization effects should be taken into account if accurate descriptions are desired. In classical computer simulations, the forces required to drive the system are typically based on interatomic interaction potentials derived in part from electronic structure calculations or from experimental data. Owing to the difficulties in including polarization effects in classical force fields, most of them are based just on pairwise additive interaction potentials. At present, major efforts are underway to develop polarizable interaction potentials for biomolecular simulations. In this review, various ways of introducing explicit polarizability into biomolecular models and force fields are reviewed, and the progress that might be achieved in applying such methods to study potassium channels is described.
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Affiliation(s)
- Christopher J. Illingworth
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of OxfordOxford OX1 3QZ, UK
| | - Carmen Domene
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of OxfordOxford OX1 3QZ, UK
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122
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Computational approaches for the design of peptides with anti-breast cancer properties. Future Med Chem 2009; 1:201-12. [DOI: 10.4155/fmc.09.13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background: Breast cancer is the most common cancer among women. Tamoxifen is the preferred drug for estrogen receptor-positive breast cancer treatment, yet many of these cancers are intrinsically resistant to tamoxifen or acquire resistance during treatment. Therefore, scientists are searching for breast cancer drugs that have different molecular targets. Methodology: Recently, a computational approach was used to successfully design peptides that are new lead compounds against breast cancer. We used replica exchange molecular dynamics to predict the structure and dynamics of active peptides, leading to the discovery of smaller bioactive peptides. Conclusions: These analogs inhibit estrogen-dependent cell growth in a mouse uterine growth assay, a test showing reliable correlation with human breast cancer inhibition. We outline the computational methods that were tried and used along with the experimental information that led to the successful completion of this research.
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123
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Abstract
Combined quantum-mechanics/molecular-mechanics (QM/MM) approaches have become the method of choice for modeling reactions in biomolecular systems. Quantum-mechanical (QM) methods are required for describing chemical reactions and other electronic processes, such as charge transfer or electronic excitation. However, QM methods are restricted to systems of up to a few hundred atoms. However, the size and conformational complexity of biopolymers calls for methods capable of treating up to several 100,000 atoms and allowing for simulations over time scales of tens of nanoseconds. This is achieved by highly efficient, force-field-based molecular mechanics (MM) methods. Thus to model large biomolecules the logical approach is to combine the two techniques and to use a QM method for the chemically active region (e.g., substrates and co-factors in an enzymatic reaction) and an MM treatment for the surroundings (e.g., protein and solvent). The resulting schemes are commonly referred to as combined or hybrid QM/MM methods. They enable the modeling of reactive biomolecular systems at a reasonable computational effort while providing the necessary accuracy.
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Affiliation(s)
- Hans Martin Senn
- Department of Chemistry, WestCHEM and University of Glasgow, Glasgow G12 8QQ, UK.
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124
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125
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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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126
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Raman SS, Vijayaraj R, Parthasarathi R, Subramanian V. Helix forming tendency of valine substituted poly-alanine: a molecular dynamics investigation. J Phys Chem B 2008; 112:9100-4. [PMID: 18597521 DOI: 10.1021/jp7119813] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In this study, classical molecular dynamics simulations have been carried out on the valine (guest) substituted poly alanine (host) using the host-guest peptide approach to understand the role of valine in the formation and stabilization of helix. Valine has been substituted in the host peptide starting from N terminal to C terminal. Various structural parameters have been obtained from the molecular dynamics simulation to understand the tolerance of helical motif to valine. Depending on the position of valine in the host peptide, it stabilizes (or destabilizes) the formation of the helical structure. The substitution of valine in the poly alanine at some positions has no effect on the helix formation (deformation). It is interesting to observe the coexistence of 3 10 and alpha-helix in the peptides due to the dynamical nature of the hydrogen bonding interaction and sterical interactions.
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Affiliation(s)
- S Sundar Raman
- Chemical Laboratory, Central Leather Research Institute, Adyar, Chennai 600 020 India
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127
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Kwac K, Lee KK, Han JB, Oh KI, Cho M. Classical and quantum mechanical/molecular mechanical molecular dynamics simulations of alanine dipeptide in water: comparisons with IR and vibrational circular dichroism spectra. J Chem Phys 2008; 128:105106. [PMID: 18345930 DOI: 10.1063/1.2837461] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
We have implemented the combined quantum mechanical (QM)/molecular mechanical (MM) molecular dynamics (MD) simulations of alanine dipeptide in water along with the polarizable and nonpolarizable classical MD simulations with different models of water. For the QM/MM MD simulation, the alanine dipeptide is treated with the AM1 or PM3 approximations and the fluctuating solute dipole moment is calculated by the Mulliken population analysis. For the classical MD simulations, the solute is treated with the polarizable or nonpolarizable AMBER and polarizable CHARMM force fields and water is treated with the TIP3P, TIP4P, or TIP5P model. It is found that the relative populations of right-handed alpha-helix and extended beta and P(II) conformations in the simulation trajectory strongly depend on the simulation method. For the QM/MM MD simulations, the PM3/MM shows that the P(II) conformation is dominant, whereas the AM1/MM predicts that the dominant conformation is alpha(R). Polarizable CHARMM force field gives almost exclusively P(II) conformation and other force fields predict that both alpha-helical and extended (beta and P(II)) conformations are populated with varying extents. Solvation environment around the dipeptide is investigated by examining the radial distribution functions and numbers and lifetimes of hydrogen bonds. Comparing the simulated IR and vibrational circular dichroism spectra with experimental results, we concluded that the dipeptide adopts the P(II) conformation and PM3/MM, AMBER03 with TIP4P water, and AMBER polarizable force fields are acceptable for structure determination of the dipeptide considered in this paper.
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Affiliation(s)
- Kijeong Kwac
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
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128
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Mackerell AD, Nilsson L. Molecular dynamics simulations of nucleic acid-protein complexes. Curr Opin Struct Biol 2008; 18:194-9. [PMID: 18281210 DOI: 10.1016/j.sbi.2007.12.012] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Revised: 12/17/2007] [Accepted: 12/21/2007] [Indexed: 10/22/2022]
Abstract
Molecular dynamics simulation studies of protein-nucleic acid complexes are more complicated than studies of either component alone-the force field has to be properly balanced, the systems tend to become very large, and a careful treatment of solvent and of electrostatic interactions is necessary. Recent investigations into several protein-DNA and protein-RNA systems have shown the feasibility of the simulation approach, yielding results of biological interest not readily accessible to experimental methods.
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Affiliation(s)
- Alexander D Mackerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA.
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129
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Nakagawa S, Mark P, Ågren H. Recipe of Polarized One-Electron Potential Optimization for Development of Polarizable Force Fields. J Chem Theory Comput 2007; 3:1947-59. [DOI: 10.1021/ct700132w] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Setsuko Nakagawa
- Department of Human Life and Environment, Kinjo Gakuin University, Omori, Moriyama-ku, Nagoya 463-8521, Japan, and Department of Theoretical Chemistry, Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Pekka Mark
- Department of Human Life and Environment, Kinjo Gakuin University, Omori, Moriyama-ku, Nagoya 463-8521, Japan, and Department of Theoretical Chemistry, Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Hans Ågren
- Department of Human Life and Environment, Kinjo Gakuin University, Omori, Moriyama-ku, Nagoya 463-8521, Japan, and Department of Theoretical Chemistry, Royal Institute of Technology, S-106 91 Stockholm, Sweden
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130
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Lin MS, Fawzi NL, Head-Gordon T. Hydrophobic potential of mean force as a solvation function for protein structure prediction. Structure 2007; 15:727-40. [PMID: 17562319 DOI: 10.1016/j.str.2007.05.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2006] [Revised: 05/04/2007] [Accepted: 05/07/2007] [Indexed: 10/23/2022]
Abstract
We have developed a solvation function that combines a Generalized Born model for polarization of protein charge by the high dielectric solvent, with a hydrophobic potential of mean force (HPMF) as a model for hydrophobic interaction, to aid in the discrimination of native structures from other misfolded states in protein structure prediction. We find that our energy function outperforms other reported scoring functions in terms of correct native ranking for 91% of proteins and low Z scores for a variety of decoy sets, including the challenging Rosetta decoys. This work shows that the stabilizing effect of hydrophobic exposure to aqueous solvent that defines the HPMF hydration physics is an apparent improvement over solvent-accessible surface area models that penalize hydrophobic exposure. Decoys generated by thermal sampling around the native-state basin reveal a potentially important role for side-chain entropy in the future development of even more accurate free energy surfaces.
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Affiliation(s)
- Matthew S Lin
- UCSF/UCB Joint Graduate Group in Bioengineering, University of California-Berkeley, Berkeley, CA 94720, USA
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131
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Kirschner KN, Lexa KW, Salisburg AM, Alser KA, Joseph L, Andersen TT, Bennett JA, Jacobson HI, Shields GC. Computational design and experimental discovery of an antiestrogenic peptide derived from alpha-fetoprotein. J Am Chem Soc 2007; 129:6263-8. [PMID: 17441722 PMCID: PMC4272344 DOI: 10.1021/ja070202w] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Breast cancer is the most common cancer among women, and tamoxifen is the preferred drug for estrogen receptor-positive breast cancer treatment. Many of these cancers are intrinsically resistant to tamoxifen or acquire resistance during treatment. Consequently, there is an ongoing need for breast cancer drugs that have different molecular targets. Previous work has shown that 8-mer and cyclic 9-mer peptides inhibit breast cancer in mouse and rat models, interacting with an unsolved receptor, while peptides smaller than eight amino acids did not. We show that the use of replica exchange molecular dynamics predicts the structure and dynamics of active peptides, leading to the discovery of smaller peptides with full biological activity. Simulations identified smaller peptide analogues with the same conserved reverse turn demonstrated in the larger peptides. These analogues were synthesized and shown to inhibit estrogen-dependent cell growth in a mouse uterine growth assay, a test showing reliable correlation with human breast cancer inhibition.
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132
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Abstract
A polarizable model potential (PMP) function for adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) is developed on the basis of ab initio molecular orbital calculations at the MP2/6-31+G* level. The PMP function consists of Coulomb, van der Waals, and polarization terms. The permanent atomic charges of the Coulomb term are determined by using electrostatic potential (ESP) optimization. The multicenter polarizabilities of the polarization term are determined by using polarized one-electron potential (POP) optimization in which the electron density changes induced by a test charge are target. Isotropic and anisotropic polarizabilities are adopted as the multicenter polarizabilities. In the PMP calculations using the optimized parameters, the interaction energies of Watson-Crick type A-T and C-G base pairs were -15.6 and -29.4 kcal/mol, respectively. The interaction energy of Hoogsteen type A-T base pair was -17.8 kcal/mol. These results reproduce well the quantum chemistry calculations at the MP2/6-311++G(3df,2pd) level within the differences of 0.6 kcal/mol. The stacking energies of A-T and C-G were -9.7 and -10.9 kcal/mol. These reproduce well the calculation results at the MP2/6-311++G (2d,2p) level within the differences of 1.3 kcal/mol. The potential energy surfaces of the system in which a sodium ion or a chloride ion is adjacent to the nucleic acid base are calculated. The interaction energies of the PMP function reproduced well the calculation results at the MP2/6-31+G* or MP2/6-311++G(2d,2p) level. The reason why the PMP function reproduces well the high-level quantum mechanical interaction energies is addressed from the viewpoint of each energy terms.
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Affiliation(s)
- Setsuko Nakagawa
- Department of Human Life and Environment, Kinjo Gakuin University, Omori, Moriyama-ku, Nagoya 463-8521, Japan
- Department of Theoretical Chemistry, Royal Institute of Technology, S-106 91 Stockholm, Sweden
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133
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Wang ZX, Wu C, Lei H, Duan Y. Accurate ab Initio Study on the Hydrogen-Bond Pairs in Protein Secondary Structures. J Chem Theory Comput 2007; 3:1527-1537. [PMID: 26221082 PMCID: PMC4515431 DOI: 10.1021/ct700021f] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Ab initio calculations up to the MP2/aug-cc-pVQZ//MP2/6-311+G** level have been carried out to characterize the four patterns of hydrogen-bond (H-bond) pairs in protein secondary structures. The unblocked and methyl-blocked glycine dipeptide dimers were arranged to model the H-bond pairs in α-helix (αHH) and antiparallel (Aββ-C5 and Aββ-C7) and parallel β-sheet (Pββ) secondary structures. The study uncovers that, in addition to the primary CO⋯NH H-bonds and the crossing secondary interactions, the CH⋯OC H-bonds and the tertiary effect (as we call it) also contribute substantially. The tertiary effect is due to the interpolarization between the donor and acceptor of a H-bond. This effect, which enhances the dipole-dipole interactions between two nearby H-bonds, stabilizes the β-sheet-like but destabilizes the helix-like H-bond pairs. The MP2 binding energies of the complexes were further refined by extrapolating to the complete basis set limit (CBS) according to Truhlar and co-workers and by a three-basis-set-based method. The best extrapolated CBS(aD-aT-aQ) binding energies of the unblocked dimers are -13.1 (αHH), -11.3 (Aββ-C5), -19.2 (Aββ-C7), and -14.8 kcal/mol (Pββ). For the methyl-blocked counterparts, the best extrapolated CBS(D-T-Q) binding energies are -14.8, -13.4, -20.8, and -16.7 kcal/mol, respectively. The interactions in the parallel β conformations are very close to the averages of the C5 and C7 antiparallel β conformations, and both are stronger than the helical dimers. Because the additive force fields are unable to account for the tertiary effect owing to the lack of polarization, all examined additive force fields significantly overestimate the interaction energies of the helix conformations relative to the β-sheet conformations. Notably, the agreement between molecular mechanical and quantum mechanical binding energies is improved after turning on the polarization. The study provides reference ab initio structures and binding energies for characterizing the backbone H-bonds of the protein secondary structures, which can be used for the parametrization of empirical molecular mechanics force fields.
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Affiliation(s)
- Zhi-Xiang Wang
- Genome Center and Department of Applied Science, University of California, Davis, California 95616
| | - Chun Wu
- Genome Center and Department of Applied Science, University of California, Davis, California 95616
| | - Hongxing Lei
- Genome Center and Department of Applied Science, University of California, Davis, California 95616
| | - Yong Duan
- Genome Center and Department of Applied Science, University of California, Davis, California 95616
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134
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Palmo K, Mannfors B, Mirkin NG, Krimm S. Inclusion of charge and polarizability fluxes provides needed physical accuracy in molecular mechanics force fields. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.08.087] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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135
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Liang T, Walsh TR. Molecular dynamics simulations of peptide carboxylate hydration. Phys Chem Chem Phys 2006; 8:4410-9. [PMID: 17001408 DOI: 10.1039/b608672a] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aqueous solvation of carboxylate groups, as present in the glycine zwitterion and the dipeptide aspartylalanine, is studied employing a force-field that includes distributed multipole electrostatics and induction contributions (Amoebapro: P. Ren and J. W. Ponder, J. Comput. Chem., 2002, 23, 1497; P. Ren and J. W. Ponder, J. Phys. Chem. B, 2003, 107, 5933; J. W. Ponder and D. A. Case, Adv. Protein Chem., 2003, 66, 27). Radial and orientation distribution functions, as well as hydration numbers, are calculated and compared with existing simulation data derived from Car-Parrinello molecular dynamics (CPMD), and also distributed-charge force-fields. Connections are also made with experimental data for solvation of carboxylates in water. Our findings show that Amoebapro yields carboxylate solvation properties in very good agreement with CPMD results, significantly closer agreement than can be obtained from traditional force-fields. We also demonstrate that the influence of solvation on the conformation of the dipeptide is markedly different using Amoebapro compared with the other force-fields.
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Affiliation(s)
- T Liang
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, UK CV4 7AL
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