51
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Cailliez F, Müller P, Firmino T, Pernot P, de la Lande A. Energetics of Photoinduced Charge Migration within the Tryptophan Tetrad of an Animal (6–4) Photolyase. J Am Chem Soc 2016; 138:1904-15. [DOI: 10.1021/jacs.5b10938] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Fabien Cailliez
- Laboratoire
de Chimie Physique, UMR 8000 CNRS/University Paris-Sud, University Paris-Saclay, 91405 Orsay, France
| | - Pavel Müller
- Institute
for Integrative Biology of the Cell (I2BC), CEA, CNRS, University
Paris-Sud, University Paris-Saclay, 91198 Gif-sur-Yvette
cedex, France
| | - Thiago Firmino
- Laboratoire
de Chimie Physique, UMR 8000 CNRS/University Paris-Sud, University Paris-Saclay, 91405 Orsay, France
| | - Pascal Pernot
- Laboratoire
de Chimie Physique, UMR 8000 CNRS/University Paris-Sud, University Paris-Saclay, 91405 Orsay, France
| | - Aurélien de la Lande
- Laboratoire
de Chimie Physique, UMR 8000 CNRS/University Paris-Sud, University Paris-Saclay, 91405 Orsay, France
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52
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Park JW, Rhee YM. Diabatic Population Matrix Formalism for Performing Molecular Mechanics Style Simulations with Multiple Electronic States. J Chem Theory Comput 2015; 10:5238-53. [PMID: 26583208 DOI: 10.1021/ct5006856] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An accurate description of nonbonded interactions is important in investigating dynamics of molecular systems. In many situations, fixed point charge models are successfully applied to explaining various chemical phenomena. However, these models with conventional formulations will not be appropriate in elucidating the detailed dynamics during nonadiabatic events. This is mainly because the chemical properties of any molecule, especially its electronic populations, significantly change with respect to molecular distortions in the vicinity of the surface crossing. To overcome this issue in molecular simulations yet within the framework of the fixed point charge model, we define a diabatic electronic population matrix and substitute it for the conventional adiabatic partial charges. We show that this matrix can be readily utilized toward attaining more reliable descriptions of Coulombic interactions, in combination with the interpolation formalism for obtaining the intramolecular interaction potential. We demonstrate how the mixed formalism with the diabatic charges and the interpolation can be applied to molecular simulations by conducting adiabatic and nonadiabatic molecular dynamics trajectory calculations of the green fluorescent protein chromophore anion in aqueous environment.
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Affiliation(s)
- Jae Woo Park
- Center for Self-Assembly and Complexity, Institute for Basic Science (IBS) , Pohang 790-784, Korea.,Department of Chemistry, Pohang University of Science and Technology (POSTECH) , Pohang 790-784, Korea
| | - Young Min Rhee
- Center for Self-Assembly and Complexity, Institute for Basic Science (IBS) , Pohang 790-784, Korea.,Department of Chemistry, Pohang University of Science and Technology (POSTECH) , Pohang 790-784, Korea
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53
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Ekesan S, Herzfeld J. Pointillist rendering of electron charge and spin density suffices to replicate trends in atomic properties. Proc Math Phys Eng Sci 2015. [DOI: 10.1098/rspa.2015.0370] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The monotonic and non-monotonic variations of atomic properties within and between the rows of the periodic table underlie our understanding of chemistry and accounting for these variations has been a signature strength of quantum mechanics (QM). However, the computational burden of QM motivates the development of more efficient means of describing electrons and reactivity. The recently developed LEWIS
•
model incorporates lessons learnt from QM into a force field that includes electrons as explicit pseudo-classical particles. Here, we extend LEWIS
•
across the 2
p
and 3
p
elements, and show that it is capable of reproducing both monotonic and non-monotonic variations of chemically important atomic properties in a cost-effective manner. An indicator of the strength of the construct is the ability of pairwise potentials trained on ionization energies and the order of spin configurations to predict atomic polarizabilities. In this manner, some insights of QM are uncoupled from its onerous computational burden.
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54
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Yin J, Fenley AT, Henriksen NM, Gilson MK. Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics. J Phys Chem B 2015; 119:10145-55. [PMID: 26181208 DOI: 10.1021/acs.jpcb.5b04262] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Improving the capability of atomistic computer models to predict the thermodynamics of noncovalent binding is critical for successful structure-based drug design, and the accuracy of such calculations remains limited by nonoptimal force field parameters. Ideally, one would incorporate protein-ligand affinity data into force field parametrization, but this would be inefficient and costly. We now demonstrate that sensitivity analysis can be used to efficiently tune Lennard-Jones parameters of aqueous host-guest systems for increasingly accurate calculations of binding enthalpy. These results highlight the promise of a comprehensive use of calorimetric host-guest binding data, along with existing validation data sets, to improve force field parameters for the simulation of noncovalent binding, with the ultimate goal of making protein-ligand modeling more accurate and hence speeding drug discovery.
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Affiliation(s)
- Jian Yin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0736, United States
| | - Andrew T Fenley
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0736, United States
| | - Niel M Henriksen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0736, United States
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0736, United States
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55
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Zgarbová M, Rosnik AM, Luque FJ, Curutchet C, Jurečka P. Transferability and additivity of dihedral parameters in polarizable and nonpolarizable empirical force fields. J Comput Chem 2015. [DOI: 10.1002/jcc.24012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Marie Zgarbová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science; Palacky University; 17. listopadu 12 Olomouc 77146 Czech Republic
| | - Andreana M. Rosnik
- Department de Fisicoquímica; Facultat de Farmàcia, Universitat de Barcelona; Av. Joan XXIII s/n Barcelona 08028 Spain
| | - F. Javier Luque
- Department de Fisicoquímica and Institut de Biomedicina (IBUB); Facultat de Farmàcia, Universitat de Barcelona; Avgda Prat de la Riba 171, Santa Coloma de Gramenet 08921 Spain
| | - Carles Curutchet
- Department de Fisicoquímica; Facultat de Farmàcia, Universitat de Barcelona; Av. Joan XXIII s/n Barcelona 08028 Spain
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science; Palacky University; 17. listopadu 12 Olomouc 77146 Czech Republic
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56
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Correct folding of an α-helix and a β-hairpin using a polarized 2D torsional potential. Sci Rep 2015; 5:10359. [PMID: 26039188 PMCID: PMC5380191 DOI: 10.1038/srep10359] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 04/09/2015] [Indexed: 01/12/2023] Open
Abstract
A new modification to the AMBER force field that incorporates the coupled two-dimensional main chain torsion energy has been evaluated for the balanced representation of secondary structures. In this modified AMBER force field (AMBER03(2D)), the main chain torsion energy is represented by 2-dimensional Fourier expansions with parameters fitted to the potential energy surface generated by high-level quantum mechanical calculations of small peptides in solution. Molecular dynamics simulations are performed to study the folding of two model peptides adopting either α-helix or β-hairpin structures. Both peptides are successfully folded into their native structures using an AMBER03(2D) force field with the implementation of a polarization scheme (AMBER03(2D)p). For comparison, simulations using a standard AMBER03 force field with and without polarization, as well as AMBER03(2D) without polarization, fail to fold both peptides successfully. The correction to secondary structure propensity in the AMBER03 force field and the polarization effect are critical to folding Trpzip2; without these factors, a helical structure is obtained. This study strongly suggests that this new force field is capable of providing a more balanced preference for helical and extended conformations. The electrostatic polarization effect is shown to be indispensable to the growth of secondary structures.
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57
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Shi Y, Ren P, Schnieders M, Piquemal JP. Polarizable Force Fields for Biomolecular Modeling. REVIEWS IN COMPUTATIONAL CHEMISTRY 2015. [DOI: 10.1002/9781118889886.ch2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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58
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Brunk E, Rothlisberger U. Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States. Chem Rev 2015; 115:6217-63. [PMID: 25880693 DOI: 10.1021/cr500628b] [Citation(s) in RCA: 301] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Elizabeth Brunk
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,‡Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94618, United States
| | - Ursula Rothlisberger
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,§National Competence Center of Research (NCCR) MARVEL-Materials' Revolution: Computational Design and Discovery of Novel Materials, 1015 Lausanne, Switzerland
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59
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Gao Y, Li Y, Mou L, Hu W, Zheng J, Zhang JZH, Mei Y. Coupled Two-Dimensional Main-Chain Torsional Potential for Protein Dynamics II: Performance and Validation. J Phys Chem B 2015; 119:4188-93. [DOI: 10.1021/jp510215c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Ya Gao
- College
of Fundamental Studies, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Yongxiu Li
- College
of Fundamental Studies, Shanghai University of Engineering Science, Shanghai 201620, China
- Key
Laboratory of Catalysis and Materials Science of the State Ethnic
Affairs Commission and Ministry of Education, Hubei Province, South-Central University for Nationalities, Wuhan 430074, China
| | - Lirong Mou
- Institutes
for Advanced Interdisciplinary Research, East China Normal University, Shanghai 200062, China
| | - Wenxin Hu
- Computing Center, School of Information Science & Technology, East China Normal University, Shanghai 200062, China
| | - Jun Zheng
- Computing Center, School of Information Science & Technology, East China Normal University, Shanghai 200062, China
| | - John Z. H. Zhang
- College
of Fundamental Studies, Shanghai University of Engineering Science, Shanghai 201620, China
- NYU-ECNU Center
for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Ye Mei
- Center
for Laser and Computational Biophysics, State Key Laboratory of Precision
Spectroscopy, Department of Physics and Institute of Theoretical and
Computational Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center
for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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60
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Ivanov MV, Talipov MR, Timerghazin QK. Genetic Algorithm Optimization of Point Charges in Force Field Development: Challenges and Insights. J Phys Chem A 2015; 119:1422-34. [DOI: 10.1021/acs.jpca.5b00218] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Maxim V. Ivanov
- Department of Chemistry, Marquette University,
P.O. Box 1881, Milwaukee, Wisconsin 53201-1881, United States
| | - Marat R. Talipov
- Department of Chemistry, Marquette University,
P.O. Box 1881, Milwaukee, Wisconsin 53201-1881, United States
| | - Qadir K. Timerghazin
- Department of Chemistry, Marquette University,
P.O. Box 1881, Milwaukee, Wisconsin 53201-1881, United States
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61
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Baker CM. Polarizable force fields for molecular dynamics simulations of biomolecules. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2015. [DOI: 10.1002/wcms.1215] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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62
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Xu S, Zhao DX, Gong LD, Liu C, Yang ZZ. Search of the conformations of Val-dipeptide and Val-tripeptide by ab initio method and ABEEMσπ polarizable force field. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.10.073] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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63
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Kumar H, Dasgupta C, Maiti PK. Structure, dynamics and thermodynamics of single-file water under confinement: effects of polarizability of water molecules. RSC Adv 2015. [DOI: 10.1039/c4ra08730e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Various structural, dynamic and thermodynamic properties of water molecules confined in single-wall carbon nanotubes are investigated using both polarizable and non-polarizable water models.
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Affiliation(s)
- Hemant Kumar
- Centre for Condensed Matter Theory
- Indian Institute of Science
- Bangalore-560012
- India
| | - Chandan Dasgupta
- Centre for Condensed Matter Theory
- Indian Institute of Science
- Bangalore-560012
- India
| | - Prabal K. Maiti
- Centre for Condensed Matter Theory
- Indian Institute of Science
- Bangalore-560012
- India
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64
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Topham CM, Smith JC. Tri-peptide reference structures for the calculation of relative solvent accessible surface area in protein amino acid residues. Comput Biol Chem 2014; 54:33-43. [PMID: 25544680 DOI: 10.1016/j.compbiolchem.2014.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Revised: 11/23/2014] [Accepted: 11/30/2014] [Indexed: 10/24/2022]
Abstract
Relative amino acid residue solvent accessibility values allow the quantitative comparison of atomic solvent-accessible surface areas in different residue types and physical environments in proteins and in protein structural alignments. Geometry-optimised tri-peptide structures in extended solvent-exposed reference conformations have been obtained for 43 amino acid residue types at a high level of quantum chemical theory. Significant increases in side-chain solvent accessibility, offset by reductions in main-chain atom solvent exposure, were observed for standard residue types in partially geometry-optimised structures when compared to non-minimised models built from identical sets of proper dihedral angles abstracted from the literature. Optimisation of proper dihedral angles led most notably to marked increases of up to 54% in proline main-chain atom solvent accessibility compared to literature values. Similar effects were observed for fully-optimised tri-peptides in implicit solvent. The relief of internal strain energy was associated with systematic variation in N, C(α) and C(β) atom solvent accessibility across all standard residue types. The results underline the importance of optimisation of 'hard' degrees of freedom (bond lengths and valence bond angles) and improper dihedral angle values from force field or other context-independent reference values, and impact on the use of standardised fixed internal co-ordinate geometry in sampling approaches to the determination of absolute values of protein amino acid residue solvent accessibility. Quantum chemical methods provide a useful and accurate alternative to molecular mechanics methods to perform energy minimisation of peptides containing non-standard (chemically modified) amino acid residues frequently present in experimental protein structure data sets, for which force field parameters may not be available. Reference tri-peptide atomic co-ordinate sets including hydrogen atoms are made freely available.
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Affiliation(s)
- Christopher M Topham
- Molecular Forces Consulting, 40 Rue Boyssonne, Toulouse 31400, France; Computational Molecular Biophysics, IWR der Universität Heidelberg, Im Neuenheimer Feld 368, Heidelberg D-69120, Germany; University of Tennessee/Oak Ridge National Laboratory, Center for Molecular Biophysics, P.O. Box 2008, Oak Ridge, TN 37831-6309, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN 37996, USA.
| | - Jeremy C Smith
- Computational Molecular Biophysics, IWR der Universität Heidelberg, Im Neuenheimer Feld 368, Heidelberg D-69120, Germany; University of Tennessee/Oak Ridge National Laboratory, Center for Molecular Biophysics, P.O. Box 2008, Oak Ridge, TN 37831-6309, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN 37996, USA
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65
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Horn AHC. A consistent force field parameter set for zwitterionic amino acid residues. J Mol Model 2014; 20:2478. [PMID: 25338816 DOI: 10.1007/s00894-014-2478-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 09/21/2014] [Indexed: 12/20/2022]
Abstract
Isolated amino acids play an important role in biochemistry and are therefore an interesting object of study. Atomistic molecular dynamics (MD) simulations can provide a high-resolution picture of the dynamic features of these species, especially in their biological environment. Unfortunately, most standard force field packages lack libraries for isolated amino acids in their zwitterionic form. Although several studies have used ad-hoc parameterizations for single amino acids, a consistent force-field parameter set for these molecules is still missing. Here, we present such a parameter library derived from the widely used parm99SB set from the AMBER program package. The parameter derivation for all 20 proteinogenic amino acids transparently followed established procedures with histidine treated in three different protonation states. All amino acids were subjected to MD simulations in four different forms for comparison: zwitterionic, N-teminally capped with acetyl, C-terminally capped with N-methyl, and capped at both termini. Simulation results show similarities between the different forms. Five zwitterionic amino acids-arginine, glutamate, glycine, phenylalanine, leucine-were simulated in a protein environment. Proteins and ligands generally retained their initial structure. The new parameter set will thus facilitate future atomistic simulations of these species.
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Affiliation(s)
- Anselm H C Horn
- Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Fahrstr. 17, 91054, Erlangen, Germany,
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66
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Cerutti DS, Swope WC, Rice J, Case DA. ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins. J Chem Theory Comput 2014; 10:4515-4534. [PMID: 25328495 PMCID: PMC4196740 DOI: 10.1021/ct500643c] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Indexed: 01/25/2023]
Abstract
We present the ff14ipq force field, implementing the previously published IPolQ charge set for simulations of complete proteins. Minor modifications to the charge derivation scheme and van der Waals interactions between polar atoms are introduced. Torsion parameters are developed through a generational learning approach, based on gas-phase MP2/cc-pVTZ single-point energies computed of structures optimized by the force field itself rather than the quantum benchmark. In this manner, we sacrifice information about the true quantum minima in order to ensure that the force field maintains optimal agreement with the MP2/cc-pVTZ benchmark for the ensembles it will actually produce in simulations. A means of making the gas-phase torsion parameters compatible with solution-phase IPolQ charges is presented. The ff14ipq model is an alternative to ff99SB and other Amber force fields for protein simulations in programs that accommodate pair-specific Lennard-Jones combining rules. The force field gives strong performance on α-helical and β-sheet oligopeptides as well as globular proteins over microsecond time scale simulations, although it has not yet been tested in conjunction with lipid and nucleic acid models. We show how our choices in parameter development influence the resulting force field and how other choices that may have appeared reasonable would actually have led to poorer results. The tools we developed may also aid in the development of future fixed-charge and even polarizable biomolecular force fields.
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Affiliation(s)
- David S. Cerutti
- Department
of Chemistry and
Chemical Biology and BioMaPS Institute, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854-8066, United States
| | - William C. Swope
- Department
of Chemistry and
Chemical Biology and BioMaPS Institute, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854-8066, United States
| | - Julia
E. Rice
- Department
of Chemistry and
Chemical Biology and BioMaPS Institute, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854-8066, United States
| | - David A. Case
- Department
of Chemistry and
Chemical Biology and BioMaPS Institute, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854-8066, United States
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67
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Gillet N, Lévy B, Moliner V, Demachy I, de la Lande A. Electron and Hydrogen Atom Transfers in the Hydride Carrier Protein EmoB. J Chem Theory Comput 2014; 10:5036-46. [DOI: 10.1021/ct500173y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Natacha Gillet
- Laboratoire
de Chimie-Physique, Université Paris Sud, CNRS, UMR 8000, 15 rue Jean Perrin, 91405 Orsay CEDEX, France
- Departament
de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Bernard Lévy
- Laboratoire
de Chimie-Physique, Université Paris Sud, CNRS, UMR 8000, 15 rue Jean Perrin, 91405 Orsay CEDEX, France
| | - Vicent Moliner
- Departament
de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Isabelle Demachy
- Laboratoire
de Chimie-Physique, Université Paris Sud, CNRS, UMR 8000, 15 rue Jean Perrin, 91405 Orsay CEDEX, France
| | - Aurélien de la Lande
- Laboratoire
de Chimie-Physique, Université Paris Sud, CNRS, UMR 8000, 15 rue Jean Perrin, 91405 Orsay CEDEX, France
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68
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Zuo ZL, Guo L, Mancera RL. Free energy of binding of coiled-coil complexes with different electrostatic environments: the influence of force field polarisation and capping. NATURAL PRODUCTS AND BIOPROSPECTING 2014; 4:285-295. [PMID: 25159896 PMCID: PMC4199946 DOI: 10.1007/s13659-014-0036-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 08/08/2014] [Indexed: 06/03/2023]
Abstract
Coiled-coils are well known protein-protein interaction motifs, with the leucine zipper region of activator protein-1 (AP-1) consisting of the c-Jun and c-Fos proteins being a typical example. Molecular dynamics (MD) simulations using the MM/GBSA method have been used to predict the free energy of interaction of these proteins. The influence of force field polarisation and capping on the predicted free energy of binding of complexes with different electrostatic environments (net charge) were investigated. Although both force field polarisation and peptide capping are important for the prediction of the absolute free energy of binding, peptide capping has the largest influence on the predicted free energy of binding. Polarisable simulations appear better suited to determine structural properties of the complexes of these proteins while non-polarisable simulations seem to give better predictions of the associated free energies of binding.
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Affiliation(s)
- Zhi-Li Zuo
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
| | - Ling Guo
- College of Animal Husbandry & Veterinary, Liaoning Medical University, Jinzhou, 121001 China
| | - Ricardo L. Mancera
- School of Biomedical Sciences, CHIRI Biosciences, Curtin University, GPO Box U1987, Perth, WA 6845 Australia
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69
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Hopkins CW, Roitberg AE. Fitting of Dihedral Terms in Classical Force Fields as an Analytic Linear Least-Squares Problem. J Chem Inf Model 2014; 54:1978-86. [DOI: 10.1021/ci500112w] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chad W. Hopkins
- Department of Physics and ‡Department of Chemistry, Quantum Theory
Project, University of Florida, Gainesville, Florida 32611, United States
| | - Adrian E. Roitberg
- Department of Physics and ‡Department of Chemistry, Quantum Theory
Project, University of Florida, Gainesville, Florida 32611, United States
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70
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Yang ZZ, Wang JJ, Zhao DX. Valence state parameters of all transition metal atoms in metalloproteins-development of ABEEMσπ fluctuating charge force field. J Comput Chem 2014; 35:1690-706. [DOI: 10.1002/jcc.23676] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 06/01/2014] [Accepted: 06/18/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering; Department of Chemistry, Liaoning Normal University; Dalian China 116029
| | - Jian-Jiang Wang
- School of Chemistry and Chemical Engineering; Department of Chemistry, Liaoning Normal University; Dalian China 116029
| | - Dong-Xia Zhao
- School of Chemistry and Chemical Engineering; Department of Chemistry, Liaoning Normal University; Dalian China 116029
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71
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Lorenzen K, Wichmann C, Tavan P. Including the Dispersion Attraction into Structure-Adapted Fast Multipole Expansions for MD Simulations. J Chem Theory Comput 2014; 10:3244-59. [DOI: 10.1021/ct500319a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Konstantin Lorenzen
- Lehrstuhl
für Biomolekulare
Optik, Ludwig-Maximilians-Universität, Oettingenstr. 67, 80538 München, Germany
| | - Christoph Wichmann
- Lehrstuhl
für Biomolekulare
Optik, Ludwig-Maximilians-Universität, Oettingenstr. 67, 80538 München, Germany
| | - Paul Tavan
- Lehrstuhl
für Biomolekulare
Optik, Ludwig-Maximilians-Universität, Oettingenstr. 67, 80538 München, Germany
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72
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Wang W, Ye W, Jiang C, Luo R, Chen H. New Force Field on Modeling Intrinsically Disordered Proteins. Chem Biol Drug Des 2014; 84:253-69. [DOI: 10.1111/cbdd.12314] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 02/15/2014] [Accepted: 02/24/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Wei Wang
- State Key Laboratory of Microbial metabolism Department of Bioinformatics and Biostatistics College of Life Sciences and Biotechnology Shanghai Jiaotong University 800 Dongchuan Road Shanghai 200240 China
| | - Wei Ye
- State Key Laboratory of Microbial metabolism Department of Bioinformatics and Biostatistics College of Life Sciences and Biotechnology Shanghai Jiaotong University 800 Dongchuan Road Shanghai 200240 China
| | - Cheng Jiang
- State Key Laboratory of Microbial metabolism Department of Bioinformatics and Biostatistics College of Life Sciences and Biotechnology Shanghai Jiaotong University 800 Dongchuan Road Shanghai 200240 China
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry and Biomedical Engineering University of California Irvine CA 92697‐3900 USA
| | - Hai‐Feng Chen
- State Key Laboratory of Microbial metabolism Department of Bioinformatics and Biostatistics College of Life Sciences and Biotechnology Shanghai Jiaotong University 800 Dongchuan Road Shanghai 200240 China
- Shanghai Center for Bioinformation Technology 1275 Keyuan Road Shanghai 200235 China
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73
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Pezeshki S, Lin H. Recent developments in QM/MM methods towards open-boundary multi-scale simulations. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.911870] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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74
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Thellamurege NM, Si D, Cui F, Li H. Quantum mechanical/molecular mechanical/continuum style solvation model: Second order Møller-Plesset perturbation theory. J Chem Phys 2014; 140:174115. [DOI: 10.1063/1.4873344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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75
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McDaniel JG, Schmidt JR. First-Principles Many-Body Force Fields from the Gas Phase to Liquid: A “Universal” Approach. J Phys Chem B 2014; 118:8042-53. [DOI: 10.1021/jp501128w] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jesse G. McDaniel
- Theoretical
Chemistry Institute
and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - J. R. Schmidt
- Theoretical
Chemistry Institute
and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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76
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Caprasecca S, Jurinovich S, Viani L, Curutchet C, Mennucci B. Geometry Optimization in Polarizable QM/MM Models: The Induced Dipole Formulation. J Chem Theory Comput 2014; 10:1588-98. [DOI: 10.1021/ct500021d] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stefano Caprasecca
- Dipartimento
di Chimica e Chimica Industriale, University of Pisa, Via Risorgimento
35, 56126 Pisa, Italy
| | - Sandro Jurinovich
- Dipartimento
di Chimica e Chimica Industriale, University of Pisa, Via Risorgimento
35, 56126 Pisa, Italy
| | - Lucas Viani
- Dipartimento
di Chimica e Chimica Industriale, University of Pisa, Via Risorgimento
35, 56126 Pisa, Italy
| | - Carles Curutchet
- Departament
de Fisicoquímica Facultat de Farmàcia, Universitat de Barcelona Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | - Benedetta Mennucci
- Dipartimento
di Chimica e Chimica Industriale, University of Pisa, Via Risorgimento
35, 56126 Pisa, Italy
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77
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Mancini G, Brancato G, Barone V. Combining the Fluctuating Charge Method, Non-Periodic Boundary Conditions and Meta-Dynamics: Aqua Ions as case studies. J Chem Theory Comput 2014; 10:1150-1163. [PMID: 26543440 DOI: 10.1021/ct400988e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We present the current status of development of our code for performing Molecular Dynamics (MD) simulations exploiting a polarizable force field based on the Fluctuating Charge (FQ) method and non-Periodic Boundary Conditions (NPBC). Continuing on the path set in a previous work, we increased the capabilities of the code by implementing a number of new features, including: a non-iterative algorithm for rigid trigonal molecule simulations; two additional temperature coupling schemes; a meta-dynamics based approach for effective free energy evaluations. Although these are well known algorithms, each present in one or more widely used MD packages, they have now been tested, for the first time, in the context of the FQ model coupled with NPBC. As case studies, we considered three aqueous ions of increasing charge, namely Na+, Ca2+ and La3+, at infinite dilution. In particular, by exploiting a computational approach recently proposed by our group and based on the metadynamics technique, we focused on the important role played by solvent polarization on ionic hydration structures, also investigating the free energy landscapes of ion coordination and the water exchange rates. Such an approach, previously tested with standard non-polarizable models, was applied here to evaluate the effects of explicit polarization on water exchange barriers between different solvent coordination structures. Moreover, we have analyzed and discussed in some detail non-linear electrostatic effects arising from solvent polarization while going from a mono- to a di- and trivalent ion.
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Affiliation(s)
- Giordano Mancini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy ; Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Giuseppe Brancato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy ; Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy ; Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
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78
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Schmidt TC, Paasche A, Grebner C, Ansorg K, Becker J, Lee W, Engels B. QM/MM investigations of organic chemistry oriented questions. Top Curr Chem (Cham) 2014; 351:25-101. [PMID: 22392477 DOI: 10.1007/128_2011_309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.
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Affiliation(s)
- Thomas C Schmidt
- Institut für Phys. und Theor. Chemie, Emil-Fischer-Strasse 42, Campus Hubland Nord, 97074, Würzburg, Germany
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79
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Vanommeslaeghe K, Guvench O, MacKerell AD. Molecular mechanics. Curr Pharm Des 2014; 20:3281-92. [PMID: 23947650 PMCID: PMC4026342 DOI: 10.2174/13816128113199990600] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/07/2013] [Indexed: 11/22/2022]
Abstract
Molecular Mechanics (MM) force fields are the methods of choice for protein simulations, which are essential in the study of conformational flexibility. Given the importance of protein flexibility in drug binding, MM is involved in most if not all Computational Structure-Based Drug Discovery (CSBDD) projects. This paper introduces the reader to the fundamentals of MM, with a special emphasis on how the target data used in the parametrization of force fields determine their strengths and weaknesses. Variations and recent developments such as polarizable force fields are discussed. The paper ends with a brief overview of common force fields in CSBDD.
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Affiliation(s)
- Kenno Vanommeslaeghe
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St, HSF-II Rm 633, Baltimore, MD 21201; tel: 410-706-7442; fax: 410-706-5017
| | - Olgun Guvench
- Department of Pharmaceutical Sciences, University of New England College of Pharmacy, 716 Stevens Ave, Portland, ME 04103
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St, HSF-II Rm 633, Baltimore, MD 21201; tel: 410-706-7442; fax: 410-706-5017
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80
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Kwac K, Geva E. A Mixed Quantum-Classical Molecular Dynamics Study of anti-Tetrol and syn-Tetrol Dissolved in Liquid Chloroform: Hydrogen-Bond Structure and Its Signature on the Infrared Absorption Spectrum. J Phys Chem B 2013; 117:16493-505. [DOI: 10.1021/jp4080724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Kijeong Kwac
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eitan Geva
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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81
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Demerdash O, Yap EH, Head-Gordon T. Advanced potential energy surfaces for condensed phase simulation. Annu Rev Phys Chem 2013; 65:149-74. [PMID: 24328448 DOI: 10.1146/annurev-physchem-040412-110040] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Computational modeling at the atomistic and mesoscopic levels has undergone dramatic development in the past 10 years to meet the challenge of adequately accounting for the many-body nature of intermolecular interactions. At the heart of this challenge is the ability to identify the strengths and specific limitations of pairwise-additive interactions, to improve classical models to explicitly account for many-body effects, and consequently to enhance their ability to describe a wider range of reference data and build confidence in their predictive capacity. However, the corresponding computational cost of these advanced classical models increases significantly enough that statistical convergence of condensed phase observables becomes more difficult to achieve. Here we review a hierarchy of potential energy surface models used in molecular simulations for systems with many degrees of freedom that best meet the trade-off between accuracy and computational speed in order to define a sweet spot for a given scientific problem of interest.
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82
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Xiao X, Zhu T, Ji CG, Zhang JZH. Development of an Effective Polarizable Bond Method for Biomolecular Simulation. J Phys Chem B 2013; 117:14885-93. [DOI: 10.1021/jp4080866] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Xudong Xiao
- State
Key Laboratory of Precision Spectroscopy, Department of Physics, Institute
of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
- Institutes
for Advanced Interdisciplinary Research, East China Normal University, Shanghai 200062, China
| | - Tong Zhu
- State
Key Laboratory of Precision Spectroscopy, Department of Physics, Institute
of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
| | - Chang G. Ji
- State
Key Laboratory of Precision Spectroscopy, Department of Physics, Institute
of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
- Institutes
for Advanced Interdisciplinary Research, East China Normal University, Shanghai 200062, China
- NYU-ECNU
Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - John Z. H. Zhang
- State
Key Laboratory of Precision Spectroscopy, Department of Physics, Institute
of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU
Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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83
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Lopes PEM, Huang J, Shim J, Luo Y, Li H, Roux B, Mackerell AD. Force Field for Peptides and Proteins based on the Classical Drude Oscillator. J Chem Theory Comput 2013; 9:5430-5449. [PMID: 24459460 DOI: 10.1021/ct400781b] [Citation(s) in RCA: 291] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Presented is a polarizable force field based on a classical Drude oscillator framework, currently implemented in the programs CHARMM and NAMD, for modeling and molecular dynamics (MD) simulation studies of peptides and proteins. Building upon parameters for model compounds representative of the functional groups in proteins, the development of the force field focused on the optimization of the parameters for the polypeptide backbone and the connectivity between the backbone and side chains. Optimization of the backbone electrostatic parameters targeted quantum mechanical conformational energies, interactions with water, molecular dipole moments and polarizabilities and experimental condensed phase data for short polypeptides such as (Ala)5. Additional optimization of the backbone φ, ψ conformational preferences included adjustments of the tabulated two-dimensional spline function through the CMAP term. Validation of the model included simulations of a collection of peptides and proteins. This 1st generation polarizable model is shown to maintain the folded state of the studied systems on the 100 ns timescale in explicit solvent MD simulations. The Drude model typically yields larger RMS differences as compared to the additive CHARMM36 force field (C36) and shows additional flexibility as compared to the additive model. Comparison with NMR chemical shift data shows a small degradation of the polarizable model with respect to the additive, though the level of agreement may be considered satisfactory, while for residues shown to have significantly underestimated S2 order parameters in the additive model, improvements are calculated with the polarizable model. Analysis of dipole moments associated with the peptide backbone and tryptophan side chains show the Drude model to have significantly larger values than those present in C36, with the dipole moments of the peptide backbone enhanced to a greater extent in sheets versus helices and the dipoles of individual moieties observed to undergo significant variations during the MD simulations. Although there are still some limitations, the presented model, termed Drude-2013, is anticipated to yield a molecular picture of peptide and protein structure and function that will be of increased physical validity and internal consistency in a computationally accessible fashion.
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Affiliation(s)
- Pedro E M Lopes
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, 20 Penn Street HSFII, Baltimore, Maryland 21201, USA
| | - Jing Huang
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, 20 Penn Street HSFII, Baltimore, Maryland 21201, USA
| | - Jihyun Shim
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, 20 Penn Street HSFII, Baltimore, Maryland 21201, USA
| | - Yun Luo
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA ; Argonne Leadership Computing Facility, Argonne National Laboratory, 9700 South Cass Avenue, Building 240, Argonne, Illinois 60439, USA
| | - Hui Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
| | - Alexander D Mackerell
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, 20 Penn Street HSFII, Baltimore, Maryland 21201, USA
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84
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Thellamurege NM, Si D, Cui F, Zhu H, Lai R, Li H. QuanPol: a full spectrum and seamless QM/MM program. J Comput Chem 2013; 34:2816-33. [PMID: 24122765 DOI: 10.1002/jcc.23435] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 08/07/2013] [Accepted: 08/10/2013] [Indexed: 12/29/2022]
Abstract
The quantum chemistry polarizable force field program (QuanPol) is implemented to perform combined quantum mechanical and molecular mechanical (QM/MM) calculations with induced dipole polarizable force fields and induced surface charge continuum solvation models. The QM methods include Hartree-Fock method, density functional theory method (DFT), generalized valence bond theory method, multiconfiguration self-consistent field method, Møller-Plesset perturbation theory method, and time-dependent DFT method. The induced dipoles of the MM atoms and the induced surface charges of the continuum solvation model are self-consistently and variationally determined together with the QM wavefunction. The MM force field methods can be user specified, or a standard force field such as MMFF94, Chemistry at Harvard Molecular Mechanics (CHARMM), Assisted Model Building with Energy Refinement (AMBER), and Optimized Potentials for Liquid Simulations-All Atom (OPLS-AA). Analytic gradients for all of these methods are implemented so geometry optimization and molecular dynamics (MD) simulation can be performed. MD free energy perturbation and umbrella sampling methods are also implemented.
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85
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Thellamurege NM, Cui F, Li H. Quantum mechanical/molecular mechanical/continuum style solvation model: Time-dependent density functional theory. J Chem Phys 2013; 139:084106. [DOI: 10.1063/1.4819139] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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86
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Baker CM, Best RB. Insights into the Binding of Intrinsically Disordered Proteins from Molecular Dynamics Simulation. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013; 4:182-198. [PMID: 34354764 DOI: 10.1002/wcms.1167] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Intrinsically disordered proteins (IDPs) are a class of protein that, in the native state, possess no well-defined secondary or tertiary structure, existing instead as dynamic ensembles of conformations. They are biologically important, with approximately 20% of all eukaryotic proteins disordered, and found at the heart of many biochemical networks. To fulfil their biological roles, many IDPs need to bind to proteins and/or nucleic acids. And while unstructured in solution, IDPs typically fold into a well-defined three-dimensional structure upon interaction with a binding partner. The flexibility and structural diversity inherent to IDPs makes this coupled folding and binding difficult to study at atomic resolution by experiment alone, and computer simulation currently offers perhaps the best opportunity to understand this process. But simulation of coupled folding and binding is itself extremely challenging; these molecules are large and highly flexible, and their binding partners, such as DNA or cyclins, are also often large. Therefore, their study requires either or both simplified representations and advanced enhanced sampling schemes. It is not always clear that existing simulation techniques, optimized for studying folded proteins, are well-suited to IDPs. In this article, we examine the progress that has been made in the study of coupled folding and binding using molecular dynamics simulation. We summarise what has been learnt, and examine the state of the art in terms of both methodologies and models. We also consider the lessons to be learnt from advances in other areas of simulation and highlight the issues that remain of be addressed.
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Affiliation(s)
- Christopher M Baker
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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87
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Li Y, Gao Y, Zhang X, Wang X, Mou L, Duan L, He X, Mei Y, Zhang JZH. A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation. J Mol Model 2013; 19:3647-57. [PMID: 23765039 DOI: 10.1007/s00894-013-1879-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 05/01/2013] [Indexed: 11/29/2022]
Abstract
Main chain torsions of alanine dipeptide are parameterized into coupled 2-dimensional Fourier expansions based on quantum mechanical (QM) calculations at M06 2X/aug-cc-pvtz//HF/6-31G** level. Solvation effect is considered by employing polarizable continuum model. Utilization of the M06 2X functional leads to precise potential energy surface that is comparable to or even better than MP2 level, but with much less computational demand. Parameterization of the 2D expansions is against the full main chain torsion space instead of just a few low energy conformations. This procedure is similar to that for the development of AMBER03 force field, except unique weighting factor was assigned to all the grid points. To avoid inconsistency between quantum mechanical calculations and molecular modeling, the model peptide is further optimized at molecular mechanics level with main chain dihedral angles fixed before the calculation of the conformational energy on molecular mechanical level at each grid point, during which generalized Born model is employed. Difference in solvation models at quantum mechanics and molecular mechanics levels makes this parameterization procedure less straightforward. All force field parameters other than main chain torsions are taken from existing AMBER force field. With this new main chain torsion terms, we have studied the main chain dihedral distributions of ALA dipeptide and pentapeptide in aqueous solution. The results demonstrate that 2D main chain torsion is effective in delineating the energy variation associated with rotations along main chain dihedrals. This work is an implication for the necessity of more accurate description of main chain torsions in the future development of ab initio force field and it also raises a challenge to the development of quantum mechanical methods, especially the quantum mechanical solvation models.
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Affiliation(s)
- Yongxiu Li
- Center for Laser and Computational Biophysics, State Key Laboratory of Precision Spectroscopy and Department of Physics and Institute of Theoretical and Computational Science, East China Normal University, Shanghai, 200062, China
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88
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Abstract
This chapter provides an overview of the most common methods for including an explicit description of electronic polarization in molecular mechanics force fields: the induced point dipole, shell, and fluctuating charge models. The importance of including polarization effects in biomolecular simulations is discussed, and some of the most important achievements in the development of polarizable biomolecular force fields to date are highlighted.
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Affiliation(s)
- Hanne S Antila
- Department of Chemistry, Aalto University, Espoo, Finland
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89
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Ren P, Chun J, Thomas DG, Schnieders MJ, Marucho M, Zhang J, Baker NA. Biomolecular electrostatics and solvation: a computational perspective. Q Rev Biophys 2012; 45:427-91. [PMID: 23217364 PMCID: PMC3533255 DOI: 10.1017/s003358351200011x] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.
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Affiliation(s)
- Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin
| | | | | | | | - Marcelo Marucho
- Department of Physics and Astronomy, The University of Texas at San Antonio
| | - Jiajing Zhang
- Department of Biomedical Engineering, The University of Texas at Austin
| | - Nathan A. Baker
- To whom correspondence should be addressed. Pacific Northwest National Laboratory, PO Box 999, MSID K7-29, Richland, WA 99352. Phone: +1-509-375-3997,
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90
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Salomon-Ferrer R, Case DA, Walker RC. An overview of the Amber biomolecular simulation package. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1121] [Citation(s) in RCA: 1192] [Impact Index Per Article: 99.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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91
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Nikolić D, Blinov N, Wishart D, Kovalenko A. 3D-RISM-Dock: A New Fragment-Based Drug Design Protocol. J Chem Theory Comput 2012; 8:3356-72. [PMID: 26605742 DOI: 10.1021/ct300257v] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We explore a new approach in the rational design of specificity in molecular recognition of small molecules based on statistical-mechanical integral equation theory of molecular liquids in the form of the three-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH). The numerically stable iterative solution of conventional 3D-RISM equations includes the fragmental decomposition of flexible ligands, which are treated as distinct species in solvent mixtures of arbitrary complexity. The computed density functions for solution (including ligand) molecules are obtained as a set of discrete spatial grids that uniquely describe the continuous solvent-site distribution around the protein solute. Potentials of mean force derived from these distributions define the scoring function interfaced with the AutoDock program for an automated ranking of docked conformations. As a case study in terms of solvent composition, we analyze cooperative interactions encountered in the binding of a flexible thiamine molecule to the prion protein at near-physiological conditions. The predicted location and residency times of computed binding modes are in excellent agreement with the available experimental data.
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Affiliation(s)
- Dragan Nikolić
- National Institute for Nanotechnology, National Research Council of Canada, Edmonton, Alberta, Canada
| | - Nikolay Blinov
- National Institute for Nanotechnology, National Research Council of Canada, Edmonton, Alberta, Canada.,Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - David Wishart
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Andriy Kovalenko
- National Institute for Nanotechnology, National Research Council of Canada, Edmonton, Alberta, Canada.,Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta, Canada
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92
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Zuo Z, Gandhi NS, Arndt KM, Mancera RL. Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein. Biopolymers 2012; 97:899-909. [DOI: 10.1002/bip.22099] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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93
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Kucukkal TG, Stuart SJ. Polarizable Molecular Dynamics Simulations of Aqueous Dipeptides. J Phys Chem B 2012; 116:8733-40. [DOI: 10.1021/jp300528m] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Tugba G. Kucukkal
- Department of Chemistry, Clemson University, Clemson, South Carolina 29634,
United States
| | - Steven J. Stuart
- Department of Chemistry, Clemson University, Clemson, South Carolina 29634,
United States
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Wang J, Cieplak P, Li J, Cai Q, Hsieh M, Luo R, Duan Y. Development of polarizable models for molecular mechanical calculations. 4. van der Waals parametrization. J Phys Chem B 2012; 116:7088-101. [PMID: 22612331 PMCID: PMC3391542 DOI: 10.1021/jp3019759] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the previous publications of this series, we presented a set of Thole induced dipole interaction models using four types of screening functions. In this work, we document our effort to refine the van der Waals parameters for the Thole polarizable models. Following the philosophy of AMBER force field development, the van der Waals (vdW) parameters were tuned for the Thole model with linear screening function to reproduce both the ab initio interaction energies and the experimental densities of pure liquids. An in-house genetic algorithm was applied to maximize the fitness of "chromosomes" which is a function of the root-mean-square errors (RMSE) of interaction energy and liquid density. To efficiently explore the vdW parameter space, a novel approach was developed to estimate the liquid densities for a given vdW parameter set using the mean residue-residue interaction energies through interpolation/extrapolation. This approach allowed the costly molecular dynamics simulations be performed at the end of each optimization cycle only and eliminated the simulations during the cycle. Test results show notable improvements over the original AMBER FF99 vdW parameter set, as indicated by the reduction in errors of the calculated pure liquid densities (d), heats of vaporization (H(vap)), and hydration energies. The average percent error (APE) of the densities of 59 pure liquids was reduced from 5.33 to 2.97%; the RMSE of H(vap) was reduced from 1.98 to 1.38 kcal/mol; the RMSE of solvation free energies of 15 compounds was reduced from 1.56 to 1.38 kcal/mol. For the interaction energies of 1639 dimers, the overall performance of the optimized vdW set is slightly better than the original FF99 vdW set (RMSE of 1.56 versus 1.63 kcal/mol). The optimized vdW parameter set was also evaluated for the exponential screening function used in the Amoeba force field to assess its applicability for different types of screening functions. Encouragingly, comparable performance was observed when the optimized vdW set was combined with the Thole Amoeba-like polarizable model, particularly for the interaction energy and liquid density calculations. Thus, the optimized vdW set is applicable to both types of Thole models with either linear or Amoeba-like screening functions.
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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 Biomedical Engineering, One Shields Avenue, Davis, CA 95616, USA
| | - 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
| | - 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 Biomedical Engineering, One Shields Avenue, Davis, CA 95616, USA
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96
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Pratas F, Sousa L, Dieterich JM, Mata RA. Computation of Induced Dipoles in Molecular Mechanics Simulations Using Graphics Processors. J Chem Inf Model 2012; 52:1159-66. [DOI: 10.1021/ci200564x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Frederico Pratas
- INESC-ID/IST, Technical University of Lisbon, Rua Alves Redol, 9, 1000-029 Lisboa,
Portugal
| | - Leonel Sousa
- INESC-ID/IST, Technical University of Lisbon, Rua Alves Redol, 9, 1000-029 Lisboa,
Portugal
| | - Johannes M. Dieterich
- Institut für
Physikalische
Chemie, Universität Göttingen, Tammannstrasse 6, D-37077 Göttingen, Germany
| | - Ricardo A. Mata
- Institut für
Physikalische
Chemie, Universität Göttingen, Tammannstrasse 6, D-37077 Göttingen, Germany
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97
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Woo Kim H, Rhee YM. Molecule-specific determination of atomic polarizabilities with the polarizable atomic multipole model. J Comput Chem 2012; 33:1662-72. [DOI: 10.1002/jcc.22985] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 03/18/2012] [Indexed: 11/07/2022]
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Verstraelen T, Pauwels E, De Proft F, Van Speybroeck V, Geerlings P, Waroquier M. Assessment of Atomic Charge Models for Gas-Phase Computations on Polypeptides. J Chem Theory Comput 2012; 8:661-76. [PMID: 26596614 DOI: 10.1021/ct200512e] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The concept of the atomic charge is extensively used to model the electrostatic properties of proteins. Atomic charges are not only the basis for the electrostatic energy term in biomolecular force fields but are also derived from quantum mechanical computations on protein fragments to get more insight into their electronic structure. Unfortunately there are many atomic charge schemes which lead to significantly different results, and it is not trivial to determine which scheme is most suitable for biomolecular studies. Therefore, we present an extensive methodological benchmark using a selection of atomic charge schemes [Mulliken, natural, restrained electrostatic potential, Hirshfeld-I, electronegativity equalization method (EEM), and split-charge equilibration (SQE)] applied to two sets of penta-alanine conformers. Our analysis clearly shows that Hirshfeld-I charges offer the best compromise between transferability (robustness with respect to conformational changes) and the ability to reproduce electrostatic properties of the penta-alanine. The benchmark also considers two charge equilibration models (EEM and SQE), which both clearly fail to describe the locally charged moieties in the zwitterionic form of penta-alanine. This issue is analyzed in detail because charge equilibration models are computationally much more attractive than the Hirshfeld-I scheme. Based on the latter analysis, a straightforward extension of the SQE model is proposed, SQE+Q(0), that is suitable to describe biological systems bearing many locally charged functional groups.
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Affiliation(s)
- Toon Verstraelen
- Center For Molecular Modeling, Ghent University , Technologiepark 903, 9050 Zwijnaarde, Belgium (Member of the QCMM Ghent-Brussels Alliance Group)
| | - Ewald Pauwels
- Center For Molecular Modeling, Ghent University , Technologiepark 903, 9050 Zwijnaarde, Belgium (Member of the QCMM Ghent-Brussels Alliance Group)
| | - Frank De Proft
- Department of General Chemistry (ALGC), Free University of Brussels-VUB , Pleinlaan 2, 1050 Brussels, Belgium (Member of the QCMM Ghent-Brussels Alliance Group)
| | - Veronique Van Speybroeck
- Center For Molecular Modeling, Ghent University , Technologiepark 903, 9050 Zwijnaarde, Belgium (Member of the QCMM Ghent-Brussels Alliance Group)
| | - Paul Geerlings
- Department of General Chemistry (ALGC), Free University of Brussels-VUB , Pleinlaan 2, 1050 Brussels, Belgium (Member of the QCMM Ghent-Brussels Alliance Group)
| | - Michel Waroquier
- Center For Molecular Modeling, Ghent University , Technologiepark 903, 9050 Zwijnaarde, Belgium (Member of the QCMM Ghent-Brussels Alliance Group)
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99
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Lu Z, Zhou N, Wu Q, Zhang Y. Directional Dependence of Hydrogen Bonds: a Density-based Energy Decomposition Analysis and Its Implications on Force Field Development. J Chem Theory Comput 2011; 7:4038-4049. [PMID: 22267958 PMCID: PMC3259744 DOI: 10.1021/ct2003226] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
One well-known shortcoming of widely-used biomolecular force fields is the description of the directional dependence of hydrogen bonding (HB). Here we aim to better understand the origin of this difficulty and thus provide some guidance for further force field development. Our theoretical approaches center on a novel density-based energy decomposition analysis (DEDA) method [J. Chem. Phys., 131, 164112 (2009)], in which the frozen density energy is variationally determined through constrained search. This unique and most significant feature of DEDA enables us to find that the frozen density interaction term is the key factor in determining the HB orientation, while the sum of polarization and charge-transfer components shows very little HB directional dependence. This new insight suggests that the difficulty for current non-polarizable force fields to describe the HB directional dependence is not due to the lack of explicit polarization or charge-transfer terms. Using the DEDA results as reference, we further demonstrate that the main failure coming from the atomic point charge model can be overcome largely by introducing extra charge sites or higher order multipole moments. Among all the electrostatic models explored, the smeared charge distributed multipole model (up to quadrupole), which also takes account of charge penetration effects, gives the best agreement with the corresponding DEDA results. Meanwhile, our results indicate that the van der Waals interaction term needs to be further improved to better model directional hydrogen bonding.
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Affiliation(s)
- Zhenyu Lu
- Department of Chemistry, New York University, New York 10003
| | - Nengjie Zhou
- Department of Chemistry, New York University, New York 10003
| | - Qin Wu
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York 10003
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Wang Q, Bryce RA. Accounting for non-optimal interactions in molecular recognition: a study of ion-π complexes using a QM/MM model with a dipole-polarisable MM region. Phys Chem Chem Phys 2011; 13:19401-8. [PMID: 21960295 DOI: 10.1039/c1cp21944h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
For a quantitative understanding of molecular structure, interaction and dynamics, accurate modelling of the energetics of both near-equilibrium and less optimal contacts is important. In this work, we explore the potential energy surfaces of representative ion-π complexes. We examine the performance of a semi-empirical QM/MM approach and the corresponding QM/MMpol model, where inducible point dipoles are additionally employed in the MM region. The predicted potential energy surfaces of cation-benzene complexes are improved by inclusion of explicit MM polarisation of the π-molecule. For cation-formamide complexes, inducible dipoles appreciably improve energetic estimates at geometries forming non-optimal interactions. Energetic component analysis suggests that the implicit MM polarisation of the fixed charge QM/MM model mirrors the behaviour of the QM/MMpol dipole model for the energetics of near-equilibrium conformations. However, for complexes at less optimal orientations, the QM/MM model exhibits higher errors than the QM/MMpol approach, being unable to capture orientation-dependent variations in polarisation energy.
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Affiliation(s)
- Qiantao Wang
- School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
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