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Liu H, Fu H, Chipot C, Shao X, Cai W. Accuracy of Alternate Nonpolarizable Force Fields for the Determination of Protein-Ligand Binding Affinities Dominated by Cation-π Interactions. J Chem Theory Comput 2021; 17:3908-3915. [PMID: 34125530 DOI: 10.1021/acs.jctc.1c00219] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Modifying pair-specific Lennard-Jones parameters through the nonbonded FIX (NBFIX) feature of the CHARMM36 force field has proven cost-effective for improving the description of cation-π interactions in biological objects by means of pairwise additive potential energy functions. Here, two sets of newly optimized CHARMM36 force-field parameters including NBFIX corrections, coined CHARMM36m-NBF and CHARMM36-WYF, and the original force fields, namely CHARMM36m and Amber ff14SB, are used to determine the standard binding free energies of seven protein-ligand complexes containing cation-π interactions. Compared with precise experimental measurements, our results indicate that the uncorrected, original force fields significantly underestimate the binding free energies, with a mean error of 5.3 kcal/mol, while the mean errors of CHARMM36m-NBF and CHARMM36-WYF amount to 0.8 and 2.1 kcal/mol, respectively. The present study cogently demonstrates that the use of modified parameters jointly with NBFIX corrections dramatically increases the accuracy of the standard binding free energy of protein-ligand complexes dominated by cation-π interactions, most notably with CHARMM36m-NBF.
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Affiliation(s)
- Han Liu
- Research Center for Analytical Sciences, College of Chemistry, and Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Haohao Fu
- Research Center for Analytical Sciences, College of Chemistry, and Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Christophe Chipot
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, UMR No. 7019, Université de Lorraine, BP 70239, F-54506 Vandœuvre-lès-Nancy, France.,Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Xueguang Shao
- Research Center for Analytical Sciences, College of Chemistry, and Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Wensheng Cai
- Research Center for Analytical Sciences, College of Chemistry, and Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
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2
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Shi Y, Laury ML, Wang Z, Ponder JW. AMOEBA binding free energies for the SAMPL7 TrimerTrip host-guest challenge. J Comput Aided Mol Des 2021; 35:79-93. [PMID: 33140208 PMCID: PMC7867568 DOI: 10.1007/s10822-020-00358-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/28/2020] [Indexed: 12/22/2022]
Abstract
As part of the SAMPL7 host-guest binding challenge, the AMOEBA force field was applied to calculate the absolute binding free energy for 16 charged organic ammonium guests to the TrimerTrip host, a recently reported acyclic cucurbituril-derived clip host structure with triptycene moieties at its termini. Here we report binding free energy calculations for this system using the AMOEBA polarizable atomic multipole force field and double annihilation free energy methodology. Conformational analysis of the host suggests three families of conformations that do not interconvert in solution on a time scale available to nanosecond molecular dynamics (MD) simulations. Two of these host conformers, referred to as the "indent" and "overlap" structures, are capable of binding guest molecules. As a result, the free energies of all 16 guests binding to both conformations were computed separately, and combined to produce values for comparison with experiment. Initial ranked results submitted as part of the SAMPL7 exercise had a mean unsigned error (MUE) from experimental binding data of 2.14 kcal/mol. Subsequently, a rigorous umbrella sampling reference calculation was used to better determine the free energy difference between unligated "indent" and "overlap" host conformations. Revised binding values for the 16 guests pegged to this umbrella sampling reference reduced the MUE to 1.41 kcal/mol, with a correlation coefficient (Pearson R) between calculated and experimental binding values of 0.832 and a rank correlation (Kendall τ) of 0.65. Overall, the AMOEBA results demonstrate no significant systematic error, suggesting the force field provides an accurate energetic description of the TrimerTrip host, and an appropriate balance of solvation and desolvation effects associated with guest binding.
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Affiliation(s)
- Yuanjun Shi
- Department of Chemistry, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Marie L Laury
- Department of Chemistry, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Zhi Wang
- Department of Chemistry, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Jay W Ponder
- Department of Chemistry, Washington University in St. Louis, Saint Louis, MO, 63130, USA.
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, 63110, USA.
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3
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Liu H, Fu H, Shao X, Cai W, Chipot C. Accurate Description of Cation-π Interactions in Proteins with a Nonpolarizable Force Field at No Additional Cost. J Chem Theory Comput 2020; 16:6397-6407. [PMID: 32852943 DOI: 10.1021/acs.jctc.0c00637] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cation-π interactions play a significant role in a host of processes eminently relevant to biology. However, polarization effects arising from the interaction of cations with aromatic moieties have long been recognized to be inadequately described by pairwise additive force fields. In the present work, we address this longstanding shortcoming through the nonbonded FIX (NBFIX) feature of the CHARMM36 force field, modifying pair-specific Lennard-Jones (LJ) parameters, while circumventing the limitations of the Lorentz-Berthelot combination rules. The potentials of mean force (PMFs) characterizing prototypical cation-π interactions in aqueous solutions are first determined using a hybrid quantum mechanical/molecular mechanics (QM/MM) strategy in conjunction with an importance-sampling algorithm. The LJ parameters describing the cation-π pairs are then optimized to match the QM/MM PMFs. The standard binding free energies of nine cation-π complexes, i.e., toluene, para-cresol, and 3-methyl-indole interacting with either ammonium, guanidinium, or tetramethylammonium, determined with this new set of parameters agree well with the experimental measurements. Additional simulations were carried out on three different classes of biological objects featuring cation-π interactions, including five individual proteins, three protein-ligand complexes, and two protein-protein complexes. Our results indicate that the description of cation-π interactions is overall improved using NBFIX corrections, compared with the standard pairwise additive force field. Moreover, an accurate binding free energy calculation for a protein-ligand complex containing cation-π interactions (2BOK) shows that using the new parameters, the experimental binding affinity can be reproduced quantitatively. Put together, the present work suggests that the NBFIX parameters optimized here can be broadly utilized in the simulation of proteins in an aqueous solution to enhance the representation of cation-π interactions, at no additional computational cost.
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Affiliation(s)
- Han Liu
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Haohao Fu
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xueguang Shao
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China.,State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, China
| | - Wensheng Cai
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Christophe Chipot
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, UMR n°7019, Université de Lorraine, BP 70239, F-54506 Vandoeuvre-lès-Nancy, France.,Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
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4
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Lin FY, MacKerell AD. Improved Modeling of Cation-π and Anion-Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins. J Comput Chem 2020; 41:439-448. [PMID: 31518010 PMCID: PMC7322827 DOI: 10.1002/jcc.26067] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/15/2019] [Accepted: 08/25/2019] [Indexed: 12/22/2022]
Abstract
Cation-π interactions are noncovalent interactions between a π-electron system and a positively charged ion that are regarded as a strong noncovalent interaction and are ubiquitous in biological systems. Similarly, though less studied, anion-ring interactions are present in proteins along with in-plane interactions of anions with aromatic rings. As these interactions are between a polarizing ion and a polarizable π system, the accuracy of the treatment of these interactions in molecular dynamics (MD) simulations using additive force fields (FFs) may be limited. In the present work, to allow for a better description of ion-π interactions in proteins in the Drude-2013 protein polarizable FF, we systematically optimized the parameters for these interactions targeting model compound quantum mechanical (QM) interaction energies with atom pair-specific Lennard-Jones parameters along with virtual particles as selected ring centroids introduced to target the QM interaction energies and geometries. Subsequently, MD simulations were performed on a series of protein structures where ion-π pairs occur to evaluate the optimized parameters in the context of the Drude-2013 FF. The resulting FF leads to a significant improvement in reproducing the ion-π pair distances observed in experimental protein structures, as well as a smaller root-mean-square differences and fluctuations of the overall protein structures from experimental structures. Accordingly, the optimized Drude-2013 protein polarizable FF is suggested for use in MD simulations of proteins where cation-π and anion-ring interactions are critical. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Fang-Yu Lin
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Alexander D. MacKerell
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
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5
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Khan HM, MacKerell AD, Reuter N. Cation-π Interactions between Methylated Ammonium Groups and Tryptophan in the CHARMM36 Additive Force Field. J Chem Theory Comput 2018; 15:7-12. [PMID: 30562013 DOI: 10.1021/acs.jctc.8b00839] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Cation-π interactions between tryptophan and choline or trimethylated lysines are vital for many biological processes. The performance of the additive CHARMM36 force field against target quantum mechanical data is shown to reproduce QM equilibrium geometries but required modified Lennard-Jones potentials to accurately reproduce the QM interaction energies. The modified parameter set allows accurate modeling, including free energies, of cation-π indole-choline and indole-trimethylated lysines interactions relevant for protein-ligand, protein-membrane, and protein-protein interfaces.
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Affiliation(s)
- Hanif M Khan
- Department of Biological Sciences , University of Bergen , N-5020 Bergen , Norway.,Computational Biology Unit, Department of Informatics , University of Bergen , N-5020 Bergen , Norway
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , Baltimore , Maryland 21201 , United States
| | - Nathalie Reuter
- Computational Biology Unit, Department of Informatics , University of Bergen , N-5020 Bergen , Norway.,Department of Chemistry , University of Bergen , N-5020 Bergen , Norway
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6
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Chen Z, Coy SL, Pannkuk EL, Laiakis EC, Fornace AJ, Vouros P. Differential Mobility Spectrometry-Mass Spectrometry (DMS-MS) in Radiation Biodosimetry: Rapid and High-Throughput Quantitation of Multiple Radiation Biomarkers in Nonhuman Primate Urine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1650-1664. [PMID: 29736597 PMCID: PMC6287943 DOI: 10.1007/s13361-018-1977-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/19/2018] [Accepted: 04/21/2018] [Indexed: 05/21/2023]
Abstract
High-throughput methods to assess radiation exposure are a priority due to concerns that include nuclear power accidents, the spread of nuclear weapon capability, and the risk of terrorist attacks. Metabolomics, the assessment of small molecules in an easily accessible sample, is the most recent method to be applied for the identification of biomarkers of the biological radiation response with a useful dose-response profile. Profiling for biomarker identification is frequently done using an LC-MS platform which has limited throughput due to the time-consuming nature of chromatography. We present here a chromatography-free simplified method for quantitative analysis of seven metabolites in urine with radiation dose-response using urine samples provided from the Pannkuk et al. (2015) study of long-term (7-day) radiation response in nonhuman primates (NHP). The stable isotope dilution (SID) analytical method consists of sample preparation by strong cation exchange-solid phase extraction (SCX-SPE) to remove interferences and concentrate the metabolites of interest, followed by differential mobility spectrometry (DMS) ion filtration to select the ion of interest and reduce chemical background, followed by mass spectrometry (overall SID-SPE-DMS-MS). Since no chromatography is used, calibration curves were prepared rapidly, in under 2 h (including SPE) for six simultaneously analyzed radiation biomarkers. The seventh, creatinine, was measured separately after 2500× dilution. Creatinine plays a dual role, measuring kidney glomerular filtration rate (GFR), and indicating kidney damage at high doses. The current quantitative method using SID-SPE-DMS-MS provides throughput which is 7.5 to 30 times higher than that of LC-MS and provides a path to pre-clinical radiation dose estimation. Graphical Abstract.
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Affiliation(s)
- Zhidan Chen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA
| | - Stephen L Coy
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA.
| | - Evan L Pannkuk
- Tumor Biology Program, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA
| | - Evagelia C Laiakis
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC, 20057, USA
| | - Albert J Fornace
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC, 20057, USA
- Department of Oncology, Georgetown University Medical Center, Washington, DC, 20057, USA
| | - Paul Vouros
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA.
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, 02115, USA.
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7
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Unke OT, Devereux M, Meuwly M. Minimal distributed charges: Multipolar quality at the cost of point charge electrostatics. J Chem Phys 2018; 147:161712. [PMID: 29096479 DOI: 10.1063/1.4993424] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Most empirical force fields use atom-centered point charges (PCs) to represent the electrostatic potential (ESP) around molecules. While such PC models are computationally efficient, they are unable to capture anisotropic electronic features, such as σ holes or lone pairs. These features are better described using atomic multipole (MTP) moments, which significantly improve the quality of the resulting ESP. However, the improvement comes at the expense of a considerably increased computational complexity and cost for calculating the interaction energies and forces. In the present work, a novel minimal distributed charge model (MDCM) based on off-centered point charges is presented and the quality of the resulting ESP is compared to the performance of MTPs and atom-centered PC models for several test molecules. All three models are fitted using the same algorithm based on differential evolution, which is available as a Fortran90 program from the authors upon request. We show that the MDCM is capable of approximating the reference ab initio ESP with an accuracy as good as, or better than, MTPs without the need for computationally expensive higher order multipoles. Further it is demonstrated that the MDCM is numerically stable in molecular dynamics simulations and is able to reproduce electrostatic interaction energies and thermodynamic quantities with the same accuracy as MTPs at reduced computational cost.
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Affiliation(s)
- Oliver T Unke
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Mike Devereux
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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8
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Cheng G, Liao M, Zhao D, Zhou J. Molecular Understanding on the Underwater Oleophobicity of Self-Assembled Monolayers: Zwitterionic versus Nonionic. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:1732-1741. [PMID: 28122450 DOI: 10.1021/acs.langmuir.6b03988] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Molecular dynamics simulations are conducted to investigate the underwater oleophobicity of self-assembled monolayers (SAMs) with different head groups. Simulation results show that the order of underwater oleophobicity of SAMs is methyl < amide < oligo(ethylene glycol) (OEG) < ethanolamine (ETA) < hydroxyl < mixed-charged zwitterionic. The underwater-oil contact angles (OCAs) are <133° for all nonionic hydrophilic SAMs, while the mixed-charged zwitterionic SAMs are underwater superoleophobic (OCA can reach 180°). It appears that surfaces with stronger underwater oleophobicity have better antifouling performance. Further study on the effect of different alkyl ammonium ions on mixed-charged SAMs reveals that the underwater OCAs are >143.6° for all SAMs; mixed-charged SAMs containing primary alkyl ammonium ion are likely to possess the best underwater oleophobicity for its strong hydration capacity. It seems that alkyl sulfonate anion (SO3-) is more hydrophilic than alkyl trimethylammonium ion (NC3+) for the hydrophobic methyl groups on nitrogen atoms and that the hydration of SO3- in mixed-charged SAMs can be seriously blocked by NC3+. The monomer of SO3- should be slightly longer than that of NC3+ to obtain better underwater oleophobicity in NC3+-/SO3--SAMs. In addition, the underwater oleophobicity of SAMs might become worse at low grafting densities. This work systematically proves that a zwitterionic surface is more underwater oleophobic than a nonionic surface. These results will help for the design and development of superoleophobic surfaces.
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Affiliation(s)
- Gang Cheng
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Laboratory for Green Chemical Product Technology, South China University of Technology , Guangzhou 510640, China
| | - Mingrui Liao
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Laboratory for Green Chemical Product Technology, South China University of Technology , Guangzhou 510640, China
| | - Daohui Zhao
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Laboratory for Green Chemical Product Technology, South China University of Technology , Guangzhou 510640, China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Laboratory for Green Chemical Product Technology, South China University of Technology , Guangzhou 510640, China
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9
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Khan HM, He T, Fuglebakk E, Grauffel C, Yang B, Roberts MF, Gershenson A, Reuter N. A Role for Weak Electrostatic Interactions in Peripheral Membrane Protein Binding. Biophys J 2016; 110:1367-78. [PMID: 27028646 PMCID: PMC4816757 DOI: 10.1016/j.bpj.2016.02.020] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 01/08/2016] [Accepted: 02/02/2016] [Indexed: 12/01/2022] Open
Abstract
Bacillus thuringiensis phosphatidylinositol-specific phospholipase C (BtPI-PLC) is a secreted virulence factor that binds specifically to phosphatidylcholine (PC) bilayers containing negatively charged phospholipids. BtPI-PLC carries a negative net charge and its interfacial binding site has no obvious cluster of basic residues. Continuum electrostatic calculations show that, as expected, nonspecific electrostatic interactions between BtPI-PLC and membranes vary as a function of the fraction of anionic lipids present in the bilayers. Yet they are strikingly weak, with a calculated ΔGel below 1 kcal/mol, largely due to a single lysine (K44). When K44 is mutated to alanine, the equilibrium dissociation constant for small unilamellar vesicles increases more than 50 times (∼2.4 kcal/mol), suggesting that interactions between K44 and lipids are not merely electrostatic. Comparisons of molecular-dynamics simulations performed using different lipid compositions reveal that the bilayer composition does not affect either hydrogen bonds or hydrophobic contacts between the protein interfacial binding site and bilayers. However, the occupancies of cation-π interactions between PC choline headgroups and protein tyrosines vary as a function of PC content. The overall contribution of basic residues to binding affinity is also context dependent and cannot be approximated by a rule-of-thumb value because these residues can contribute to both nonspecific electrostatic and short-range protein-lipid interactions. Additionally, statistics on the distribution of basic amino acids in a data set of membrane-binding domains reveal that weak electrostatics, as observed for BtPI-PLC, might be a less unusual mechanism for peripheral membrane binding than is generally thought.
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Affiliation(s)
- Hanif M Khan
- Department of Molecular Biology, University of Bergen, Bergen, Norway; Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Tao He
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts
| | - Edvin Fuglebakk
- Department of Molecular Biology, University of Bergen, Bergen, Norway; Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Cédric Grauffel
- Department of Molecular Biology, University of Bergen, Bergen, Norway; Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Boqian Yang
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts; Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts
| | - Mary F Roberts
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts
| | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts
| | - Nathalie Reuter
- Department of Molecular Biology, University of Bergen, Bergen, Norway; Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
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10
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Khan HM, Grauffel C, Broer R, MacKerell AD, Havenith RWA, Reuter N. Improving the Force Field Description of Tyrosine-Choline Cation-π Interactions: QM Investigation of Phenol-N(Me) 4+ Interactions. J Chem Theory Comput 2016; 12:5585-5595. [PMID: 27682345 PMCID: PMC5148683 DOI: 10.1021/acs.jctc.6b00654] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cation-π interactions between tyrosine amino acids and compounds containing N,N,N-trimethylethanolammonium (N(CH3)3) are involved in the recognition of histone tails by chromodomains and in the recognition of phosphatidylcholine (PC) phospholipids by membrane-binding proteins. Yet, the lack of explicit polarization or charge transfer effects in molecular mechanics force fields raises questions about the reliability of the representation of these interactions in biomolecular simulations. Here, we investigate the nature of phenol-tetramethylammonium (TMA) interactions using quantum mechanical (QM) calculations, which we also use to evaluate the accuracy of the additive CHARMM36 and Drude polarizable force fields in modeling tyrosine-choline interactions. We show that the potential energy surface (PES) obtained using SAPT2+/aug-cc-pVDZ compares well with the large basis-set CCSD(T) PES when TMA approaches the phenol ring perpendicularly. Furthermore, the SAPT energy decomposition reveals comparable contributions from electrostatics and dispersion in phenol-TMA interactions. We then compared the SAPT2+/aug-cc-pVDZ PES obtained along various approach directions to the corresponding PES obtained with CHARMM, and we show that the force field accurately reproduces the minimum distances while the interaction energies are underestimated. The use of the Drude polarizable force field significantly improves the interaction energies but decreases the agreement on distances at energy minima. The best agreement between force field and QM PES is obtained by modifying the Lennard-Jones terms for atom pairs involved in the phenol-TMA cation-π interactions. This is further shown to improve the correlation between the occupancy of tyrosine-choline cation-π interactions obtained from molecular dynamics simulations of a bilayer-bound bacterial phospholipase and experimental affinity data of the wild-type protein and selected mutants.
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Affiliation(s)
- Hanif M Khan
- Department of Molecular Biology, University of Bergen , N-5020 Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen , N-5020 Bergen, Norway
| | - Cédric Grauffel
- Institute of Biomedical Sciences, Academia Sinica , Taipei 11529, Taiwan
| | | | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , Baltimore, Maryland 21201, United States
| | - Remco W A Havenith
- Ghent Quantum Chemistry Group, Department of Inorganic and Physical Chemistry, Ghent University , 9000 Ghent, Belgium
| | - Nathalie Reuter
- Department of Molecular Biology, University of Bergen , N-5020 Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen , N-5020 Bergen, Norway
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11
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Arbor SC, LaFontaine M, Cumbay M. Amyloid-beta Alzheimer targets - protein processing, lipid rafts, and amyloid-beta pores. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2016; 89:5-21. [PMID: 27505013 PMCID: PMC4797837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Amyloid beta (Aβ), the hallmark of Alzheimer's Disease (AD), now appears to be deleterious in its low number aggregate form as opposed to the macroscopic Aβ fibers historically seen postmortem. While Alzheimer targets, such as the tau protein, amyloid precursor protein (APP) processing, and immune system activation continue to be investigated, the recent discovery that amyloid beta aggregates at lipid rafts and likely forms neurotoxic pores has led to a new paradigm regarding why past therapeutics may have failed and how to design the next round of compounds for clinical trials. An atomic resolution understanding of Aβ aggregates, which appear to exist in multiple conformations, is most desirable for future therapeutic development. The investigative difficulties, structures of these small Aβ aggregates, and current therapeutics are summarized in this review.
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Affiliation(s)
- Sage C. Arbor
- Marian University College of Osteopathic Medicine, 3200 Cold Spring Road, Indianapolis, Indiana, 46222
| | - Mike LaFontaine
- Marian University College of Osteopathic Medicine, 3200 Cold Spring Road, Indianapolis, Indiana, 46222
| | - Medhane Cumbay
- Marian University College of Osteopathic Medicine, 3200 Cold Spring Road, Indianapolis, Indiana, 46222
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12
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Pathak AK, Bandyopadhyay T. Ortho-7 bound to the active-site gorge of free and OP-conjugated acetylcholinesterase: cation-π interactions. Biopolymers 2015; 105:10-20. [PMID: 26270602 DOI: 10.1002/bip.22712] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/10/2015] [Accepted: 08/10/2015] [Indexed: 02/02/2023]
Abstract
Despite the immense importance of cation-π interactions prevailing in bispyridinium drug acetylcholinesterase (AChE) complexes, a precise description of cation-π interactions at molecular level has remained elusive. Here, we consider a bispyridinium drug, namely, ortho-7 in three different structures of AChE, with and without complexation with organophosphorus (OP) compounds for detailed investigation using all atom molecular dynamics simulation. By quantum mechanical calculations, Y72, W86, Y124, W286, Y337, and Y341 aromatic residues of the enzyme are investigated for possible cation-π interactions with ortho-7. The cation-π interactions in each of the protein-drug complexes are studied using distance, angle, a suitable functional form of them, and electrostatic criteria. The variation of cation-π functional is remarkably consistent with that of the Columbic variation. It is clearly observed that cation-π interactions for some of the residues in the catalytic active site (CAS) and peripheral anionic site (PAS) of the enzyme are either enhanced or reduced based on the nature of OP conjugation (i.e., nerve gas, tabun or pesticide, fenamiphos) when compared with the OP-free enzyme. The strength of cation-π interaction is strongly dependent on the type OP conjugation. The effect of conjugation at CAS is also seen to influence the cation-π interaction at the PAS region. The variation of cation-π interactions on the type of conjugating OP compounds might be suggestive of a reason as to why wide spectrum drug against any OP poisoning is yet to arrive in the market.
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Affiliation(s)
- Arup Kumar Pathak
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Tusar Bandyopadhyay
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai, 400085, India
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13
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Kuster DJ, Liu C, Fang Z, Ponder JW, Marshall GR. High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics. PLoS One 2015; 10:e0123146. [PMID: 25894612 PMCID: PMC4403875 DOI: 10.1371/journal.pone.0123146] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/24/2015] [Indexed: 11/25/2022] Open
Abstract
Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.613 α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.613/10-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole force fields and assumed secondary structures used in low-resolution refinement of electron density of proteins, such structures in the PDB often show linear hydrogen bonding.
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Affiliation(s)
- Daniel J. Kuster
- Department of Biomedical Engineering, Washington University, St. Louis, MO, United States of America
| | - Chengyu Liu
- Department of Chemistry, Washington University, St. Louis, MO, United States of America
| | - Zheng Fang
- Department of Biomedical Engineering, Washington University, St. Louis, MO, United States of America
| | - Jay W. Ponder
- Department of Chemistry, Washington University, St. Louis, MO, United States of America
| | - Garland R. Marshall
- Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, MO, United States of America
- * E-mail:
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14
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Zhou B, Xu B, Ma L, Wang M, Chen K, Chen Y. Synthesis, Crystal Structure of the Receptor Derived from Diethoxycarbonyl Glycoluril for Aromatic Amide Guest. CHINESE J CHEM 2014. [DOI: 10.1002/cjoc.201400477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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Liu C, Ponder JW, Marshall GR. Helix stability of oligoglycine, oligoalanine, and oligo-β-alanine dodecamers reflected by hydrogen-bond persistence. Proteins 2014; 82:3043-61. [PMID: 25116421 PMCID: PMC4206583 DOI: 10.1002/prot.24665] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 08/03/2014] [Indexed: 02/03/2023]
Abstract
Helices are important structural/recognition elements in proteins and peptides. Stability and conformational differences between helices composed of α- and β-amino acids as scaffolds for mimicry of helix recognition has become a theme in medicinal chemistry. Furthermore, helices formed by β-amino acids are experimentally more stable than those formed by α-amino acids. This is paradoxical because the larger sizes of the hydrogen-bonding rings required by the extra methylene groups should lead to entropic destabilization. In this study, molecular dynamics simulations using the second-generation force field, AMOEBA (Ponder, J.W., et al., Current status of the AMOEBA polarizable force field. J Phys Chem B, 2010. 114(8): p. 2549-64.) explored the stability and hydrogen-bonding patterns of capped oligo-β-alanine, oligoalanine, and oligoglycine dodecamers in water. The MD simulations showed that oligo-β-alanine has strong acceptor+2 hydrogen bonds, but surprisingly did not contain a large content of 3(12) -helical structures, possibly due to the sparse distribution of the 3(12) -helical structure and other structures with acceptor+2 hydrogen bonds. On the other hand, despite its backbone flexibility, the β-alanine dodecamer had more stable and persistent <3.0 Å hydrogen bonds. Its structure was dominated more by multicentered hydrogen bonds than either oligoglycine or oligoalanine helices. The 3(1) (PII) helical structure, prevalent in oligoglycine and oligoalanine, does not appear to be stable in oligo-β-alanine indicating its competition with other structures (stacking structure as indicated by MD analyses). These differences are among the factors that shape helical structural preferences and the relative stabilities of these three oligopeptides.
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Affiliation(s)
- Chengyu Liu
- Department of Chemistry, Washington University, St. Louis, Missouri, 63130
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16
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Devereux M, Raghunathan S, Fedorov DG, Meuwly M. A Novel, Computationally Efficient Multipolar Model Employing Distributed Charges for Molecular Dynamics Simulations. J Chem Theory Comput 2014; 10:4229-41. [PMID: 26588121 DOI: 10.1021/ct500511t] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A truncated multipole expansion can be re-expressed exactly using an appropriate arrangement of point charges. This means that groups of point charges that are shifted away from nuclear coordinates can be used to achieve accurate electrostatics for molecular systems. We introduce a multipolar electrostatic model formulated in this way for use in computationally efficient multipolar molecular dynamics simulations with well-defined forces and energy conservation in NVE (constant number-volume-energy) simulations. A framework is introduced to distribute torques arising from multipole moments throughout a molecule, and a refined fitting approach is suggested to obtain atomic multipole moments that are optimized for accuracy and numerical stability in a force field context. The formulation of the charge model is outlined as it has been implemented into CHARMM, with application to test systems involving H2O and chlorobenzene. As well as ease of implementation and computational efficiency, the approach can be used to provide snapshots for multipolar QM/MM calculations in QM/MM-MD studies and easily combined with a standard point-charge force field to allow mixed multipolar/point charge simulations of large systems.
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Affiliation(s)
- Mike Devereux
- Universität Basel , Departement Chemie, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Shampa Raghunathan
- Universität Basel , Departement Chemie, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Dmitri G Fedorov
- NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Markus Meuwly
- Universität Basel , Departement Chemie, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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17
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Devereux M, Gresh N, Piquemal JP, Meuwly M. A supervised fitting approach to force field parametrization with application to the SIBFA polarizable force field. J Comput Chem 2014; 35:1577-91. [DOI: 10.1002/jcc.23661] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 04/14/2014] [Accepted: 05/25/2014] [Indexed: 01/07/2023]
Affiliation(s)
- Mike Devereux
- Department of Chemistry; University of Basel; Klingelbergstr 80 CH 4056 Switzerland
| | - Nohad Gresh
- Chemistry & Biology, Nucleo(s)tides & Immunology for Therapy (CBNIT), UMR 8601, CNRS, UFR Biomedicale; Paris France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, UPMC, Sorbonne Université, Campus de Jussieu; 4 place Jussieu Paris France
| | - Markus Meuwly
- Department of Chemistry; University of Basel; Klingelbergstr 80 CH 4056 Switzerland
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18
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Semrouni D, Sharma A, Dognon JP, Ohanessian G, Clavaguéra C. Finite Temperature Infrared Spectra from Polarizable Molecular Dynamics Simulations. J Chem Theory Comput 2014; 10:3190-9. [DOI: 10.1021/ct5004065] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- David Semrouni
- Laboratoire de
Chimie Moléculaire, Ecole polytechnique, CNRS, 91128 Palaiseau Cedex, France, and
| | - Ashwani Sharma
- Laboratoire de
Chimie Moléculaire, Ecole polytechnique, CNRS, 91128 Palaiseau Cedex, France, and
| | - Jean-Pierre Dognon
- CEA/Saclay, DSM/IRAMIS/NIMBE,
CNRS, Laboratoire de Chimie Moléculaire et de Catalyse pour
l’Energie, 91191 Gif-sur-Yvette, France
| | - Gilles Ohanessian
- Laboratoire de
Chimie Moléculaire, Ecole polytechnique, CNRS, 91128 Palaiseau Cedex, France, and
| | - Carine Clavaguéra
- Laboratoire de
Chimie Moléculaire, Ecole polytechnique, CNRS, 91128 Palaiseau Cedex, France, and
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19
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Pathak AK, Bandyopadhyay T. Unbinding free energy of acetylcholinesterase bound oxime drugs along the gorge pathway from metadynamics-umbrella sampling investigation. Proteins 2014; 82:1799-818. [PMID: 24549829 DOI: 10.1002/prot.24533] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 01/17/2014] [Accepted: 01/28/2014] [Indexed: 12/20/2022]
Abstract
Because of the pivotal role that the nerve enzyme, acetylcholinesterase plays in terminating nerve impulses at cholinergic synapses. Its active site, located deep inside a 20 Å gorge, is a vulnerable target of the lethal organophosphorus compounds. Potent reactivators of the intoxicated enzyme are nucleophiles, such as bispyridinium oxime that binds to the peripheral anionic site and the active site of the enzyme through suitable cation-π interactions. Atomic scale molecular dynamics and free energy calculations in explicit water are used to study unbinding pathways of two oxime drugs (Ortho-7 and Obidoxime) from the gorge of the enzyme. The role of enzyme-drug cation-π interactions are explored with the metadynamics simulation. The metadynamics discovered potential of mean force (PMF) of the unbinding events is refined by the umbrella sampling (US) corrections. The bidimensional free energy landscape of the metadynamics runs are further subjected to finite temperature string analysis to obtain the transition tube connecting the minima and bottlenecks of the unbinding pathway. The PMF is also obtained from US simulations using the biasing potential constructed from the transition tube and are found to be consistent with the metadynamics-US corrected results. Although experimental structural data clearly shows analogous coordination of the two drugs inside the gorge in the bound state, the PMF of the drug trafficking along the gorge pathway point, within an equilibrium free energy context, to a multistep process that differs from one another. Routes, milestones and subtlety toward the unbinding pathway of the two oximes at finite temperature are identified.
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Affiliation(s)
- Arup K Pathak
- Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre, Trombay, Mumbai, India
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20
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21
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Yuan Y, Mills MJL, Popelier PLA. Multipolar electrostatics for proteins: Atom-atom electrostatic energies in crambin. J Comput Chem 2013; 35:343-59. [DOI: 10.1002/jcc.23469] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 09/04/2013] [Accepted: 09/29/2013] [Indexed: 12/31/2022]
Affiliation(s)
- Yongna Yuan
- Manchester Institute of Biotechnology (MIB); 131 Princess Street Manchester M1 7DN United Kingdom
- School of Chemistry, University of Manchester; Oxford Road Manchester M13 9PL United Kingdom
| | - Matthew J. L. Mills
- Manchester Institute of Biotechnology (MIB); 131 Princess Street Manchester M1 7DN United Kingdom
- School of Chemistry, University of Manchester; Oxford Road Manchester M13 9PL United Kingdom
| | - Paul L. A. Popelier
- Manchester Institute of Biotechnology (MIB); 131 Princess Street Manchester M1 7DN United Kingdom
- School of Chemistry, University of Manchester; Oxford Road Manchester M13 9PL United Kingdom
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22
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Ansorg K, Tafipolsky M, Engels B. Cation−π Interactions: Accurate Intermolecular Potential from Symmetry-Adapted Perturbation Theory. J Phys Chem B 2013; 117:10093-102. [DOI: 10.1021/jp403578r] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kay Ansorg
- Institut
für Physikalische und Theoretische
Chemie, Universität Würzburg, Campus Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg,
Germany
| | - Maxim Tafipolsky
- Institut
für Physikalische und Theoretische
Chemie, Universität Würzburg, Campus Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg,
Germany
| | - Bernd Engels
- Institut
für Physikalische und Theoretische
Chemie, Universität Würzburg, Campus Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg,
Germany
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23
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Limiting assumptions in molecular modeling: electrostatics. J Comput Aided Mol Des 2013; 27:107-14. [PMID: 23354627 DOI: 10.1007/s10822-013-9634-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 01/15/2013] [Indexed: 10/27/2022]
Abstract
Molecular mechanics attempts to represent intermolecular interactions in terms of classical physics. Initial efforts assumed a point charge located at the atom center and coulombic interactions. It is been recognized over multiple decades that simply representing electrostatics with a charge on each atom failed to reproduce the electrostatic potential surrounding a molecule as estimated by quantum mechanics. Molecular orbitals are not spherically symmetrical, an implicit assumption of monopole electrostatics. This perspective reviews recent evidence that requires use of multipole electrostatics and polarizability in molecular modeling.
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24
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Mahadevi AS, Sastry GN. Cation-π interaction: its role and relevance in chemistry, biology, and material science. Chem Rev 2012; 113:2100-38. [PMID: 23145968 DOI: 10.1021/cr300222d] [Citation(s) in RCA: 719] [Impact Index Per Article: 59.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- A Subha Mahadevi
- Molecular Modeling Group, CSIR-Indian Institute of Chemical Technology Tarnaka, Hyderabad 500 607, Andhra Pradesh, India
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