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Chang H, Adibnia V, Qi W, Su R, Banquy X. Ternary Synergy of Lys, Dopa, and Phe Results in Strong Cohesion of Peptide Films. ACS APPLIED BIO MATERIALS 2023; 6:865-873. [PMID: 36625035 DOI: 10.1021/acsabm.2c01009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Synergistic interactions between 3,4-dihydroxyphenylalanine (Dopa, Y*), cationic residues, and the aromatic rings have been recently highlighted as influential factors that enhance the underwater adhesion strength of mussel foot proteins and their derivatives. In this study, we report the first ever evidence of a cation-catechol-benzene ternary synergy between Y*, lysine (Lys, K), and phenylalanine (Phe, F) in adhesive peptides. We synthesized three hexapeptides containing a different combination of Y*, K, and F, i.e., (KY*)3, (KF)3, and (KY*F)2, respectively, exploring the relationship between the cohesive performance and molecular architecture of peptides. The peptide with the (KY*F)2 sequence displays the strongest underwater cohesion energy of 10.3 ± 0.3 mJ m-2 from direct nanoscale surface force measurements. Combined with molecular dynamics simulation, we demonstrated that there are more bonding interactions (including cation-π, π-π, and hydrogen bond interactions) in (KY*F)2 compared to the other two peptides. In addition, peptide (KY*F)2 still shows the strongest cohesive energies of 7.6 ± 0.7 and 3.7 ± 0.5 mJ m-2 in acidic and high-ionic strength environments, respectively, although the cohesive energy decreases compared to the value in pure water. Our results further explain the underwater cohesion mechanisms combining multiple interactions and offer insights on designing Dopa containing underwater adhesives.
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Affiliation(s)
- Heng Chang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China.,Faculty of Pharmacy, Université de Montréal, 2900 Edouard-Montpetit, Montréal, Québec H3C 3J7, Canada
| | - Vahid Adibnia
- School of Biomedical Engineering, Dalhousie University, Halifax, Nova Scotia B3J 1B6, Canada.,Department of Applied Oral Sciences, Dalhousie University, Halifax, Nova Scotia B3J 1B6, Canada
| | - Wei Qi
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China.,School of Marine Science and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Xavier Banquy
- Faculty of Pharmacy, Université de Montréal, 2900 Edouard-Montpetit, Montréal, Québec H3C 3J7, Canada.,Department of Chemistry, Faculty of Art and Science, Université de Montréal, Montreal, Québec H3C 3J7, Canada.,Institute of Biomedical Engineering Faculty of Medicine, Université de Montréal, Montreal, Québec H3C 3J7, Canada
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2
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Comparative study of the unbinding process of some HTLV-1 protease inhibitors using unbiased molecular dynamics simulations. PLoS One 2022; 17:e0263200. [PMID: 35834445 PMCID: PMC9282663 DOI: 10.1371/journal.pone.0263200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 06/28/2022] [Indexed: 12/15/2022] Open
Abstract
The HTLV-1 protease is one of the major antiviral targets to overwhelm this virus. Several research groups have developed protease inhibitors, but none has been successful. In this regard, developing new HTLV-1 protease inhibitors to fix the defects in previous inhibitors may overcome the lack of curative treatment for this oncovirus. Thus, we decided to study the unbinding pathways of the most potent (compound 10, PDB ID 4YDF, Ki = 15 nM) and one of the weakest (compound 9, PDB ID 4YDG, Ki = 7900 nM) protease inhibitors, which are very structurally similar. We conducted 12 successful short and long simulations (totaling 14.8 μs) to unbind the compounds from two monoprotonated (mp) forms of protease using the Supervised Molecular Dynamics (SuMD) without applying any biasing force. The results revealed that Asp32 or Asp32′ in the two forms of mp state similarly exert powerful effects on maintaining both potent and weak inhibitors in the binding pocket of HTLV-1 protease. In the potent inhibitor’s unbinding process, His66′ was a great supporter that was absent in the weak inhibitor’s unbinding pathway. In contrast, in the weak inhibitor’s unbinding process, Trp98/Trp98′ by pi-pi stacking interactions were unfavorable for the stability of the inhibitor in the binding site. In our opinion, these results will assist in designing more potent and effective inhibitors for the HTLV-1 protease.
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3
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Orabi EA, Öztürk TN, Bernhardt N, Faraldo-Gómez JD. Corrections in the CHARMM36 Parametrization of Chloride Interactions with Proteins, Lipids, and Alkali Cations, and Extension to Other Halide Anions. J Chem Theory Comput 2021; 17:6240-6261. [PMID: 34516741 DOI: 10.1021/acs.jctc.1c00550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The nonpolarizable CHARMM force field is one of the most widely used energy functions for all-atom biomolecular simulations. Chloride is the only halide ion included in the latest version, CHARMM36m, and is used widely in simulation studies, often as an electrolyte ion but also as the biological substrate of transport proteins and enzymes. Here, we find that existing parameters systematically underestimate the interaction of Cl- with proteins and lipids. Accordingly, when examined in solution, little to no Cl-association can be observed with most components of the protein, including backbone, polar side chains and aromatic rings. The strength of the interaction with cationic side chains and with alkali ions is also incongruent with experimental measurements, specifically osmotic coefficients of concentrated solutions. Consistent with these findings, a 4-μs trajectory of the Cl--specific transport protein CLC-ec1 shows irreversible Cl- dissociation from the so-called Scen binding site, even in a 150 mM NaCl buffer. To correct for these deficiencies, we formulate a series of pair-specific Lennard-Jones parameters that override those resulting from the conventional Lorentz-Berthelot combination rules. These parameters, referred to as NBFIX, are systematically calibrated against available experimental data as well as ab initio geometry optimizations and energy evaluations, for a wide set of binary and ternary Cl- complexes with protein and lipid analogs and alkali cations. Analogously, we also formulate parameter sets for the other three biological halide ions, namely, fluoride, bromide, and iodide. The resulting parameters are used to calculate the potential of mean force defining the interaction of each anion and each of the protein and lipid analogues in bulk water, revealing association free energies in the range of -0.3 to -3.3 kcal/mol, with the F- complexes being the least stable. The NBFIX corrections also preserve the Cl- occupancy of CLC-ec1 in a second 4-μs trajectory. We posit that these optimized molecular-mechanics models provide a more realistic foundation for all-atom simulation studies of processes entailing changes in hydration, recognition, or transport of halide anions.
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Affiliation(s)
- Esam A Orabi
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
| | - Tuǧba N Öztürk
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States.,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Nathan Bernhardt
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
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4
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Vuorte M, Kuitunen S, Sammalkorpi M. Physisorption of bio oil nitrogen compounds onto montmorillonite. Phys Chem Chem Phys 2021; 23:21840-21851. [PMID: 34554171 DOI: 10.1039/d1cp01880a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We assess computationally the adsorption of a series of nitrogen containing heterocycles and fatty acid amides from bio-oil on a model clay surface, Na-montmorillonite. The adsorption energies and conformations predicted by atomistic detail molecular dynamics (MD) simulations are compared against density functional theory (DFT) based molecular electrostatic potentials (MEP) and Hirshfeld, AIM, Merz-Singh-Kollman, and ChelpG charges. MD predicts systematically adsorption via cation bridging with adsorption strength of the heterocycles following purine > pyridine > imidazole > pyrrole > indole > quinoline. The fatty acid amides adsorption strength follows the steric availability and bulkiness of the head group. A comparison against the DFT calculations shows that MEP predicts adsorption geometries and the MD simulations reproduce the conformations for single adsorption site species. However, the DFT derived charge distibutions show that MD force-fields with non-polarizable fixed partial charge representations parametrized for aqueous environments cannot be used in apolar solvent environments without careful accuracy considerations. The overall trends in adsorption energies are reproduced by the Charmm GenFF employed in the MD simulations but the adsorption energies are systematically overestimated in this apolar solvent environment. The work has significance both for revealing nitrogen compound adsorption trends in technologically relevant bio oil environments but also as a methodological assessment revealing the limits of state of the art biomolecular force-fields and simulation protocols in apolar bioenvironments.
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Affiliation(s)
- Maisa Vuorte
- Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland.
| | - Susanna Kuitunen
- Neste Engineering Solutions Oy, P.O. Box 310, FI-06101 Porvoo, Finland
| | - Maria Sammalkorpi
- Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland. .,Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
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6
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Mu L, Yang Y, Liu J, Du W, Chen J, Shi G, Fang H. Hydrated cation-π interactions of π-electrons with hydrated Li +, Na +, and K + cations. Phys Chem Chem Phys 2021; 23:14662-14670. [PMID: 34213518 DOI: 10.1039/d1cp01609a] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cation-π interactions are essential for many chemical, biological, and material processes, and these processes usually involve an aqueous salt solution. However, there is still a lack of a full understanding of the hydrated cation-π interactions between the hydrated cations and the aromatic ring structures on the molecular level. Here, we report a molecular picture of hydrated cation-π interactions, by using the calculations of density functional theory (DFT). Specifically, the graphene sheet can distort the hydration shell of the hydrated K+ to interact with K+ directly, which is hereafter called water-cation-π interactions. In contrast, the hydration shell of the hydrated Li+ is quite stable and the graphene sheet interacts with Li+ indirectly, mediated by water molecules, which we hereafter call the cation-water-π interactions. The behavior of hydrated cations adsorbed on a graphene surface is mainly attributed to the competition between the cation-π interactions and hydration effects. These findings provide valuable details of the structures and the adsorption energy of hydrated cations adsorbed onto the graphene surface.
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Affiliation(s)
- Liuhua Mu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yizhou Yang
- Department of Physics, East China University of Science and Technology, Shanghai 200237, China.
| | - Jian Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wei Du
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jige Chen
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China and Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Guosheng Shi
- Shanghai Applied Radiation Institute and State Key Lab. Advanced Special Steel, Shanghai University, Shanghai 200444, China.
| | - Haiping Fang
- Department of Physics, East China University of Science and Technology, Shanghai 200237, China. and Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
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7
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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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8
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Al Mughram MH, Catalano C, Bowry JP, Safo MK, Scarsdale JN, Kellogg GE. 3D Interaction Homology: Hydropathic Analyses of the "π-Cation" and "π-π" Interaction Motifs in Phenylalanine, Tyrosine, and Tryptophan Residues. J Chem Inf Model 2021; 61:2937-2956. [PMID: 34101460 DOI: 10.1021/acs.jcim.1c00235] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Three-dimensional (3D) maps of the hydropathic environments of protein amino acid residues are information-rich descriptors of preferred conformations, interaction types and energetics, and solvent accessibility. The interactions made by each residue are the primary factor for rotamer selection and the secondary, tertiary, and even quaternary protein structure. Our evolving basis set of environmental data for each residue type can be used to understand the protein structure. This work focuses on the aromatic residues phenylalanine, tyrosine, and tryptophan and their structural roles. We calculated and analyzed side chain-to-environment 3D maps for over 70,000 residues of these three types that reveal, with respect to hydrophobic and polar interactions, the environment around each. After binning with backbone ϕ/ψ and side chain χ1, we clustered each bin by 3D similarities between map-map pairs. For each of the three residue types, four bins were examined in detail: one in the β-pleat, two in the right-hand α-helix, and one in the left-hand α-helix regions of the Ramachandran plot. For high degrees of side chain burial, encapsulation of the side chain by hydrophobic interactions is ubiquitous. The more solvent-exposed side chains are more likely to be involved in polar interactions with their environments. Evidence for π-π interactions was observed in about half of the residues surveyed [phenylalanine (PHE): 53.3%, tyrosine (TYR): 34.1%, and tryptophan (TRP): 55.7%], but on an energy basis, this contributed to only ∼4% of the total. Evidence for π-cation interactions was observed in 14.1% of PHE, 8.3% of TYR, and 26.8% of TRP residues, but on an energy basis, this contributed to only ∼1%. This recognition of even these subtle interactions in the 3D hydropathic environment maps is key support for our interaction homology paradigm of protein structure elucidation and possibly prediction.
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Affiliation(s)
- Mohammed H Al Mughram
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States
| | - Claudio Catalano
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States
| | - John P Bowry
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States
| | - Martin K Safo
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States.,Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States
| | - J Neel Scarsdale
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States.,Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States
| | - Glen E Kellogg
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States.,Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States.,Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States
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9
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Du WT, Orabi EA, Mohamed MG, Kuo SW. Inter/intramolecular hydrogen bonding mediate miscible blend formation between near-perfect alternating Poly(styrene-alt- hydroxyphenylmaleimide) copolymers and Poly(vinyl pyrrolidone). POLYMER 2021. [DOI: 10.1016/j.polymer.2021.123542] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Aydin F, Moradzadeh A, Bilodeau CL, Lau EY, Schwegler E, Aluru NR, Pham TA. Ion Solvation and Transport in Narrow Carbon Nanotubes: Effects of Polarizability, Cation-π Interaction, and Confinement. J Chem Theory Comput 2021; 17:1596-1605. [PMID: 33625224 DOI: 10.1021/acs.jctc.0c00827] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Understanding ion solvation and transport under confinement is critical for a wide range of emerging technologies, including water desalination and energy storage. While molecular dynamics (MD) simulations have been widely used to study the behavior of confined ions, considerable deviations between simulation results depending on the specific treatment of intermolecular interactions remain. In the following, we present a systematic investigation of the structure and dynamics of two representative solutions, that is, KCl and LiCl, confined in narrow carbon nanotubes (CNTs) with a diameter of 1.1 and 1.5 nm, using a combination of first-principles and classical MD simulations. Our simulations show that the inclusion of both polarization and cation-π interactions is essential for the description of ion solvation under confinement, particularly for large ions with weak hydration energies. Beyond the variation in ion solvation, we find that cation-π interactions can significantly influence the transport properties of ions in CNTs, particularly for KCl, where our simulations point to a strong correlation between ion dehydration and diffusion. Our study highlights the complex interplay between nanoconfinement and specific intermolecular interactions that strongly control the solvation and transport properties of ions.
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Affiliation(s)
- Fikret Aydin
- Quantum Simulations Group, Materials Science Division, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, California 94550, United States
| | - Alireza Moradzadeh
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Camille L Bilodeau
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Edmond Y Lau
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, California 94550, United States
| | - Eric Schwegler
- Quantum Simulations Group, Materials Science Division, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, California 94550, United States
| | - Narayana R Aluru
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Tuan Anh Pham
- Quantum Simulations Group, Materials Science Division, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, California 94550, United States
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11
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Orabi EA, English AM. Modeling Shows that Rotation about the Peroxide O-O Bond Assists Protein and Lipid Functional Groups in Discriminating between H 2O 2 and H 2O. J Phys Chem B 2020; 125:137-147. [PMID: 33356279 DOI: 10.1021/acs.jpcb.0c10326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Long associated with cell death, hydrogen peroxide (H2O2) is now known to perform many physiological roles. Unraveling its biological mechanisms of action requires atomic-level knowledge of its association with proteins and lipids, which we address here. High-level [MP2(full)/6-311++G(3df,3pd)] ab initio calculations reveal skew rotamers as the lowest-energy states of isolated H2O2 (ϕHOOH ∼ 112°) with minimum and maximum electrostatic potentials (kcal/mol) of -24.8 (Vs,min) and 36.5 (Vs,max), respectively. Transition-state, nonpolar trans rotamers (ϕHOOH ∼ 180°) at 1.2 kcal/mol higher in energy are poorer H-bond acceptors (Vs,min = -16.6) than the skew rotamers, while highly polar cis rotamers (ϕHOOH ∼ 0°) at 7.8 kcal/mol are much better H-bond donors (Vs,max = 52.7). Modeling H2O2 association with neutral and charged analogs of protein residues and lipid groups (e.g., ester, phosphate, choline) reveals that skew rotamers (ϕHOOH = 84-122°) are favored in the neutral and cationic complexes, which display gas-phase interaction energies (ECP, kcal/mol) of -1.5 to -18. The neutral and cationic complexes of H2O exhibit a similar range of stabilities (ECP ∼ -1 to -18). However, considerably higher energies (ECP ∼ -14 to -36) are found for the H2O2 complexes of the anionic ligands, which are stabilized by charge-assisted H-bond donation from cis and distorted cis rotamers (ϕHOOH = 0-60°). H2O is a much poorer H-bond donor (Vs,max = 33.4) than cis-H2O2, so its anionic complexes are significantly weaker (ECP ∼ -11 to -20). Thus, by dictating the rotamer preference of H2O2, functional groups in biomolecules can discriminate between H2O2 and H2O. Finally, exploiting the present ab initio data, we calibrated and validated our published molecular mechanics model for H2O2 (Orabi, E. A.; English, A. M. J. Chem. Theory Comput. 2018, 14, 2808-2821) to provide an important tool for simulating H2O2 in biology.
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Affiliation(s)
- Esam A Orabi
- Department of Chemistry, Faculty of Science, Assiut University, Assiut 71516, Egypt.,Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada
| | - Ann M English
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.,Center for Research in Molecular Modeling (CERMM) and Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Concordia University, Montreal, Quebec H4B 1R6, Canada
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12
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Liu C, Zhao J, Yang ZZ, Zhao DX. Dividing the Periodic Box into Subdivisions with Their Surroundings to Accelerate Molecular Dynamics Simulation with High Accuracy. J Chem Theory Comput 2020; 16:7618-7631. [PMID: 33231445 DOI: 10.1021/acs.jctc.0c00808] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A major field of current research in chemistry and biology is the development of the tools that enable in situ analysis of complex systems. However, the long-time dynamics simulation for an extremely large system in solution is almost impossible by an all-atom force field combined with an explicit solvent model. The results show that the larger the periodic box is, the closer the properties of the system are to the experimental values. Therefore, how can we carry out simulations for systems that are fast, accurate, and large enough? A method of dividing the periodic box into subdivisions with their surroundings (DBSS) is presented here, and it clearly increases the computation speed without losing accuracy and enables the simulation of extremely large systems by strongly decreasing the dimension of the charge matrix. The DBSS method divides a single periodic box or unit in an extremely large system into several subdivisions with a suitable choice according to atomic coordinates. This method ensures that these subdivisions are always changing and allows the atoms to communicate with each other. Intermolecular communication is important for molecular properties and functions but is not possible with other fragment methods. The partial charges are calculated in each subdivision with an overlapping surrounding used to take hydrogen bond interaction between the subdivisions into account. This is an iterative process because the charge population will be recalculated at intervals during the dynamics simulations. Taking a water system as an example, each subdivision is extended by 4 Å as the surrounding. The computation time scales almost linearly with the size of the system, and the slope is small. MD simulations for several properties have been performed by the ABEEM-DBSS method. The results indicate that the ABEEM-DBSS method can accurately simulate the properties of water system, and the accuracy can reach or approach that of the experimental data or of other water potentials. Interestingly, the properties become closer to the experimental data as the sizes of the periodic box increase, further validating the need for the simulation of a large system and demonstrating the value of the DBSS method.
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Affiliation(s)
- Cui Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Jian Zhao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Dong-Xia Zhao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
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13
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Turupcu A, Tirado-Rives J, Jorgensen WL. Explicit Representation of Cation-π Interactions in Force Fields with 1/ r4 Nonbonded Terms. J Chem Theory Comput 2020; 16:7184-7194. [PMID: 33048555 DOI: 10.1021/acs.jctc.0c00847] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The binding energies for cation-π complexation are underestimated by traditional fixed-charge force fields owing to their lack of explicit treatment of ion-induced dipole interactions. To address this deficiency, an explicit treatment of cation-π interactions has been introduced into the OPLS-AA force field. Following prior work with atomic cations, it is found that cation-π interactions can be handled efficiently by augmenting the usual 12-6 Lennard-Jones potentials with 1/r4 terms. Results are provided for prototypical complexes as well as protein-ligand systems of relevance for drug design. Alkali cation, ammonium, guanidinium, and tetramethylammonium were chosen for the representative cations, while benzene and six heteroaromatic molecules were used as the π systems. The required nonbonded parameters were fit to reproduce structure and interaction energies for gas-phase complexes from density functional theory (DFT) calculations at the ωB97X-D/6-311++G(d,p) level. The impact of the solvent was then examined by computing potentials of mean force (pmfs) in both aqueous and tetrahydrofuran (THF) solutions using the free-energy perturbation (FEP) theory. Further testing was carried out for two cases of strong and one case of weak cation-π interactions between druglike molecules and their protein hosts, namely, the JH2 domain of JAK2 kinase and macrophage migration inhibitory factor. FEP results reveal greater binding by 1.5-4.4 kcal/mol from the addition of the explicit cation-π contributions. Thus, in the absence of such treatment of cation-π interactions, errors for computed binding or inhibition constants of 101-103 are expected.
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Affiliation(s)
- Aysegul Turupcu
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Julian Tirado-Rives
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - William L Jorgensen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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14
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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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15
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Younis O, Tolba MS, Orabi EA, Kamal AM, Hassanien R, Tsutsumi O, Ahmed M. Biologically-Active Heterocyclic Molecules with Aggregation-Induced Blue-Shifted Emission and Efficient Luminescence both in Solution and Solid States. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2020.112642] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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16
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Badizad MH, Koleini MM, Hartkamp R, Ayatollahi S, Ghazanfari MH. How do ions contribute to brine-hydrophobic hydrocarbon Interfaces? An in silico study. J Colloid Interface Sci 2020; 575:337-346. [DOI: 10.1016/j.jcis.2020.04.060] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 10/24/2022]
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17
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Orabi EA, Faraldo-Gómez JD. New Molecular-Mechanics Model for Simulations of Hydrogen Fluoride in Chemistry and Biology. J Chem Theory Comput 2020; 16:5105-5126. [PMID: 32615034 DOI: 10.1021/acs.jctc.0c00247] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hydrogen fluoride (HF) is the most polar diatomic molecule and one of the simplest molecules capable of hydrogen-bonding. HF deviates from ideality both in the gas phase and in solution and is thus of great interest from a fundamental standpoint. Pure and aqueous HF solutions are broadly used in chemical and industrial processes, despite their high toxicity. HF is a stable species also in some biological conditions, because it does not readily dissociate in water unlike other hydrogen halides; yet, little is known about how HF interacts with biomolecules. Here, we set out to develop a molecular-mechanics model to enable computer simulations of HF in chemical and biological applications. This model is based on a comprehensive high-level ab initio quantum chemical investigation of the structure and energetics of the HF monomer and dimer; (HF)n clusters, for n = 3-7; various clusters of HF and H2O; and complexes of HF with analogs of all 20 amino acids and of several commonly occurring lipids, both neutral and ionized. This systematic analysis explains the unique properties of this molecule: for example, that interacting HF molecules favor nonlinear geometries despite being diatomic and that HF is a strong H-bond donor but a poor acceptor. The ab initio data also enables us to calibrate a three-site molecular-mechanics model, with which we investigate the structure and thermodynamic properties of gaseous, liquid, and supercritical HF in a wide range of temperatures and pressures; the solvation structure of HF in water and of H2O in liquid HF; and the free diffusion of HF across a lipid bilayer, a key process underlying the high cytotoxicity of HF. Despite its inherent simplifications, the model presented significantly improves upon previous efforts to capture the properties of pure and aqueous HF fluids by molecular-mechanics methods and to our knowledge constitutes the first parameter set calibrated for biomolecular simulations.
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Affiliation(s)
- Esam A Orabi
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
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18
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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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19
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Kumar A, Mahato J, Dixit M, Patwari GN. Progressive Hydrophobicity of Fluorobenzenes. J Phys Chem B 2019; 123:10083-10088. [PMID: 31661279 DOI: 10.1021/acs.jpcb.9b08057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The potentials of mean force for the dimers of fluorobenzenes sample both π-stacked and T-shaped structures for partially fluorinated benzenes, namely, 1,4-difluorobenzene, 1,3,5-trifluorobenzene, and 1,2,4,5-tetrafluorobenzene, and sample only the T-shaped structures for benzene and hexafluorobenzene. While the free energy for the dimerization in water is very weakly dependent on the number of fluorine atoms, the formation of π-stacked structures is entropy-driven and the T-shaped structures appear due to an enthalpic minimum. Interestingly, the solvation behavior suggests that the accumulation of water around the contact and solvent-separated pairs decreases with the increase in the number of fluorine atoms, which signifies progressive hydrophobicity of fluorobenzenes.
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Affiliation(s)
- Anuj Kumar
- Department of Chemistry , Indian Institute of Technology Bombay , Powai, Mumbai 400076 India.,Prithwi Chand Vigyan College, Jai Prakash Vishwavidyalaya , Chapra , Saran, Bihar 841301 , India
| | - Jaladhar Mahato
- Department of Chemistry , Indian Institute of Technology Bombay , Powai, Mumbai 400076 India
| | - Mayank Dixit
- Department of Chemistry , Indian Institute of Technology Bombay , Powai, Mumbai 400076 India
| | - G Naresh Patwari
- Department of Chemistry , Indian Institute of Technology Bombay , Powai, Mumbai 400076 India
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20
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Orabi EA, Davis RL, Lamoureux G. Drude polarizable force field for cation–π interactions of alkali and quaternary ammonium ions with aromatic amino acid side chains. J Comput Chem 2019; 41:472-481. [DOI: 10.1002/jcc.26084] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/14/2019] [Accepted: 09/16/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Esam A. Orabi
- Department of ChemistryFaculty of Science, Assiut University Assiut 71516 Egypt
- Department of ChemistryUniversity of Manitoba Winnipeg Manitoba R3T 2N2 Canada
| | - Rebecca L. Davis
- Department of ChemistryUniversity of Manitoba Winnipeg Manitoba R3T 2N2 Canada
| | - Guillaume Lamoureux
- Department of Chemistry and Center for Computational and Integrative Biology (CCIB)Rutgers University Camden New Jersey 08102
- Centre for Research in Molecular Modeling (CERMM), Concordia University Montréal Québec H4B 1R6 Canada
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21
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Sewring T, Zhu W, Sedin M, Theliander H. Predictions of Pair Interaction Potentials between Kraft Lignin Macromolecules in Black Liquors by Utilization of a Modified Poisson–Boltzmann Approach. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.8b05929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tor Sewring
- Forest Products and Chemical Engineering, Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
- Wallenberg Wood Science Centre, Chalmers University of Technology/Royal Institute of Technology, Kemigården 4, SE-412 96 Gothenburg, Sweden
| | - Weizhen Zhu
- Forest Products and Chemical Engineering, Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Maria Sedin
- RISE Innventia AB, SE-114 86 Stockholm, Sweden
| | - Hans Theliander
- Forest Products and Chemical Engineering, Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
- Wallenberg Wood Science Centre, Chalmers University of Technology/Royal Institute of Technology, Kemigården 4, SE-412 96 Gothenburg, Sweden
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22
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Abstract
Molecular dynamics (MD) simulations have been widely applied to computer-aided drug design (CADD). While MD has been used in a variety of applications such as free energy perturbation and long-time simulations, the accuracy of the results from those methods depends strongly on the force field used. Force fields for small molecules are crucial, as they not only serve as building blocks for developing force fields for larger biomolecules but also act as model compounds that will be transferred to ligands used in CADD. Currently, a wide range of small molecule force fields based on additive or nonpolarizable models have been developed. While these nonpolarizable force fields can produce reasonable estimations of physical properties and have shown success in a variety of systems, there is still room for improvements due to inherent limitations in these models including the lack of an electronic polarization response. For this reason, incorporating polarization effects into the energy function underlying a force field is believed to be an important step forward, giving rise to the development of polarizable force fields. Recent simulations of biological systems have indicated that polarizable force fields are able to provide a better physical representation of intermolecular interactions and, in many cases, better agreement with experimental properties than nonpolarizable, additive force fields. Therefore, this chapter focuses on the development of small molecule force fields with emphasis on polarizable models. It begins with a brief introduction on the importance of small molecule force fields and their evolution from additive to polarizable force fields. Emphasis is placed on the additive CHARMM General Force Field and the polarizable force field based on the classical Drude oscillator. The theory for the Drude polarizable force field and results for small molecules are presented showing their improvements over the additive model. The potential importance of polarization for their application in a wide range of biological systems including CADD is then discussed.
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Affiliation(s)
- Fang-Yu Lin
- Department of Pharmaceutical Sciences, Computer-Aided Drug Design Center, School of Pharmacy, University of Maryland, Baltimore, MD, USA
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, Computer-Aided Drug Design Center, School of Pharmacy, University of Maryland, Baltimore, MD, USA.
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23
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Hagler AT. Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics. J Comput Aided Mol Des 2018; 33:205-264. [DOI: 10.1007/s10822-018-0134-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/18/2018] [Indexed: 01/04/2023]
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24
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25
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Orabi EA, Lamoureux G. Cation-π Interactions between Quaternary Ammonium Ions and Amino Acid Aromatic Groups in Aqueous Solution. J Phys Chem B 2018; 122:2251-2260. [PMID: 29397727 DOI: 10.1021/acs.jpcb.7b11983] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cation-π interactions play important roles in the stabilization of protein structures and protein-ligand complexes. They contribute to the binding of quaternary ammonium ligands (mainly RNH3+ and RN(CH3)3+) to various protein receptors and are likely involved in the blockage of potassium channels by tetramethylammonium (TMA+) and tetraethylammonium (TEA+). Polarizable molecular models are calibrated for NH4+, TMA+, and TEA+ interacting with benzene, toluene, 4-methylphenol, and 3-methylindole (representing aromatic amino acid side chains) based on the ab initio MP2(full)/6-311++G(d,p) properties of the complexes. Whereas the gas-phase affinity of the ions with a given aromatic follows the trend NH4+ > TMA+ > TEA+, molecular dynamics simulations using the polarizable models show a reverse trend in water, likely due to a contribution from the hydrophobic effect. This reversed trend follows the solubility of aromatic hydrocarbons in quaternary ammonium salt solutions, which suggests a role for cation-π interactions in the salting-in of aromatic compounds in solution. Simulations in water show that the complexes possess binding free energies ranging from -1.3 to -3.3 kcal/mol (compared to gas-phase binding energies between -8.5 and -25.0 kcal/mol). Interestingly, whereas the most stable complexes involve TEA+ (the largest ion), the most stable solvent-separated complexes involve TMA+ (the intermediate-size ion).
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Affiliation(s)
- Esam A Orabi
- Department of Chemistry and Biochemistry and Centre for Research in Molecular Modeling (CERMM), Concordia University , 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada
| | - Guillaume Lamoureux
- Department of Chemistry and Biochemistry and Centre for Research in Molecular Modeling (CERMM), Concordia University , 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada
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26
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Su H, Wu Q, Wang H, Wang H. An assessment of the random-phase approximation functional and characteristics analysis for noncovalent cation-π interactions. Phys Chem Chem Phys 2017; 19:26014-26021. [PMID: 28920597 DOI: 10.1039/c7cp04504b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding energy is of great importance in understanding the formation and stability of noncovalent interactions. However, the determination of the binding energy with high precision and efficiency in medium- and long-range noncovalent interactions is still challenging for quantum chemistry. Here, we assess the performance of random-phase approximation (RPA), a fully non-local fifth-rung of the Jacob ladder functional, in determining the binding energy of cation-π systems (cation = Li+, Na+, Be2+, Mg2+, Al+, and NH4+; π = C6H6), which, to the best of our knowledge, has not been investigated. Using experimental results as the benchmark, we systematically compared the RPA method to the other ab initio methods (DFT/B3LYP, MP2, CCSD(T), and QCISD(T)) both in calculation accuracy and efficiency. From the perspective of accuracy, RPA is the best among these approaches, followed by the CCSD(T) and QCISD(T) methods. DFT/B3LYP and MP2 provide the worst accuracy. In addition, the computational efficiency of RPA is much faster than that of CCSD(T) and QCISD(T). We believe that RPA is a robust method for the precise description of medium- and long-range noncovalent interactions and is capable of providing benchmarking data. The interaction strength and interaction nature of cation-π systems are further analyzed by atoms in molecules (AIM) and the color-mapped reduced density gradient (RDG) isosurface, which are consistent with the characteristics of a typical cation-π interaction.
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Affiliation(s)
- He Su
- School of Physical Science and Technology, Southwest Jiaotong University, Chengdu 610031, P. R. China.
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27
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Pašalić H, Aquino AJA, Tunega D, Haberhauer G, Gerzabek MH, Lischka H. Cation-π interactions in competition with cation microhydration: a theoretical study of alkali metal cation-pyrene complexes. J Mol Model 2017; 23:131. [PMID: 28337678 PMCID: PMC5364259 DOI: 10.1007/s00894-017-3302-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 02/27/2017] [Indexed: 11/19/2022]
Abstract
Cation–π interactions were systematically investigated for the adsorption of H+ and alkali metal cations M+ to pyrene by means of Møller–Plesset perturbation theory (MP2) and density functional theory (DFT). The main aims were to determine the preferred adsorption sites and how the microhydration shell influences the adsorption process. The preferred adsorption sites were characterized in terms of structural parameters and energetic stability. Stability analysis of the M+–pyrene complexes revealed that the binding strength and the barrier to transitions between neighboring sites generally decreased with increasing cation size from Li+ to Cs+. Such transitions were practically barrierless (<<1 kcal/mol) for the large Rb+ and Cs+ ions. Further, the influence of the first hydration shell on the adsorption behavior was investigated for Li+ and K+ as representatives of small and large (alkali metal) cations, respectively. While the isolated complexes possessed only one minimum, two minima—corresponding to an inner and an outer complex—were observed for microhydrated complexes. The small Li+ ion formed a stable hydration shell and preferentially interacted with water rather than pyrene. In contrast, K+ favored cation–π over cation–water interactions. It was found that the mechanism for complex formation depends on the balance between cation–π interactions, cation–water complexation, and the hydrogen bonding of water to the π-system.
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Affiliation(s)
- Hasan Pašalić
- Institute for Theoretical Chemistry, University of Vienna, Währinger Strasse 17, 1090, Vienna, Austria
| | - Adelia J A Aquino
- School of Pharmaceutical Sciences and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, People's Republic of China.,Institute for Soil Research, University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Strasse 82, 1190, Vienna, Austria
| | - Daniel Tunega
- Institute for Soil Research, University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Strasse 82, 1190, Vienna, Austria.
| | - Georg Haberhauer
- Institute for Soil Research, University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Strasse 82, 1190, Vienna, Austria
| | - Martin H Gerzabek
- Institute for Soil Research, University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Strasse 82, 1190, Vienna, Austria
| | - Hans Lischka
- Institute for Theoretical Chemistry, University of Vienna, Währinger Strasse 17, 1090, Vienna, Austria. .,School of Pharmaceutical Sciences and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, People's Republic of China.
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28
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Studies on hydrolysis mechanism of anticancer ruthenium drug ImH[trans-Ru(Im)2Cl4] via ABEEMσπ polarizable force field combined with QM and MD-FEP. Chem Res Chin Univ 2017. [DOI: 10.1007/s40242-017-6401-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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29
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Abstract
Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.
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Affiliation(s)
| | - Kenneth M. Merz
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute of Cyber-Enabled Research, Michigan State University, East Lansing, Michigan 48824, United States
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30
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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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31
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Orabi EA, English AM. Sulfur-Aromatic Interactions: Modeling Cysteine and Methionine Binding to Tyrosinate and Histidinium Ions to Assess Their Influence on Protein Electron Transfer. Isr J Chem 2016. [DOI: 10.1002/ijch.201600047] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Esam A. Orabi
- Department of Chemistry and Biochemistry; Concordia University; 7141 Sherbrooke Street West Montréal Québec H4B 1R6 Canada
- Center for Research in Molecular Modeling (CERMM)Quebec; Network for Research on Protein Function, Engineering, and Applications (PROTEO)
- On leave from Department of Chemistry, Faculty of Science; Assiut University; Assiut 71516 Egypt
| | - Ann M. English
- Department of Chemistry and Biochemistry; Concordia University; 7141 Sherbrooke Street West Montréal Québec H4B 1R6 Canada
- Center for Research in Molecular Modeling (CERMM)Quebec; Network for Research on Protein Function, Engineering, and Applications (PROTEO)
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32
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Lemkul J, Huang J, Roux B, MacKerell AD. An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications. Chem Rev 2016; 116:4983-5013. [PMID: 26815602 PMCID: PMC4865892 DOI: 10.1021/acs.chemrev.5b00505] [Citation(s) in RCA: 371] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Indexed: 11/28/2022]
Abstract
Molecular mechanics force fields that explicitly account for induced polarization represent the next generation of physical models for molecular dynamics simulations. Several methods exist for modeling induced polarization, and here we review the classical Drude oscillator model, in which electronic degrees of freedom are modeled by charged particles attached to the nuclei of their core atoms by harmonic springs. We describe the latest developments in Drude force field parametrization and application, primarily in the last 15 years. Emphasis is placed on the Drude-2013 polarizable force field for proteins, DNA, lipids, and carbohydrates. We discuss its parametrization protocol, development history, and recent simulations of biologically interesting systems, highlighting specific studies in which induced polarization plays a critical role in reproducing experimental observables and understanding physical behavior. As the Drude oscillator model is computationally tractable and available in a wide range of simulation packages, it is anticipated that use of these more complex physical models will lead to new and important discoveries of the physical forces driving a range of chemical and biological phenomena.
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Affiliation(s)
- Justin
A. Lemkul
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, Maryland 21201, United States
| | - Jing Huang
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, Maryland 21201, United States
| | - Benoît Roux
- Department
of Biochemistry and Molecular Biology, University
of Chicago, Chicago, Illinois 60637, United
States
| | - Alexander D. MacKerell
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, Maryland 21201, United States
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Matyska Liskova P, Fiser R, Macek P, Chmelik J, Sykora J, Bednarova L, Konopasek I, Bumba L. Probing the Ca(2+)-assisted π-π interaction during Ca(2+)-dependent protein folding. SOFT MATTER 2016; 12:531-541. [PMID: 26489523 DOI: 10.1039/c5sm01796c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Protein folding is governed by a balance of non-covalent interactions, of which cation-π and π-π play important roles. Theoretical calculations revealed a strong cooperativity between cation-π involving alkali and alkaline earth metal ions and π-π interactions, but however, no experimental evidence was provided in this regard. Here, we characterized a Ca(2+)-binding self-processing module (SPM), which mediates a highly-specific Ca(2+)-dependent autocatalytic processing of iron-regulated protein FrpC secreted by the pathogenic Gram-negative bacterium Neisseria meningitidis. The SPM undergoes a Ca(2+)-induced transition from an intrinsically unstructured conformation to the compact protein fold that is ultimately stabilized by the π-π interaction between two unique tryptophan residues arranged in the T-shaped orientation. Moreover, the pair of tryptophans is located in a close vicinity of a calcium-binding site, suggesting the involvement of a Ca(2+)-assisted π-π interaction in the stabilization of the tertiary structure of the SPM. This makes the SPM an excellent model for the investigation of the Ca(2+)-assisted π-π interaction during Ca(2+)-induced protein folding.
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Affiliation(s)
- Petra Matyska Liskova
- Laboratory of Molecular Biology of Bacterial Pathogens, Institute of Microbiology of the ASCR, v.v.i., Videnska 1083, 14200 Prague, Czech Republic.
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34
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Hussain MA, Mahadevi AS, Sastry GN. Estimating the binding ability of onium ions with CO2 and π systems: a computational investigation. Phys Chem Chem Phys 2015; 17:1763-75. [DOI: 10.1039/c4cp03434a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The impact of increasing methyl substitution on onium ions in their complexes with CO2 and aromatic systems has been analyzed using DFT calculations.
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Affiliation(s)
- M. Althaf Hussain
- Center for Molecular Modeling
- Indian Institute of Chemical Technology
- Hyderabad 500607
- India
| | - A. Subha Mahadevi
- Center for Molecular Modeling
- Indian Institute of Chemical Technology
- Hyderabad 500607
- India
| | - G. Narahari Sastry
- Center for Molecular Modeling
- Indian Institute of Chemical Technology
- Hyderabad 500607
- India
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35
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Affiliation(s)
- J. Richard Premkumar
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - G. Narahari Sastry
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
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36
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Ghiassi H, Raissi H. Comprehensive study of the structural and electronic properties of complexes formed by Mz+ (Li+, Na+, K+, Be2+, Mg2+, Ca2+) cation and thiophene and its derivatives. J Sulphur Chem 2014. [DOI: 10.1080/17415993.2014.962537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
| | - Heidar Raissi
- Chemistry Department, University of Birjand, Birjand, Iran
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37
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Orabi EA, Lamoureux G. Simulation of Liquid and Supercritical Hydrogen Sulfide and of Alkali Ions in the Pure and Aqueous Liquid. J Chem Theory Comput 2014; 10:3221-35. [DOI: 10.1021/ct5002335] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Esam A. Orabi
- Department of Chemistry and Biochemistry
and Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada
| | - Guillaume Lamoureux
- Department of Chemistry and Biochemistry
and Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada
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38
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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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39
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Boulanger E, Thiel W. Toward QM/MM Simulation of Enzymatic Reactions with the Drude Oscillator Polarizable Force Field. J Chem Theory Comput 2014; 10:1795-809. [DOI: 10.1021/ct401095k] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eliot Boulanger
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim
an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim
an der Ruhr, Germany
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40
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Development of ABEEMσπ polarizable force field for oxidized adenine base pairs: investigation of the interaction and mutagenic mechanism. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1469-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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41
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Rapp C, Goldberger E, Tishbi N, Kirshenbaum R. Cation-π interactions of methylated ammonium ions: a quantum mechanical study. Proteins 2014; 82:1494-502. [PMID: 24464782 DOI: 10.1002/prot.24519] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/12/2014] [Accepted: 01/16/2014] [Indexed: 11/05/2022]
Abstract
Cation-π interactions of methylated ammonium ions play a key role in a broad range of biochemical systems. These include methyl-lysine binding proteins which bind to methylated sites on histone proteins, lysine demethylase enzymes which demethylate these sites, and neurotransmitter receptor complexes which bind choline-derived ligands. Recognition in these systems is achieved through an 'aromatic cage' motif in the binding site. Here we use high-level quantum mechanical calculations to address how cation-π interactions of methylated ammonium ions are modulated by a change in methylation state and interaction geometry. We survey methyl-lysine and choline-derived complexes in the Protein Databank to validate our results against available structural data. A quantitative description of cation-π interactions of methylated ammonium systems is critical to structure-based efforts to target methyl-lysine binding proteins and demethylase enzymes in the treatment of unregulated transcriptional control, and neurotransmitter receptors in the treatment of neurological disease. It is our hope that our work will serve as a benchmark for the development of physical chemistry based force fields that can accurately model the contribution of cation-π interactions to binding and specificity in these systems.
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Affiliation(s)
- Chaya Rapp
- Department of Chemistry and Biochemistry, Stern College for Women, Yeshiva University, New York, New York
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42
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Liu C, Wang Y, Zhao D, Gong L, Yang Z. Investigation of base pairs containing oxidized guanine using ab initio method and ABEEMσπ polarizable force field. J Mol Graph Model 2014; 47:62-76. [DOI: 10.1016/j.jmgm.2013.10.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 10/21/2013] [Accepted: 10/21/2013] [Indexed: 12/21/2022]
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43
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Baday S, Wang S, Lamoureux G, Bernèche S. Different hydration patterns in the pores of AmtB and RhCG could determine their transport mechanisms. Biochemistry 2013; 52:7091-8. [PMID: 24021113 DOI: 10.1021/bi400015f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The ammonium transporters of the Amt/Rh family facilitate the diffusion of ammonium across cellular membranes. Functional data suggest that Amt proteins, notably found in plants, transport the ammonium ion (NH4(+)), whereas human Rhesus (Rh) proteins transport ammonia (NH3). Comparison between the X-ray structures of the prokaryotic AmtB, assumed to be representative of Amt proteins, and the human RhCG reveals important differences at the level of their pore. Despite these important functional and structural differences between Amt and Rh proteins, studies of the AmtB transporter have led to the suggestion that proteins of both subfamilies work according to the same mechanism and transport ammonia. We performed molecular dynamics simulations of the AmtB and RhCG proteins under different water and ammonia occupancy states of their pore. Free energy calculations suggest that the probability of finding NH3 molecules in the pore of AmtB is negligible in comparison to finding water. The presence of water in the pore of AmtB could support the transport of proton. The pore lumen of RhCG is found to be more hydrophobic due to the presence of a phenylalanine conserved among Rh proteins. Simulations of RhCG also reveal that the signature histidine dyad is occasionally exposed to the extracellular bulk, which is never observed in AmtB. These different hydration patterns are consistent with the idea that Amt and Rh proteins are not functionally equivalent and that permeation takes place according to two distinct mechanisms.
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Affiliation(s)
- Sefer Baday
- Swiss Institute of Bioinformatics and Biozentrum University of Basel , Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
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44
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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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45
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Baker CM, Best RB. Matching of additive and polarizable force fields for multiscale condensed phase simulations. J Chem Theory Comput 2013; 9:2826-2837. [PMID: 23997691 PMCID: PMC3752912 DOI: 10.1021/ct400116g] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Inclusion of electronic polarization effects is one of the key aspects in which the accuracy of current biomolecular force fields may be improved. The principal drawback of such approaches is the computational cost, which typically ranges from 3 - 10 times that of the equivalent additive model, and may be greater for more sophisticated treatments of polarization or other many-body effects. Here, we present a multiscale approach which may be used to enhance the sampling in simulations with polarizable models, by using the additive model as a tool to explore configuration space. We use a method based on information theory to determine the charges for an additive model that has optimal overlap with the polarizable one, and we demonstrate the feasibility of enhancing sampling via a hybrid replica exchange scheme for several model systems. An additional advantage is that, in the process, we obtain a systematic method for deriving charges for an additive model that will be the natural complement to its polarizable parent. The additive charges are found by an effective coarse-graining of the polarizable force field, rather than by ad hoc procedures.
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Affiliation(s)
- Christopher M. Baker
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Robert B. Best
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, U.S.A
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46
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Orabi EA, Lamoureux G. Molecular Dynamics Investigation of Alkali Metal Ions in Liquid and Aqueous Ammonia. J Chem Theory Comput 2013; 9:2324-38. [DOI: 10.1021/ct4001069] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Esam A. Orabi
- Department of Chemistry
and Biochemistry and Centre
for Research in Molecular Modeling (CERMM), Concordia University,
7141 Sherbrooke Street West, Montréal, Québec H4B 1R6,
Canada
| | - Guillaume Lamoureux
- Department of Chemistry
and Biochemistry and Centre
for Research in Molecular Modeling (CERMM), Concordia University,
7141 Sherbrooke Street West, Montréal, Québec H4B 1R6,
Canada
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47
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Bereau T, Kramer C, Monnard FW, Nogueira ES, Ward TR, Meuwly M. Scoring Multipole Electrostatics in Condensed-Phase Atomistic Simulations. J Phys Chem B 2013; 117:5460-71. [DOI: 10.1021/jp400593c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Tristan Bereau
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Christian Kramer
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Fabien W. Monnard
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Elisa S. Nogueira
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Thomas R. Ward
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
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48
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Orabi EA, Lamoureux G. Polarizable Interaction Model for Liquid, Supercritical, and Aqueous Ammonia. J Chem Theory Comput 2013; 9:2035-51. [DOI: 10.1021/ct301123j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Esam A. Orabi
- Department of Chemistry
and Biochemistry and Centre
for Research in Molecular Modeling (CERMM), Concordia University,
7141 Sherbrooke Street West, Montréal, Québec H4B 1R6,
Canada
| | - Guillaume Lamoureux
- Department of Chemistry
and Biochemistry and Centre
for Research in Molecular Modeling (CERMM), Concordia University,
7141 Sherbrooke Street West, Montréal, Québec H4B 1R6,
Canada
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49
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Wireduaah S, Parker TM, Lewis M. Effects of the aromatic substitution pattern in cation-π sandwich complexes. J Phys Chem A 2013; 117:2598-604. [PMID: 23452189 DOI: 10.1021/jp309740r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A computational study investigating the effects of the aromatic substitution pattern on the structure and binding energies of cation-π sandwich complexes is reported. The correlation between the binding energies (Ebind) and Hammett substituent constants is approximately the same as what is observed for cation-π half-sandwich complexes. For cation-π sandwich complexes where both aromatics contain substituents the issue of relative conformation is a possible factor in the strength of the binding; however, the work presented here shows the Ebind values are approximately the same regardless of the relative conformation of the two substituted aromatics. Finally, recent computational work has shown conflicting results on whether cation-π sandwich Ebind values (Ebind,S) are approximately equal to twice the respective half-sandwich Ebind values (Ebind,HS), or if cation-π sandwich Ebind,S values are less than double the respective half-sandwich Ebind,HS values. The work presented here shows that for cation-π sandwich complexes involving substituted aromatics the Ebind,S values are less than twice the respective half-sandwich Ebind,HS values, and this is termed nonadditive. The extent to which the cation-π sandwich complexes investigated here are nonadditive is greater for B3LYP calculated values than for MP2 calculated values and for sandwich complexes with electron-donating substituents than those with electron-withdrawing groups.
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Affiliation(s)
- Selina Wireduaah
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, Saint Louis, Missouri 63103, USA
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50
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Hassan A, Dinadayalane TC, Grabowski SJ, Leszczynski J. Structural, energetic, spectroscopic and QTAIM analyses of cation–π interactions involving mono- and bi-cyclic ring fused benzene systems. Phys Chem Chem Phys 2013; 15:20839-56. [PMID: 24196371 DOI: 10.1039/c3cp53927j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Ayorinde Hassan
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, 1400 J.R. Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA.
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