51
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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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52
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Franconetti A, Jiménez-Barbero J, Cabrera-Escribano F. The Stabilization of Glycosyl Cations Through Cooperative Noncovalent Interactions: A Theoretical Perspective. Chemphyschem 2018; 19:659-665. [DOI: 10.1002/cphc.201700988] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 10/25/2017] [Indexed: 01/18/2023]
Affiliation(s)
- Antonio Franconetti
- Department of Organic Chemistry; Faculty of Chemistry; University of Seville; C/ Profesor García González 1 41012 Sevilla Spain
| | - Jesús Jiménez-Barbero
- Molecular Recognition and Host-Pathogen Interactions; CIC bioGUNE; Bizkaia Technology Park, Building 801 A 48170 Derio Spain
- Basque Foundation for Science; Maria Diaz de Haro 13 48009 Bilbao Spain
- Department of Organic Chemistry II; Faculty of Science and Technology; University of the BasqueCountry; 48940 Leioa Bizkaia Spain
| | - Francisca Cabrera-Escribano
- Department of Organic Chemistry; Faculty of Chemistry; University of Seville; C/ Profesor García González 1 41012 Sevilla Spain
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53
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Mirchi A, Sizochenko N, Dinadayalane T, Leszczynski J. Binding of Alkali Metal Ions with 1,3,5-Tri(phenyl)benzene and 1,3,5-Tri(naphthyl)benzene: The Effect of Phenyl and Naphthyl Ring Substitution on Cation−π Interactions Revealed by DFT Study. J Phys Chem A 2017; 121:8927-8938. [DOI: 10.1021/acs.jpca.7b08725] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Ali Mirchi
- Interdisciplinary
Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric
Sciences, Jackson State University, 1400 J. R. Lynch Street, Jackson, Mississippi 39217, United States
| | - Natalia Sizochenko
- Interdisciplinary
Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric
Sciences, Jackson State University, 1400 J. R. Lynch Street, Jackson, Mississippi 39217, United States
| | - Tandabany Dinadayalane
- Department
of Chemistry, Clark Atlanta University, 223 James P. Brawley Drive, S.W., Atlanta, Georgia 30314, United States
| | - Jerzy Leszczynski
- Interdisciplinary
Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric
Sciences, Jackson State University, 1400 J. R. Lynch Street, Jackson, Mississippi 39217, United States
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54
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Marro EA, Press EM, Purkait TK, Jimenez D, Siegler MA, Klausen RS. Cooperative Noncovalent Interactions Induce Ion Pair Separation in Diphenylsilanides. Chemistry 2017; 23:15633-15637. [PMID: 28940844 DOI: 10.1002/chem.201704217] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Eric A. Marro
- Department of Chemistry Johns Hopkins University 3400 N. Charles St Baltimore MD 21218 USA
| | - Eric M. Press
- Department of Chemistry Johns Hopkins University 3400 N. Charles St Baltimore MD 21218 USA
| | - Tapas K. Purkait
- Department of Chemistry Johns Hopkins University 3400 N. Charles St Baltimore MD 21218 USA
| | - Daniel Jimenez
- Department of Chemistry Johns Hopkins University 3400 N. Charles St Baltimore MD 21218 USA
| | - Maxime A. Siegler
- Department of Chemistry Johns Hopkins University 3400 N. Charles St Baltimore MD 21218 USA
| | - Rebekka S. Klausen
- Department of Chemistry Johns Hopkins University 3400 N. Charles St Baltimore MD 21218 USA
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55
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Wang B, Zhang Q, Jiang J, Yu H, Fu Y. Mechanistic Study on Nickel-Catalyzed Silylation of Aryl Methyl Ethers. Chemistry 2017; 23:17249-17256. [DOI: 10.1002/chem.201703266] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Bing Wang
- Hefei National Laboratory for Physical Sciences at the Microscale; CAS Key Laboratory of Urban Pollutant Conversion; Anhui Province Key Laboratory of Biomass Clean Energy; iChEM; Department of Chemistry; University of Science and Technology of China; Hefei Anhui 230026 P.R. China
| | - Qi Zhang
- Institute of Industry & Equipment Technology; Hefei University of Technology; Hefei Anhui 230009 P.R. China
| | - Julong Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale; CAS Key Laboratory of Urban Pollutant Conversion; Anhui Province Key Laboratory of Biomass Clean Energy; iChEM; Department of Chemistry; University of Science and Technology of China; Hefei Anhui 230026 P.R. China
| | - Haizhu Yu
- Department of Chemistry and Centre for Atomic Engineering; of Advanced Materials; Anhui University; Hefei Anhui 230601 P.R. China
| | - Yao Fu
- Hefei National Laboratory for Physical Sciences at the Microscale; CAS Key Laboratory of Urban Pollutant Conversion; Anhui Province Key Laboratory of Biomass Clean Energy; iChEM; Department of Chemistry; University of Science and Technology of China; Hefei Anhui 230026 P.R. China
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56
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Demircan ÇA, Bozkaya U. Transition Metal Cation−π Interactions: Complexes Formed by Fe2+, Co2+, Ni2+, Cu2+, and Zn2+ Binding with Benzene Molecules. J Phys Chem A 2017; 121:6500-6509. [DOI: 10.1021/acs.jpca.7b05759] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Uğur Bozkaya
- Department of Chemistry, Hacettepe University, Ankara, 06800, Turkey
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57
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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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58
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Deka BC, Purkayastha SK, Bhattacharyya PK. Formation of thiophene sandwiches through cation–π interaction: A DFT study. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.09.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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59
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Borca CH, Slipchenko LV, Wasserman A. Ground-State Charge Transfer: Lithium-Benzene and the Role of Hartree-Fock Exchange. J Phys Chem A 2016; 120:8190-8198. [PMID: 27661445 DOI: 10.1021/acs.jpca.6b09014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Most approximations to the exchange-correlation functional of Kohn-Sham density functional theory lead to delocalization errors that undermine the description of charge-transfer phenomena. We explore how various approximate functionals and charge-distribution schemes describe ground-state atomic-charge distributions in the lithium-benzene complex, a model system of relevance to carbon-based supercapacitors. To understand the trends, we compare Hartree-Fock (HF) and correlated post-HF calculations, confirming that the HOMO-LUMO gap is narrower in semilocal functionals but widened by hybrid functionals with large fractions of HF exchange. For semilocal functionals, natural bond orbital (NBO) and Mulliken schemes yield opposite pictures of how charge transfer occurs. In PBE, for example, when lithium and benzene are <1.5 Å apart, NBO yields a positive charge on the lithium atom, but the Mulliken scheme yields a negative charge. Furthermore, the partial charges in conjugated materials depend on the interplay between the charge-distribution scheme employed and the underlying exchange-correlation functional, being critically sensitive to the admixture of HF exchange. We analyze and explain why this happens, discuss implications, and conclude that hybrid functionals with an admixture of about one-fourth of HF exchange are particularly useful in describing charge transfer in the lithium-benzene model.
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Affiliation(s)
- Carlos H Borca
- Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Lyudmila V Slipchenko
- Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Adam Wasserman
- Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907, United States.,Department of Physics and Astronomy, Purdue University , 525 Northwestern Avenue, West Lafayette, Indiana 47907, United States
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60
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Generation of self-clusters of galectin-1 in the farnesyl-bound form. Sci Rep 2016; 6:32999. [PMID: 27624845 PMCID: PMC5021961 DOI: 10.1038/srep32999] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/18/2016] [Indexed: 12/17/2022] Open
Abstract
Ras protein is involved in a signal transduction cascade in cell growth, and cluster formation of H-Ras and human galectin-1 (Gal-1) complex is considered to be crucial to achieve its physiological roles. It is considered that the complex is formed through interactions between Gal-1 and the farnesyl group (farnesyl-dependent model), post-translationally modified to the C-terminal Cys, of H-Ras. We investigated the role of farnesyl-bound Gal-1 in the cluster formation by analyzing the structure and properties of Gal-1 bound to farnesyl thiosalicylic acid (FTS), a competitive inhibitor of the binding of H-Ras to Gal-1. Gal-1 exhibited self-cluster formation upon interaction with FTS, and small- and large-size clusters were formed depending on FTS concentration. The galactoside-binding pocket of Gal-1 in the FTS-bound form was found to play an important role in small-size cluster formation. Large-size clusters were likely formed by the interaction among the hydrophobic sites of Gal-1 in the FTS-bound form. The present results indicate that Gal-1 in the FTS-bound form has the ability to form self-clusters as well as intrinsic lectin activity. Relevance of the self-clustering of FTS-bound Gal-1 to the cluster formation of the H-Ras–Gal-1complex was discussed by taking account of the farnesyl-dependent model and another (Raf-dependent) model.
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61
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Light-activated electrochemistry on alkyne-terminated Si(100) surfaces towards solution-based redox probes. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2016.07.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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62
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Pereverzev AY, Cheng X, Nagornova NS, Reese DL, Steele RP, Boyarkin OV. Vibrational Signatures of Conformer-Specific Intramolecular Interactions in Protonated Tryptophan. J Phys Chem A 2016; 120:5598-608. [DOI: 10.1021/acs.jpca.6b05605] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aleksandr Y. Pereverzev
- Laboratoire
de Chimie Physique Moléculaire, Ecole Polytechnique Federale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Xiaolu Cheng
- Department
of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Natalia S. Nagornova
- Laboratoire
de Chimie Physique Moléculaire, Ecole Polytechnique Federale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Diana L. Reese
- Department
of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Ryan P. Steele
- Department
of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Oleg V. Boyarkin
- Laboratoire
de Chimie Physique Moléculaire, Ecole Polytechnique Federale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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63
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Structure, Bonding, and Electronic Properties of Four Rare Earth Complexes with a Phenoxyacetic Acid Ligand: X-ray Diffraction and DFT Studies. Ind Eng Chem Res 2016. [DOI: 10.1021/acs.iecr.6b01077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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64
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Habka S, Brenner V, Mons M, Gloaguen E. Gas-Phase Spectroscopic Signatures of Carboxylate-Li(+) Contact Ion Pairs: New Benchmarks For Characterizing Ion Pairing in Solution. J Phys Chem Lett 2016; 7:1192-1197. [PMID: 26978595 DOI: 10.1021/acs.jpclett.6b00454] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The coexistence of several types of ion pairs in solution together with their elusive nature hampers their experimental characterization, which relies in practice on theoretical models resorting to numerous approximations. In this context, a series of isolated contact ion pairs between a lithium cation and phenyl-tagged carboxylate anions of various lengths (Ph-(CH2)n-COO(-), n = 1-3) has been investigated in a conformer-selective manner by IR and UV laser spectroscopy, in conjunction with quantum chemistry calculations. The typical gas-phase IR signature of the bidentate structure formed between the carboxylate moiety and Li(+) has thus been obtained in the CO2(-) stretch region. In addition to the cation-anion interaction, a cation-π interaction occurs simultaneously in the largest system investigated (n = 3). The resulting distorted ion pair structure has been evidenced from both the IR signature of the CO2(-) stretches and the unique vibrationally resolved UV spectroscopy of a phenyl ring interacting with a cation. Such specific spectroscopic signatures of contact ion pairs provide experimental benchmarks, alternative to theoretical predictions, that can assist the assignment of vibrational spectra in solution.
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Affiliation(s)
- Sana Habka
- LIDYL, CEA, CNRS, Université Paris-Saclay , CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris-Saclay , CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- LIDYL, CEA, CNRS, Université Paris-Saclay , CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Eric Gloaguen
- LIDYL, CEA, CNRS, Université Paris-Saclay , CEA Saclay, 91191 Gif-sur-Yvette, France
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65
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Krossa S, Faust A, Ober D, Scheidig AJ. Comprehensive Structural Characterization of the Bacterial Homospermidine Synthase-an Essential Enzyme of the Polyamine Metabolism. Sci Rep 2016; 6:19501. [PMID: 26776105 PMCID: PMC4725965 DOI: 10.1038/srep19501] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/15/2015] [Indexed: 12/14/2022] Open
Abstract
The highly conserved bacterial homospermidine synthase (HSS) is a key enzyme of the polyamine metabolism of many proteobacteria including pathogenic strains such as Legionella pneumophila and Pseudomonas aeruginosa; The unique usage of NAD(H) as a prosthetic group is a common feature of bacterial HSS, eukaryotic HSS and deoxyhypusine synthase (DHS). The structure of the bacterial enzyme does not possess a lysine residue in the active center and thus does not form an enzyme-substrate Schiff base intermediate as observed for the DHS. In contrast to the DHS the active site is not formed by the interface of two subunits but resides within one subunit of the bacterial HSS. Crystal structures of Blastochloris viridis HSS (BvHSS) reveal two distinct substrate binding sites, one of which is highly specific for putrescine. BvHSS features a side pocket in the direct vicinity of the active site formed by conserved amino acids and a potential substrate discrimination, guiding, and sensing mechanism. The proposed reaction steps for the catalysis of BvHSS emphasize cation-π interaction through a conserved Trp residue as a key stabilizer of high energetic transition states.
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Affiliation(s)
- Sebastian Krossa
- Structural Biology-Zoological Institute, Kiel University, Am Botanischen Garten 11, 24118 Kiel, Germany
| | - Annette Faust
- Structural Biology-Zoological Institute, Kiel University, Am Botanischen Garten 11, 24118 Kiel, Germany
| | - Dietrich Ober
- Botanical Institute - Biochemical Ecology and Molecular Evolution, Kiel University, Am Botanischen Garten 1-9, 24118 Kiel, Germany
| | - Axel J Scheidig
- Structural Biology-Zoological Institute, Kiel University, Am Botanischen Garten 11, 24118 Kiel, Germany
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66
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Ataie N, Xiang J, Cheng N, Brea EJ, Lu W, Scheinberg DA, Liu C, Ng HL. Structure of a TCR-Mimic Antibody with Target Predicts Pharmacogenetics. J Mol Biol 2016; 428:194-205. [PMID: 26688548 PMCID: PMC4738012 DOI: 10.1016/j.jmb.2015.12.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/25/2015] [Accepted: 12/03/2015] [Indexed: 11/21/2022]
Abstract
Antibody therapies currently target only extracellular antigens. A strategy to recognize intracellular antigens is to target peptides presented by immune HLA receptors. ESK1 is a human, T-cell receptor (TCR)-mimic antibody that binds with subnanomolar affinity to the RMF peptide from the intracellular Wilms tumor oncoprotein WT1 in complex with HLA-A*02:01. ESK1 is therapeutically effective in mouse models of WT1(+) human cancers. TCR-based therapies have been presumed to be restricted to one HLA subtype. The mechanism for the specificity and high affinity of ESK1 is unknown. We show in a crystal structure that ESK1 Fab binds to RMF/HLA-A*02:01 in a mode different from that of TCRs. From the structure, we predict and then experimentally confirm high-affinity binding with multiple other HLA-A*02 subtypes, broadening the potential patient pool for ESK1 therapy. Using the crystal structure, we also predict potential off-target binding that we experimentally confirm. Our results demonstrate how protein structure information can contribute to personalized immunotherapy.
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Affiliation(s)
- Niloufar Ataie
- University of Hawaii at Manoa, Department of Chemistry, 2545 McCarthy Mall, Honolulu, HI 96822-2275, USA
| | - Jingyi Xiang
- Eureka Therapeutics Inc., 5858 Horton Street, Emeryville, CA 94608, USA
| | - Neal Cheng
- Eureka Therapeutics Inc., 5858 Horton Street, Emeryville, CA 94608, USA
| | - Elliott J Brea
- Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Wenjie Lu
- University of Hawaii at Manoa, Department of Chemistry, 2545 McCarthy Mall, Honolulu, HI 96822-2275, USA
| | - David A Scheinberg
- Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA; Weill Cornell Medical College, 1305 York Avenue, New York, NY 10021, USA
| | - Cheng Liu
- Eureka Therapeutics Inc., 5858 Horton Street, Emeryville, CA 94608, USA
| | - Ho Leung Ng
- University of Hawaii at Manoa, Department of Chemistry, 2545 McCarthy Mall, Honolulu, HI 96822-2275, USA; University of Hawaii Cancer Center, 2545 McCarthy Mall, Honolulu, HI 96822-2275, USA.
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67
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Berg L, Mishra BK, Andersson CD, Ekström F, Linusson A. The Nature of Activated Non-classical Hydrogen Bonds: A Case Study on Acetylcholinesterase-Ligand Complexes. Chemistry 2016; 22:2672-81. [DOI: 10.1002/chem.201503973] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 01/25/2023]
Affiliation(s)
- Lotta Berg
- Department of Chemistry; Umeå University; 901 87 Umeå Sweden
| | | | | | - Fredrik Ekström
- CBRN Defense and Security; Swedish Defense Research Agency; 906 21 Umeå Sweden
| | - Anna Linusson
- Department of Chemistry; Umeå University; 901 87 Umeå Sweden
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68
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Nagar M, Bearne SL. An additional role for the Brønsted acid-base catalysts of mandelate racemase in transition state stabilization. Biochemistry 2015; 54:6743-52. [PMID: 26480244 DOI: 10.1021/acs.biochem.5b00982] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mandelate racemase (MR) catalyzes the interconversion of the enantiomers of mandelate and serves as a paradigm for understanding the enzyme-catalyzed abstraction of an α-proton from a carbon acid substrate with a high pKa. The enzyme utilizes a two-base mechanism with Lys 166 and His 297 acting as Brønsted acid and base catalysts, respectively, in the R → S reaction direction. In the S → R reaction direction, their roles are reversed. Using isothermal titration calorimetry (ITC), MR is shown to bind the intermediate/transition state (TS) analogue inhibitor benzohydroxamate (BzH) in an entropy-driven process with a value of ΔCp equal to -358 ± 3 cal mol(-1) K(-1), consistent with an increased number of hydrophobic interactions. However, MR binds BzH with an affinity that is ∼2 orders of magnitude greater than that predicted solely on the basis of hydrophobic interactions [St. Maurice, M., and Bearne, S. L. (2004) Biochemistry 43, 2524], suggesting that additional specific interactions contribute to binding. To test the hypothesis that cation-π/NH-π interactions between the side chains of Lys 166 and His 297 and the aromatic ring and/or the hydroxamate/hydroximate moiety of BzH contribute to the binding of BzH, site-directed mutagenesis was used to generate the MR variants K166M, K166C, H297N, and K166M/H297N and their binding affinity for various ligands determined using ITC. Comparison of the binding affinities of these MR variants with the intermediate/TS analogues BzH and cyclohexanecarbohydroxamate revealed that cation-π/NH-π interactions between His 297 and the hydroxamate/hydroximate moiety and the phenyl ring of BzH contribute approximately 0.26 and 0.91 kcal/mol to binding, respectively, while interactions with Lys 166 contribute approximately 1.74 and 1.74 kcal/mol, respectively. Similarly, comparison of the binding affinities of these mutants with substrate analogues revealed that Lys 166 contributes >2.93 kcal/mol to the binding of (R)-atrolactate, and His 297 contributes 2.46 kcal/mol to the binding of (S)-atrolactate. These results are consistent with Lys 166 and His 297 playing dual roles in catalysis: they act as Brønsted acid-base catalysts, and they stabilize both the enolate moiety and phenyl ring of the altered substrate in the TS.
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Affiliation(s)
- Mitesh Nagar
- Department of Biochemistry and Molecular Biology, Dalhousie University , Halifax, NS B3H 4R2, Canada
| | - Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University , Halifax, NS B3H 4R2, Canada.,Department of Chemistry, Dalhousie University , Halifax, NS B3H 4R2, Canada
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69
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Liu J, Shi G, Guo P, Yang J, Fang H. Blockage of Water Flow in Carbon Nanotubes by Ions Due to Interactions between Cations and Aromatic Rings. PHYSICAL REVIEW LETTERS 2015; 115:164502. [PMID: 26550880 DOI: 10.1103/physrevlett.115.164502] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Indexed: 06/05/2023]
Abstract
Combining classical molecular dynamics simulations and density functional theory calculations, we find that cations block water flow through narrow (6,6)-type carbon nanotubes (CNTs) because of interactions between cations and aromatic rings in CNTs. In wide CNTs, these interactions trap the cations in the interior of the CNT, inducing unexpected open or closed state switching of ion transfer under a strong electric field, which is consistent with experiments. These findings will help to develop new methods to facilitate water and ion transport across CNTs.
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Affiliation(s)
- Jian Liu
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guosheng Shi
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Pan Guo
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinrong Yang
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiping Fang
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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70
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Xie NZ, Du QS, Li JX, Huang RB. Exploring Strong Interactions in Proteins with Quantum Chemistry and Examples of Their Applications in Drug Design. PLoS One 2015; 10:e0137113. [PMID: 26339784 PMCID: PMC4560430 DOI: 10.1371/journal.pone.0137113] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 08/12/2015] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES Three strong interactions between amino acid side chains (salt bridge, cation-π, and amide bridge) are studied that are stronger than (or comparable to) the common hydrogen bond interactions, and play important roles in protein-protein interactions. METHODS Quantum chemical methods MP2 and CCSD(T) are used in calculations of interaction energies and structural optimizations. RESULTS The energies of three types of amino acid side chain interactions in gaseous phase and in aqueous solutions are calculated using high level quantum chemical methods and basis sets. Typical examples of amino acid salt bridge, cation-π, and amide bridge interactions are analyzed, including the inhibitor design targeting neuraminidase (NA) enzyme of influenza A virus, and the ligand binding interactions in the HCV p7 ion channel. The inhibition mechanism of the M2 proton channel in the influenza A virus is analyzed based on strong amino acid interactions. CONCLUSION (1) The salt bridge interactions between acidic amino acids (Glu- and Asp-) and alkaline amino acids (Arg+, Lys+ and His+) are the strongest residue-residue interactions. However, this type of interaction may be weakened by solvation effects and broken by lower pH conditions. (2) The cation- interactions between protonated amino acids (Arg+, Lys+ and His+) and aromatic amino acids (Phe, Tyr, Trp and His) are 2.5 to 5-fold stronger than common hydrogen bond interactions and are less affected by the solvation environment. (3) The amide bridge interactions between the two amide-containing amino acids (Asn and Gln) are three times stronger than hydrogen bond interactions, which are less influenced by the pH of the solution. (4) Ten of the twenty natural amino acids are involved in salt bridge, or cation-, or amide bridge interactions that often play important roles in protein-protein, protein-peptide, protein-ligand, and protein-DNA interactions.
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Affiliation(s)
- Neng-Zhong Xie
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
| | - Qi-Shi Du
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
- Gordon Life Science Institute, 53 South Cottage Road, Belmont, MA, 02478, United States of America
| | - Jian-Xiu Li
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
- Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi, 530004, China
| | - Ri-Bo Huang
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
- Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi, 530004, China
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71
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Rana S, Sahoo AR, Majhi BK. Allosterism in human complement component 5a ((h)C5a): a damper of C5a receptor (C5aR) signaling. J Biomol Struct Dyn 2015. [PMID: 26212097 DOI: 10.1080/07391102.2015.1073634] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The phenomena of allosterism continues to advance the field of drug discovery, by illuminating gainful insights for many key processes, related to the structure-function relationships in proteins and enzymes, including the transmembrane G-protein coupled receptors (GPCRs), both in normal as well as in the disease states. However, allosterism is completely unexplored in the native protein ligands, especially when a small covalent change significantly modulates the pharmacology of the protein ligands toward the signaling axes of the GPCRs. One such example is the human C5a ((h)C5a), the potent cationic anaphylatoxin that engages C5aR and C5L2 to elicit numerous immunological and non-immunological responses in humans. From the recently available structure-function data, it is clear that unlike the mouse C5a ((m)C5a), the (h)C5a displays conformational heterogeneity. However, the molecular basis of such conformational heterogeneity, otherwise allosterism in (h)C5a and its precise contribution toward the overall C5aR signaling is not known. This study attempts to decipher the functional role of allosterism in (h)C5a, by exploring the inherent conformational dynamics in (m)C5a, (h)C5a and in its point mutants, including the proteolytic mutant des-Arg(74)-(h)C5a. Prima facie, the comparative molecular dynamics study, over total 500 ns, identifies Arg(74)-Tyr(23) and Arg(37)-Phe(51) "cation-π" pairs as the molecular "allosteric switches" on (h)C5a that potentially functions as a damper of C5aR signaling.
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Affiliation(s)
- Soumendra Rana
- a Chemical Biology Laboratory, School of Basic Sciences , Indian Institute of Technology Bhubaneswar , Bhubaneswar , Odisha 751007 , India
| | - Amita Rani Sahoo
- a Chemical Biology Laboratory, School of Basic Sciences , Indian Institute of Technology Bhubaneswar , Bhubaneswar , Odisha 751007 , India
| | - Bharat Kumar Majhi
- a Chemical Biology Laboratory, School of Basic Sciences , Indian Institute of Technology Bhubaneswar , Bhubaneswar , Odisha 751007 , India
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72
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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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73
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Parrish RM, Sherrill CD. Spatial assignment of symmetry adapted perturbation theory interaction energy components: The atomic SAPT partition. J Chem Phys 2015; 141:044115. [PMID: 25084889 DOI: 10.1063/1.4889855] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
We develop a physically-motivated assignment of symmetry adapted perturbation theory for intermolecular interactions (SAPT) into atom-pairwise contributions (the A-SAPT partition). The basic precept of A-SAPT is that the many-body interaction energy components are computed normally under the formalism of SAPT, following which a spatially-localized two-body quasiparticle interaction is extracted from the many-body interaction terms. For electrostatics and induction source terms, the relevant quasiparticles are atoms, which are obtained in this work through the iterative stockholder analysis (ISA) procedure. For the exchange, induction response, and dispersion terms, the relevant quasiparticles are local occupied orbitals, which are obtained in this work through the Pipek-Mezey procedure. The local orbital atomic charges obtained from ISA additionally allow the terms involving local orbitals to be assigned in an atom-pairwise manner. Further summation over the atoms of one or the other monomer allows for a chemically intuitive visualization of the contribution of each atom and interaction component to the overall noncovalent interaction strength. Herein, we present the intuitive development and mathematical form for A-SAPT applied in the SAPT0 approximation (the A-SAPT0 partition). We also provide an efficient series of algorithms for the computation of the A-SAPT0 partition with essentially the same computational cost as the corresponding SAPT0 decomposition. We probe the sensitivity of the A-SAPT0 partition to the ISA grid and convergence parameter, orbital localization metric, and induction coupling treatment, and recommend a set of practical choices which closes the definition of the A-SAPT0 partition. We demonstrate the utility and computational tractability of the A-SAPT0 partition in the context of side-on cation-π interactions and the intercalation of DNA by proflavine. A-SAPT0 clearly shows the key processes in these complicated noncovalent interactions, in systems with up to 220 atoms and 2845 basis functions.
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Affiliation(s)
- Robert M Parrish
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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74
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Paul AK, Kolakkandy S, Hase WL. Dynamics of Na+(Benzene) + Benzene Association and Ensuing Na+(Benzene)2* Dissociation. J Phys Chem A 2015; 119:7894-904. [DOI: 10.1021/acs.jpca.5b01922] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Amit K. Paul
- Department
of Chemistry and
Biochemistry Texas Tech University, Lubbock, Texas 79409, United States
| | - Sujitha Kolakkandy
- Department
of Chemistry and
Biochemistry Texas Tech University, Lubbock, Texas 79409, United States
| | - William L. Hase
- Department
of Chemistry and
Biochemistry Texas Tech University, Lubbock, Texas 79409, United States
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75
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Rana S, Sahoo AR. Model structures of inactive and peptide agonist bound C5aR: Insights into agonist binding, selectivity and activation. Biochem Biophys Rep 2015; 1:85-96. [PMID: 29124137 PMCID: PMC5668562 DOI: 10.1016/j.bbrep.2015.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 03/10/2015] [Accepted: 03/11/2015] [Indexed: 11/30/2022] Open
Abstract
C5a receptor (C5aR) is one of the major chemoattractant receptors of the druggable proteome that binds C5a, the proinflammatory polypeptide of complement cascade, triggering inflammation and SEPSIS. Here, we report the model structures of C5aR in both inactive and peptide agonist (YSFKPMPLaR; a=D-Ala) bound meta-active state. Assembled in CYANA and evolved over molecular dynamics (MD) in POPC bilayer, the inactive C5aR demonstrates a topologically unique compact heptahelical bundle topology harboring a β-hairpin in extracellular loop 2 (ECL2), derived from the atomistic folding simulations. The peptide agonist bound meta-active C5aR deciphers the “site2” at an atomistic resolution in the extracellular surface (ECS), in contrast to the previously hypothesized inter-helical crevice. With estimated Ki≈2.75 μM, the meta-active C5aR excellently rationalizes the IC50 (0.1–13 μM) and EC50 (0.01–6 μM) values, displayed by the peptide agonist in several signaling studies. Moreover, with Ki≈5.3×105 μM, the “site2” also illustrates selectivity, by discriminating the stereochemical mutant peptide (YSFkPMPLaR; k=D-Lys), known to be inert toward C5aR, up to 1 mM concentration. Topologically juxtaposed between the structures of rhodopsin and CXCR1, the C5aR models also display excellent structural correlations with the other G-protein coupled receptors (GPCRs). The models elaborated in the current study unravel many important structural insights previously not known for regulating the agonist binding and activation mechanism of C5aR. Topologically unique inactive and meta-active atomistic models of C5aR. Model demonstrates excellent structural correlation with the other reported GPCRs. Model deciphers the “site2” in the ECS and also demonstrates agonist selectivity. Agonist binding and activation requires “cation–π” interaction with F275 of C5aR. Inactive to meta-active transition involves TM3–TM6 movements (ΔΘ≈+11.1°) in C5aR.
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Affiliation(s)
- Soumendra Rana
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Odisha 751007, India
| | - Amita Rani Sahoo
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Odisha 751007, India
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76
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Kolakkandy S, Paul AK, Pratihar S, Kohale SC, Barnes GL, Wang H, Hase WL. Energy and temperature dependent dissociation of the Na+(benzene)1,2 clusters: Importance of anharmonicity. J Chem Phys 2015; 142:044306. [DOI: 10.1063/1.4906232] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sujitha Kolakkandy
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, USA
| | - Amit K. Paul
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, USA
| | - Subha Pratihar
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, USA
| | - Swapnil C. Kohale
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, USA
| | - George L. Barnes
- Department of Chemistry and Biochemistry, Siena College, Loudonville, New York 12211-1462, USA
| | - Hai Wang
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, USA
| | - William L. Hase
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, USA
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77
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Lima CFRAC, Fernandes AM, Melo A, Gonçalves LM, Silva AMS, Santos LMNBF. Diarylferrocene tweezers for cation binding. Phys Chem Chem Phys 2015; 17:23917-23. [DOI: 10.1039/c5cp04530d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Diarylferrocenes can act as molecular tweezers of cations. Their unique molecular shape and low torsional potentials allow for strong binding of small cations in the gas phase.
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Affiliation(s)
- Carlos F. R. A. C. Lima
- CIQ
- Departamento de Química e Bioquímica
- Faculdade de Ciências da Universidade do Porto
- Porto
- Portugal
| | - Ana M. Fernandes
- Department of Chemistry & QOPNA
- University of Aveiro
- Aveiro
- Portugal
| | - André Melo
- LAQV-REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências da Universidade do Porto
- Porto
- Portugal
| | - Luís M. Gonçalves
- LAQV-REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências da Universidade do Porto
- Porto
- Portugal
| | | | - Luís M. N. B. F. Santos
- CIQ
- Departamento de Química e Bioquímica
- Faculdade de Ciências da Universidade do Porto
- Porto
- Portugal
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78
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Arias S, Freire F, Quiñoá E, Riguera R. The leading role of cation–π interactions in polymer chemistry: the control of the helical sense in solution. Polym Chem 2015. [DOI: 10.1039/c5py00587f] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cation–π interactions determine the helical sense adopted by a polyphenylacetylene bearing (R)-α-methoxy-α-phenylacetamide as a pendant group (poly-1).
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Affiliation(s)
- Sandra Arias
- Department of Organic Chemistry and Center for Research in Biological Chemistry and Molecular Materials (CIQUS)
- University of Santiago de Compostela
- E-15782 Santiago de Compostela
- Spain
| | - Félix Freire
- Department of Organic Chemistry and Center for Research in Biological Chemistry and Molecular Materials (CIQUS)
- University of Santiago de Compostela
- E-15782 Santiago de Compostela
- Spain
| | - Emilio Quiñoá
- Department of Organic Chemistry and Center for Research in Biological Chemistry and Molecular Materials (CIQUS)
- University of Santiago de Compostela
- E-15782 Santiago de Compostela
- Spain
| | - Ricardo Riguera
- Department of Organic Chemistry and Center for Research in Biological Chemistry and Molecular Materials (CIQUS)
- University of Santiago de Compostela
- E-15782 Santiago de Compostela
- Spain
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79
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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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80
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Linder T, Saxena P, Timin E, Hering S, Stary-Weinzinger A. Structural Insights into Trapping and Dissociation of Small Molecules in K+ Channels. J Chem Inf Model 2014; 54:3218-28. [DOI: 10.1021/ci500353r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tobias Linder
- Department for Pharmacology and Toxicology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Priyanka Saxena
- Department for Pharmacology and Toxicology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Eugen Timin
- Department for Pharmacology and Toxicology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Steffen Hering
- Department for Pharmacology and Toxicology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Anna Stary-Weinzinger
- Department for Pharmacology and Toxicology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
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81
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Kolakkandy S, Pratihar S, Aquino AJA, Wang H, Hase WL. Properties of Complexes Formed by Na+, Mg2+, and Fe2+ Binding with Benzene Molecules. J Phys Chem A 2014; 118:9500-11. [DOI: 10.1021/jp5029257] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sujitha Kolakkandy
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Subha Pratihar
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Adelia J. A. Aquino
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Hai Wang
- Department
of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
| | - William L. Hase
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
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82
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Chiavarino B, Crestoni ME, Schütz M, Bouchet A, Piccirillo S, Steinmetz V, Dopfer O, Fornarini S. Cation-π interactions in protonated phenylalkylamines. J Phys Chem A 2014; 118:7130-8. [PMID: 25061749 DOI: 10.1021/jp505037n] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Phenylalkylamines of the general formula C6H5(CH2)nNH2 (n = 1-4) have been delivered to the gas phase as protonated species using electrospray ionization. The ions thus formed have been assayed by IRMPD spectroscopy in two different spectroscopic domains, namely, the 600-1800 and the 3000-3500 cm(-1) regions using either an IR free electron laser or a tabletop OPO/OPA laser source. The interpretation of the experimental spectra is aided by density functional theory calculations of candidate species and vibrational frequency analyses. Protonated benzylamine presents a relatively straightforward instance of a single stable conformer, providing a trial case for the adopted approach. Turning to the higher homologues, C6H5(CH2)nNH3(+) (n = 2-4), more conformations become accessible. For each C6H5(CH2)nNH3(+) ion (n = 2-4), the most stable geometry is characterized by cation-π interactions between the positively charged ammonium group and the aromatic π-electronic system, permitted by the folding of the polymethylene chain. The IRMPD spectra of the sampled ions confirm the presence of the folded structures by comparison with the calculated IR spectra of the various possible conformers. An inspection of the NH stretching region is helpful in this regard.
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Affiliation(s)
- Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza , P. le A. Moro 5, I-00185 Roma, Italy
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83
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Bania KK, Guha AK, Bhattacharyya PK, Sinha S. Effect of substituent and solvent on cation-π interactions in benzene and borazine: a computational study. Dalton Trans 2014; 43:1769-84. [PMID: 24248426 DOI: 10.1039/c3dt52081a] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A DFT and ab initio quantum chemical study has been carried out at different theoretical levels to delve into the role of the cation-π interaction within the main group metal cations (Li(+), Na(+) and K(+)), substituted benzene and borazine. The effects of electron withdrawing and electron donating groups on these non-covalent forces of interaction were also studied. The excellent correlation between Hammett constants and binding energy values indicates that the cation-π interaction is influenced by both inductive and resonance effects. Electron donating groups (EDG) such as -CH3 and -NH2 attached to benzene at the 1, 3 and 5 position and the three boron atoms of borazine were found to strengthen these interactions, while electron withdrawing groups (EWG) such as -NO2 did the reverse. These results were further substantiated by topological analysis using the quantum theory of atoms in molecules (QTAIM). The polarized continuum model (PCM) and the discrete solvation model were used to elucidate the effect of solvation on the cation-π interaction. The size of the cations and the nature of the substituents were found to influence the enthalpy and binding energy of the systems (or complex). In the gas phase, the cation-π interaction was found to be exothermic, whereas in the presence of a polar solvent the interaction was highly endothermic. Thermochemical analysis predicts the presence of thermodynamic driving forces for borazine and benzene substituted with EDG. DFT based reactivity descriptors, such as global hardness (η), chemical potential (μ) and the electrophilicity index (ω) were used to elucidate the effect of the substituent on the reactivity of the cation-π complexes.
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84
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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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85
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Datta A, Das K, Massera C, Clegg JK, Sinha C, Huang JH, Garribba E. A mixed valent heterometallic CuII/NaI coordination polymer with sodium–phenyl bonds. Dalton Trans 2014; 43:5558-63. [DOI: 10.1039/c4dt00189c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A mixed valent heterometallic CuII/NaI coordination polymer (1) is generated by the reaction of a Schiff base ligand, (6,6′-(1E,1′E)-(2-hydroxypropane-1,3-diyl)bis(azan-1-yl-1-ylidene)bis(methan-1-yl-1-ylidene)bis(2-methoxyphenol)) with copper(ii) acetate and sodium perchlorate.
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Affiliation(s)
- Amitabha Datta
- Department of Chemistry
- National Changhua University of Education
- Changhua 50058, Taiwan
| | - Kuheli Das
- Department of Chemistry
- Inorganic Chemistry Section
- Jadavpur University
- Kolkata – 700032, India
| | - Chiara Massera
- Dipartimento di Chimica
- Università degli Studi di Parma
- 43124 Parma, Italy
| | - Jack K. Clegg
- School of Chemistry and Molecular Biosciences
- The University of Queensland
- Brisbane St Lucia, Australia
| | - Chittaranjan Sinha
- Department of Chemistry
- Inorganic Chemistry Section
- Jadavpur University
- Kolkata – 700032, India
| | - Jui-Hsien Huang
- Department of Chemistry
- National Changhua University of Education
- Changhua 50058, Taiwan
| | - Eugenio Garribba
- Dipartimento di Chimica e Farmacia
- and Centro Interdisciplinare per lo Sviluppo della Ricerca Biotecnologica e per lo Studio della Biodiversità della Sardegna
- Università di Sassari
- I-07100 Sassari, Italy
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86
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Shang R, Wang S, Xu X, Yi Y, Guo W, YuLiu, Liang J. Chemical synthesis and biological activities of novel pleuromutilin derivatives with substituted amino moiety. PLoS One 2013; 8:e82595. [PMID: 24376551 PMCID: PMC3871055 DOI: 10.1371/journal.pone.0082595] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 10/25/2013] [Indexed: 11/18/2022] Open
Abstract
Novel pleuromutilin derivatives designed based on the structure of valnemulin were synthesized and evaluated for their in vitro antibacterial activities. These pleuromutilin derivatives with substituted amino moiety exhibited excellent activities against methicillin-resistant Staphylococcus aureus, methicillin-resistant Staphylococcus epidermidis, Escherichia coli, and Streptococcus agalactiae. Compound 5b showed the highest antibacterial activities and even exceeded tiamulin. Moreover, the docking experiments provided information about the binding model between the synthesized compounds and peptidyl transferase center (PTC) of 23S rRNA.
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Affiliation(s)
- Ruofeng Shang
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmacceutical Development, Ministry of Agriculture, Lanzhou Institute of Animal Science and Veterinary Pharmaceutics Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Shengyu Wang
- University Hospital of Gansu Traditional Chinese Medicine, Lanzhou, Gansu, China
| | - Ximing Xu
- Université Paris Diderot, Sorbonne Paris Cité, Unité de Biologie Fonctionnelle et Adaptative, CNRS, Paris, France
| | - Yunpeng Yi
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmacceutical Development, Ministry of Agriculture, Lanzhou Institute of Animal Science and Veterinary Pharmaceutics Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Wenzhu Guo
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmacceutical Development, Ministry of Agriculture, Lanzhou Institute of Animal Science and Veterinary Pharmaceutics Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - YuLiu
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmacceutical Development, Ministry of Agriculture, Lanzhou Institute of Animal Science and Veterinary Pharmaceutics Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Jianping Liang
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmacceutical Development, Ministry of Agriculture, Lanzhou Institute of Animal Science and Veterinary Pharmaceutics Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
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87
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Kolmann SJ, D'Arcy JH, Jordan MJT. Quantum effects and anharmonicity in the H2-Li+-benzene complex: A model for hydrogen storage materials. J Chem Phys 2013; 139:234305. [DOI: 10.1063/1.4831715] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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88
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Soydaş E, Bozkaya U. Accurate Open-Shell Noncovalent Interaction Energies from the Orbital-Optimized Møller–Plesset Perturbation Theory: Achieving CCSD Quality at the MP2 Level by Orbital Optimization. J Chem Theory Comput 2013; 9:4679-83. [DOI: 10.1021/ct4008124] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emine Soydaş
- Department of Chemistry, Atatürk University, Erzurum 25240, Turkey
| | - Uğur Bozkaya
- Department of Chemistry, Atatürk University, Erzurum 25240, Turkey
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89
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Song J, Ng SC, Tompa P, Lee KAW, Chan HS. Polycation-π interactions are a driving force for molecular recognition by an intrinsically disordered oncoprotein family. PLoS Comput Biol 2013; 9:e1003239. [PMID: 24086122 PMCID: PMC3784488 DOI: 10.1371/journal.pcbi.1003239] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 08/12/2013] [Indexed: 12/20/2022] Open
Abstract
Molecular recognition by intrinsically disordered proteins (IDPs) commonly involves specific localized contacts and target-induced disorder to order transitions. However, some IDPs remain disordered in the bound state, a phenomenon coined “fuzziness”, often characterized by IDP polyvalency, sequence-insensitivity and a dynamic ensemble of disordered bound-state conformations. Besides the above general features, specific biophysical models for fuzzy interactions are mostly lacking. The transcriptional activation domain of the Ewing's Sarcoma oncoprotein family (EAD) is an IDP that exhibits many features of fuzziness, with multiple EAD aromatic side chains driving molecular recognition. Considering the prevalent role of cation-π interactions at various protein-protein interfaces, we hypothesized that EAD-target binding involves polycation- π contacts between a disordered EAD and basic residues on the target. Herein we evaluated the polycation-π hypothesis via functional and theoretical interrogation of EAD variants. The experimental effects of a range of EAD sequence variations, including aromatic number, aromatic density and charge perturbations, all support the cation-π model. Moreover, the activity trends observed are well captured by a coarse-grained EAD chain model and a corresponding analytical model based on interaction between EAD aromatics and surface cations of a generic globular target. EAD-target binding, in the context of pathological Ewing's Sarcoma oncoproteins, is thus seen to be driven by a balance between EAD conformational entropy and favorable EAD-target cation-π contacts. Such a highly versatile mode of molecular recognition offers a general conceptual framework for promiscuous target recognition by polyvalent IDPs. Understanding how proteins recognize each other is central to deciphering the inner workings of living things and for biomedical research. It has long been known that the sequence of a protein, which is a string of different amino acids, can dictate how a protein molecule folds into a well-defined shape required for biological tasks. Many folded proteins recognize and bind with each other by a tight geometric fit similar to that between a lock and its key. Recently, however, it has become clear that some proteins function as a flexible string, in constant motion, without forming a stable shape. Understanding how such “disordered” proteins work is challenging. To gain insight, we studied a disordered protein region that causes a large family of human cancers. Employing an innovative combination of experimental and theoretical techniques, we describe a new mode of protein interaction based on multiple simple contacts between one type of amino acid (aromatic) in the disordered protein and another type (positively charged) on the partner protein. Because this mechanism also underlies the ability of the disordered protein to cause cancer, further investigation of this unprecedented mode of protein-protein interaction may open up new avenues for cancer therapy.
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Affiliation(s)
- Jianhui Song
- Departments of Biochemistry, Molecular Genetics, and Physics, University of Toronto, Toronto, Ontario, Canada
| | - Sheung Chun Ng
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong S.A.R., China
| | - Peter Tompa
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
| | - Kevin A. W. Lee
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong S.A.R., China
- * E-mail: (KAWL); (HSC)
| | - Hue Sun Chan
- Departments of Biochemistry, Molecular Genetics, and Physics, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (KAWL); (HSC)
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90
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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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91
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Abstract
Fundamental features of biomolecules, such as their structure, solvation, and crystal packing and even the docking of drugs, rely on noncovalent interactions. Theory can help elucidate the nature of these interactions, and energy component analysis reveals the contributions from the various intermolecular forces: electrostatics, London dispersion terms, induction (polarization), and short-range exchange-repulsion. Symmetry-adapted perturbation theory (SAPT) provides one method for this type of analysis. In this Account, we show several examples of how SAPT provides insight into the nature of noncovalent π-interactions. In cation-π interactions, the cation strongly polarizes electrons in π-orbitals, leading to substantially attractive induction terms. This polarization is so important that a cation and a benzene attract each other when placed in the same plane, even though a consideration of the electrostatic interactions alone would suggest otherwise. SAPT analysis can also support an understanding of substituent effects in π-π interactions. Trends in face-to-face sandwich benzene dimers cannot be understood solely in terms of electrostatic effects, especially for multiply substituted dimers, but SAPT analysis demonstrates the importance of London dispersion forces. Moreover, detailed SAPT studies also reveal the critical importance of charge penetration effects in π-stacking interactions. These effects arise in cases with substantial orbital overlap, such as in π-stacking in DNA or in crystal structures of π-conjugated materials. These charge penetration effects lead to attractive electrostatic terms where a simpler analysis based on atom-centered charges, electrostatic potential plots, or even distributed multipole analysis would incorrectly predict repulsive electrostatics. SAPT analysis of sandwich benzene, benzene-pyridine, and pyridine dimers indicates that dipole/induced-dipole terms present in benzene-pyridine but not in benzene dimer are relatively unimportant. In general, a nitrogen heteroatom contracts the electron density, reducing the magnitude of both the London dispersion and the exchange-repulsion terms, but with an overall net increase in attraction. Finally, using recent advances in SAPT algorithms, researchers can now perform SAPT computations on systems with 200 atoms or more. We discuss a recent study of the intercalation complex of proflavine with a trinucleotide duplex of DNA. Here, London dispersion forces are the strongest contributors to binding, as is typical for π-π interactions. However, the electrostatic terms are larger than usual on a fractional basis, which likely results from the positive charge on the intercalator and its location between two electron-rich base pairs. These cation-π interactions also increase the induction term beyond those of typical noncovalent π-interactions.
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Affiliation(s)
- C. David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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92
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Schouwey C, Scopelliti R, Severin K. An Imine-Based Molecular Cage with Distinct Binding Sites for Small and Large Alkali Metal Cations. Chemistry 2013; 19:6274-81. [DOI: 10.1002/chem.201300098] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Indexed: 12/30/2022]
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93
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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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94
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Lu Q, Oh DX, Lee Y, Jho Y, Hwang DS, Zeng H. Nanomechanics of Cation-π Interactions in Aqueous Solution. Angew Chem Int Ed Engl 2013; 52:3944-8. [DOI: 10.1002/anie.201210365] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Indexed: 02/06/2023]
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95
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96
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Schyman P, Jorgensen WL. Exploring Adsorption of Water and Ions on Carbon Surfaces using a Polarizable Force Field. J Phys Chem Lett 2013; 4:468-474. [PMID: 23440601 PMCID: PMC3579643 DOI: 10.1021/jz302085c] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Graphene, carbon nanotubes, and fullerenes are of great interest due to their unique properties and diverse applications in biology, molecular electronics, and materials science. Therefore, there is demand for methods that can accurately model the interface between carbon surfaces and their environment. In this letter we compare results for complexes of water, potassium ion, and chloride ion with graphene, carbon nanotube, and fullerene surfaces using a standard non-polarizable force field (OPLS-AA), a polarizable force field (OPLS-AAP), DFT, and ab initio theory. For interactions with water, OPLS-AA with the TIP3P or TIP4P water models describes the interactions with benzene (C(6)H(6)) and coronene (C(24)H(12)) well; however, for acenes larger than circumcoronene (C(54)H(18)) and especially for C(60), the interaction energies are somewhat too weak and polarization is needed. For ions interacting with carbon surfaces, inclusion of polarization is essential, and OPLS-AAP is found to perform well in comparison to the highest-level quantum mechanical methods. Overall, OPLS-AAP provides an accurate and computationally efficient force field for modeling condensed-phase systems featuring carbon surfaces.
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97
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Artem'ev AV, Gusarova NK, Bagryanskaya IY, Doronina EP, Verkhoturova SI, Sidorkin VF, Trofimov BA. Alkali Metal Thioselenophosphinates, M[SeSPR2]: One-Pot Multicomponent Synthesis, DFT Study, and Synthetic Application. Eur J Inorg Chem 2012. [DOI: 10.1002/ejic.201200947] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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98
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Yang J, Waller MP. JACOB: a dynamic database for computational chemistry benchmarking. J Chem Inf Model 2012; 52:3255-62. [PMID: 23157388 DOI: 10.1021/ci300374g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
JACOB (just a collection of benchmarks) is a database that contains four diverse benchmark studies, which in-turn included 72 data sets, with a total of 122,356 individual results. The database is constructed upon a dynamic web framework that allows users to retrieve data from the database via predefined categories. Additional flexibility is made available via user-defined text-based queries. Requested sets of results are then automatically presented as bar graphs, with parameters of the graphs being controllable via the URL. JACOB is currently available at www.wallerlab.org/jacob.
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Affiliation(s)
- Jack Yang
- Theoretische Organische Chemie, Organisch-Chemisches Institut der Westfälische Wilhelms Universität Münster, Corrensstraße 40, 48149 Münster, Germany
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99
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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: 731] [Impact Index Per Article: 60.9] [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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100
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Rueda-Zubiaurre A, Herrero-García N, del Rosario Torres M, Fernández I, Osío Barcina J. Rational Design of a Nonbasic Molecular Receptor for Selective NH4+/K+Complexation in the Gas Phase. Chemistry 2012; 18:16884-9. [DOI: 10.1002/chem.201201642] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 09/16/2012] [Indexed: 11/08/2022]
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