1
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Calinsky R, Levy Y. Histidine in Proteins: pH-Dependent Interplay between π-π, Cation-π, and CH-π Interactions. J Chem Theory Comput 2024; 20:6930-6945. [PMID: 39037905 PMCID: PMC11325542 DOI: 10.1021/acs.jctc.4c00606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Histidine (His) stands out as the most versatile natural amino acid due to its side chain's facile propensity to protonate at physiological pH, leading to a transition from aromatic to cationic characteristics and thereby enabling diverse biomolecular interactions. In this study, our objective was to quantify the energetics and geometries of pairwise interactions involving His at varying pH levels. Through quantum chemical calculations, we discovered that His exhibits robust participation in both π-π and cation-π interactions, underscoring its ability to adopt a π or cationic nature, akin to other common residues. Of particular note, we found that the affinity of protonated His for aromatic residues (via cation-π interactions) is greater than the affinity of neutral His for either cationic residues (also via cation-π interactions) or aromatic residues (via π-π interactions). Furthermore, His frequently engages in CH-π interactions, and notably, depending on its protonation state, we found that some instances of hydrogen bonding by His exhibit greater stability than is typical for interamino acid hydrogen bonds. The strength of the pH-dependent pairwise energies of His with aromatic residues is supported by the abundance of pairwise interactions with His of low and high predicted pKa values. Overall, our findings illustrate the contribution of His interactions to protein stability and its potential involvement in conformational changes despite its relatively low abundance in proteins.
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Affiliation(s)
- Rivka Calinsky
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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2
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Zaorska E, Malinska M. Cucurbit[7]uril-mediated Histidine Dimerization: Exploring the Structure and Binding Mechanism. Chemistry 2024; 30:e202302250. [PMID: 38055216 DOI: 10.1002/chem.202302250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/07/2023]
Abstract
Cucurbit[7,8]urils are known to form inclusion complexes with hydrophobic amino acids such as Trp, Tyr, Phe, and Met, as well as peptides containing these residues at the N-terminus. Despite their widespread use in protein purification, the affinity of histidine (His) for cucurbit[7,8]urils has not been extensively explored. In this study, X-ray diffraction experiments were conducted to investigate the binding of two histidine moieties to the cucurbit[7]uril (CB7) cavity, resulting in a network of π-π and hydrogen bonds. This assembly was found to induce a His pKa shift of ΔpKa=-4. Histidine weakly bound to CB7 or CB8; however, isothermal titration calorimetry revealed micromolar equilibrium dissociation constant values for CB7 and CB8 when bound to dipeptides containing His at the C-terminus. Conversely, dipeptides with His at the N-terminus exhibited millimolar values. Additionally, the His-Gly-Gly tripeptide formed a 2 : 1 complex with CB7. These findings suggest the potential use of histidine and histidine-containing tags in conjunction with CB7 for various biological applications.
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Affiliation(s)
- Ewelina Zaorska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Maura Malinska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
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3
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Tang C, Saielli G, Wang Y. Influence of Anion Species on Liquid-Liquid Phase Separation in [EMIm +][X -]/Benzene Mixtures. J Phys Chem B 2023. [PMID: 38031410 DOI: 10.1021/acs.jpcb.3c06205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
When a molar excess of benzene is mixed with an ionic liquid (IL), liquid-liquid phase separation may appear with a pure liquid phase almost composed of only benzene molecules separated from a liquid clathrate phase with benzene molecules dissolved in the IL. Our previous study (J. Phys. Chem. B, 124, 7929, 2020) on long-chain IL/benzene systems has concluded that benzene molecules, as planar nonpolar ones, majorly dissolve in the IL nonpolar domains consisting of cationic alkyl side chains. Nevertheless, the above mechanism is inadequate for explaining the experimental observations that benzene can also dissolve in IL systems with very short alkyl side chains. In this study, by molecular dynamics simulation of the [EMIm+][X-]/benzene mixtures with X- being Cl-, NO3-, PF6-, or Tf2N-, we still observe liquid-liquid phase separation of the pure benzene phase from a liquid clathrate (mixed IL/benzene) phase where benzene molecules are almost equally distributed near imidazolium rings through π-stacking or near alkyl side chains. The anion species strongly influences the solubility of benzene and the ratio of the two liquid phases via the alteration of anionic charge density, which tunes the strength of the electrostatic interaction among ions and thus the probability of benzene molecules interacting with both imidazolium rings and alkyl side chains: a larger anionic charge density corresponds to a lower solubility of benzene.
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Affiliation(s)
- Chenyu Tang
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Giacomo Saielli
- CNR Institute on Membrane Technology, Unit of Padova, Via Marzolo, Padova 1-35131, Italy
- Department of Chemical Sciences, University of Padova, Via Marzolo, Padova 1-35131, Italy
| | - Yanting Wang
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Theoretical Interdisciplinary Sciences, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, China
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4
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El Harrar T, Gohlke H. Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions. J Chem Inf Model 2023; 63:281-298. [PMID: 36520535 DOI: 10.1021/acs.jcim.2c01123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The interactions of amino acid side-chains confer diverse energetic contributions and physical properties to a protein's stability and function. Various computational tools estimate the effect of changing a given amino acid on the protein's stability based on parametrized (free) energy functions. When parametrized for the prediction of protein stability in water, such energy functions can lead to suboptimal results for other solvents, such as ionic liquids (IL), aqueous ionic liquids (aIL), or salt solutions. However, to our knowledge, no comprehensive data are available describing the energetic effects of aIL on intramolecular protein interactions. Here, we present the most comprehensive set of potential of mean force (PMF) profiles of pairwise protein-residue interactions to date, covering 50 relevant interactions in water, the two biotechnologically relevant aIL [BMIM/Cl] and [BMIM/TfO], and [Na/Cl]. These results are based on a cumulated simulation time of >1 ms. aIL and salt ions can weaken, but also strengthen, specific residue interactions by more than 3 kcal mol-1, depending on the residue pair, residue-residue configuration, participating ions, and concentration, necessitating considering such interactions specifically. These changes originate from a complex interplay of competitive or cooperative noncovalent ion-residue interactions, changes in solvent structural dynamics, or unspecific charge screening effects and occur at the contact distance but also at larger, solvent-separated distances. This data provide explanations at the atomistic and energetic levels for complex IL effects on protein stability and should help improve the prediction accuracies of computational tools that estimate protein stability based on (free) energy functions.
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Affiliation(s)
- Till El Harrar
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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5
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Wakchaure PD, Ganguly B. Unraveling the Role of π-Stacking Interactions in Ligand Binding to the Thiamine Pyrophosphate Riboswitch with High-level Quantum Chemical Calculations and Docking Study. J Phys Chem B 2022; 126:1076-1084. [PMID: 35089046 DOI: 10.1021/acs.jpcb.1c08587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The thiamine pyrophosphate (TPP) riboswitch has emerged as the new target for designing new ligands for antibiotic purpose. Binding of the natural ligand TPP to the TPP riboswitch causes downregulation of the genes responsible for its biosynthesis. We have reported the role of π-stacking energy contributions to ligand binding with a TPP riboswitch. In conjunction with the docking study, the higher-level quantum chemical calculations performed with the wB97XD and Def2TZVPP basis set in the aqueous phase revealed that the optimum ring size is crucial to attain the effective binding efficiency of ligands with a TPP riboswitch. The π-stacking energy contributions observed for the ligands studied are largely similar; however, the cases studied with higher π-stacking energies with larger rings have a weaker ability to displace the radiolabeled thiamine from the riboswitch. The EDA and NCI analyses suggest the role of larger dispersive interactions in stabilizing the π-stacking rings. The contribution from hydrogen-bonding interactions of the hydrogen-bond donor groups on the A ring augments the binding affinity of the ligand. This study sheds light on various factors that contribute to the design of new ligands for efficient binding with a TPP riboswitch and inhibition of gene expression.
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Affiliation(s)
- Padmaja D Wakchaure
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, Gujarat, India.,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201 002, India
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, Gujarat, India.,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201 002, India
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6
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Arrigoni F, Rizza F, Tisi R, De Gioia L, Zampella G, Bertini L. On the propagation of the OH radical produced by Cu-amyloid beta peptide model complexes. Insight from molecular modelling. Metallomics 2020; 12:1765-1780. [PMID: 33052996 DOI: 10.1039/d0mt00113a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Oxidative stress and metal dyshomeostasis are considered as crucial factors in the pathogenesis of Alzheimer's disease (AD). Indeed, transition metal ions such as Cu(ii) can generate Reactive Oxygen Species (ROS) via O2 Fenton-like reduction, catalyzed by Cu(ii) coordinated to the Amyloid beta (Aβ) peptide. Despite intensive effort, the mechanisms of ROS-induced molecular damage remain poorly understood. In the present paper, we investigate on the basis of molecular modelling computations the mechanism of OH radical propagation toward the Aβ peptide, starting from the end-product of OH radical generation by Cu(ii)·Aβ. We evaluate (i) the OH oxidative capacity, as well as the energetics of the possible Aβ oxidation target residues, by quantum chemistry Density Functional Theory (DFT) on coordination models of Cu(ii)/OH/Aβ and (ii) the motion of the OH˙ approaching the Aβ target residues by classical Molecular Dynamics (MD) on the full peptide Cu(ii)/OH/Aβ(1-16). The results show that the oxidative capacity of OH coordinated Cu(ii)Aβ is significantly lower than that of the free OH radical and that propagation toward Aβ Asp and His residues is favoured over Tyr residues. These results are discussed on the basis of the recent literature on in vitro Aβ metal-catalyzed oxidation and on the possible implications for the AD oxidative stress mechanism.
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Affiliation(s)
- Federica Arrigoni
- Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
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7
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Perumalla DS, Govind G, Anjukandi P. Folding‐Unfolding Dynamics of pH‐Assisted Structures of S‐Peptide. ChemistrySelect 2020. [DOI: 10.1002/slct.202000360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Gokul Govind
- Department of Chemistry Central University of Tamil Nadu Tiruvarur India
| | - Padmesh Anjukandi
- Department of Chemistry Indian Institute of Technology Palakkad India
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8
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Bootsma AN, Doney AC, Wheeler SE. Predicting the Strength of Stacking Interactions between Heterocycles and Aromatic Amino Acid Side Chains. J Am Chem Soc 2019; 141:11027-11035. [DOI: 10.1021/jacs.9b00936] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Andrea N. Bootsma
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Analise C. Doney
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Steven E. Wheeler
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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9
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Mayes ML, Perreault L. Probing the Nature of Noncovalent Interactions in Dimers of Linear Tyrosine-Based Dipeptides. ACS OMEGA 2019; 4:911-919. [PMID: 31459367 PMCID: PMC6648619 DOI: 10.1021/acsomega.8b02934] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/27/2018] [Indexed: 06/10/2023]
Abstract
Tyrosine-based dipeptides self-assemble to form higher order structures. To gain insights into the nature of intermolecular interactions contributing to the early stages of the self-assembly of aromatic dipeptides, we study the dimers of linear dityrosine (YY) and tryptophan-tyrosine (WY) using quantum-chemical methods with dispersion corrections and universal solvation model based on density in combination with energy decomposition and natural bond orbital (NBO) analyses. We find that hydrogen bonding is a dominant stabilizing force. The lowest energy structure for the linear YY dimer is characterized by Ocarboxyl···H(O)tyr. In contrast, the lowest energy dimer of linear WY is stabilized by Ocarboxyl···H(N)trp and πtyr···πtyr. The solvent plays a critical role as it can change the strength and nature of interactions. The lowest energy for linear WY dimer in acetone is stabilized by Ocarboxyl···H(O)tyr, πtrp···H(C), and πtrp···H(N). The ΔG of dimerization and stabilization energies of solvated dipeptides reveal that the dipeptide systems are more stable in the solvent phase than in gas phase. NBO confirms increased magnitudes for donor-acceptor interaction for the solvated dipeptides.
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10
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Hori Y, Chikai T, Ida T, Mizuno M. Local structure and hydrogen bond characteristics of imidazole molecules for proton conduction in acid and base proton-conducting composite materials. Phys Chem Chem Phys 2018; 20:10311-10318. [DOI: 10.1039/c7cp08396c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protons in composite materials of acidic polymers and imidazole molecules transport with rotational motion of imidazole in hydrogen bonds.
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Affiliation(s)
- Yuta Hori
- Chemistry Course, Division of Material Chemistry
- Graduate School of Natural Science and Technology
- Kanazawa University
- Kanazawa 920-1192
- Japan
| | - Takuma Chikai
- Chemistry Course, Division of Material Chemistry
- Graduate School of Natural Science and Technology
- Kanazawa University
- Kanazawa 920-1192
- Japan
| | - Tomonori Ida
- Chemistry Course, Division of Material Chemistry
- Graduate School of Natural Science and Technology
- Kanazawa University
- Kanazawa 920-1192
- Japan
| | - Motohiro Mizuno
- Chemistry Course, Division of Material Chemistry
- Graduate School of Natural Science and Technology
- Kanazawa University
- Kanazawa 920-1192
- Japan
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11
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Holzer C, Klopper W. Communication: Symmetry-adapted perturbation theory with intermolecular induction and dispersion energies from the Bethe–Salpeter equation. J Chem Phys 2017; 147:181101. [DOI: 10.1063/1.5007929] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Christof Holzer
- Institute of Physical Chemistry, Theoretical Chemistry Group, Karlsruhe Institute of Technology (KIT), KIT Campus South, P.O. Box 6980, D-76049 Karlsruhe, Germany
| | - Wim Klopper
- Institute of Physical Chemistry, Theoretical Chemistry Group, Karlsruhe Institute of Technology (KIT), KIT Campus South, P.O. Box 6980, D-76049 Karlsruhe, Germany
- Centre for Advanced Study (CAS) at The Norwegian Academy of Science and Letters, Drammensveien 78, N-0271 Oslo, Norway
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12
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Cabaleiro-Lago EM, Rodríguez-Otero J. σ-σ, σ-π, and π-π Stacking Interactions between Six-Membered Cyclic Systems. Dispersion Dominates and Electrostatics Commands. ChemistrySelect 2017. [DOI: 10.1002/slct.201700671] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Enrique M. Cabaleiro-Lago
- Facultade de Ciencias (Dpto. de Química Física); Universidade de Santiago de Compostela; Avda. Alfonso X El Sabio s/n 27002 Lugo, Galicia Spain
| | - Jesús Rodríguez-Otero
- CIQUS and Facultade de Química (Dpto. de Química Física); Universidade de Santiago de Compostela; 15782 Santiago de Compostela, Galicia Spain)
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13
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An Y, Doney AC, Andrade RB, Wheeler SE. Stacking Interactions between 9-Methyladenine and Heterocycles Commonly Found in Pharmaceuticals. J Chem Inf Model 2016; 56:906-14. [DOI: 10.1021/acs.jcim.5b00651] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yi An
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Analise C. Doney
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Rodrigo B. Andrade
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Steven E. Wheeler
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
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14
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Mullaney JC, Zaleski DP, Tew DP, Walker NR, Legon AC. Geometry of an Isolated Dimer of Imidazole Characterised by Rotational Spectroscopy and Ab Initio Calculations. Chemphyschem 2016; 17:1154-8. [DOI: 10.1002/cphc.201501179] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Indexed: 11/07/2022]
Affiliation(s)
- John C. Mullaney
- School of Chemistry, Bedson Building; Newcastle University; Newcastle upon Tyne, Tyne and Wear NE1 7RU UK
| | - Daniel P. Zaleski
- School of Chemistry, Bedson Building; Newcastle University; Newcastle upon Tyne, Tyne and Wear NE1 7RU UK
- Argonne National Laboratory; Chemical Sciences & Engineering; 9700 S. Cass Ave., Bldg. 200 Lemont IL 60439 USA
| | - David P. Tew
- School of Chemistry; University of Bristol; Bristol BS8 1TS UK
| | - Nicholas R. Walker
- School of Chemistry, Bedson Building; Newcastle University; Newcastle upon Tyne, Tyne and Wear NE1 7RU UK
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15
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Boussouf K, Khairat T, Prakash M, Komiha N, Chambaud G, Hochlaf M. Structure, Spectroscopy, and Bonding within the Zn(q+)-Imidazole(n) (q = 0, 1, 2; n = 1-4) Clusters and Implications for Zeolitic Imidazolate Frameworks and Zn-Enzymes. J Phys Chem A 2015; 119:11928-40. [PMID: 26565743 DOI: 10.1021/acs.jpca.5b09500] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using density functional theory (DFT) with dispersion correction and ab initio post Hartree-Fock methods, we treat the bonding, the structure, the stability, and the spectroscopy of the complexes between Zn(q+) and imidazole (Im), Zn(q+)Imn (where q = 0, 1 and 2; n = 1-4). These entities are subunits of zeolitic imidazolate frameworks (ZIFs) and Zn-enzymes, which possess relevant roles in industrial and biological domains, respectively. We also investigate the Imn (n = 2-4) clusters for comparison. For each species, we determine several new structures that were not found previously. Our calculations show a competition between atomic metal solvation, by either σ-type interactions or π-stacking type interaction, and proton transfer through hydrogen bonding (H-bonding) in charged species. This results in several geometrical environments around the metal. These are connected with structural properties and the functional role of Zn cation within ZIFs and Zn-enzymes. Moreover, we show that the Zn(2+)Imn subunits do not absorb in the visible domain, which may be related to the photostability of ZIFs. Our findings are important for the development of new applications of ZIFs and metalloenzymes.
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Affiliation(s)
- K Boussouf
- LS3ME-Equipe de Chimie Théorique et Modélisation, Faculté des Sciences Rabat, Université Mohamed V , Rabat, Morocco.,Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est , 5 bd Descartes, 77454 Marne-la-Vallée, France
| | - T Khairat
- LS3ME-Equipe de Chimie Théorique et Modélisation, Faculté des Sciences Rabat, Université Mohamed V , Rabat, Morocco
| | - M Prakash
- Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est , 5 bd Descartes, 77454 Marne-la-Vallée, France
| | - N Komiha
- LS3ME-Equipe de Chimie Théorique et Modélisation, Faculté des Sciences Rabat, Université Mohamed V , Rabat, Morocco
| | - G Chambaud
- Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est , 5 bd Descartes, 77454 Marne-la-Vallée, France
| | - M Hochlaf
- Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est , 5 bd Descartes, 77454 Marne-la-Vallée, France
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16
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Trachsel MA, Ottiger P, Frey HM, Pfaffen C, Bihlmeier A, Klopper W, Leutwyler S. Modeling the Histidine–Phenylalanine Interaction: The NH···π Hydrogen Bond of Imidazole·Benzene. J Phys Chem B 2015; 119:7778-90. [DOI: 10.1021/jp512766r] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Maria A. Trachsel
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Philipp Ottiger
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Hans-Martin Frey
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Chantal Pfaffen
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Angela Bihlmeier
- Institute of Physical
Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg
2, D-76131 Karlsruhe, Germany
| | - Wim Klopper
- Institute of Physical
Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg
2, D-76131 Karlsruhe, Germany
| | - Samuel Leutwyler
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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17
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Ahnen S, Hehn AS, Vogiatzis KD, Trachsel MA, Leutwyler S, Klopper W. Accurate computations of the structures and binding energies of the imidazole ⋯benzene and pyrrole ⋯benzene complexes. Chem Phys 2014. [DOI: 10.1016/j.chemphys.2014.05.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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Santos LA, da Cunha EFF, Freitas MP, Ramalho TC. Hydrophobic noncovalent interactions of inosine-phenylalanine: a theoretical model for investigating the molecular recognition of nucleobases. J Phys Chem A 2014; 118:5808-17. [PMID: 24814712 DOI: 10.1021/jp411230w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Understanding the molecular recognition process of nucleobases is one of the greatest challenges for both computational chemistry and biophysics fields. In fact, our results point out that it is a hard task to take into account the hydrophobic interactions, such as π-π and T-stacking interactions, by theoretical calculations using conventional force fields due to quantum effects of hyperconjugation and electronic correlation. In this line, our findings put in evidence that simple modifications in the Lennard-Jones potential can improve theoretical predictions in scenarios where hydrophobic interactions can drive the molecular recognition.
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Affiliation(s)
- Lucas A Santos
- Department of Chemistry, Federal University of Lavras , CEP 37200-000 Lavras, Minas Gerais Brazil
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19
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Karthikeyan S, Lee JY. Tuning the C–X…π interaction of benzene–chloroacetylene complexes by aromatic substitutions. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.04.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Kadam RU, Garg D, Schwartz J, Visini R, Sattler M, Stocker A, Darbre T, Reymond JL. CH-π "T-shape" interaction with histidine explains binding of aromatic galactosides to Pseudomonas aeruginosa lectin LecA. ACS Chem Biol 2013; 8:1925-30. [PMID: 23869965 DOI: 10.1021/cb400303w] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The galactose specific lectin LecA mediates biofilm formation in the opportunistic pathogen P. aeruginosa . The interaction between LecA and aromatic β-galactoside biofilm inhibitors involves an intermolecular CH-π T-shape interaction between C(ε1)-H of residue His50 in LecA and the aromatic ring of the galactoside aglycone. The generality of this interaction was tested in a diverse family of β-galactosides. LecA binding to aromatic β-galactosides (KD ∼ 8 μM) was consistently stronger than to aliphatic β-galactosides (KD ∼ 36 μM). The CH-π interaction was observed in the X-ray crystal structures of six different LecA complexes, with shorter than the van der Waals distances indicating productive binding. Related XH/cation/π-π interactions involving other residues were identified in complexes of aromatic glycosides with a variety of carbohydrate binding proteins such as concanavalin A. Exploiting such interactions might be generally useful in drug design against these targets.
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Affiliation(s)
- Rameshwar U. Kadam
- Department of Chemistry and
Biochemistry, University of Berne, Freiestrasse
3, 3012 Berne, Switzerland
| | - Divita Garg
- Institute of Structural Biology,
Helmholtz Zentrum München and Center for integrated Protein
Science Munich at Dept Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Julian Schwartz
- Department of Chemistry and
Biochemistry, University of Berne, Freiestrasse
3, 3012 Berne, Switzerland
| | - Ricardo Visini
- Department of Chemistry and
Biochemistry, University of Berne, Freiestrasse
3, 3012 Berne, Switzerland
| | - Michael Sattler
- Institute of Structural Biology,
Helmholtz Zentrum München and Center for integrated Protein
Science Munich at Dept Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Achim Stocker
- Department of Chemistry and
Biochemistry, University of Berne, Freiestrasse
3, 3012 Berne, Switzerland
| | - Tamis Darbre
- Department of Chemistry and
Biochemistry, University of Berne, Freiestrasse
3, 3012 Berne, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and
Biochemistry, University of Berne, Freiestrasse
3, 3012 Berne, Switzerland
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Chen H, Zhang Y, Ye C, Feng TT, Han JG. Insight into the binding modes and inhibition mechanisms of adamantyl-based 1,3-disubstituted urea inhibitors in the active site of the human soluble epoxide hydrolase. J Biomol Struct Dyn 2013; 32:1231-47. [DOI: 10.1080/07391102.2013.812981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Kellie JL, Wetmore SD. Selecting DFT methods for use in optimizations of enzyme active sites: applications to ONIOM treatments of DNA glycosylases. CAN J CHEM 2013. [DOI: 10.1139/cjc-2012-0506] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
When using a hybrid methodology to treat an enzymatic reaction, many factors contribute to selecting the method for the high-level region, which can be complicated by the presence of dispersion-driven interactions such as π–π stacking. In addition, the proper treatment of the reaction center often requires a large number of heavy atoms to be included in the high-level region, precluding the use of ab initio methods such as MP2 as well as large basis sets, in the optimization step. In the present work, popular DFT methods were tested to identify an appropriate functional for treating the high-level region in ONIOM optimizations of reactions catalyzed by nonmetalloenzymes. Eight different DFT methods (B3LYP, B97-2, MPW1K, MPWB1K, BB1K, B1B95, M06-2X, and ωB97X-D) in combination with four double-ζ quality Pople basis sets were tested for their ability to optimize noncovalent interactions (hydrogen bonding and π–π) and characterize reactions (proton transfer, SN2 hydrolysis, and unimolecular cleavage). Although the primary focus of this study is accurate structure determination, energetics were also examined at both the optimization level of theory, and with triple-ζ quality basis set and select (M06-2X or ωB97X-D) methods. If dispersion-driven interactions exist within the active site, then MPWB1K/6-31G(d,p) or M06-2X/6-31+G(d,p) are recommended for the optimization step with subsequent triple-ζ quality single-point energies. However, since dispersion-corrected functionals (M06-2X and ωB97X-D) generally require diffuse functions to yield appropriate geometries, the possible size of the high-level region is greatly limited with these methods. In contrast, if the model is large enough to recover steric constraints on π–π interactions, then B3LYP with a small basis set performs comparatively well for the optimization step and is significantly less computationally expensive. Interestingly, the functionals that afford the best geometries often do not yield the best energetics, which emphasizes the importance of structural benchmark studies.
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Affiliation(s)
- Jennifer L. Kellie
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada
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Mó O, Yáñez M, Alkorta I, Elguero J. Modulating the Strength of Hydrogen Bonds through Beryllium Bonds. J Chem Theory Comput 2012; 8:2293-300. [PMID: 26588962 DOI: 10.1021/ct300243b] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mutual influence between beryllium bonds and inter- or intramolecular hydrogen bonds (HBs) has been investigated at the B3LYP/6-311++G(3df,2p) level of theory, using the complexes between imidazole dimer and malonaldehyde with BeH2 and BeF2 as suitable model systems. Imidazole and its dimer form very strong beryllium bonds with both BeH2 and BeF2, accompanied by a significant geometry distortion of the Lewis acid. More importantly, we have found a clear cooperativity between these two noncovalent interactions, since the intermolecular HB between the two imidazole molecules in the dimer-BeX2 complex becomes much stronger than in the isolated dimer, whereas the beryllium bond becomes also stronger in the dimer-BeX2 complex, with respect to that found in the imidazole-BeX2 complex. The effects of beryllium bonds are also dramatic on the strength of intramolecular HBs. Depending on to which center the BeX2 is attached, the intramolecular HB becomes much stronger or much weaker. The first situation is found when the beryllium derivative is attached to the HB donor, whereas the second occurs if it is attached to the HB acceptor. The first effect can be so strong as to produce a spontaneous proton transfer, as it is actually the case of the malonaldehyde-BeF2 complex.
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Affiliation(s)
- Otilia Mó
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid , Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Manuel Yáñez
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid , Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC) , Juan de la Cierva, 3, 28006-Madrid, Spain
| | - José Elguero
- Instituto de Química Médica (CSIC) , Juan de la Cierva, 3, 28006-Madrid, Spain
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