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Wu J, Lv J, Zhao L, Zhao R, Gao T, Xu Q, Liu D, Yu Q, Ma F. Exploring the role of microbial proteins in controlling environmental pollutants based on molecular simulation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167028. [PMID: 37704131 DOI: 10.1016/j.scitotenv.2023.167028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/03/2023] [Accepted: 09/10/2023] [Indexed: 09/15/2023]
Abstract
Molecular simulation has been widely used to study microbial proteins' structural composition and dynamic properties, such as volatility, flexibility, and stability at the microscopic scale. Herein, this review describes the key elements of molecular docking and molecular dynamics (MD) simulations in molecular simulation; reviews the techniques combined with molecular simulation, such as crystallography, spectroscopy, molecular biology, and machine learning, to validate simulation results and bridge information gaps in the structure, microenvironmental changes, expression mechanisms, and intensity quantification; illustrates the application of molecular simulation, in characterizing the molecular mechanisms of interaction of microbial proteins with four different types of contaminants, namely heavy metals (HMs), pesticides, dyes and emerging contaminants (ECs). Finally, the review outlines the important role of molecular simulations in the study of microbial proteins for controlling environmental contamination and provides ideas for the application of molecular simulation in screening microbial proteins and incorporating targeted mutagenesis to obtain more effective contaminant control proteins.
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Affiliation(s)
- Jieting Wu
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Jin Lv
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resources & Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Ruofan Zhao
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Tian Gao
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, China
| | - Qi Xu
- PetroChina Fushun Petrochemical Company, Fushun 113000, China
| | - Dongbo Liu
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Qiqi Yu
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Fang Ma
- State Key Laboratory of Urban Water Resources & Environment, Harbin Institute of Technology, Harbin 150090, China.
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2
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Tekwani Movellan K, Wegstroth M, Overkamp K, Leonov A, Becker S, Andreas LB. Real-time tracking of drug binding to influenza A M2 reveals a high energy barrier. J Struct Biol X 2023; 8:100090. [PMID: 37363040 PMCID: PMC10285276 DOI: 10.1016/j.yjsbx.2023.100090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 05/18/2023] [Accepted: 06/02/2023] [Indexed: 06/28/2023] Open
Abstract
The drug Rimantadine binds to two different sites in the M2 protein from influenza A, a peripheral site and a pore site that is the primary site of efficacy. It remained enigmatic that pore binding did not occur in certain detergent micelles, and in particular incomplete binding was observed in a mixture of lipids selected to match the viral membrane. Here we show that two effects are responsible, namely changes in the protein upon pore binding that prevented detergent solubilization, and slow binding kinetics in the lipid samples. Using 55-100 kHz magic-angle spinning NMR, we characterize kinetics of drug binding in three different lipid environments: DPhPC, DPhPC with cholesterol and viral mimetic membrane lipid bilayers. Slow pharmacological binding kinetics allowed the characterization of spectral changes associated with non-specific binding to the protein periphery in the kinetically trapped pore-apo state. Resonance assignments were determined from a set of proton-detected 3D spectra. Chemical shift changes associated with functional binding in the pore of M2 were tracked in real time in order to estimate the activation energy. The binding kinetics are affected by pH and the lipid environment and in particular cholesterol. We found that the imidazole-imidazole hydrogen bond at residue histidine 37 is a stable feature of the protein across several lipid compositions. Pore binding breaks the imidazole-imidazole hydrogen bond and limits solubilization in DHPC detergent.
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3
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Qian Y, Wu Y, Qiu S, He X, Liu Y, Kong X, Tian W, Jiang L, Wen L. A Bioinspired Free‐Standing 2D Crown‐Ether‐Based Polyimine Membrane for Selective Proton Transport. Angew Chem Int Ed Engl 2023. [DOI: 10.1002/ange.202300167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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4
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Lai Z, Shen M, Shen Y, Ye YX, Zhu F, Xu J, Ouyang G. Hydrogen bond networks in gas-phase complex anions. RSC Adv 2022; 12:29137-29142. [PMID: 36320744 PMCID: PMC9558071 DOI: 10.1039/d2ra05029c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/02/2022] [Indexed: 11/05/2022] Open
Abstract
Hydrogen bond networks (HBNs) have piqued the interest of the scientific community due to their crucial roles in nature. However, HBNs that are isolated from complicated backgrounds for unraveling their characteristics are still scarce. Herein, we propose that HBNs exist in complex anions formed between α-cyclodextrin (α-CD) and four benzoic acids (RBAs) in the gas phase. The complex anions are facilely extracted from solutions via the electrospray ionization technique, and subsequently activated through collision for the investigation of their transition dynamics. It is revealed that the generation of deprotonated α-CD and neutral RBAs is the unexpected dominant dissociation pathway for all the four complex anions, and the complex anions formed from more acidic RBAs exhibit higher stabilities. These dissociation results are successfully explained by the cooperative stretching dynamics of the proposed HBNs that are formed involving the intramolecular HBN of α-CD and the intermolecular hydrogen bonds (HBs) between α-CD and RBAs. Furthermore, the rarely observed low barrier HBs (LBHBs) are suggested to be present in the HBNs. It is believed that the present complex anions can serve as a facilely accessible and informative model for studying HBNs in the future. Hydrogen bond networks and low barrier hydrogen bonds are demonstrated in the complex anions formed between α-cyclodextrin and benzoic acids.![]()
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Affiliation(s)
- Zhisheng Lai
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China
| | - Minhui Shen
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China
| | - Yong Shen
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China
| | - Yu-Xin Ye
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China
| | - Fang Zhu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China
| | - Jianqiao Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China
| | - Gangfeng Ouyang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China,College of Chemistry, Center of Advanced Analysis and Gene Sequencing, Zhengzhou UniversityZhengzhou450001China,Guangdong Provincial Key Laboratory of Emergency Testing for Dangerous Chemicals, Guangdong Institute of Analysis (China National Analytical Center Guangzhou), Guangdong Academy of SciencesGuangzhou510070China
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5
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Lazaratos M, Siemers M, Brown LS, Bondar AN. Conserved hydrogen-bond motifs of membrane transporters and receptors. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183896. [PMID: 35217000 DOI: 10.1016/j.bbamem.2022.183896] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/04/2022] [Accepted: 02/16/2022] [Indexed: 01/18/2023]
Abstract
Membrane transporters and receptors often rely on conserved hydrogen bonds to assemble transient paths for ion transfer or long-distance conformational couplings. For transporters and receptors that use proton binding and proton transfer for function, inter-helical hydrogen bonds of titratable protein sidechains that could change protonation are of central interest to formulate hypotheses about reaction mechanisms. Knowledge of hydrogen bonds common at sites of potential interest for proton binding could thus inform and guide studies on functional mechanisms of protonation-coupled membrane proteins. Here we apply graph-theory approaches to identify hydrogen-bond motifs of carboxylate and histidine sidechains in a large data set of static membrane protein structures. We find that carboxylate-hydroxyl hydrogen bonds are present in numerous structures of the dataset, and can be part of more extended H-bond clusters that could be relevant to conformational coupling. Carboxylate-carboxyamide and imidazole-imidazole hydrogen bonds are represented in comparably fewer protein structures of the dataset. Atomistic simulations on two membrane transporters in lipid membranes suggest that many of the hydrogen bond motifs present in static protein structures tend to be robust, and can be part of larger hydrogen-bond clusters that recruit additional hydrogen bonds.
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Affiliation(s)
- Michalis Lazaratos
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
| | - Malte Siemers
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
| | - Leonid S Brown
- University of Guelph, Department of Physics, 50 Stone Road E., Guelph, Ontario N1G 2W1, Canada
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany; University of Bucharest, Faculty of Physics, Atomiștilor 405, Măgurele 077125, Romania; Forschungszentrum Jülich, Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Wilhelm-Johnen Straße, 52428 Jülich, Germany.
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6
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Le Marchand T, Schubeis T, Bonaccorsi M, Paluch P, Lalli D, Pell AJ, Andreas LB, Jaudzems K, Stanek J, Pintacuda G. 1H-Detected Biomolecular NMR under Fast Magic-Angle Spinning. Chem Rev 2022; 122:9943-10018. [PMID: 35536915 PMCID: PMC9136936 DOI: 10.1021/acs.chemrev.1c00918] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Indexed: 02/08/2023]
Abstract
Since the first pioneering studies on small deuterated peptides dating more than 20 years ago, 1H detection has evolved into the most efficient approach for investigation of biomolecular structure, dynamics, and interactions by solid-state NMR. The development of faster and faster magic-angle spinning (MAS) rates (up to 150 kHz today) at ultrahigh magnetic fields has triggered a real revolution in the field. This new spinning regime reduces the 1H-1H dipolar couplings, so that a direct detection of 1H signals, for long impossible without proton dilution, has become possible at high resolution. The switch from the traditional MAS NMR approaches with 13C and 15N detection to 1H boosts the signal by more than an order of magnitude, accelerating the site-specific analysis and opening the way to more complex immobilized biological systems of higher molecular weight and available in limited amounts. This paper reviews the concepts underlying this recent leap forward in sensitivity and resolution, presents a detailed description of the experimental aspects of acquisition of multidimensional correlation spectra with fast MAS, and summarizes the most successful strategies for the assignment of the resonances and for the elucidation of protein structure and conformational dynamics. It finally outlines the many examples where 1H-detected MAS NMR has contributed to the detailed characterization of a variety of crystalline and noncrystalline biomolecular targets involved in biological processes ranging from catalysis through drug binding, viral infectivity, amyloid fibril formation, to transport across lipid membranes.
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Affiliation(s)
- Tanguy Le Marchand
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Tobias Schubeis
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Marta Bonaccorsi
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
- Department
of Biochemistry and Biophysics, Stockholm
University, Svante Arrhenius
väg 16C SE-106 91, Stockholm, Sweden
| | - Piotr Paluch
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Daniela Lalli
- Dipartimento
di Scienze e Innovazione Tecnologica, Università
del Piemonte Orientale “A. Avogadro”, Viale Teresa Michel 11, 15121 Alessandria, Italy
| | - Andrew J. Pell
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
- Department
of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Svante Arrhenius väg 16 C, SE-106
91 Stockholm, Sweden
| | - Loren B. Andreas
- Department
for NMR-Based Structural Biology, Max-Planck-Institute
for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Kristaps Jaudzems
- Latvian
Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006 Latvia
- Faculty
of Chemistry, University of Latvia, Jelgavas 1, Riga LV-1004, Latvia
| | - Jan Stanek
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Guido Pintacuda
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
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7
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Salnikov E, Aisenbrey C, Bechinger B. Lipid saturation and head group composition have a pronounced influence on the membrane insertion equilibrium of amphipathic helical polypeptides. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183844. [PMID: 34954200 DOI: 10.1016/j.bbamem.2021.183844] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 10/19/2022]
Abstract
The histidine-rich peptides of the LAH4 family were designed using cationic antimicrobial peptides such as magainin and PGLa as templates. The LAH4 amphipathic helical sequences exhibit a multitude of interesting biological properties such as antimicrobial activity, cell penetration of a large variety of cargo and lentiviral transduction enhancement. The parent peptide associates with lipid bilayers where it changes from an orientation along the membrane interface into a transmembrane configuration in a pH-dependent manner. Here we show that LAH4 adopts a transmembrane configuration in fully saturated DMPC membranes already at pH 3.5, i.e. much below the pKa of the histidines whereas the transition pH in POPC correlates closely with histidine neutralization. In contrast in POPG membranes the in-planar configuration is stabilized by about one pH unit. The differences in pH can be converted into energetic contributions for the in-plane to transmembrane transition equilibrium, where the shift in the transition pH due to lipid saturation corresponds to energies which are otherwise obtained by the exchange of several cationic with hydrophobic residues. A similar dependence on lipid saturation has also been observed when the PGLa and magainin antimicrobial peptides interact within lipid bilayers suggesting that the quantitative evaluation presented in this paper also applies to other membrane polypeptides.
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Affiliation(s)
- Evgeniy Salnikov
- University of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics and NMR, Strasbourg, France
| | - Christopher Aisenbrey
- University of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics and NMR, Strasbourg, France
| | - Burkhard Bechinger
- University of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics and NMR, Strasbourg, France; Institut Universitaire de France, France.
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8
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Lu J, Li X, Yuan S, Wang Y, Sun H, Weng W, Shi Y, Wang X, Huang K, Sun X, Wu T. Identification, Synthesis, and Comprehension of an Imidazole N-3 Regioisomeric Impurity of Olmesartan Medoxomil Key Intermediate. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.2c00002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jianwu Lu
- Department of Natural Medicine, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
- State Key Lab of New Drug & Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Shanghai 201203, China
| | - Xiao Li
- State Key Lab of New Drug & Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Shanghai 201203, China
| | - Shun Yuan
- State Key Lab of New Drug & Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Shanghai 201203, China
| | - Yinquan Wang
- State Key Lab of New Drug & Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Shanghai 201203, China
| | - Han Sun
- State Key Lab of New Drug & Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Shanghai 201203, China
| | - Weizhao Weng
- Department of Natural Medicine, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
- State Key Lab of New Drug & Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Shanghai 201203, China
| | - Yinfei Shi
- State Key Lab of New Drug & Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Shanghai 201203, China
| | - Xiaoxu Wang
- State Key Lab of New Drug & Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Shanghai 201203, China
| | - Kongcheng Huang
- State Key Lab of New Drug & Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Shanghai 201203, China
| | - Xun Sun
- Department of Natural Medicine, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Taizhi Wu
- Department of Natural Medicine, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
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9
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Wright AK, Paulino J, Cross TA. Emulating Membrane Protein Environments─How Much Lipid Is Required for a Native Structure: Influenza S31N M2. J Am Chem Soc 2022; 144:2137-2148. [PMID: 35089701 DOI: 10.1021/jacs.1c10174] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This report investigates the homotetrameric membrane protein structure of the S31N M2 protein from Influenza A virus in the presence of a high molar ratio of lipid. The structured regions of this protein include a single transmembrane helix and an amphipathic helix. Two structures of the S31N M2 conductance domain from Influenza A virus have been deposited in the Protein Data Bank (PDB). These structures present different symmetries about the channel main axis. We present new magic angle spinning and oriented sample solid-state NMR spectroscopic data for S31N M2 in liquid crystalline lipid bilayers using protein tetramer:lipid molar ratios ranging from 1:120 to 1:240. The data is consistent with an essentially 4-fold-symmetric structure very similar to the M2 WT structure that also has a single conformation for the four monomers, except at the His37 and Trp41 functional sites when characterized in samples with a high molar ratio of lipid. While detergent solubilization is well recognized today as a nonideal environment for small membrane proteins, here we discuss the influence of a high lipid to protein ratio for samples of the S31N M2 protein to stabilize an essentially 4-fold-symmetric conformation of the M2 membrane protein. While it is generally accepted that the chemical and physical properties of the native environment of membrane proteins needs to be reproduced judiciously to achieve the native protein structure, here we show that not only the character of the emulated membrane environment is important but also the abundance of the environment is important for achieving the native structure. This is a critical finding as a membrane protein spectroscopist's goal is always to generate a sample with the highest possible protein sensitivity while obtaining spectra of the native-like structure.
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Affiliation(s)
- Anna K Wright
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, United States.,National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Joana Paulino
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, United States.,National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Timothy A Cross
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, United States.,Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States.,National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
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10
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Bondar AN. Mechanisms of long-distance allosteric couplings in proton-binding membrane transporters. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 128:199-239. [PMID: 35034719 DOI: 10.1016/bs.apcsb.2021.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Membrane transporters that use proton binding and proton transfer for function couple local protonation change with changes in protein conformation and water dynamics. Changes of protein conformation might be required to allow transient formation of hydrogen-bond networks that bridge proton donor and acceptor pairs separated by long distances. Inter-helical hydrogen-bond networks adjust rapidly to protonation change, and ensure rapid response of the protein structure and dynamics. Membrane transporters with known three-dimensional structures and proton-binding groups inform on general principles of protonation-coupled protein conformational dynamics. Inter-helical hydrogen bond motifs between proton-binding carboxylate groups and a polar sidechain are observed in unrelated membrane transporters, suggesting common principles of coupling protonation change with protein conformational dynamics.
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Affiliation(s)
- Ana-Nicoleta Bondar
- University of Bucharest, Faculty of Physics, Măgurele, Romania; Forschungszentrum Jülich, Institute of Computational Biomedicine, Jülich, Germany.
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11
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Aledavood E, Selmi B, Estarellas C, Masetti M, Luque FJ. From Acid Activation Mechanisms of Proton Conduction to Design of Inhibitors of the M2 Proton Channel of Influenza A Virus. Front Mol Biosci 2022; 8:796229. [PMID: 35096969 PMCID: PMC8795881 DOI: 10.3389/fmolb.2021.796229] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/24/2021] [Indexed: 11/26/2022] Open
Abstract
With an estimated 1 billion people affected across the globe, influenza is one of the most serious health concerns worldwide. Therapeutic treatments have encompassed a number of key functional viral proteins, mainly focused on the M2 proton channel and neuraminidase. This review highlights the efforts spent in targeting the M2 proton channel, which mediates the proton transport toward the interior of the viral particle as a preliminary step leading to the release of the fusion peptide in hemagglutinin and the fusion of the viral and endosomal membranes. Besides the structural and mechanistic aspects of the M2 proton channel, attention is paid to the challenges posed by the development of efficient small molecule inhibitors and the evolution toward novel ligands and scaffolds motivated by the emergence of resistant strains.
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Affiliation(s)
- Elnaz Aledavood
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Institut de Biomedicina and Institut de Química Teòrica i Computacional, University of Barcelona, Barcelona, Spain
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum – Università di Bologna, Bologna, Italy
| | - Beatrice Selmi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum – Università di Bologna, Bologna, Italy
| | - Carolina Estarellas
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Institut de Biomedicina and Institut de Química Teòrica i Computacional, University of Barcelona, Barcelona, Spain
- *Correspondence: Carolina Estarellas, ; Matteo Masetti, ; F. Javier Luque,
| | - Matteo Masetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum – Università di Bologna, Bologna, Italy
- *Correspondence: Carolina Estarellas, ; Matteo Masetti, ; F. Javier Luque,
| | - F. Javier Luque
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Institut de Biomedicina and Institut de Química Teòrica i Computacional, University of Barcelona, Barcelona, Spain
- *Correspondence: Carolina Estarellas, ; Matteo Masetti, ; F. Javier Luque,
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12
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Barbosa GD, Bara JE, Weinman ST, Turner CH. Molecular aspects of temperature swing solvent extraction for brine desalination using imidazole-based solvents. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2021.116866] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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13
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Kratochvil HT, Newberry RW, Mensa B, Mravic M, DeGrado WF. Spiers Memorial Lecture: Analysis and de novo design of membrane-interactive peptides. Faraday Discuss 2021; 232:9-48. [PMID: 34693965 PMCID: PMC8979563 DOI: 10.1039/d1fd00061f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Membrane-peptide interactions play critical roles in many cellular and organismic functions, including protection from infection, remodeling of membranes, signaling, and ion transport. Peptides interact with membranes in a variety of ways: some associate with membrane surfaces in either intrinsically disordered conformations or well-defined secondary structures. Peptides with sufficient hydrophobicity can also insert vertically as transmembrane monomers, and many associate further into membrane-spanning helical bundles. Indeed, some peptides progress through each of these stages in the process of forming oligomeric bundles. In each case, the structure of the peptide and the membrane represent a delicate balance between peptide-membrane and peptide-peptide interactions. We will review this literature from the perspective of several biologically important systems, including antimicrobial peptides and their mimics, α-synuclein, receptor tyrosine kinases, and ion channels. We also discuss the use of de novo design to construct models to test our understanding of the underlying principles and to provide useful leads for pharmaceutical intervention of diseases.
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Affiliation(s)
- Huong T Kratochvil
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Robert W Newberry
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Bruk Mensa
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Marco Mravic
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
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14
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Kolokouris D, Kalenderoglou IE, Kolocouris A. Inside and Out of the Pore: Comparing Interactions and Molecular Dynamics of Influenza A M2 Viroporin Complexes in Standard Lipid Bilayers. J Chem Inf Model 2021; 61:5550-5568. [PMID: 34714655 DOI: 10.1021/acs.jcim.1c00264] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ion channels located at viral envelopes (viroporins) have a critical function for the replication of infectious viruses and are important drug targets. Over the last decade, the number and duration of molecular dynamics (MD) simulations of the influenza A M2 ion channel owing to the increased computational efficiency. Here, we aimed to define the system setup and simulation conditions for the correct description of the protein-pore and the protein-lipid interactions for influenza A M2 in comparison with experimental data. We performed numerous MD simulations of the influenza A M2 protein in complex with adamantane blockers in standard lipid bilayers using OPLS2005 and CHARMM36 (C36) force fields. We explored the effect of varying the M2 construct (M2(22-46) and M2(22-62)), the lipid buffer size and type (stiffer DMPC or softer POPC with or without 20% cholesterol), the simulation time, the H37 protonation site (Nδ or Νε), the conformational state of the W41 channel gate, and M2's cholesterol binding sites (BSs). We report that the 200 ns MD with M2(22-62) (having Nε Η37) in the 20 Å lipid buffer with the C36 force field accurately describe: (a) the M2 pore structure and interactions inside the pore, that is, adamantane channel blocker location, water clathrate structure, and water or chloride anion blockage/passage from the M2 pore in the presence of a channel blocker and (b) interactions between M2 and the membrane environment as reflected by the calculation of the M2 bundle tilt, folding of amphipathic helices, and cholesterol BSs. Strikingly, we also observed that the C36 1 μs MD simulations using M2(22-62) embedded in a 20 Å POPC:cholesterol (5:1) scrambled membrane produced frequent interactions with cholesterol, which when combined with computational kinetic analysis, revealed the experimentally observed BSs of cholesterol and suggested three similarly long-interacting positions in the top leaflet that have previously not been observed experimentally. These findings promise to be useful for other viroporin systems.
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Affiliation(s)
- Dimitrios Kolokouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
| | - Iris E Kalenderoglou
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
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15
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Simultaneous determination of multiple coupling networks by high-resolution 2D J-edited NMR spectroscopy. Anal Chim Acta 2021; 1185:339055. [PMID: 34711310 DOI: 10.1016/j.aca.2021.339055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 09/10/2021] [Accepted: 09/11/2021] [Indexed: 11/24/2022]
Abstract
J coupling constitutes an important NMR parameter for molecular-level composition analysis and conformation elucidation. Dozens of J-based approaches have been exploited for J coupling measurement and coupling network determination, however, they are generally imposed to insufficient spectral resolution to resolve crowded NMR resonances and low measurement efficiency that a single experiment records one J coupling network. Herein, we propose a general NMR method to collect high-resolution 2D J-edited NMR spectra, which are characterized with advantages of pure absorptive lineshapes, decoupled chemical shift dimension, as well as eliminated axial peaks, thus facilitating J coupling partner assignments and J coupling constant measurements. More meaningfully, this protocol allows simultaneous determination of multiple coupling networks for highly efficient multiplet analyses via addressing multiple protons within one single experiment. Additionally, another variant is proposed for high-resolution applications under adverse magnetic field conditions. Therefore, this study provides a useful NMR protocol for configurational and structural studies with extensive applications in chemistry, biology, and material science.
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16
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Movellan KT, Dervişoğlu R, Becker S, Andreas LB. Porengebundenes Wasser an der Schlüsselaminosäure Histidin‐37 in Influenza A M2. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kumar Tekwani Movellan
- NMR-basierte Strukturbiologie Max-Planck-Institut für biophysikalische Chemie Am Faßberg 11 Göttingen 37077 Deutschland
| | - Rıza Dervişoğlu
- NMR-basierte Strukturbiologie Max-Planck-Institut für biophysikalische Chemie Am Faßberg 11 Göttingen 37077 Deutschland
| | - Stefan Becker
- NMR-basierte Strukturbiologie Max-Planck-Institut für biophysikalische Chemie Am Faßberg 11 Göttingen 37077 Deutschland
| | - Loren B. Andreas
- NMR-basierte Strukturbiologie Max-Planck-Institut für biophysikalische Chemie Am Faßberg 11 Göttingen 37077 Deutschland
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17
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Movellan KT, Dervişoğlu R, Becker S, Andreas LB. Pore-Bound Water at the Key Residue Histidine 37 in Influenza A M2. Angew Chem Int Ed Engl 2021; 60:24075-24079. [PMID: 34477305 PMCID: PMC8597138 DOI: 10.1002/anie.202103955] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 08/02/2021] [Indexed: 01/14/2023]
Abstract
Atomic details of structured water molecules are indispensable to understand the thermodynamics of important biological processes including the proton conduction mechanism of the M2 protein. Despite the expectation of structured water molecules based on crystal structures of Influenza A M2, only two water populations have been observed by NMR in reconstituted lipid bilayer samples. These are the bulk‐ and lipid‐associated water populations typically seen in membrane samples. Here, we detect a bound water molecule at a chemical shift of 11 ppm, located near the functional histidine 37 residue in the M2 conductance domain, which comprises residues 18 to 60. Combining 100 kHz magic‐angle spinning NMR, dynamic nuclear polarization and density functional theory calculations, we show that the bound water forms a hydrogen bond to the δ1 nitrogen of histidine 37.
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Affiliation(s)
- Kumar Tekwani Movellan
- NMR based Structural Biology, Max Planck Institute for biophysical Chemistry, Am Fassberg 11, Göttingen, 37077, Germany
| | - Rıza Dervişoğlu
- NMR based Structural Biology, Max Planck Institute for biophysical Chemistry, Am Fassberg 11, Göttingen, 37077, Germany
| | - Stefan Becker
- NMR based Structural Biology, Max Planck Institute for biophysical Chemistry, Am Fassberg 11, Göttingen, 37077, Germany
| | - Loren B Andreas
- NMR based Structural Biology, Max Planck Institute for biophysical Chemistry, Am Fassberg 11, Göttingen, 37077, Germany
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18
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Porat-Dahlerbruch G, Goldbourt A, Polenova T. Virus Structures and Dynamics by Magic-Angle Spinning NMR. Annu Rev Virol 2021; 8:219-237. [PMID: 34586870 DOI: 10.1146/annurev-virology-011921-064653] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Techniques for atomic-resolution structural biology have evolved during the past several decades. Breakthroughs in instrumentation, sample preparation, and data analysis that occurred in the past decade have enabled characterization of viruses with an unprecedented level of detail. Here we review the recent advances in magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy for structural analysis of viruses and viral assemblies. MAS NMR is a powerful method that yields information on 3D structures and dynamics in a broad range of experimental conditions. After a brief introduction, we discuss recent structural and functional studies of several viruses investigated with atomic resolution at various levels of structural organization, from individual domains of a membrane protein reconstituted into lipid bilayers to virus-like particles and intact viruses. We present examples of the unique information revealed by MAS NMR about drug binding, conduction mechanisms, interactions with cellular host factors, and DNA packaging in biologically relevant environments that are inaccessible by other methods.
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Affiliation(s)
- Gal Porat-Dahlerbruch
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA;
| | - Amir Goldbourt
- School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA; .,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
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19
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Zhan H, Zhan F, Gao C, Lin E, Huang C, Lin X, Huang Y, Chen Z. Multiplet analysis by strong-coupling-artifact-suppression 2D J-resolved NMR spectroscopy. J Chem Phys 2021; 155:034202. [PMID: 34293873 DOI: 10.1063/5.0056999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Benefitting from the capability of recording scalar (J) couplings and bonding information, 2D J-resolved NMR spectroscopy constitutes an important tool for molecular structure analysis and mixture component identification. Unfortunately, conventional 2D J-resolved experiments generally encounter challenges of insufficient spectral resolution and strong coupling artifacts. In this study, a general NMR approach is exploited to record absorption-mode artifact-free 2D J-resolved spectra. This proposal adopts the advanced triple-spin-echo pure shift yielded by chirp excitation element to eliminate J coupling splittings and preserve chemical shifts along the F2 dimension, and it additionally utilizes the echo-train J acquisition to reveal the multiplet structure along the F1 dimension in accelerated experimental acquisition. Thus, it permits one to extract multiplet structure information from crowded spectral regions in one-shot experiments, with considerable resolution advantage resulting from completely decoupling F2 dimension and absorption-mode presentation, thus facilitating analysis on complex samples. More importantly, this method grants the superior performance on suppressing strong coupling artifacts, which have been affirmed by experiments on a series of chemical samples. As a consequence, this proposed method serves as a useful tool for J coupling measurements and multiplet structure analyses on complex samples that contain crowded NMR resonances and strong coupling spin systems, and it may exhibit broad application potentials in fields of physics, chemistry, and medical science, among others.
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Affiliation(s)
- Haolin Zhan
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Fengqi Zhan
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Cunyuan Gao
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Enping Lin
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Chengda Huang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Xiaoqing Lin
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Yuqing Huang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Zhong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
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20
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Bondar AN. Proton-Binding Motifs of Membrane-Bound Proteins: From Bacteriorhodopsin to Spike Protein S. Front Chem 2021; 9:685761. [PMID: 34136464 PMCID: PMC8203321 DOI: 10.3389/fchem.2021.685761] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/18/2021] [Indexed: 11/13/2022] Open
Abstract
Membrane-bound proteins that change protonation during function use specific protein groups to bind and transfer protons. Knowledge of the identity of the proton-binding groups is of paramount importance to decipher the reaction mechanism of the protein, and protonation states of prominent are studied extensively using experimental and computational approaches. Analyses of model transporters and receptors from different organisms, and with widely different biological functions, indicate common structure-sequence motifs at internal proton-binding sites. Proton-binding dynamic hydrogen-bond networks that are exposed to the bulk might provide alternative proton-binding sites and proton-binding pathways. In this perspective article I discuss protonation coupling and proton binding at internal and external carboxylate sites of proteins that use proton transfer for function. An inter-helical carboxylate-hydroxyl hydrogen-bond motif is present at functionally important sites of membrane proteins from archaea to the brain. External carboxylate-containing H-bond clusters are observed at putative proton-binding sites of protonation-coupled model proteins, raising the question of similar functionality in spike protein S.
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Affiliation(s)
- Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
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21
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Siemers M, Bondar AN. Interactive Interface for Graph-Based Analyses of Dynamic H-Bond Networks: Application to Spike Protein S. J Chem Inf Model 2021; 61:2998-3014. [PMID: 34133162 DOI: 10.1021/acs.jcim.1c00306] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Dynamic hydrogen-bond networks are key determinants of protein conformational dynamics. In the case of macromolecular protein complexes, which can have a large number of hydrogen bonds giving rise to extensive hydrogen-bond networks, efficient algorithms are required to analyze interactions that could be important for the dynamics and biological function of the complex. We present here a highly efficient, standalone interface designed for analyses of dynamical hydrogen-bond networks of biomolecules and macromolecular complexes. To facilitate a comprehensive description of protein dynamics, the interface includes analyses of hydrophobic interactions. We illustrate the usefulness and workflow of the interface by dissecting the dynamics of the ectodomain of SARS-CoV-2 protein S in its closed conformation. We find that protein S contains numerous local clusters of dynamic hydrogen bonds and identify hydrogen bonds that are sampled persistently. The receptor binding domain of the spike protein hosts only a handful of persistent hydrogen-bond clusters, suggesting structural plasticity. Our data analysis interface is released here for open use.
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Affiliation(s)
- Malte Siemers
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
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22
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Bonaccorsi M, Le Marchand T, Pintacuda G. Protein structural dynamics by Magic-Angle Spinning NMR. Curr Opin Struct Biol 2021; 70:34-43. [PMID: 33915352 DOI: 10.1016/j.sbi.2021.02.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 02/20/2021] [Indexed: 02/07/2023]
Abstract
Magic-Angle Spinning (MAS) Nuclear Magnetic Resonance (NMR) is a fast-developing technique, capable of complementing solution NMR, X-ray crystallography, and electron microscopy for the biophysical characterization of microcrystalline, poorly crystalline or disordered protein samples, such as enzymes, biomolecular assemblies, membrane-embedded systems or fibrils. Beyond structures, MAS NMR is an ideal tool for the investigation of dynamics, since it is unique in its ability to distinguish static and dynamic disorder, and to characterize not only amplitudes but also timescales of motion. Building on seminal work on model proteins, the technique is now ripe for widespread application in structural biology. This review briefly summarizes the recent evolutions in biomolecular MAS NMR and accounts for the growing number of systems where this spectroscopy has provided a description of conformational dynamics over the very last few years.
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Affiliation(s)
- Marta Bonaccorsi
- Université de Lyon, Centre de RMN à Très hauts Champs, UMR 5280 (CNRS / Ecole Normale Supérieure de Lyon / Université Claude Bernard Lyon 1), 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Tanguy Le Marchand
- Université de Lyon, Centre de RMN à Très hauts Champs, UMR 5280 (CNRS / Ecole Normale Supérieure de Lyon / Université Claude Bernard Lyon 1), 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Guido Pintacuda
- Université de Lyon, Centre de RMN à Très hauts Champs, UMR 5280 (CNRS / Ecole Normale Supérieure de Lyon / Université Claude Bernard Lyon 1), 5 rue de la Doua, F-69100, Villeurbanne, France.
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23
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Mechanism and Kinetics of Copper Complexes Binding to the Influenza A M2 S31N and S31N/G34E Channels. Biophys J 2020; 120:168-177. [PMID: 33248127 DOI: 10.1016/j.bpj.2020.11.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/21/2020] [Accepted: 11/13/2020] [Indexed: 01/13/2023] Open
Abstract
Copper(II) is known to bind in the influenza virus His37 cluster in the homotetrameric M2 proton channel and block the proton current needed for uncoating. Copper complexes based on iminodiacetate also block the M2 proton channel and show reduced cytotoxicity and zebrafish-embryo toxicity. In voltage-clamp oocyte studies using the ubiquitous amantadine-insensitive M2 S31N variant, the current block showed fast and slow phases, in contrast to the single phase found for amantadine block of wild-type M2. Here, we evaluate the mechanism of block by copper adamantyl iminodiacitate and copper cyclooctyl iminodiacitate complexes and address whether the complexes can coordinate with one or more of the His37 imidazoles. The current traces were fitted to parametrized master equations. The energetics of binding and the rate constants suggest that the first step is copper complex binding within the channel, and the slow step in the current block is the formation of a Cu-histidine coordination complex. Solution-phase isothermal titration calorimetry and density functional theory (DFT) calculations indicate that imidazole binds to the copper complexes. Structural optimization using DFT reveals that the complexes fit inside the channel and project the Cu(II) toward the His37 cluster, allowing one imidazole to form a coordination complex with Cu(II). Electrophysiology and DFT studies also show that the complexes block the G34E amantadine-resistant mutant despite some crowding in the binding site by the glutamates.
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24
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Wang Y, Zhang WX, Xi Z. Carbodiimide-based synthesis of N-heterocycles: moving from two classical reactive sites to chemical bond breaking/forming reaction. Chem Soc Rev 2020; 49:5810-5849. [PMID: 32658233 DOI: 10.1039/c9cs00478e] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Carbodiimides are a unique class of heterocumulene compounds that display distinctive chemical properties. The rich chemistry of carbodiimides has drawn increasing attention from chemists in recent years and has made them exceedingly useful compounds in modern organic chemistry, especially in the synthesis of N-heterocycles. This review has outlined the extensive application of carbodiimides in the synthesis of N-heterocycles from the 1980s to today. A wide range of reactions for the synthesis of various types of N-heterocyclic systems (three-, four-, five-, six-, seven-, larger-membered and fused heterocycles) have been developed on the basis of carbodiimides and their derivatives.
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Affiliation(s)
- Yang Wang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China. and Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology (QNLM), Qingdao 266237, China
| | - Wen-Xiong Zhang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China.
| | - Zhenfeng Xi
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China.
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25
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Tan C, Chen Y, Peng X, Chen Z, Cai S, Cross TA, Fu R. Revealing weak histidine 15N homonuclear scalar couplings using Solid-State Magic-Angle-Spinning NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 316:106757. [PMID: 32535401 PMCID: PMC7426724 DOI: 10.1016/j.jmr.2020.106757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/12/2020] [Accepted: 05/27/2020] [Indexed: 05/05/2023]
Abstract
The tautomeric structure and chemistry of the histidine imidazole ring play active roles in many structurally and functionally important proteins and polypeptides. While in NMR spectroscopy histidine chemical shifts (e.g. 15N, 13C, and 1H) have been commonly used to characterize the tautomeric structure, hydrogen bonding, and torsion angles, homonuclear 15N scalar couplings in histidine have rarely been reported. Here, we propose double spin-echo sequences to compare the observed signals with and without a 90° pulse between the two spin-echo periods, such that their signal ratio as a function of the echo time solely depends on homonuclear scalar couplings, allowing for measuring weak homonuclear scalar couplings without influence from transverse dephasing effects, thus capable of revealing hydrogen-bond mediated 15N-15N J-couplings that can provide direct and definitive evidence for the formation of N…H…N hydrogen-bonding associated with the imidazole ring. We used two 13C,15N labeled histidine samples recrystallized from solutions at pH 6.3 and pH 11.0 to demonstrate the feasibility of this method and reveal the existence of a weak two-bond scalar coupling between the Nδ1 and Nε2 sites in the histidine imidazole ring in three tautomeric states and the presence of a hydrogen-bond mediated scalar coupling between the Nδ1 site in the imidazole ring and the backbone Nα site in the histidine neutral τ and π states. Our results demonstrate that weak 15N homonuclear scalar couplings can be measured even when their values are less than their corresponding intrinsic natural linewidths, thus providing direct and definitive evidence for the formation of N…H…N hydrogen bonding that is associated with the histidine imidazole ring.
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Affiliation(s)
- Chunhua Tan
- National High Magnet Field Lab, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA; Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, Fujian 361005, China
| | - Yuquan Chen
- CAS Key Laboratory of Microscale Magnetic Resonance and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - Xinhua Peng
- CAS Key Laboratory of Microscale Magnetic Resonance and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - Zhong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, Fujian 361005, China
| | - Shuhui Cai
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, Fujian 361005, China
| | - Timothy A Cross
- National High Magnet Field Lab, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Riqiang Fu
- National High Magnet Field Lab, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA.
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