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Noui Mehidi I, Ait Ouazzou A, Tachoua W, Hosni K. Investigating the Antimicrobial Properties of Essential Oil Constituents and Their Mode of Action. Molecules 2024; 29:4119. [PMID: 39274967 PMCID: PMC11397014 DOI: 10.3390/molecules29174119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 06/20/2024] [Accepted: 06/20/2024] [Indexed: 09/16/2024] Open
Abstract
Essential oils (EOs) and plant extracts, rich in beneficial chemical compounds, have diverse applications in medicine, food, cosmetics, and agriculture. This study investigates the antibacterial activity of nine essential oil constituents (EOCs) against Escherichia coli, focusing on the effects of treatment pH and biosynthetic requirements. The impact of EOCs on bacterial inactivation in E. coli strains was examined using both nonselective and selective culture media. Computer-assisted drug design (CADD) methods were employed to identify critical binding sites and predict the main binding modes of ligands to proteins. The EOCs, including citral, α-terpinyl acetate, α-terpineol, and linalool, demonstrated significant bacterial inactivation, particularly under acidic conditions. This study revealed that EOCs have an effect on the presence of sublethal damage to both the cytoplasmic membrane and the outer membrane in Gram-negative bacteria. Adding penicillin G to the repair medium prevents the recovery of sublethal injuries in E. coli treated with α-terpinyl acetate, α-terpineol, linalool, and citral, indicating that peptidoglycan synthesis is essential for recovering from these injuries. However, penicillin G did not hinder the recovery process of most sublethally injured cells treated with the other assessed EOCs. Molecular docking studies revealed the favorable binding interactions of α-terpinyl acetate, α-terpineol, linalool, and citral with the β-lactamase enzyme Toho-1, indicating their potential as effective antibacterial agents. The findings suggest that EOCs could serve as viable alternatives to synthetic preservatives, offering new strategies for combating antibiotic-resistant bacteria.
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Affiliation(s)
- Ilham Noui Mehidi
- Natural Resources Valorization and Bioengineering Laboratory, University Benyoucef Benkhedda Algiers 1, Alger Centre 16000, Algeria
| | - Abdenour Ait Ouazzou
- Natural Resources Valorization and Bioengineering Laboratory, University Benyoucef Benkhedda Algiers 1, Alger Centre 16000, Algeria
- Department of Nature and Life Sciences, Faculty of Sciences, Algiers 1 University-Benyoucef Benkhedda, 2 Rue Didouche Mourad, Alger Centre 16000, Algeria
| | - Wafa Tachoua
- Department of Nature and Life Sciences, Faculty of Sciences, Algiers 1 University-Benyoucef Benkhedda, 2 Rue Didouche Mourad, Alger Centre 16000, Algeria
| | - Karim Hosni
- Laboratoire des Substances Naturelles, Institut National de Recherche et d'Analyse Physico-Chimique, Sidi Thabet 2020, Tunisia
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2
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Song Z, Trozzi F, Palzkill T, Tao P. QM/MM modeling of class A β-lactamases reveals distinct acylation pathways for ampicillin and cefalexin. Org Biomol Chem 2021; 19:9182-9189. [PMID: 34647114 PMCID: PMC8613693 DOI: 10.1039/d1ob01593a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Efficient mechanism-based design of antibiotics that are not susceptible to β-lactamases is hindered by the lack of comprehensive knowledge on the energetic landscapes for the hydrolysis of various β-lactams. Herein, we adopted efficient quantum mechanics/molecular mechanics simulations to explore the acylation reaction catalyzed by CTX-M-44 (Toho-1) β-lactamase. We show that the catalytic pathways for β-lactam hydrolysis are correlated to substrate scaffolds: using Glu166 as the only general base for acylation is viable for ampicillin but prohibitive for cefalexin. The present computational workflow provides quantitative insights to facilitate the optimization of future β-lactam antibiotics.
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Affiliation(s)
- Zilin Song
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75205, USA.
| | - Francesco Trozzi
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75205, USA.
| | - Timothy Palzkill
- The Verna and Marrs McLean Department of Biochemistry and Molecular Biology and Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75205, USA.
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3
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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4
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Langan PS, Sullivan B, Weiss KL, Coates L. Probing the role of the conserved residue Glu166 in a class A β-lactamase using neutron and X-ray protein crystallography. Acta Crystallogr D Struct Biol 2020; 76:118-123. [PMID: 32038042 PMCID: PMC7008513 DOI: 10.1107/s2059798319016334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/03/2019] [Indexed: 11/10/2022] Open
Abstract
The amino-acid sequence of the Toho-1 β-lactamase contains several conserved residues in the active site, including Ser70, Lys73, Ser130 and Glu166, some of which coordinate a catalytic water molecule. This catalytic water molecule is essential in the acylation and deacylation parts of the reaction mechanism through which Toho-1 inactivates specific antibiotics and provides resistance to its expressing bacterial strains. To investigate the function of Glu166 in the acylation part of the catalytic mechanism, neutron and X-ray crystallographic studies were performed on a Glu166Gln mutant. The structure of this class A β-lactamase mutant provides several insights into its previously reported reduced drug-binding kinetic rates. A joint refinement of both X-ray and neutron diffraction data was used to study the effects of the Glu166Gln mutation on the active site of Toho-1. This structure reveals that while the Glu166Gln mutation has a somewhat limited impact on the positions of the conserved amino acids within the active site, it displaces the catalytic water molecule from the active site. These subtle changes offer a structural explanation for the previously observed decreases in the binding of non-β-lactam inhibitors such as the recently developed diazobicyclooctane inhibitor avibactam.
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Affiliation(s)
- Patricia S. Langan
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Brendan Sullivan
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Kevin L. Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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5
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Abstract
The use of neutron protein crystallography (NPX) is expanding rapidly, with most structures determined in the last decade. This growth is stimulated by a number of developments, spanning from the building of new NPX beamlines to the availability of improved software for structure refinement. The main bottleneck preventing structural biologists from adding NPX to the suite of methods commonly used is the large volume of the individual crystals required for a successful experiment. A survey of deposited NPX structures in the Protein Data Bank shows that about two-thirds came from crystals prepared using vapor diffusion, while batch and dialysis-based methods all-together contribute to most of the remaining one-third. This chapter explains the underlying principles of these protein crystallization methods and provides practical examples that may help others to successfully prepare large crystals for NPX.
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Tooke CL, Hinchliffe P, Bragginton EC, Colenso CK, Hirvonen VHA, Takebayashi Y, Spencer J. β-Lactamases and β-Lactamase Inhibitors in the 21st Century. J Mol Biol 2019; 431:3472-3500. [PMID: 30959050 PMCID: PMC6723624 DOI: 10.1016/j.jmb.2019.04.002] [Citation(s) in RCA: 440] [Impact Index Per Article: 88.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/27/2019] [Accepted: 04/01/2019] [Indexed: 12/31/2022]
Abstract
The β-lactams retain a central place in the antibacterial armamentarium. In Gram-negative bacteria, β-lactamase enzymes that hydrolyze the amide bond of the four-membered β-lactam ring are the primary resistance mechanism, with multiple enzymes disseminating on mobile genetic elements across opportunistic pathogens such as Enterobacteriaceae (e.g., Escherichia coli) and non-fermenting organisms (e.g., Pseudomonas aeruginosa). β-Lactamases divide into four classes; the active-site serine β-lactamases (classes A, C and D) and the zinc-dependent or metallo-β-lactamases (MBLs; class B). Here we review recent advances in mechanistic understanding of each class, focusing upon how growing numbers of crystal structures, in particular for β-lactam complexes, and methods such as neutron diffraction and molecular simulations, have improved understanding of the biochemistry of β-lactam breakdown. A second focus is β-lactamase interactions with carbapenems, as carbapenem-resistant bacteria are of grave clinical concern and carbapenem-hydrolyzing enzymes such as KPC (class A) NDM (class B) and OXA-48 (class D) are proliferating worldwide. An overview is provided of the changing landscape of β-lactamase inhibitors, exemplified by the introduction to the clinic of combinations of β-lactams with diazabicyclooctanone and cyclic boronate serine β-lactamase inhibitors, and of progress and strategies toward clinically useful MBL inhibitors. Despite the long history of β-lactamase research, we contend that issues including continuing unresolved questions around mechanism; opportunities afforded by new technologies such as serial femtosecond crystallography; the need for new inhibitors, particularly for MBLs; the likely impact of new β-lactam:inhibitor combinations and the continuing clinical importance of β-lactams mean that this remains a rewarding research area.
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Affiliation(s)
- Catherine L Tooke
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Eilis C Bragginton
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Charlotte K Colenso
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Viivi H A Hirvonen
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Yuiko Takebayashi
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom.
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7
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Neutron macromolecular crystallography. Emerg Top Life Sci 2018; 2:39-55. [DOI: 10.1042/etls20170083] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/12/2017] [Accepted: 12/19/2017] [Indexed: 01/02/2023]
Abstract
Neutron diffraction techniques permit direct determination of the hydrogen (H) and deuterium (D) positions in crystal structures of biological macromolecules at resolutions of ∼1.5 and 2.5 Å, respectively. In addition, neutron diffraction data can be collected from a single crystal at room temperature without radiation damage issues. By locating the positions of H/D-atoms, protonation states and water molecule orientations can be determined, leading to a more complete understanding of many biological processes and drug-binding. In the last ca. 5 years, new beamlines have come online at reactor neutron sources, such as BIODIFF at Heinz Maier-Leibnitz Zentrum and IMAGINE at Oak Ridge National Laboratory (ORNL), and at spallation neutron sources, such as MaNDi at ORNL and iBIX at the Japan Proton Accelerator Research Complex. In addition, significant improvements have been made to existing beamlines, such as LADI-III at the Institut Laue-Langevin. The new and improved instrumentations are allowing sub-mm3 crystals to be regularly used for data collection and permitting the study of larger systems (unit-cell edges >100 Å). Owing to this increase in capacity and capability, many more studies have been performed and for a wider range of macromolecules, including enzymes, signalling proteins, transport proteins, sugar-binding proteins, fluorescent proteins, hormones and oligonucleotides; of the 126 structures deposited in the Protein Data Bank, more than half have been released since 2013 (65/126, 52%). Although the overall number is still relatively small, there are a growing number of examples for which neutron macromolecular crystallography has provided the answers to questions that otherwise remained elusive.
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8
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Langan PS, Vandavasi VG, Cooper CJ, Weiss KL, Ginell SL, Parks JM, Coates L. Substrate Binding Induces Conformational Changes in a Class A β-lactamase That Prime It for Catalysis. ACS Catal 2018. [DOI: 10.1021/acscatal.7b04114] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Patricia S. Langan
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Venu Gopal Vandavasi
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Connor J. Cooper
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Kevin L. Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Stephan L. Ginell
- Structural Biology Center, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Jerry M. Parks
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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9
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Yee AW, Blakeley MP, Moulin M, Haertlein M, Mitchell E, Forsyth VT. Back-exchange of deuterium in neutron crystallography: characterization by IR spectroscopy. J Appl Crystallogr 2017; 50:660-664. [PMID: 28381984 PMCID: PMC5377354 DOI: 10.1107/s1600576717003624] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/07/2017] [Indexed: 01/02/2023] Open
Abstract
The application of IR spectroscopy to the characterization and quality control of samples used in neutron crystallography is described. While neutron crystallography is a growing field, the limited availability of neutron beamtime means that there may be a delay between crystallogenesis and data collection. Since essentially all neutron crystallographic work is carried out using D2O-based solvent buffers, a particular concern for these experiments is the possibility of H2O back-exchange across reservoir or capillary sealants. This may limit the quality of neutron scattering length density maps and of the associated analysis. Given the expense of central facility beamtime and the effort that goes into the production of suitably sized (usually perdeuterated) crystals, a systematic method of exploiting IR spectroscopy for the analysis of back-exchange phenomena in the reservoirs used for crystal growth is valuable. Examples are given in which the characterization of D2O/H2O back-exchange in transthyretin crystals is described.
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Affiliation(s)
- Ai Woon Yee
- Life Sciences Group, Institut Laue–Langevin, 71 avenue des Martyrs, Grenoble 38042, France
- Faculty of Natural Sciences, Keele University, Keele ST5 5BG, UK
| | - Matthew P. Blakeley
- Large-Scale Structures Group, Institut Laue–Langevin, 71 avenue des Martyrs, Grenoble 38042, France
| | - Martine Moulin
- Life Sciences Group, Institut Laue–Langevin, 71 avenue des Martyrs, Grenoble 38042, France
- Faculty of Natural Sciences, Keele University, Keele ST5 5BG, UK
| | - Michael Haertlein
- Life Sciences Group, Institut Laue–Langevin, 71 avenue des Martyrs, Grenoble 38042, France
| | - Edward Mitchell
- Faculty of Natural Sciences, Keele University, Keele ST5 5BG, UK
- European Synchrotron Research Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - V. Trevor Forsyth
- Life Sciences Group, Institut Laue–Langevin, 71 avenue des Martyrs, Grenoble 38042, France
- Faculty of Natural Sciences, Keele University, Keele ST5 5BG, UK
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Chen JCH, Unkefer CJ. Fifteen years of the Protein Crystallography Station: the coming of age of macromolecular neutron crystallography. IUCRJ 2017; 4:72-86. [PMID: 28250943 PMCID: PMC5331467 DOI: 10.1107/s205225251601664x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 10/17/2016] [Indexed: 06/06/2023]
Abstract
The Protein Crystallography Station (PCS), located at the Los Alamos Neutron Scattering Center (LANSCE), was the first macromolecular crystallography beamline to be built at a spallation neutron source. Following testing and commissioning, the PCS user program was funded by the Biology and Environmental Research program of the Department of Energy Office of Science (DOE-OBER) for 13 years (2002-2014). The PCS remained the only dedicated macromolecular neutron crystallography station in North America until the construction and commissioning of the MaNDi and IMAGINE instruments at Oak Ridge National Laboratory, which started in 2012. The instrument produced a number of research and technical outcomes that have contributed to the field, clearly demonstrating the power of neutron crystallo-graphy in helping scientists to understand enzyme reaction mechanisms, hydrogen bonding and visualization of H-atom positions, which are critical to nearly all chemical reactions. During this period, neutron crystallography became a technique that increasingly gained traction, and became more integrated into macromolecular crystallography through software developments led by investigators at the PCS. This review highlights the contributions of the PCS to macromolecular neutron crystallography, and gives an overview of the history of neutron crystallography and the development of macromolecular neutron crystallography from the 1960s to the 1990s and onwards through the 2000s.
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Affiliation(s)
- Julian C.-H. Chen
- Bioscience Division, Protein Crystallography Station, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606, USA
| | - Clifford J. Unkefer
- Bioscience Division, Protein Crystallography Station, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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Active-Site Protonation States in an Acyl-Enzyme Intermediate of a Class A β-Lactamase with a Monobactam Substrate. Antimicrob Agents Chemother 2016; 61:AAC.01636-16. [PMID: 27795378 PMCID: PMC5192116 DOI: 10.1128/aac.01636-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 09/29/2016] [Indexed: 11/20/2022] Open
Abstract
The monobactam antibiotic aztreonam is used to treat cystic fibrosis patients with chronic pulmonary infections colonized by Pseudomonas aeruginosa strains expressing CTX-M extended-spectrum β-lactamases. The protonation states of active-site residues that are responsible for hydrolysis have been determined previously for the apo form of a CTX-M β-lactamase but not for a monobactam acyl-enzyme intermediate. Here we used neutron and high-resolution X-ray crystallography to probe the mechanism by which CTX-M extended-spectrum β-lactamases hydrolyze monobactam antibiotics. In these first reported structures of a class A β-lactamase in an acyl-enzyme complex with aztreonam, we directly observed most of the hydrogen atoms (as deuterium) within the active site. Although Lys 234 is fully protonated in the acyl intermediate, we found that Lys 73 is neutral. These findings are consistent with Lys 73 being able to serve as a general base during the acylation part of the catalytic mechanism, as previously proposed.
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12
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Cortina GA, Kasson PM. Excess positional mutual information predicts both local and allosteric mutations affecting beta lactamase drug resistance. Bioinformatics 2016; 32:3420-3427. [PMID: 27466622 PMCID: PMC6078173 DOI: 10.1093/bioinformatics/btw492] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 06/30/2016] [Accepted: 07/18/2016] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Bacterial resistance to antibiotics, particularly plasmid-encoded resistance to beta lactam drugs, poses an increasing threat to human health. Point mutations to beta-lactamase enzymes can greatly alter the level of resistance conferred, but predicting the effects of such mutations has been challenging due to the large combinatorial space involved and the subtle relationships of distant residues to catalytic function. Therefore we desire an information-theoretic metric to sensitively and robustly detect both local and distant residues that affect substrate conformation and catalytic activity. RESULTS Here, we report the use of positional mutual information in multiple microsecond-length molecular dynamics (MD) simulations to predict residues linked to catalytic activity of the CTX-M9 beta lactamase. We find that motions of the bound drug are relatively isolated from motions of the protein as a whole, which we interpret in the context of prior theories of catalysis. In order to robustly identify residues that are weakly coupled to drug motions but nonetheless affect catalysis, we utilize an excess mutual information metric. We predict 31 such residues for the cephalosporin antibiotic cefotaxime. Nine of these have previously been tested experimentally, and all decrease both enzyme rate constants and empirical drug resistance. We prospectively validate our method by testing eight high-scoring mutations and eight low-scoring controls in bacteria. Six of eight predicted mutations decrease cefotaxime resistance greater than 2-fold, while only one control shows such an effect. The ability to prospectively predict new variants affecting bacterial drug resistance is of great interest to clinical and epidemiological surveillance. AVAILABILITY AND IMPLEMENTATION Excess mutual information code is available at https://github.com/kassonlab/positionalmi CONTACT: kasson@virginia.edu.
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Affiliation(s)
- George A Cortina
- Departments of Biomedical Engineering and Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Peter M Kasson
- Departments of Biomedical Engineering and Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
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13
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Langan PS, Vandavasi VG, Weiss KL, Cooper JB, Ginell SL, Coates L. The structure of Toho1 β-lactamase in complex with penicillin reveals the role of Tyr105 in substrate recognition. FEBS Open Bio 2016; 6:1170-1177. [PMID: 28255534 PMCID: PMC5324766 DOI: 10.1002/2211-5463.12132] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 09/26/2016] [Accepted: 09/28/2016] [Indexed: 11/06/2022] Open
Abstract
The role of the conserved residue Tyr105 in class A β‐lactamases has been the subject of investigation using both structural studies and saturation mutagenesis. Both have shown that while it does not need to be strictly conserved for activity, it is important for substrate recognition. With this in mind we determined the crystal structure of Toho1 β‐lactamase at 15 K to 1.10 Å resolution in complex with penicillin. As expected a ring‐opened penicillin molecule bound to Ser70 the catalytic nucleophile, can clearly be seen in electron density in the active site. In addition to the trapped penicillin, however, are two additional intact ring‐closed penicillin molecules, captured by the enzyme through noncovalent interactions at the edge of the active site.
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Affiliation(s)
- Patricia S Langan
- Biology and Soft Matter Division Oak Ridge National Laboratory TN USA
| | | | - Kevin L Weiss
- Biology and Soft Matter Division Oak Ridge National Laboratory TN USA
| | | | | | - Leighton Coates
- Biology and Soft Matter Division Oak Ridge National Laboratory TN USA
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14
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O'Dell WB, Bodenheimer AM, Meilleur F. Neutron protein crystallography: A complementary tool for locating hydrogens in proteins. Arch Biochem Biophys 2016; 602:48-60. [DOI: 10.1016/j.abb.2015.11.033] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/12/2015] [Accepted: 11/16/2015] [Indexed: 10/22/2022]
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15
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Vandavasi VG, Weiss KL, Cooper JB, Erskine PT, Tomanicek SJ, Ostermann A, Schrader TE, Ginell SL, Coates L. Exploring the Mechanism of β-Lactam Ring Protonation in the Class A β-lactamase Acylation Mechanism Using Neutron and X-ray Crystallography. J Med Chem 2015; 59:474-9. [PMID: 26630115 DOI: 10.1021/acs.jmedchem.5b01215] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The catalytic mechanism of class A β-lactamases is often debated due in part to the large number of amino acids that interact with bound β-lactam substrates. The role and function of the conserved residue Lys 73 in the catalytic mechanism of class A type β-lactamase enzymes is still not well understood after decades of scientific research. To better elucidate the functions of this vital residue, we used both neutron and high-resolution X-ray diffraction to examine both the structures of the ligand free protein and the acyl-enzyme complex of perdeuterated E166A Toho-1 β-lactamase with the antibiotic cefotaxime. The E166A mutant lacks a critical glutamate residue that has a key role in the deacylation step of the catalytic mechanism, allowing the acyl-enzyme adduct to be captured for study. In our ligand free structures, Lys 73 is present in a single conformation, however in all of our acyl-enzyme structures, Lys 73 is present in two different conformations, in which one conformer is closer to Ser 70 while the other conformer is positioned closer to Ser 130, which supports the existence of a possible pathway by which proton transfer from Lys 73 to Ser 130 can occur. This and further clarifications of the role of Lys 73 in the acylation mechanism may facilitate the design of inhibitors that capitalize on the enzyme's native machinery.
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Affiliation(s)
- Venu Gopal Vandavasi
- Oak Ridge National Laboratory , 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Kevin L Weiss
- Oak Ridge National Laboratory , 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Jonathan B Cooper
- Birkbeck University of London , Malet Street, London WC1E 7HX, United Kingdom
| | - Peter T Erskine
- Birkbeck University of London , Malet Street, London WC1E 7HX, United Kingdom
| | - Stephen J Tomanicek
- Oak Ridge National Laboratory , 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München , Lichtenbergstr. 1, 85748 Garching, Germany
| | - Tobias E Schrader
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH , Lichtenbergstr. 1, 85747 Garching, Germany
| | - Stephan L Ginell
- Structural Biology Center, Argonne National Laboratory , 9700 St. Cass Avenue, Argonne, Illinois 60439, United States
| | - Leighton Coates
- Oak Ridge National Laboratory , 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
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16
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Yesselman JD, Horowitz S, Brooks CL, Trievel RC. Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures. Proteins 2015; 83:403-410. [PMID: 25401519 DOI: 10.1002/prot.24724] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 10/19/2014] [Accepted: 11/10/2014] [Indexed: 11/11/2022]
Abstract
The propensity of backbone Cα atoms to engage in carbon-oxygen (CH · · · O) hydrogen bonding is well-appreciated in protein structure, but side chain CH · · · O hydrogen bonding remains largely uncharacterized. The extent to which side chain methyl groups in proteins participate in CH · · · O hydrogen bonding is examined through a survey of neutron crystal structures, quantum chemistry calculations, and molecular dynamics simulations. Using these approaches, methyl groups were observed to form stabilizing CH · · · O hydrogen bonds within protein structure that are maintained through protein dynamics and participate in correlated motion. Collectively, these findings illustrate that side chain methyl CH · · · O hydrogen bonding contributes to the energetics of protein structure and folding.
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Affiliation(s)
- Joseph D Yesselman
- Departments of Biophysics and Molecular, Cellular, University of Michigan, Ann Arbor, MI 48109, USA.,Departments of Biochemistry & Physics, Stanford University, Stanford, CA 94305
| | - Scott Horowitz
- Departments of Biophysics and Molecular, Cellular, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Biological Chemistry, Howard Hughes Medical Institute, University of Michigan, Ann Arbor MI 48109 USA
| | - Charles L Brooks
- Departments of Biophysics and Molecular, Cellular, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Raymond C Trievel
- Department of Biological Chemistry, Howard Hughes Medical Institute, University of Michigan, Ann Arbor MI 48109 USA
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17
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Haupt M, Blakeley MP, Fisher SJ, Mason SA, Cooper JB, Mitchell EP, Forsyth VT. Binding site asymmetry in human transthyretin: insights from a joint neutron and X-ray crystallographic analysis using perdeuterated protein. IUCRJ 2014; 1:429-38. [PMID: 25485123 PMCID: PMC4224461 DOI: 10.1107/s2052252514021113] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 09/22/2014] [Indexed: 05/12/2023]
Abstract
Human transthyretin has an intrinsic tendency to form amyloid fibrils and is heavily implicated in senile systemic amyloidosis. Here, detailed neutron structural studies of perdeuterated transthyretin are described. The analyses, which fully exploit the enhanced visibility of isotopically replaced hydrogen atoms, yield new information on the stability of the protein and the possible mechanisms of amyloid formation. Residue Ser117 may play a pivotal role in that a single water molecule is closely associated with the γ-hydrogen atoms in one of the binding pockets, and could be important in determining which of the two sites is available to the substrate. The hydrogen-bond network at the monomer-monomer interface is more extensive than that at the dimer-dimer interface. Additionally, the edge strands of the primary dimer are seen to be favourable for continuation of the β-sheet and the formation of an extended cross-β structure through sequential dimer couplings. It is argued that the precursor to fibril formation is the dimeric form of the protein.
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Affiliation(s)
- Melina Haupt
- Facility of Natural Sciences, Institute of Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
- Institut Laue-Langevin, 71, avenue des Martyrs, Grenoble, CS 20156, France
- Partnership for Structural Biology, 71, avenue des Martyrs, Grenoble, CS 20156, France
| | - Matthew P. Blakeley
- Institut Laue-Langevin, 71, avenue des Martyrs, Grenoble, CS 20156, France
- Partnership for Structural Biology, 71, avenue des Martyrs, Grenoble, CS 20156, France
| | - Stuart J. Fisher
- Department of Molecular Biology, University of Salzburg, Billrothstrasse 11, Salzburg, 5020, Austria
- Diamond Light Source, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Sax A. Mason
- Institut Laue-Langevin, 71, avenue des Martyrs, Grenoble, CS 20156, France
| | - Jon B. Cooper
- Division of Medicine (Royal Free Campus), University College London, Rowland Hill Street, London NW3 2PF, United Kingdom
| | - Edward P. Mitchell
- Facility of Natural Sciences, Institute of Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
- Partnership for Structural Biology, 71, avenue des Martyrs, Grenoble, CS 20156, France
- Business Development Office, European Synchrotron Radiation Facility, Grenoble, 38042, France
| | - V. Trevor Forsyth
- Facility of Natural Sciences, Institute of Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
- Institut Laue-Langevin, 71, avenue des Martyrs, Grenoble, CS 20156, France
- Partnership for Structural Biology, 71, avenue des Martyrs, Grenoble, CS 20156, France
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18
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Heller WT, Urban VS, Lynn GW, Weiss KL, O'Neill HM, Pingali SV, Qian S, Littrell KC, Melnichenko YB, Buchanan MV, Selby DL, Wignall GD, Butler PD, Myles DA. The Bio-SANS instrument at the High Flux Isotope Reactor of Oak Ridge National Laboratory. J Appl Crystallogr 2014. [DOI: 10.1107/s1600576714011285] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Small-angle neutron scattering (SANS) is a powerful tool for characterizing complex disordered materials, including biological materials. The Bio-SANS instrument of the High Flux Isotope Reactor of Oak Ridge National Laboratory (ORNL) is a high-flux low-background SANS instrument that is, uniquely among SANS instruments, dedicated to serving the needs of the structural biology and biomaterials communities as an open-access user facility. Here, the technical specifications and performance of the Bio-SANS are presented. Sample environments developed to address the needs of the user program of the instrument are also presented. Further, the isotopic labeling and sample preparation capabilities available in the Bio-Deuteration Laboratory for users of the Bio-SANS and other neutron scattering instruments at ORNL are described. Finally, a brief survey of research performed using the Bio-SANS is presented, which demonstrates the breadth of the research that the instrument's user community engages in.
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19
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Coates L, Tomanicek S, Schrader TE, Weiss KL, Ng JD, Jüttner P, Ostermann A. Cryogenic neutron protein crystallography: routine methods and potential benefits. J Appl Crystallogr 2014. [DOI: 10.1107/s1600576714010772] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The use of cryocooling in neutron diffraction has been hampered by several technical challenges, such as the need for specialized equipment and techniques. This article reports the recent development and deployment of equipment and strategies that allow routine neutron data collection on cryocooled crystals using off-the-shelf components. This system has several advantages compared to a closed displex cooling system, such as fast cooling coupled with easier crystal mounting and centering. The ability to routinely collect cryogenic neutron data for analysis will significantly broaden the range of scientific questions that can be examined by neutron protein crystallography. Cryogenic neutron data collection for macromolecules has recently become available at the new Biological Diffractometer BIODIFF at the FRM II and the Macromolecular Diffractometer (MaNDi) at the Spallation Neutron Source, Oak Ridge National Laboratory. To evaluate the benefits of a cryocooled neutron structure, a full neutron data set was collected on the BIODIFF instrument on a Toho-1 β-lactamase structure at 100 K.
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20
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Golden EA, Vrielink A. Looking for Hydrogen Atoms: Neutron Crystallography Provides Novel Insights Into Protein Structure and Function. Aust J Chem 2014. [DOI: 10.1071/ch14337] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Neutron crystallography allows direct localization of hydrogen positions in biological macromolecules. Within enzymes, hydrogen atoms play a pivotal role in catalysis. Recent advances in instrumentation and sample preparation have helped to overcome the difficulties of performing neutron diffraction experiments on protein crystals. The application of neutron macromolecular crystallography to a growing number of proteins has yielded novel structural insights. The ability to accurately position water molecules, hydronium ions, and hydrogen atoms within protein structures has helped in the study of low-barrier hydrogen bonds and hydrogen-bonding networks. The determination of protonation states of protein side chains, substrates, and inhibitors in the context of the macromolecule has provided important insights into enzyme chemistry and ligand binding affinities, which can assist in the design of potent therapeutic agents. In this review, we give an overview of the method and highlight advances in knowledge attained through the application of neutron protein crystallography.
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21
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Meilleur F, Munshi P, Robertson L, Stoica AD, Crow L, Kovalevsky A, Koritsanszky T, Chakoumakos BC, Blessing R, Myles DAA. The IMAGINE instrument: first neutron protein structure and new capabilities for neutron macromolecular crystallography. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2157-60. [DOI: 10.1107/s0907444913019604] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 07/15/2013] [Indexed: 11/11/2022]
Abstract
The first high-resolution neutron protein structure of perdeuterated rubredoxin fromPyrococcus furiosus(PfRd) determined using the new IMAGINE macromolecular neutron crystallography instrument at the Oak Ridge National Laboratory is reported. Neutron diffraction data extending to 1.65 Å resolution were collected from a relatively small 0.7 mm3PfRd crystal using 2.5 d (60 h) of beam time. The refined structure contains 371 out of 391, or 95%, of the D atoms of the protein and 58 solvent molecules. The IMAGINE instrument is designed to provide neutron data at or near atomic resolution (1.5 Å) from crystals with volume <1.0 mm3and with unit-cell edges <100 Å. Beamline features include novel elliptical focusing mirrors that deliver neutrons into a 2.0 × 3.2 mm focal spot at the sample position with full-width vertical and horizontal divergences of 0.5 and 0.6°, respectively. Variable short- and long-wavelength cutoff optics provide automated exchange between multiple-wavelength configurations (λmin= 2.0, 2.8, 3.3 Å to λmax= 3.0, 4.0, 4.5, ∼20 Å). These optics produce a more than 20-fold increase in the flux density at the sample and should help to enable more routine collection of high-resolution data from submillimetre-cubed crystals. Notably, the crystal used to collect thesePfRd data was 5–10 times smaller than those previously reported.
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22
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Ankner JF, Heller WT, Herwig KW, Meilleur F, Myles DAA. Neutron scattering techniques and applications in structural biology. ACTA ACUST UNITED AC 2013; Chapter 17:Unit17.16. [PMID: 23546619 DOI: 10.1002/0471140864.ps1716s72] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Neutron scattering is exquisitely sensitive to the position, concentration, and dynamics of hydrogen atoms in materials and is a powerful tool for the characterization of structure-function and interfacial relationships in biological systems. Modern neutron scattering facilities offer access to a sophisticated, nondestructive suite of instruments for biophysical characterization that provides spatial and dynamic information spanning from Ångstroms to microns and from picoseconds to microseconds, respectively. Applications in structural biology range from the atomic-resolution analysis of individual hydrogen atoms in enzymes through to meso- and macro-scale analysis of complex biological structures, membranes, and assemblies. The large difference in neutron scattering length between hydrogen and deuterium allows contrast variation experiments to be performed and enables H/D isotopic labeling to be used for selective and systematic analysis of the local structure, dynamics, and interactions of multi-component systems. This overview describes the available techniques and summarizes their practical application to the study of biomolecular systems.
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Affiliation(s)
- John F Ankner
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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23
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van der Kamp MW, Mulholland AJ. Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology. Biochemistry 2013; 52:2708-28. [PMID: 23557014 DOI: 10.1021/bi400215w] [Citation(s) in RCA: 399] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Computational enzymology is a rapidly maturing field that is increasingly integral to understanding mechanisms of enzyme-catalyzed reactions and their practical applications. Combined quantum mechanics/molecular mechanics (QM/MM) methods are important in this field. By treating the reacting species with a quantum mechanical method (i.e., a method that calculates the electronic structure of the active site) and including the enzyme environment with simpler molecular mechanical methods, enzyme reactions can be modeled. Here, we review QM/MM methods and their application to enzyme-catalyzed reactions to investigate fundamental and practical problems in enzymology. A range of QM/MM methods is available, from cheaper and more approximate methods, which can be used for molecular dynamics simulations, to highly accurate electronic structure methods. We discuss how modeling of reactions using such methods can provide detailed insight into enzyme mechanisms and illustrate this by reviewing some recent applications. We outline some practical considerations for such simulations. Further, we highlight applications that show how QM/MM methods can contribute to the practical development and application of enzymology, e.g., in the interpretation and prediction of the effects of mutagenesis and in drug and catalyst design.
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Affiliation(s)
- Marc W van der Kamp
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
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24
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Chakraborty S. A quantitative measure of electrostatic perturbation in holo and apo enzymes induced by structural changes. PLoS One 2013; 8:e59352. [PMID: 23516628 PMCID: PMC3597595 DOI: 10.1371/journal.pone.0059352] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 02/13/2013] [Indexed: 11/19/2022] Open
Abstract
Biological pathways are subject to subtle manipulations that achieve a wide range of functional variation in differing physiological niches. In many instances, changes in the structure of an enzyme on ligand binding germinate electrostatic perturbations that form the basis of its changed catalytic or transcriptional efficiency. Computational methods that seek to gain insights into the electrostatic changes in enzymes require expertise to setup and computing prowess. In the current work, we present a fast, easy and reliable methodology to compute electrostatic perturbations induced by ligand binding (MEPP). The theoretical foundation of MEPP is the conserved electrostatic potential difference (EPD) in cognate pairs of active site residues in proteins with the same functionality. Previously, this invariance has been used to unravel promiscuous serine protease and metallo-β-lactamase scaffolds in alkaline phosphatases. Given that a similarity in EPD is significant, we expect differences in the EPD to be significant too. MEPP identifies residues or domains that undergo significant electrostatic perturbations, and also enumerates residue pairs that undergo significant polarity change. The gain in a certain polarity of a residue with respect to neighboring residues, or the reversal of polarity between two residues might indicate a change in the preferred ligand. The methodology of MEPP has been demonstrated on several enzymes that employ varying mechanisms to perform their roles. For example, we have attributed the change in polarity in residue pairs to be responsible for the loss of metal ion binding in fructose 1,6-bisphosphatases, and corroborated the pre-organized state of the active site of the enzyme with respect to functionally relevant changes in electric fields in ketosteroid isomerases.
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Affiliation(s)
- Sandeep Chakraborty
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India.
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25
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Tomanicek SJ, Standaert RF, Weiss KL, Ostermann A, Schrader TE, Ng JD, Coates L. Neutron and X-ray crystal structures of a perdeuterated enzyme inhibitor complex reveal the catalytic proton network of the Toho-1 β-lactamase for the acylation reaction. J Biol Chem 2012; 288:4715-22. [PMID: 23255594 DOI: 10.1074/jbc.m112.436238] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mechanism by which class A β-lactamases hydrolyze β-lactam antibiotics has been the subject of intensive investigation using many different experimental techniques. Here, we report on the novel use of both neutron and high resolution x-ray diffraction to help elucidate the identity of the catalytic base in the acylation part of the catalytic cycle, wherein the β-lactam ring is opened and an acyl-enzyme intermediate forms. To generate protein crystals optimized for neutron diffraction, we produced a perdeuterated form of the Toho-1 β-lactamase R274N/R276N mutant. Protein perdeuteration, which involves replacing all of the hydrogen atoms in a protein with deuterium, gives a much stronger signal in neutron diffraction and enables the positions of individual deuterium atoms to be located. We also synthesized a perdeuterated acylation transition state analog, benzothiophene-2-boronic acid, which was also isotopically enriched with (11)B, as (10)B is a known neutron absorber. Using the neutron diffraction data from the perdeuterated enzyme-inhibitor complex, we were able to determine the positions of deuterium atoms in the active site directly rather than by inference. The neutron diffraction results, along with supporting bond-length analysis from high resolution x-ray diffraction, strongly suggest that Glu-166 acts as the general base during the acylation reaction.
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26
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Direct observation of hydrogen atom dynamics and interactions by ultrahigh resolution neutron protein crystallography. Proc Natl Acad Sci U S A 2012; 109:15301-6. [PMID: 22949690 DOI: 10.1073/pnas.1208341109] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The 1.1 Å, ultrahigh resolution neutron structure of hydrogen/deuterium (H/D) exchanged crambin is reported. Two hundred ninety-nine out of 315, or 94.9%, of the hydrogen atom positions in the protein have been experimentally derived and resolved through nuclear density maps. A number of unconventional interactions are clearly defined, including a potential O─H…π interaction between a water molecule and the aromatic ring of residue Y44, as well as a number of potential C─H…O hydrogen bonds. Hydrogen bonding networks that are ambiguous in the 0.85 Å ultrahigh resolution X-ray structure can be resolved by accurate orientation of water molecules. Furthermore, the high resolution of the reported structure has allowed for the anisotropic description of 36 deuterium atoms in the protein. The visibility of hydrogen and deuterium atoms in the nuclear density maps is discussed in relation to the resolution of the neutron data.
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27
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Chakraborty S. Enumerating pathways of proton abstraction based on a spatial and electrostatic analysis of residues in the catalytic site. PLoS One 2012; 7:e39577. [PMID: 22745790 PMCID: PMC3379984 DOI: 10.1371/journal.pone.0039577] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 05/28/2012] [Indexed: 11/19/2022] Open
Abstract
The pathways of proton abstraction (PA), a key aspect of most catalytic reactions, is often controversial and highly debated. Ultrahigh-resolution diffraction studies, molecular dynamics, quantum mechanics and molecular mechanic simulations are often adopted to gain insights in the PA mechanisms in enzymes. These methods require expertise and effort to setup and can be computationally intensive. We present a push button methodology--Proton abstraction Simulation (PRISM)--to enumerate the possible pathways of PA in a protein with known 3D structure based on the spatial and electrostatic properties of residues in the proximity of a given nucleophilic residue. Proton movements are evaluated in the vicinity of this nucleophilic residue based on distances, potential differences, spatial channels and characteristics of the individual residues (polarity, acidic, basic, etc). Modulating these parameters eliminates their empirical nature and also might reveal pathways that originate from conformational changes. We have validated our method using serine proteases and concurred with the dichotomy in PA in Class A β-lactamases, both of which are hydrolases. The PA mechanism in a transferase has also been corroborated. The source code is made available at www.sanchak.com/prism.
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Affiliation(s)
- Sandeep Chakraborty
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India.
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28
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Bush K, Fisher JF. Epidemiological expansion, structural studies, and clinical challenges of new β-lactamases from gram-negative bacteria. Annu Rev Microbiol 2012; 65:455-78. [PMID: 21740228 DOI: 10.1146/annurev-micro-090110-102911] [Citation(s) in RCA: 297] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
β-Lactamase evolution presents to the infectious disease community a major challenge in the treatment of infections caused by multidrug-resistant gram-negative bacteria. Because over 1,000 of these naturally occurring β-lactamases exist, attempts to correlate structure and function have become daunting. Although new enzymes in the extended-spectrum β-lactamase (ESBL) families are frequently identified, the older CTX-M-14 and CTX-M-15 enzymes have become the most prevalent ESBLs in global surveillance. Carbapenemases with either serine-based or zinc-facilitated hydrolysis mechanisms are posing some of the most critical problems. Most geographical regions now report KPC serine carbapenemases and the metallo-β-lactamases VIM, IMP, and NDM-1, even though NDM-1 was only recently identified. The rapid emergence of these newer enzymes, with multiple β-lactamases appearing in a single organism, makes the design of new β-lactamase inactivators or β-lactamase-stable β-lactams all the more difficult. Combination therapy will likely be required to counteract the continuing evolution of these insidious enzymes in multidrug-resistant pathogens.
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Affiliation(s)
- Karen Bush
- Biology Department, Indiana University, Bloomington, Indiana 47401, USA.
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29
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Munshi P, Chung SL, Blakeley MP, Weiss KL, Myles DAA, Meilleur F. Rapid visualization of hydrogen positions in protein neutron crystallographic structures. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2011; 68:35-41. [PMID: 22194331 DOI: 10.1107/s0907444911048402] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 11/15/2011] [Indexed: 11/10/2022]
Abstract
Neutron crystallography is a powerful technique for experimental visualization of the positions of light atoms, including hydrogen and its isotope deuterium. In recent years, structural biologists have shown increasing interest in the technique as it uniquely complements X-ray crystallographic data by revealing the positions of D atoms in macromolecules. With this regained interest, access to macromolecular neutron crystallography beamlines is becoming a limiting step. In this report, it is shown that a rapid data-collection strategy can be a valuable alternative to longer data-collection times in appropriate cases. Comparison of perdeuterated rubredoxin structures refined against neutron data sets collected over hours and up to 5 d shows that rapid neutron data collection in just 14 h is sufficient to provide the positions of 269 D atoms without ambiguity.
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Affiliation(s)
- Parthapratim Munshi
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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30
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Haupt M, Blakeley MP, Teixeira SCM, Mason SA, Mitchell EP, Cooper JB, Forsyth VT. Preliminary neutron crystallographic study of human transthyretin. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1428-31. [PMID: 22102249 PMCID: PMC3212468 DOI: 10.1107/s1744309111036244] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 09/05/2011] [Indexed: 11/10/2022]
Abstract
Preliminary studies of perdeuterated crystals of human transthyretin (TTR) have been carried out using the LADI-III and D19 diffractometers at the Institut Laue-Langevin in Grenoble. The results demonstrate the feasibility of a full crystallographic analysis to a resolution of 2.0 Å using Laue diffraction and also illustrate the potential of using monochromatic instruments such as D19 for higher resolution studies where larger crystals having smaller unit cells are available. This study will yield important information on hydrogen bonding, amino-acid protonation states and hydration in the protein. Such information will be of general interest for an understanding of the factors that stabilize/destabilize TTR and for the design of ligands that may be used to counter TTR amyloid fibrillogenesis.
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Affiliation(s)
- Melina Haupt
- EPSAM, Keele University, Keele, Staffordshire ST5 5BG, England
- Institut Laue–Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
- Partnership for Structural Biology (PSB), Institut Laue–Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | | | - Susana C. M. Teixeira
- EPSAM, Keele University, Keele, Staffordshire ST5 5BG, England
- Institut Laue–Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | - Sax A. Mason
- Institut Laue–Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | - Edward P. Mitchell
- EPSAM, Keele University, Keele, Staffordshire ST5 5BG, England
- European Synchrotron Radiation Facility (ESRF), 6 Rue Jules Horowitz, 38043 Grenoble, France
| | - Jonathan B. Cooper
- Division of Medicine, University College London, Rowland Hill Street, London NW3 2PF, England
| | - V. Trevor Forsyth
- EPSAM, Keele University, Keele, Staffordshire ST5 5BG, England
- Institut Laue–Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
- Partnership for Structural Biology (PSB), Institut Laue–Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
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