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Abstract
Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate-carbohydrate interactions, glycolipids, and N- and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics.
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Affiliation(s)
- Serge Perez
- Centre de Recherche sur les Macromolecules Vegetales, University of Grenoble-Alpes, Centre National de la Recherche Scientifique, Grenoble F-38041, France
| | - Olga Makshakova
- FRC Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, Kazan 420111, Russia
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Jothi R, Hari Prasath N, Gowrishankar S, Pandian SK. Bacterial Quorum-Sensing Molecules as Promising Natural Inhibitors of Candida albicans Virulence Dimorphism: An In Silico and In Vitro Study. Front Cell Infect Microbiol 2021; 11:781790. [PMID: 34926324 PMCID: PMC8677694 DOI: 10.3389/fcimb.2021.781790] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/12/2021] [Indexed: 11/25/2022] Open
Abstract
Farnesol, a self-secreted quorum-sensing molecule (QSM) of Candida albicans, has been known to limit yeast-to-hyphal transition by blocking the RAS1-cAMP-PKA pathway. In a similar fashion, certain bacterial QSMs have also been reported to be successful in attenuating C. albicans biofilm and hyphal formation at relatively high cell density. This prompted us to investigate the antihyphal efficacy of certain bacterial QSMs through virtual docking against seminal drug targets, viz., CYCc and RAS1, that have been reported to be the hallmark players in C. albicans dimorphic virulence cascade. Against this backdrop, 64 QSMs belonging to five different bacterial QS signaling systems were subjected to initial virtual screening with farnesol as reference. Data of the virtual screening unveiled QSMs belonging to diketopiperazines (DKPs), i.e., 3-benzyl-6-isobutylidene-2,5-piperazinedione (QSSM 1157) and cyclo(l-Pro-l-Leu) (QSSM 1112), as potential inhibitors of CYCc and RAS1 with binding energies of -8.2 and -7.3 kcal mol-1, respectively. Further, the molecular dynamics simulations (for 50 ns) of CYCc-QSSM 1157 and RAS1-QSSM 1112 complexes revealed the mean ligand root mean square deviation (RMSD) values of 0.35 and 0.27 Å, respectively, which endorsed the rigid nature, less fluctuation in binding stiffness, and conformation of binding complexes. Furthermore, the identified two QSMs were found to be good in solubility, absorption, and permeation and less toxic in nature, as revealed by pharmacokinetics and toxicity analyses. In addition, the in vitro antihyphal assays using liquid and solid media, germ-tube experiment, and microscopic analysis strongly validated DKP-QSSM 1112 as a promising inhibitor of hyphal transition. Taken together, the present study unequivocally proves that DKPs can be used as potent inhibitors of C. albicans virulence dimorphism.
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Vardi-Kilshtain A, Nitoker N, Major DT. Nuclear quantum effects and kinetic isotope effects in enzyme reactions. Arch Biochem Biophys 2015; 582:18-27. [DOI: 10.1016/j.abb.2015.03.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/02/2015] [Accepted: 03/03/2015] [Indexed: 11/28/2022]
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Abstract
The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of carbohydrate-protein interactions, the survey provides a thorough coverage of the available computational methods and tools. At the quantum-mechanical level, the use of both molecular orbitals and density-functional theory is critically assessed. These are followed by a presentation and critical evaluation of the applications of semiempirical and empirical methods: QM/MM, molecular dynamics, free-energy calculations, metadynamics, molecular robotics, and others. The usefulness of molecular docking in structural glycobiology is evaluated by considering recent docking- validation studies on a range of protein targets. The range of applications of these theoretical methods provides insights into the structural, energetic, and mechanistic facets that occur in the course of the recognition processes. Selected examples are provided to exemplify the usefulness and the present limitations of these computational methods in their ability to assist in elucidation of the structural basis underlying the diverse function and biological roles of carbohydrates in their dialogue with proteins. These test cases cover the field of both carbohydrate biosynthesis and glycosyltransferases, as well as glycoside hydrolases. The phenomenon of (macro)molecular recognition is illustrated for the interactions of carbohydrates with such proteins as lectins, monoclonal antibodies, GAG-binding proteins, porins, and viruses.
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Affiliation(s)
- Serge Pérez
- Department of Molecular Pharmacochemistry, CNRS, University Grenoble-Alpes, Grenoble, France.
| | - Igor Tvaroška
- Department of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic; Department of Chemistry, Faculty of Natural Sciences, Constantine The Philosopher University, Nitra, Slovak Republic.
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Liu M, Wang Y, Chen Y, Field MJ, Gao J. QM/MM through the 1990s: The First Twenty Years of Method Development and Applications. Isr J Chem 2014; 54:1250-1263. [PMID: 29386687 PMCID: PMC5788202 DOI: 10.1002/ijch.201400036] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The 2013 Nobel Prize in Chemistry was awarded to the authors of the first two publications utilizing the concept of combined quantum mechanical and molecular mechanical (QM/MM) methods. In celebrating this great event in computational chemistry, we review the early development of combined QM/MM techniques and the associated events that took place through the mid-1990s. We also offer some prospects for the future development of quantum mechanical techniques for macromolecular systems.
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Affiliation(s)
- Meiyi Liu
- State Key Laboratory of Theoretical and Computational Chemistry, Theoretical Chemistry Institute, Jilin University, Changchun, Jilin Province (China)
| | - Yingjie Wang
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis MN 55455 (USA)
| | - Yakun Chen
- State Key Laboratory of Theoretical and Computational Chemistry, Theoretical Chemistry Institute, Jilin University, Changchun, Jilin Province (China)
| | - Martin J Field
- Institut de Biologie Structrale, CEA, CNRS, umr5075, Université Joseph Fourier - Grenoble I, 6 rue Jules Horowitz, 38000 Grenoble (France)
| | - Jiali Gao
- State Key Laboratory of Theoretical and Computational Chemistry, Theoretical Chemistry Institute, Jilin University, Changchun, Jilin Province (China)
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis MN 55455 (USA)
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Ruiz Pernía JJ, Williams IH. Ensemble-Averaged QM/MM Kinetic Isotope Effects for the SN2 Reaction of Cyanide Anions with Chloroethane in DMSO Solution. Chemistry 2012; 18:9405-14. [DOI: 10.1002/chem.201200443] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Indexed: 11/11/2022]
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Williams IH. Kinetic Isotope Effects from QM/MM Subset Hessians: "Cut-Off" Analysis for SN2 Methyl Transfer in Solution. J Chem Theory Comput 2012; 8:542-53. [PMID: 26596603 DOI: 10.1021/ct200771t] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Isotopic partition-function ratios and kinetic isotope effects for reaction of S-adenosylmethionine with catecholate in water are evaluated using a subset of 324 atoms within its surrounding aqueous environment at the AM1/TIP3P level. Two alternative methods for treating motion in the six librational degrees of freedom of the subset atoms relative to their environment are compared. A series of successively smaller subset Hessians are generated by cumulative deletion of rows and columns from the initial 972 × 972 Hessian. We find that it is better to treat these librations as vibrations than as translations and rotations and that there is no need to invoke the Teller-Redlich product rule. The validity of "cut-off" procedures for computation of isotope effects with truncated atomic subsets is assessed: to ensure errors in ln(KIE) < 1% (or 2% for the quantum-corrected KIE) for all isotopic substitutions considered, it is necessary to use a less-restrictive procedure than is suggested by the familiar two-bond cutoff rule.
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Affiliation(s)
- Ian H Williams
- Department of Chemistry, University of Bath , Bath BA2 7AY, United Kingdom
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Zhang Y, Lin H, Truhlar DG. Self-Consistent Polarization of the Boundary in the Redistributed Charge and Dipole Scheme for Combined Quantum-Mechanical and Molecular-Mechanical Calculations. J Chem Theory Comput 2007; 3:1378-98. [DOI: 10.1021/ct7000107] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yan Zhang
- Chemistry Department, University of Colorado at Denver and Health Sciences Center, Denver, Colorado 80217-3364, and Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Hai Lin
- Chemistry Department, University of Colorado at Denver and Health Sciences Center, Denver, Colorado 80217-3364, and Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Chemistry Department, University of Colorado at Denver and Health Sciences Center, Denver, Colorado 80217-3364, and Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
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Lin H, Zhao Y, Tishchenko O, Truhlar DG. Multiconfiguration Molecular Mechanics Based on Combined Quantum Mechanical and Molecular Mechanical Calculations. J Chem Theory Comput 2006; 2:1237-54. [DOI: 10.1021/ct600171u] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Hai Lin
- Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Chemistry Department, University of Colorado at Denver and Health Science Center, Denver, Colorado 80217-3364
| | - Yan Zhao
- Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Chemistry Department, University of Colorado at Denver and Health Science Center, Denver, Colorado 80217-3364
| | - Oksana Tishchenko
- Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Chemistry Department, University of Colorado at Denver and Health Science Center, Denver, Colorado 80217-3364
| | - Donald G. Truhlar
- Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Chemistry Department, University of Colorado at Denver and Health Science Center, Denver, Colorado 80217-3364
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Newstead S, Watson JN, Knoll TL, Bennet AJ, Taylor G. Structure and Mechanism of Action of an Inverting Mutant Sialidase. Biochemistry 2005; 44:9117-22. [PMID: 15966735 DOI: 10.1021/bi050517t] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mutagenesis of the conserved tyrosine (Y370) of the Micromonospora viridifaciens sialidase to small amino acids changes the mechanism of catalysis from retention of anomeric configuration to inversion [Watson, J. N., et al. (2003) Biochemistry 42, 12682-12690]. For the Y370G mutant enzyme-catalyzed hydrolysis of a series of aryl sialosides and 3'-sialyllactose, the derived Brønsted parameters (beta(lg)) on k(cat) and k(cat)/K(m) are -0.63 +/- 0.05 and -0.80 +/- 0.08, respectively. Thus, for the Y370G enzyme, glycosidic C-O bond cleavage is rate-determining. Analysis of the activity of the Y370G mutant and wild-type enzymes against a substrate [3,4-dihydro-2H-pyrano[3,2-c]pyridinium alpha-d-N-acetylneuraminide (DHP-alphaNeu5Ac)] whose hydrolysis cannot be accelerated by acid catalysis is consistent with these reactions proceeding via S(N)1 and S(N)2 mechanisms, respectively. The overall structure of the Y370G mutant sialidase active site is very similar to the previously reported wild-type structure [Gaskell, A., et al. (1995) Structure 3, 1197-1205], although removal of the tyrosine residue creates two significant changes to the active site. First, the anomeric oxygen atom of the hydrolysis product (beta-N-acetylneuraminic acid) and four water molecules bind in the large cavity created by the Y370G mutation. Second, the side chain of Asn310 moves to make a strong hydrogen bond to one of the bound water molecules.
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Affiliation(s)
- Simon Newstead
- Centre for Biomolecular Science, University of St. Andrews, St. Andrews, Fife KY16 9ST, Scotland
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Ferrer S, Silla E, Tuñón I, Martí S, Moliner V. Catalytic Mechanism of Dihydrofolate Reductase Enzyme. A Combined Quantum-Mechanical/Molecular-Mechanical Characterization of the N5 Protonation Step. J Phys Chem B 2003. [DOI: 10.1021/jp0354898] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Martí S, Andrés J, Moliner V, Silla E, Tuñón I, Bertrán J. A QM/MM Study of the Conformational Equilibria in the Chorismate Mutase Active Site. The Role of the Enzymatic Deformation Energy Contribution. J Phys Chem B 2000. [DOI: 10.1021/jp001888g] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sergio Martí
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castellón (Spain), and Departament de Química Física, Universidad de Valencia, 46100 Burjasot, Valencia (Spain), and Departament de Química, Universidad Autónoma de Barcelona, 08193 Bellaterra, Barcelona (Spain)
| | - Juan Andrés
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castellón (Spain), and Departament de Química Física, Universidad de Valencia, 46100 Burjasot, Valencia (Spain), and Departament de Química, Universidad Autónoma de Barcelona, 08193 Bellaterra, Barcelona (Spain)
| | - Vicent Moliner
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castellón (Spain), and Departament de Química Física, Universidad de Valencia, 46100 Burjasot, Valencia (Spain), and Departament de Química, Universidad Autónoma de Barcelona, 08193 Bellaterra, Barcelona (Spain)
| | - Estanislao Silla
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castellón (Spain), and Departament de Química Física, Universidad de Valencia, 46100 Burjasot, Valencia (Spain), and Departament de Química, Universidad Autónoma de Barcelona, 08193 Bellaterra, Barcelona (Spain)
| | - Iñaki Tuñón
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castellón (Spain), and Departament de Química Física, Universidad de Valencia, 46100 Burjasot, Valencia (Spain), and Departament de Química, Universidad Autónoma de Barcelona, 08193 Bellaterra, Barcelona (Spain)
| | - Juan Bertrán
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castellón (Spain), and Departament de Química Física, Universidad de Valencia, 46100 Burjasot, Valencia (Spain), and Departament de Química, Universidad Autónoma de Barcelona, 08193 Bellaterra, Barcelona (Spain)
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Chou DTH, Watson JN, Scholte AA, Borgford TJ, Bennet AJ. Effect of Neutral Pyridine Leaving Groups on the Mechanisms of Influenza Type A Viral Sialidase-Catalyzed and Spontaneous Hydrolysis Reactions of α-d-N-Acetylneuraminides. J Am Chem Soc 2000. [DOI: 10.1021/ja001641x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Doug T. H. Chou
- Contribution from the Department of Chemistry and the Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Jacqueline N. Watson
- Contribution from the Department of Chemistry and the Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Andrew A. Scholte
- Contribution from the Department of Chemistry and the Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Thor J. Borgford
- Contribution from the Department of Chemistry and the Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Andrew J. Bennet
- Contribution from the Department of Chemistry and the Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
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Castillo R, Andrés J, Moliner V. Catalytic Mechanism of Dihydrofolate Reductase Enzyme. A Combined Quantum-Mechanical/Molecular-Mechanical Characterization of Transition State Structure for the Hydride Transfer Step. J Am Chem Soc 1999. [DOI: 10.1021/ja9843019] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- R. Castillo
- Contribution from the Departament de Ciències Experimentals, Universitat Jaume I, Castelló, Spain
| | - J. Andrés
- Contribution from the Departament de Ciències Experimentals, Universitat Jaume I, Castelló, Spain
| | - V. Moliner
- Contribution from the Departament de Ciències Experimentals, Universitat Jaume I, Castelló, Spain
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Thomas A, Jourand D, Bret C, Amara P, Field MJ. Is There a Covalent Intermediate in the Viral Neuraminidase Reaction? A Hybrid Potential Free-Energy Study. J Am Chem Soc 1999. [DOI: 10.1021/ja991603h] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aline Thomas
- Contribution from the Laboratoire de Dynamique Moléculaire, Institut de Biologie StructuraleJean-Pierre Ebel, 41, rue Jules Horowitz, F-38027 Grenoble Cedex 01, France
| | - David Jourand
- Contribution from the Laboratoire de Dynamique Moléculaire, Institut de Biologie StructuraleJean-Pierre Ebel, 41, rue Jules Horowitz, F-38027 Grenoble Cedex 01, France
| | - Celine Bret
- Contribution from the Laboratoire de Dynamique Moléculaire, Institut de Biologie StructuraleJean-Pierre Ebel, 41, rue Jules Horowitz, F-38027 Grenoble Cedex 01, France
| | - Patricia Amara
- Contribution from the Laboratoire de Dynamique Moléculaire, Institut de Biologie StructuraleJean-Pierre Ebel, 41, rue Jules Horowitz, F-38027 Grenoble Cedex 01, France
| | - Martin J. Field
- Contribution from the Laboratoire de Dynamique Moléculaire, Institut de Biologie StructuraleJean-Pierre Ebel, 41, rue Jules Horowitz, F-38027 Grenoble Cedex 01, France
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Abstract
Numerical simulations of enzyme reaction mechanisms are beginning to provide quantitative as well as qualitative insights. Methods based on hybrid quantum mechanical/molecular mechanical technique permit the natural inclusion of protein solvation effects. Coupled with modern experimental techniques, the numerical simulations are providing details at the atomic level about how enzyme structure influences its function.
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Affiliation(s)
- M A Cunningham
- Center for Mechanistic Biology and Biotechnology, Argonne National Laboratory, IL 60439, USA
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Smith BJ. A Conformational Study of 2-Oxanol: Insight into the Role of Ring Distortion on Enzyme-Catalyzed Glycosidic Bond Cleavage. J Am Chem Soc 1997. [DOI: 10.1021/ja9623020] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Brian J. Smith
- Contribution from the Biomolecular Research Institute, Parkville, Victoria 3052, Australia
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