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Lemay-St-Denis C, Pelletier JN. From a binding module to essential catalytic activity: how nature stumbled on a good thing. Chem Commun (Camb) 2023; 59:12560-12572. [PMID: 37791701 DOI: 10.1039/d3cc04209j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Enzymes are complex macromolecules capable of catalyzing a wide variety of chemical reactions with high efficiency. Nonetheless, biological catalysis can be rudimentary. Here, we describe an enzyme that is built from a simple protein fold. This short protein sequence - almost a peptide - belongs to the ancient SH3 family of binding modules. Surprisingly, this binding module catalyzes the specific reduction of dihydrofolate using NADPH as a reducing cofactor, making this a dihydrofolate reductase. Too small to provide all the required binding and catalytic machinery on its own, it homotetramerizes, thus creating a large, central active site environment. Remarkably, none of the active site residues is essential to the catalytic function. Instead, backbone interactions juxtapose the reducing cofactor proximal to the target imine of the folate substrate, and a specific motion of the substrate promotes formation of the transition state. In this feature article, we describe the features that make this small protein a functional enzyme capable of catalyzing a metabolically essential reaction, highlighting the characteristics that make it a model for the evolution of primitive enzymes from binding modules.
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Affiliation(s)
- Claudèle Lemay-St-Denis
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
| | - Joelle N Pelletier
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
- Chemistry Department, Université de Montréal, Montreal, QC, Canada.
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2
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Fuente-Gómez GJ, Kellum CL, Miranda AC, Duff MR, Howell EE. Differentiation of the binding of two ligands to a tetrameric protein with a single symmetric active site by 19 F NMR. Protein Sci 2020; 30:477-484. [PMID: 33269489 PMCID: PMC7784773 DOI: 10.1002/pro.4007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/20/2020] [Accepted: 11/26/2020] [Indexed: 01/31/2023]
Abstract
R67 dihydrofolate reductase (R67 DHFR) is a plasmid‐encoded enzyme that confers resistance to the antibacterial drug trimethoprim. R67 DHFR is a tetramer with a single active site that is unusual as both cofactor and substrate are recognized by symmetry‐related residues. Such promiscuity has limited our previous efforts to differentiate ligand binding by NMR. To address this problem, we incorporated fluorine at positions 4, 5, 6, or 7 of the indole rings of tryptophans 38 and 45 and characterized the spectra to determine which probe was optimal for studying ligand binding. Two resonances were observed for all apo proteins. Unexpectedly, the W45 resonance appeared broad, and truncation of the disordered N‐termini resulted in the appearance of one sharp W45 resonance. These results are consistent with interaction of the N‐terminus with W45. Binding of the cofactor broadened W38 for all fluorine probes, whereas substrate, dihydrofolate, binding resulted in the appearance of three new resonances for 4‐ and 5‐fluoroindole labeled protein and severe line broadening for 6‐ and 7‐fluoroindole R67 DHFR. W45 became slightly broader upon ligand binding. With only two peaks in the 19F NMR spectra, our data were able to differentiate cofactor and substrate binding to the single, symmetric active site of R67 DHFR and yield binding affinities.
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Affiliation(s)
- Gabriel J Fuente-Gómez
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee, USA
| | - Creighton L Kellum
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee, USA
| | - Alexis C Miranda
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee, USA
| | - Michael R Duff
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee, USA
| | - Elizabeth E Howell
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee, USA
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3
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Bastien D, Ebert MCCJC, Forge D, Toulouse J, Kadnikova N, Perron F, Mayence A, Huang TL, Vanden Eynde JJ, Pelletier JN. Fragment-Based Design of Symmetrical Bis-benzimidazoles as Selective Inhibitors of the Trimethoprim-Resistant, Type II R67 Dihydrofolate Reductase. J Med Chem 2012; 55:3182-92. [DOI: 10.1021/jm201645r] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dominic Bastien
- Département de Biochimie, Université de Montréal, C.P. 6128, Succ.
Centre-ville Montréal, Québec H3C 3J7, Canada
| | - Maximilian C. C. J. C. Ebert
- Département de Biochimie, Université de Montréal, C.P. 6128, Succ.
Centre-ville Montréal, Québec H3C 3J7, Canada
| | - Delphine Forge
- Laboratoire de Chimie Organique, Université de Mons-UMONS, 20 Place du Parc,
B-7000 Mons, Belgium
| | - Jacynthe Toulouse
- Département de Biochimie, Université de Montréal, C.P. 6128, Succ.
Centre-ville Montréal, Québec H3C 3J7, Canada
| | - Natalia Kadnikova
- Département
de Chimie, Université de Montréal, C.P. 6128, Succursale
Centre-ville Montréal, Québec H3C 3J7, Canada
| | - Florent Perron
- Laboratoire de Chimie Organique, Université de Mons-UMONS, 20 Place du Parc,
B-7000 Mons, Belgium
| | - Annie Mayence
- Division of Basic Pharmaceutical
Sciences, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125, United States
| | - Tien L. Huang
- Division of Basic Pharmaceutical
Sciences, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125, United States
| | | | - Joelle N. Pelletier
- Département de Biochimie, Université de Montréal, C.P. 6128, Succ.
Centre-ville Montréal, Québec H3C 3J7, Canada
- Département
de Chimie, Université de Montréal, C.P. 6128, Succursale
Centre-ville Montréal, Québec H3C 3J7, Canada
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4
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Jogalekar AS, Damodaran K, Kriel FH, Jung WH, Alcaraz AA, Zhong S, Curran DP, Snyder JP. Dictyostatin Flexibility Bridges Conformations in Solution and in the β-Tubulin Taxane Binding Site. J Am Chem Soc 2011; 133:2427-36. [DOI: 10.1021/ja1023817] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ashutosh S. Jogalekar
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Krishnan Damodaran
- Department of Chemistry, University of Pittsburgh, 1101 Chevron Science Center, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260-3900, United States
| | - Frederik H. Kriel
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Won-Hyuk Jung
- Department of Chemistry, University of Pittsburgh, 1101 Chevron Science Center, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260-3900, United States
| | - Ana A. Alcaraz
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Shi Zhong
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Dennis P. Curran
- Department of Chemistry, University of Pittsburgh, 1101 Chevron Science Center, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260-3900, United States
| | - James P. Snyder
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
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Kamath G, Howell EE, Agarwal PK. The Tail Wagging the Dog: Insights into Catalysis in R67 Dihydrofolate Reductase. Biochemistry 2010; 49:9078-88. [DOI: 10.1021/bi1007222] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ganesh Kamath
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Elizabeth E. Howell
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Pratul K. Agarwal
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
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6
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Krahn JM, Jackson MR, DeRose EF, Howell EE, London RE. Crystal structure of a type II dihydrofolate reductase catalytic ternary complex. Biochemistry 2007; 46:14878-88. [PMID: 18052202 PMCID: PMC3743094 DOI: 10.1021/bi701532r] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Type II dihydrofolate reductase (DHFR) is a plasmid-encoded enzyme that confers resistance to bacterial DHFR-targeted antifolate drugs. It forms a symmetric homotetramer with a central pore which functions as the active site. Its unusual structure, which results in a promiscuous binding surface that accommodates either the dihydrofolate (DHF) substrate or the NADPH cofactor, has constituted a significant limitation to efforts to understand its substrate specificity and reaction mechanism. We describe here the first structure of a ternary R67 DHFR.DHF.NADP+ catalytic complex, resolved to 1.26 A. This structure provides the first clear picture of how this enzyme, which lacks the active site carboxyl residue that is ubiquitous in Type I DHFRs, is able to function. In the catalytic complex, the polar backbone atoms of two symmetry-related I68 residues provide recognition motifs that interact with the carboxamide on the nicotinamide ring, and the N3-O4 amide function on the pteridine ring. This set of interactions orients the aromatic rings of substrate and cofactor in a relative endo geometry in which the reactive centers are held in close proximity. Additionally, a central, hydrogen-bonded network consisting of two pairs of Y69-Q67-Q67'-Y69' residues provides an unusually tight interface, which appears to serve as a "molecular clamp" holding the substrates in place in an orientation conducive to hydride transfer. In addition to providing the first clear insight regarding how this extremely unusual enzyme is able to function, the structure of the ternary complex provides general insights into how a mutationally challenged enzyme, i.e., an enzyme whose evolution is restricted to four-residues-at-a-time active site mutations, overcomes this fundamental limitation.
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Affiliation(s)
- Joseph M. Krahn
- Laboratory of Structural Biology, MR-01, National Institute of Environmental Health Sciences, National Institutes of Health, Box 12233, Research Triangle Park, North Carolina 27709
| | - Michael R. Jackson
- Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996-0840
| | - Eugene F. DeRose
- Laboratory of Structural Biology, MR-01, National Institute of Environmental Health Sciences, National Institutes of Health, Box 12233, Research Triangle Park, North Carolina 27709
| | - Elizabeth E. Howell
- Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996-0840
| | - Robert E. London
- Laboratory of Structural Biology, MR-01, National Institute of Environmental Health Sciences, National Institutes of Health, Box 12233, Research Triangle Park, North Carolina 27709
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7
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Rational design of peptide ligand for affinity chromatography of tissue-type plasminogen activator by the combination of docking and molecular dynamics simulations. J Chromatogr A 2007; 1175:249-58. [DOI: 10.1016/j.chroma.2007.10.074] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Revised: 10/22/2007] [Accepted: 10/23/2007] [Indexed: 10/22/2022]
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Chopra S, Lynch R, Kim SH, Jackson M, Howell EE. Effects of temperature and viscosity on R67 dihydrofolate reductase catalysis. Biochemistry 2006; 45:6596-605. [PMID: 16716070 DOI: 10.1021/bi052504l] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
R67 dihydrofolate reductase (DHFR) is a novel homotetrameric protein that possesses 222 symmetry and a single, voluminous active site pore. This symmetry poses numerous limitations on catalysis; for example, two dihydrofolate (DHF) molecules or two NADPH molecules, or one substrate plus one cofactor can bind. Only the latter combination leads to catalysis. To garner additional information on how this enzyme facilitates transition-state formation, the temperature dependence of binding and catalysis was monitored. The binding of NADPH and DHF is enthalpy-driven. Previous primary isotope effect studies indicate hydride transfer is at least partially rate-determining. Accordingly, the activation energy associated with transition-state formation was measured and is found to be 6.9 kcal/mol (DeltaH(++)(25) = 6.3 kcal/mol). A large entropic component is also found associated with catalysis, TDeltaS(++)(25) = -11.3 kcal/mol. The poor substrate, dihydropteroate, binds more weakly than dihydrofolate (DeltaDeltaG = 1.4 kcal/mol) and displays a large loss in the binding enthalpy value (DeltaDeltaH = 3.8 kcal/mol). The k(cat) value for dihydropteroate reduction is decreased 1600-fold compared to DHF usage. This effect appears to derive mostly from the DeltaDeltaH difference in binding, demonstrating that the glutamate tail is important for catalysis. This result is surprising, as the para-aminobenzoyl-glutamate tail of DHF has been previously shown to be disordered by both NMR and crystallography studies. Viscosity studies were also performed and confirmed that the hydride transfer rate is not sensitive to sucrose addition. Surprisingly, binding of DHF, by both K(m) and K(d) determination, was found to be sensitive to added viscogens, suggesting a role for water in DHF binding.
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Affiliation(s)
- Shaileja Chopra
- Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, USA
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9
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Alonso H, Gready JE. Integron-sequestered dihydrofolate reductase: a recently redeployed enzyme. Trends Microbiol 2006; 14:236-42. [PMID: 16584884 DOI: 10.1016/j.tim.2006.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2005] [Revised: 03/01/2006] [Accepted: 03/21/2006] [Indexed: 11/21/2022]
Abstract
The introduction and wide use of antibacterial drugs has resulted in the emergence of resistant organisms. DfrB dihydrofolate reductase (DHFR) is a bacterial enzyme that is uniquely associated with mobile gene cassettes within integrons, and confers resistance to the drug trimethoprim. This enzyme has intrigued microbiologists since it was discovered more than thirty years ago because of its simple structure, enzymatic inefficiency and its virtual insensitivity to trimethoprim. Here, for the first time, a comprehensive discussion of genetic, evolutionary, structural and functional studies of this enzyme is presented together. This information supports the ideas that DfrB DHFR is a poorly adapted catalyst and has recently been recruited to perform a novel enzymatic activity in response to selective pressure.
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Affiliation(s)
- Hernán Alonso
- Division of Molecular Bioscience, John Curtin School of Medical Research, Australian National University, Canberra, ACT 0200, Australia
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10
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Hetényi C, van der Spoel D. Blind docking of drug-sized compounds to proteins with up to a thousand residues. FEBS Lett 2006; 580:1447-50. [PMID: 16460734 DOI: 10.1016/j.febslet.2006.01.074] [Citation(s) in RCA: 219] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2005] [Revised: 12/20/2005] [Accepted: 01/24/2006] [Indexed: 10/25/2022]
Abstract
Blind docking was introduced for the detection of possible binding sites and modes of peptide ligands by scanning the entire surface of protein targets. In the present study, the method is tested on a group of drug-sized compounds and proteins with up to a thousand amino acid residues. Both proteins from complex structures and ligand-free proteins were used as targets. Robustness, limitations and future perspectives of the method are discussed. It is concluded that blind docking can be used for unbiased mapping of the binding patterns of drug candidates.
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Affiliation(s)
- Csaba Hetényi
- Department of Biochemistry, Eötvös Loránd University, 1/C Pázmány P. sétány, 1117 Budapest, Hungary.
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Alonso H, Bliznyuk AA, Gready JE. Combining docking and molecular dynamic simulations in drug design. Med Res Rev 2006; 26:531-68. [PMID: 16758486 DOI: 10.1002/med.20067] [Citation(s) in RCA: 438] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A rational approach is needed to maximize the chances of finding new drugs, and to exploit the opportunities of potential new drug targets emerging from genomic and proteomic initiatives, and from the large libraries of small compounds now readily available through combinatorial chemistry. Despite a shaky early history, computer-aided drug design techniques can now be effective in reducing costs and speeding up drug discovery. This happy outcome results from development of more accurate and reliable algorithms, use of more thoughtfully planned strategies to apply them, and greatly increased computer power to allow studies with the necessary reliability to be performed. Our review focuses on applications and protocols, with the main emphasis on critical analysis of recent studies where docking calculations and molecular dynamics (MD) simulations were combined to dock small molecules into protein receptors. We highlight successes to demonstrate what is possible now, but also point out drawbacks and future directions. The review is structured to lead the reader from the simpler to more compute-intensive methods. Thus, while inexpensive and fast docking algorithms can be used to scan large compound libraries and reduce their size, more accurate but expensive MD simulations can be applied when a few selected ligand candidates remain. MD simulations can be used: during the preparation of the protein receptor before docking, to optimize its structure and account for protein flexibility; for the refinement of docked complexes, to include solvent effects and account for induced fit; to calculate binding free energies, to provide an accurate ranking of the potential ligands; and in the latest developments, during the docking process itself to find the binding site and correctly dock the ligand a priori.
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Affiliation(s)
- Hernán Alonso
- Computational Proteomics Group, John Curtin School of Medical Research, The Australian National University, Canberra ACT 0200, Australia
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