1
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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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Mhashal AR, Major DT. Temperature-Dependent Kinetic Isotope Effects in R67 Dihydrofolate Reductase from Path-Integral Simulations. J Phys Chem B 2021; 125:1369-1377. [PMID: 33522797 PMCID: PMC7883348 DOI: 10.1021/acs.jpcb.0c10318] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/05/2021] [Indexed: 11/28/2022]
Abstract
Calculation of temperature-dependent kinetic isotope effects (KIE) in enzymes presents a significant theoretical challenge. Additionally, it is not trivial to identify enzymes with available experimental accurate intrinsic KIEs in a range of temperatures. In the current work, we present a theoretical study of KIEs in the primitive R67 dihydrofolate reductase (DHFR) enzyme and compare with experimental work. The advantage of R67 DHFR is its significantly lower kinetic complexity compared to more evolved DHFR isoforms. We employ mass-perturbation-based path-integral simulations in conjunction with umbrella sampling and a hybrid quantum mechanics-molecular mechanics Hamiltonian. We obtain temperature-dependent KIEs in good agreement with experiments and ascribe the temperature-dependent KIEs primarily to zero-point energy effects. The active site in the primitive enzyme is found to be poorly preorganized, which allows excessive water access to the active site and results in loosely bound reacting ligands.
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Affiliation(s)
- Anil R. Mhashal
- Department of Chemistry and Institute
for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and Institute
for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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3
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Toulouse JL, Shi G, Lemay-St-Denis C, Ebert MCCJC, Deon D, Gagnon M, Ruediger E, Saint-Jacques K, Forge D, Vanden Eynde JJ, Marinier A, Ji X, Pelletier JN. Dual-Target Inhibitors of the Folate Pathway Inhibit Intrinsically Trimethoprim-Resistant DfrB Dihydrofolate Reductases. ACS Med Chem Lett 2020; 11:2261-2267. [PMID: 33214838 DOI: 10.1021/acsmedchemlett.0c00393] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/28/2020] [Indexed: 12/11/2022] Open
Abstract
Trimethoprim (TMP) is widely used to treat infections in humans and in livestock, accelerating the incidence of TMP resistance. The emergent and largely untracked type II dihydrofolate reductases (DfrBs) are intrinsically TMP-resistant plasmid-borne Dfrs that are structurally and evolutionarily unrelated to chromosomal Dfrs. We report kinetic characterization of the known DfrB family members. Their kinetic constants are conserved and all are poorly inhibited by TMP, consistent with TMP resistance. We investigate their inhibition with known and novel bisubstrate inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK). Importantly, all are inhibited by the HPPK inhibitors, making these molecules dual-target inhibitors of two folate pathway enzymes that are strictly microbial.
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Affiliation(s)
- Jacynthe L. Toulouse
- Département de biochimie, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
- PROTEO, Quebec G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, Quebec H2V 0B3, Canada
| | - Genbin Shi
- Macromolecular Crystallography Laboratory, NCI, Frederick, Maryland 21702, United States
| | - Claudèle Lemay-St-Denis
- Département de biochimie, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
- PROTEO, Quebec G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, Quebec H2V 0B3, Canada
| | | | - Daniel Deon
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Marc Gagnon
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Edward Ruediger
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Kévin Saint-Jacques
- Département de chimie, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Delphine Forge
- Laboratoire de chimie organique, Université de Mons, 7000 Mons, Belgium
| | | | - Anne Marinier
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Xinhua Ji
- Macromolecular Crystallography Laboratory, NCI, Frederick, Maryland 21702, United States
| | - Joelle N. Pelletier
- Département de biochimie, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
- PROTEO, Quebec G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, Quebec H2V 0B3, Canada
- Département de biochimie, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
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4
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Toulouse J, Yachnin BJ, Ruediger EH, Deon D, Gagnon M, Saint-Jacques K, Ebert MCCC, Forge D, Bastien D, Colin DY, Vanden Eynde JJ, Marinier A, Berghuis AM, Pelletier JN. Structure-Based Design of Dimeric Bisbenzimidazole Inhibitors to an Emergent Trimethoprim-Resistant Type II Dihydrofolate Reductase Guides the Design of Monomeric Analogues. ACS OMEGA 2019; 4:10056-10069. [PMID: 31460098 PMCID: PMC6648814 DOI: 10.1021/acsomega.9b00640] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/22/2019] [Indexed: 05/18/2023]
Abstract
The worldwide use of the broad-spectrum antimicrobial trimethoprim (TMP) has induced the rise of TMP-resistant microorganisms. In addition to resistance-causing mutations of the microbial chromosomal dihydrofolate reductase (Dfr), the evolutionarily and structurally unrelated type II Dfrs (DfrBs) have been identified in TMP-resistant microorganisms. DfrBs are intrinsically TMP-resistant and allow bacterial proliferation when the microbial chromosomal Dfr is TMP-inhibited, making these enzymes important targets for inhibitor development. Furthermore, DfrBs occur in multiresistance plasmids, potentially accelerating their dissemination. We previously reported symmetrical bisbenzimidazoles that are the first selective inhibitors of the only well-characterized DfrB, DfrB1. Here, their diversification provides a new series of inhibitors (K i = 1.7-12.0 μM). Our results reveal two prominent features: terminal carboxylates and inhibitor length allow the establishment of essential interactions with DfrB1. Two crystal structures demonstrate the simultaneous binding of two inhibitor molecules in the symmetrical active site. Observations of those dimeric inhibitors inspired the design of monomeric analogues, binding in a single copy yet offering similar inhibition potency (K i = 1.1 and 7.4 μM). Inhibition of a second member of the DfrB family, DfrB4, suggests the generality of these inhibitors. These results provide key insights into inhibition of the highly TMP-resistant DfrBs, opening avenues to downstream development of antibiotics for combatting this emergent source of resistance.
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Affiliation(s)
- Jacynthe
L. Toulouse
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
- PROTEO,
the Québec Network for Research on Protein, Function, Engineering
and Applications, Quebec G1V 0A6, Canada
- CGCC,
The Center in Green Chemistry and Catalysis, Montréal H3A
0B8, Quebec, Canada
| | - Brahm J. Yachnin
- PROTEO,
the Québec Network for Research on Protein, Function, Engineering
and Applications, Quebec G1V 0A6, Canada
- Department
of Biochemistry, McGill University, Montréal H3A 0G4, Quebec, Canada
| | - Edward H. Ruediger
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
| | - Daniel Deon
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
| | - Marc Gagnon
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
| | - Kévin Saint-Jacques
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
- Département
de Chimie, Université de Sherbrooke, Sherbrooke J1K 0A5, Quebec, Canada
| | | | - Delphine Forge
- Laboratoire
de Chimie Organique, Université de
Mons, Mons 7000, Belgium
| | - Dominic Bastien
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
- PROTEO,
the Québec Network for Research on Protein, Function, Engineering
and Applications, Quebec G1V 0A6, Canada
- CGCC,
The Center in Green Chemistry and Catalysis, Montréal H3A
0B8, Quebec, Canada
| | - Damien Y. Colin
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
- PROTEO,
the Québec Network for Research on Protein, Function, Engineering
and Applications, Quebec G1V 0A6, Canada
- CGCC,
The Center in Green Chemistry and Catalysis, Montréal H3A
0B8, Quebec, Canada
| | | | - Anne Marinier
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
| | - Albert M. Berghuis
- PROTEO,
the Québec Network for Research on Protein, Function, Engineering
and Applications, Quebec G1V 0A6, Canada
- Department
of Biochemistry, McGill University, Montréal H3A 0G4, Quebec, Canada
| | - Joelle N. Pelletier
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
- PROTEO,
the Québec Network for Research on Protein, Function, Engineering
and Applications, Quebec G1V 0A6, Canada
- CGCC,
The Center in Green Chemistry and Catalysis, Montréal H3A
0B8, Quebec, Canada
- E-mail: . Phone: 514-343-2124. Fax: 514-343-7586
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5
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Bhojane P, Duff MR, Bafna K, Agarwal P, Stanley C, Howell EE. Small Angle Neutron Scattering Studies of R67 Dihydrofolate Reductase, a Tetrameric Protein with Intrinsically Disordered N-Termini. Biochemistry 2017; 56:5886-5899. [PMID: 29020453 PMCID: PMC5678894 DOI: 10.1021/acs.biochem.7b00822] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/02/2017] [Indexed: 11/28/2022]
Abstract
R67 dihydrofolate reductase (DHFR) is a homotetramer with a single active site pore and no sequence or structural homology with chromosomal DHFRs. The R67 enzyme provides resistance to trimethoprim, an active site-directed inhibitor of Escherichia coli DHFR. Sixteen to twenty N-terminal amino acids are intrinsically disordered in the R67 dimer crystal structure. Chymotrypsin cleavage of 16 N-terminal residues results in an active enzyme with a decreased stability. The space sampled by the disordered N-termini of R67 DHFR was investigated using small angle neutron scattering. From a combined analysis using molecular dynamics and the program SASSIE ( http://www.smallangles.net/sassie/SASSIE_HOME.html ), the apoenzyme displays a radius of gyration (Rg) of 21.46 ± 0.50 Å. Addition of glycine betaine, an osmolyte, does not result in folding of the termini as the Rg increases slightly to 22.78 ± 0.87 Å. SASSIE fits of the latter SANS data indicate that the disordered N-termini sample larger regions of space and remain disordered, suggesting they might function as entropic bristles. Pressure perturbation calorimetry also indicated that the volume of R67 DHFR increases upon addition of 10% betaine and decreased at 20% betaine because of the dehydration of the protein. Studies of the hydration of full-length R67 DHFR in the presence of the osmolytes betaine and dimethyl sulfoxide find around 1250 water molecules hydrating the protein. Similar studies with truncated R67 DHFR yield around 400 water molecules hydrating the protein in the presence of betaine. The difference of ∼900 waters indicates the N-termini are well-hydrated.
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Affiliation(s)
- Purva
P. Bhojane
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
| | - Michael R. Duff
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
| | - Khushboo Bafna
- Genome
Science and Technology Program, University
of Tennessee, Knoxville, Tennessee 37996-0840, United States
| | - Pratul Agarwal
- Computer
Science and Mathematics Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Christopher Stanley
- Biology
and Soft Matter Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Elizabeth E. Howell
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
- Genome
Science and Technology Program, University
of Tennessee, Knoxville, Tennessee 37996-0840, United States
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6
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Integron-Associated DfrB4, a Previously Uncharacterized Member of the Trimethoprim-Resistant Dihydrofolate Reductase B Family, Is a Clinically Identified Emergent Source of Antibiotic Resistance. Antimicrob Agents Chemother 2017; 61:AAC.02665-16. [PMID: 28242670 DOI: 10.1128/aac.02665-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/11/2017] [Indexed: 01/01/2023] Open
Abstract
Whole-genome sequencing of trimethoprim-resistant Escherichia coli clinical isolates identified a member of the trimethoprim-resistant type II dihydrofolate reductase gene family (dfrB). The dfrB4 gene was located within a class I integron flanked by multiple resistance genes. This arrangement was previously reported in a 130.6-kb multiresistance plasmid. The DfrB4 protein conferred a >2,000-fold increased trimethoprim resistance on overexpression in E. coli Our results are consistent with the finding that dfrB4 contributes to clinical trimethoprim resistance.
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7
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Bhojane P, Duff MR, Bafna K, Rimmer GP, Agarwal PK, Howell EE. Aspects of Weak Interactions between Folate and Glycine Betaine. Biochemistry 2016; 55:6282-6294. [PMID: 27768285 PMCID: PMC5198541 DOI: 10.1021/acs.biochem.6b00873] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/19/2016] [Indexed: 01/22/2023]
Abstract
Folate, or vitamin B9, is an important compound in one-carbon metabolism. Previous studies have found weaker binding of dihydrofolate to dihydrofolate reductase in the presence of osmolytes. In other words, osmolytes are more difficult to remove from the dihydrofolate solvation shell than water; this shifts the equilibrium toward the free ligand and protein species. This study uses vapor-pressure osmometry to explore the interaction of folate with the model osmolyte, glycine betaine. This method yields a preferential interaction potential (μ23/RT value). This value is concentration-dependent as folate dimerizes. The μ23/RT value also tracks the deprotonation of folate's N3-O4 keto-enol group, yielding a pKa of 8.1. To determine which folate atoms interact most strongly with betaine, the interaction of heterocyclic aromatic compounds (as well as other small molecules) with betaine was monitored. Using an accessible surface area approach coupled with osmometry measurements, deconvolution of the μ23/RT values into α values for atom types was achieved. This allows prediction of μ23/RT values for larger molecules such as folate. Molecular dynamics simulations of folate show a variety of structures from extended to L-shaped. These conformers possess μ23/RT values from -0.18 to 0.09 m-1, where a negative value indicates a preference for solvation by betaine and a positive value indicates a preference for water. This range of values is consistent with values observed in osmometry and solubility experiments. As the average predicted folate μ23/RT value is near zero, this indicates folate interacts almost equally well with betaine and water. Specifically, the glutamate tail prefers to interact with water, while the aromatic rings prefer betaine. In general, the more protonated species in our small molecule survey interact better with betaine as they provide a source of hydrogens (betaine is not a hydrogen bond donor). Upon deprotonation of the small molecule, the preference swings toward water interaction because of its hydrogen bond donating capacities.
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Affiliation(s)
- Purva
P. Bhojane
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
| | - Michael R. Duff
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
| | - Khushboo Bafna
- Genome
Science and Technology Program, University
of Tennessee, Knoxville, Tennessee 37996-0840, United States
| | - Gabriella P. Rimmer
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
| | - Pratul K. Agarwal
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
- Genome
Science and Technology Program, University
of Tennessee, Knoxville, Tennessee 37996-0840, United States
- Computer
Science and Mathematics Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Elizabeth E. Howell
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
- Genome
Science and Technology Program, University
of Tennessee, Knoxville, Tennessee 37996-0840, United States
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8
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Halalipour A, Duff MR, Howell EE, Reyes-De-Corcuera JI. Glucose oxidase stabilization against thermal inactivation using high hydrostatic pressure and hydrophobic modification. Biotechnol Bioeng 2016; 114:516-525. [DOI: 10.1002/bit.26185] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/14/2016] [Accepted: 09/13/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Ali Halalipour
- Department of Food Science and Technology; University of Georgia; Food Science Building, 100 Cedar St. Athens, Georgia 30602
| | - Michael R. Duff
- Department of Biochemistry, Cellular and Molecular Biology; University of Tennessee; Knoxville Tennessee
| | - Elizabeth E. Howell
- Department of Biochemistry, Cellular and Molecular Biology; University of Tennessee; Knoxville Tennessee
| | - José I. Reyes-De-Corcuera
- Department of Food Science and Technology; University of Georgia; Food Science Building, 100 Cedar St. Athens, Georgia 30602
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