1
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van Neer RHP, Dranchak PK, Liu L, Aitha M, Queme B, Kimura H, Katoh T, Battaile KP, Lovell S, Inglese J, Suga H. Serum-Stable and Selective Backbone-N-Methylated Cyclic Peptides That Inhibit Prokaryotic Glycolytic Mutases. ACS Chem Biol 2022; 17:2284-2295. [PMID: 35904259 PMCID: PMC9900472 DOI: 10.1021/acschembio.2c00403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
N-Methylated amino acids (N-MeAAs) are privileged residues of naturally occurring peptides critical to bioactivity. However, de novo discovery from ribosome display is limited by poor incorporation of N-methylated amino acids into the nascent peptide chain attributed to a poor EF-Tu affinity for the N-methyl-aminoacyl-tRNA. By reconfiguring the tRNA's T-stem region to compensate and tune the EF-Tu affinity, we conducted Random nonstandard Peptides Integrated Discovery (RaPID) display of a macrocyclic peptide (MCP) library containing six different N-MeAAs. We have here devised a "pool-and-split" enrichment strategy using the RaPID display and identified N-methylated MCPs against three species of prokaryotic metal-ion-dependent phosphoglycerate mutases. The enriched MCPs reached 57% N-methylation with up to three consecutively incorporated N-MeAAs, rivaling natural products. Potent nanomolar inhibitors ranging in ortholog selectivity, strongly mediated by N-methylation, were identified. Co-crystal structures reveal an architecturally related Ce-2 Ipglycermide active-site metal-ion-coordinating Cys lariat MCP, functionally dependent on two cis N-MeAAs with broadened iPGM species selectivity over the original nematode-selective MCPs. Furthermore, the isolation of a novel metal-ion-independent Staphylococcus aureus iPGM inhibitor utilizing a phosphoglycerate mimetic mechanism illustrates the diversity of possible chemotypes encoded by the N-MeAA MCP library.
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Affiliation(s)
- R H P van Neer
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - P K Dranchak
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - L Liu
- Protein Structure and X-ray Crystallography Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas 66045, United States
| | - M Aitha
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - B Queme
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - H Kimura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - T Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - K P Battaile
- New York Structural Biology Center, NSLS-II, Upton, New York 11973, United States
| | - S Lovell
- Protein Structure and X-ray Crystallography Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas 66045, United States
| | - J Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - H Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
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2
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Wiedmann M, Dranchak PK, Aitha M, Queme B, Collmus CD, Kashipathy MM, Kanter L, Lamy L, Rogers JM, Tao D, Battaile KP, Rai G, Lovell S, Suga H, Inglese J. Structure-activity relationship of ipglycermide binding to phosphoglycerate mutases. J Biol Chem 2021; 296:100628. [PMID: 33812994 PMCID: PMC8113725 DOI: 10.1016/j.jbc.2021.100628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/26/2021] [Accepted: 03/31/2021] [Indexed: 01/11/2023] Open
Abstract
Catalysis of human phosphoglycerate mutase is dependent on a 2,3-bisphosphoglycerate cofactor (dPGM), whereas the nonhomologous isozyme in many parasitic species is cofactor independent (iPGM). This mechanistic and phylogenetic diversity offers an opportunity for selective pharmacologic targeting of glycolysis in disease-causing organisms. We previously discovered ipglycermide, a potent inhibitor of iPGM, from a large combinatorial cyclic peptide library. To fully delineate the ipglycermide pharmacophore, herein we construct a detailed structure–activity relationship using 280 substituted ipglycermide analogs. Binding affinities of these analogs to immobilized Caenorhabditis elegans iPGM, measured as fold enrichment relative to the index residue by deep sequencing of an mRNA display library, illuminated the significance of each amino acid to the pharmacophore. Using cocrystal structures and binding kinetics, we show that the high affinity of ipglycermide for iPGM orthologs, from Brugia malayi, Onchocerca volvulus, Dirofilaria immitis, and Escherichia coli, is achieved by a codependence between (1) the off-rate mediated by the macrocycle Cys14 thiolate coordination to an active-site Zn2+ in the iPGM phosphatase domain and (2) shape complementarity surrounding the macrocyclic core at the phosphotransferase–phosphatase domain interface. Our results show that the high-affinity binding of ipglycermide to iPGMs freezes these structurally dynamic enzymes into an inactive, stable complex.
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Affiliation(s)
- Mareike Wiedmann
- Department of Chemistry, Graduate School of Sciences, The University of Tokyo, Tokyo, Japan
| | - Patricia K Dranchak
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Mahesh Aitha
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Bryan Queme
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Christopher D Collmus
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Maithri M Kashipathy
- Protein Structure Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas, USA
| | - Liza Kanter
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Laurence Lamy
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Joseph M Rogers
- Department of Chemistry, Graduate School of Sciences, The University of Tokyo, Tokyo, Japan
| | - Dingyin Tao
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Kevin P Battaile
- IMCA-CAT Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, USA
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Scott Lovell
- Protein Structure Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas, USA
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Sciences, The University of Tokyo, Tokyo, Japan.
| | - James Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA; National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA.
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3
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Hedglin M, Aitha M, Pedley A, Benkovic SJ. Replication protein A dynamically regulates monoubiquitination of proliferating cell nuclear antigen. J Biol Chem 2019; 294:5157-5168. [PMID: 30700555 DOI: 10.1074/jbc.ra118.005297] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 01/17/2019] [Indexed: 11/06/2022] Open
Abstract
DNA damage tolerance permits bypass of DNA lesions encountered during S-phase and may be carried out by translesion DNA synthesis (TLS). Human TLS requires selective monoubiquitination of proliferating cell nuclear antigen (PCNA) sliding clamps encircling damaged DNA. This posttranslational modification (PTM) is catalyzed by Rad6/Rad18. Recent studies revealed that replication protein A (RPA), the major ssDNA-binding protein, is involved in the regulation of PCNA monoubiquitination and interacts directly with Rad18 on chromatin and in the nucleoplasm. However, it is unclear how RPA regulates this critical PTM and what functional role(s) these interactions serve. Here, we developed an in vitro assay to quantitatively monitor PCNA monoubiquitination under in vivo scenarios. Results from extensive experiments revealed that RPA regulates Rad6/Rad18 activity in an ssDNA-dependent manner. We found that "DNA-free" RPA inhibits monoubiquitination of free PCNA by directly interacting with Rad18. This interaction is promoted under native conditions when there is an overabundance of free RPA in the nucleoplasm where Rad6/Rad18 and a significant fraction of PCNA reside. During DNA replication stress, RPA binds the ssDNA exposed downstream of stalled primer/template (P/T) junctions, releasing Rad6/Rad18. RPA restricted the resident PCNAs to the upstream duplex regions by physically blocking diffusion of PCNA along ssDNA, and this activity was required for efficient monoubiquitination of PCNA on DNA. Furthermore, upon binding ssDNA, RPA underwent a conformational change that increased its affinity for Rad18. Rad6/Rad18 complexed with ssDNA-bound RPA was active, and this interaction may selectively promote monoubiquitination of PCNA on long RPA-coated ssDNA.
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Affiliation(s)
- Mark Hedglin
- From the Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Mahesh Aitha
- From the Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Anthony Pedley
- From the Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Stephen J Benkovic
- From the Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
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4
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Bergstrom A, Katko A, Adkins Z, Hill J, Cheng Z, Burnett M, Yang H, Aitha M, Mehaffey MR, Brodbelt JS, Tehrani KHME, Martin NI, Bonomo RA, Page RC, Tierney DL, Fast W, Wright GD, Crowder MW. Probing the Interaction of Aspergillomarasmine A with Metallo-β-lactamases NDM-1, VIM-2, and IMP-7. ACS Infect Dis 2018; 4:135-145. [PMID: 29091730 DOI: 10.1021/acsinfecdis.7b00106] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Metallo-β-lactamases (MBLs) are a growing threat to the continued efficacy of β-lactam antibiotics. Recently, aspergillomarasmine A (AMA) was identified as an MBL inhibitor, but the mode of inhibition was not fully characterized. Equilibrium dialysis and metal analysis studies revealed that 2 equiv of AMA effectively removes 1 equiv of Zn(II) from MBLs NDM-1, VIM-2, and IMP-7 when the MBL is at micromolar concentrations. Conversely, 1H NMR studies revealed that 2 equiv of AMA remove 2 equiv of Co(II) from Co(II)-substituted NDM-1, VIM-2, and IMP-7 when the MBL/AMA are at millimolar concentrations. Our findings reveal that AMA inhibits the MBLs by removal of the active site metal ions required for β-lactam hydrolysis among the most clinically significant MBLs.
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Affiliation(s)
- Alexander Bergstrom
- Department of Chemistry
and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Andrew Katko
- Department of Chemistry
and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Zach Adkins
- Department of Chemistry
and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Jessica Hill
- Department of Chemistry
and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Zishuo Cheng
- Department of Chemistry
and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Mia Burnett
- Department of Chemistry
and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Hao Yang
- Department of Chemistry
and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Mahesh Aitha
- Department of Chemistry
and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - M. Rachel Mehaffey
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Kamaleddin H. M. E. Tehrani
- Department of Chemical Biology and Drug
Discovery Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Nathaniel I. Martin
- Department of Chemical Biology and Drug
Discovery Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Robert A. Bonomo
- Research
Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 10701 East Boulevard, Cleveland, Ohio 44106, United States
| | - Richard C. Page
- Department of Chemistry
and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - David L. Tierney
- Department of Chemistry
and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Walter Fast
- Division of Chemical Biology and Medicinal Chemistry,
College of Pharmacy, University of Texas, 107 W. Dean Keeton, Austin, Texas 78712, United States
| | - Gerard D. Wright
- Michael
G DeGroote Institute for Infectious Disease and Department of Biochemistry
and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4L8, Canada
| | - Michael W. Crowder
- Department of Chemistry
and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
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5
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Hedglin M, Aitha M, Benkovic SJ. Monitoring the Retention of Human Proliferating Cell Nuclear Antigen at Primer/Template Junctions by Proteins That Bind Single-Stranded DNA. Biochemistry 2017; 56:3415-3421. [PMID: 28590137 DOI: 10.1021/acs.biochem.7b00386] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In humans, proliferating cell nuclear antigen (PCNA) sliding clamps encircling DNA coordinate various aspects of DNA metabolism throughout the cell cycle. A critical aspect of this is restricting PCNA to the vicinity of its DNA target site. For example, PCNA must be maintained at or near primer/template (P/T) junctions during DNA synthesis. With a diverse array of cellular factors implicated, many of which interact with PCNA, DNA, or both, it is unknown how this critical feat is achieved. Furthermore, current biochemical assays that examine the retention of PCNA near P/T junctions are inefficient, discontinuous, and qualitative and significantly deviate from physiologically relevant conditions. To overcome these challenges and limitations, we recently developed a novel and convenient Förster resonance energy transfer (FRET) assay that directly and continuously monitors the retention of human PCNA at a P/T junction. Here we describe in detail the design, methodology, interpretation, and limitations of this quantitative FRET assay using the single-stranded DNA-binding protein, SSB, from Escherichia coli as an example. This powerful tool is broadly applicable to any single-stranded DNA-binding protein and may be utilized and/or expanded upon to dissect DNA metabolic pathways that are dependent upon PCNA.
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Affiliation(s)
- Mark Hedglin
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Mahesh Aitha
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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6
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Meng F, Yang H, Aitha M, George S, Tierney DL, Crowder MW. Biochemical and spectroscopic characterization of the catalytic domain of MMP16 (cdMMP16). J Biol Inorg Chem 2016; 21:523-35. [PMID: 27229514 DOI: 10.1007/s00775-016-1362-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/07/2016] [Indexed: 11/25/2022]
Abstract
Membrane-bound matrix metalloproteinase 16 (MMP16/MT3-MMP) is considered a drug target due to its role(s) in disease processes such as cancer and inflammation. Biochemical characterization of MMP16 is critical for developing new generation MMP inhibitors (MMPi), which exhibit high efficacies and selectivities. Herein, a modified over-expression and purification protocol was used to prepare the catalytic domain of MMP16 (cdMMP16). The resulting recombinant enzyme exhibited steady-state kinetic constants of K m = 10.6 ± 0.7 μM and k cat = 1.14 ± 0.02 s(-1), when using FS-6 as substrate, and the enzyme bound 1.8 ± 0.1 eq of Zn(II). The enzymatic activity of cdMMP16 is salt concentration-dependent, and cdMMP16 exhibits autoproteolytic activity under certain conditions, which may be related to an in vivo regulatory mechanism of MMP16 and of other membrane-type MMPs (MT-MMPs). Co(II)-substituted analogs (Co2- and ZnCo) of cdMMP16 were prepared and characterized using several spectroscopic techniques, such as UV-Vis, (1)H NMR, and EXAFS spectroscopies. A well-characterized cdMMP16 is now available for future inhibitor screening efforts.
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Affiliation(s)
- Fan Meng
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Hao Yang
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Mahesh Aitha
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Sam George
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - David L Tierney
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA.
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA.
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7
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Aitha M, Moller AJ, Sahu ID, Horitani M, Tierney DL, Crowder MW. Investigating the position of the hairpin loop in New Delhi metallo-β-lactamase, NDM-1, during catalysis and inhibitor binding. J Inorg Biochem 2016; 156:35-9. [PMID: 26717260 PMCID: PMC4843777 DOI: 10.1016/j.jinorgbio.2015.10.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 10/07/2015] [Accepted: 10/19/2015] [Indexed: 12/29/2022]
Abstract
In an effort to examine the relative position of a hairpin loop in New Delhi metallo-β-lactamase, NDM-1, during catalysis, rapid freeze quench double electron electron resonance (RFQ-DEER) spectroscopy was used. A doubly-labeled mutant of NDM-1, which had one spin label on the invariant loop at position 69 and another label at position 235, was prepared and characterized. The reaction of the doubly spin labeled mutant with chromacef was freeze quenched at 500μs and 10ms. DEER results showed that the average distance between labels decreased by 4Å in the 500μs quenched sample and by 2Å in the 10ms quenched sample, as compared to the distance in the unreacted enzyme, although the peaks corresponding to distance distributions were very broad. DEER spectra with the doubly spin labeled enzyme with two inhibitors showed that the distance between the loop residue at position 69 and the spin label at position 235 does not change upon inhibitor binding. This study suggests that the hairpin loop in NDM-1 moves over the metal ion during the catalysis and then moves back to its original position after hydrolysis, which is consistent with a previous hypothesis based on NMR solution studies on a related metallo-β-lactamase. This study also demonstrates that this loop motion occurs in the millisecond time domain.
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Affiliation(s)
- Mahesh Aitha
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, OH 45056, USA
| | - Abraham J Moller
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, OH 45056, USA
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, OH 45056, USA
| | - Masaki Horitani
- Department of Chemistry, Northwestern University, Evanston, IL 60208-3113, USA
| | - David L Tierney
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, OH 45056, USA
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, OH 45056, USA.
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8
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Aitha M, Al-Adbul-Wahid S, Tierney DL, Crowder MW. Probing substrate binding to the metal binding sites in metallo-β-lactamase L1 during catalysis. Medchemcomm 2016; 7:194-201. [PMID: 27087914 DOI: 10.1039/c5md00358j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metal ions in metallo-β-lactamases (MBLs) play a major role in catalysis. In this study we investigated the role of the metal ions in the Zn1 and Zn2 sites of MBL L1 during catalysis. A ZnCo (with Zn(II) in the invariant Zn1 site and Co(II) in the Zn2 site) analog of MBL L1 was prepared by using a biological incorporation method. Extended X-ray Absorption Fine Structure (EXAFS) spectroscopic studies were used to confirm that the ZnCo analog was prepared. To study the roles of the Zn(II) and Co(II) ions during catalysis, rapid freeze quench (RFQ)-EXAFS studies were used to probe the reaction of the ZnCo-L1 analog with chromacef when quenched at 10 ms, 50 ms, and 100 ms. The L1-product complex was also analyzed with EXAFS spectroscopy. The data show that the Zn-Co distance is 3.49 Å in the resting enzyme and that this distance increases by 0.3 Å in the sample that was quenched at 10 ms. The average Zn-Co distance decreases at the other time points until reaching a distance of 3.58 Å in the L1-product complex. The data also show that a Co-S interaction is present in the 100 ms quenched sample and in the L1-product complex, which suggests that there is a significant rearrangement of product in the active site.
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Affiliation(s)
- Mahesh Aitha
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Sameer Al-Adbul-Wahid
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - David L Tierney
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
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9
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Aitha M, Al-Abdul-Wahid S, Tierney DL, Crowder MW. Correction: Probing substrate binding to the metal binding sites in metallo-β-lactamase L1 during catalysis. Med Chem Commun 2016. [DOI: 10.1039/c6md90019d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Mahesh Aitha
- Department of Chemistry and Biochemistry
- Miami University
- Oxford
- USA
| | | | - David L. Tierney
- Department of Chemistry and Biochemistry
- Miami University
- Oxford
- USA
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10
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Abstract
Matrix metalloproteinase-1 (MMP-1) plays crucial roles in disease-related physiologies and pathological processes in the human body. We report here solution studies of MMP-1, including characterization of a series of mutants designed to bind metal in either the catalytic site or the structural site (but not both). Circular dichroism and fluorescence spectroscopy of the mutants demonstrate the importance of the structural Zn(II) in maintaining both secondary and tertiary structure, while UV-visible, nuclear magnetic resonance, electron paramagnetic resonance, and extended X-ray absorption fine structure show its presence influences the catalytic metal ion's coordination number. The mutants allow us to demonstrate convincingly the preparation of a mixed-metal analogue, Co(C)Zn(S)-MMP-1, with Zn(II) in the structural site and Co(II) in the catalytic site. Stopped-flow fluorescence of the native form, Zn(C)Zn(S)-MMP-1, and the mixed-metal Co(C)Zn(S)-MMP-1 analogue shows that the internal fluorescence of a nearby Trp residue is modulated with catalysis and can be used to monitor reactivity under a number of conditions, opening the door to substrate profiling.
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Affiliation(s)
- Hao Yang
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Katherine Makaroff
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Nicholas Paz
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Mahesh Aitha
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - David L Tierney
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
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11
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Aitha M, Moritz L, Sahu ID, Sanyurah O, Roche Z, McCarrick R, Lorigan GA, Bennett B, Crowder MW. Conformational dynamics of metallo-β-lactamase CcrA during catalysis investigated by using DEER spectroscopy. J Biol Inorg Chem 2015; 20:585-94. [PMID: 25827593 PMCID: PMC4733638 DOI: 10.1007/s00775-015-1244-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 01/26/2015] [Indexed: 10/24/2022]
Abstract
Previous crystallographic and mutagenesis studies have implicated the role of a position-conserved hairpin loop in the metallo-β-lactamases in substrate binding and catalysis. In an effort to probe the motion of that loop during catalysis, rapid-freeze-quench double electron-electron resonance (RFQ-DEER) spectroscopy was used to interrogate metallo-β-lactamase CcrA, which had a spin label at position 49 on the loop and spin labels (at positions 82, 126, or 233) 20-35 Å away from residue 49, during catalysis. At 10 ms after mixing, the DEER spectra show distance increases of 7, 10, and 13 Å between the spin label at position 49 and the spin labels at positions 82, 126, and 233, respectively. In contrast to previous hypotheses, these data suggest that the loop moves nearly 10 Å away from the metal center during catalysis and that the loop does not clamp down on the substrate during catalysis. This study demonstrates that loop motion during catalysis can be interrogated on the millisecond time scale.
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Affiliation(s)
- Mahesh Aitha
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Lindsay Moritz
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Indra D. Sahu
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Omar Sanyurah
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Zahilyn Roche
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Robert McCarrick
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Gary A. Lorigan
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Brian Bennett
- Physics Department, Marquette University, 540 N. 15th Street, Milwaukee, Wisconsin 53233, USA, and Department of Biophysics, Medical College of Wisconsin, 8701 W. Watertown Plank Road, Milwaukee, Wisconsin 53226, USA
| | - Michael W. Crowder
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
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Aitha M, Marts AR, Bergstrom A, Møller A, Moritz L, Turner L, Nix JC, Bonomo RA, Page RC, Tierney DL, Crowder MW. Biochemical, mechanistic, and spectroscopic characterization of metallo-β-lactamase VIM-2. Biochemistry 2014; 53:7321-31. [PMID: 25356958 PMCID: PMC4245990 DOI: 10.1021/bi500916y] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/10/2014] [Indexed: 11/29/2022]
Abstract
This study examines metal binding to metallo-β-lactamase VIM-2, demonstrating the first successful preparation of a Co(II)-substituted VIM-2 analogue. Spectroscopic studies of the half- and fully metal loaded enzymes show that both Zn(II) and Co(II) bind cooperatively, where the major species present, regardless of stoichiometry, are apo- and di-Zn (or di-Co) enzymes. We determined the di-Zn VIM-2 structure to a resolution of 1.55 Å, and this structure supports results from spectroscopic studies. Kinetics, both steady-state and pre-steady-state, show that VIM-2 utilizes a mechanism that proceeds through a very short-lived anionic intermediate when chromacef is used as the substrate. Comparison with other B1 enzymes shows that those that bind Zn(II) cooperatively are better poised to protonate the intermediate on its formation, compared to those that bind Zn(II) non-cooperatively, which uniformly build up substantial amounts of the intermediate.
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Affiliation(s)
- Mahesh Aitha
- Department
of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Amy R. Marts
- Department
of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Alex Bergstrom
- Department
of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Abraham
Jon Møller
- Department
of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Lindsay Moritz
- Department
of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Lucien Turner
- Department
of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Jay C. Nix
- Molecular
Biology Consortium, Beamline 4.2.2, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Robert A. Bonomo
- Research
Service, Louis Stokes Cleveland Department
of Veterans Affairs Medical Center, 10701 East Boulevard, Cleveland, Ohio 44106, United
States
- Department
of Medicine, Pharmacology, and Molecular Biology and Microbiology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Richard C. Page
- Department
of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - David L. Tierney
- Department
of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Michael W. Crowder
- Department
of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
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Aitha M, Richmond TK, Hu Z, Hetrick A, Reese R, Gunther A, McCarrick R, Bennett B, Crowder MW. Dilution of dipolar interactions in a spin-labeled, multimeric metalloenzyme for DEER studies. J Inorg Biochem 2014; 136:40-6. [PMID: 24742748 PMCID: PMC4733626 DOI: 10.1016/j.jinorgbio.2014.03.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 03/17/2014] [Accepted: 03/18/2014] [Indexed: 01/28/2023]
Abstract
The metallo-β-lactamases (MβLs), which require one or two Zn(II) ions in their active sites for activity, hydrolyze the amide bond in β-lactam-containing antibiotics, and render the antibiotics inactive. All known MβLs contain a mobile element near their active sites, and these mobile elements have been implicated in the catalytic mechanisms of these enzymes. However little is known about the dynamics of these elements. In this study, we prepared a site-specific, double spin-labeled analog of homotetrameric MβL L1 with spin labels at positions 163 and 286 and analyzed the sample with DEER (double electron electron resonance) spectroscopy. Four unique distances were observed in the DEER distance distribution, and these distances were assigned to the desired intramolecular dipolar coupling (between spin labels at positions 163 and 286 in one subunit) and to intermolecular dipolar couplings. To rid the spin-labeled analog of L1 of the intermolecular couplings, spin-labeled L1 was "diluted" by unfolding/refolding the spin-labeled enzyme in the presence of excess wild-type L1. DEER spectra of the resulting, spin-diluted enzyme revealed a single distance corresponding to the desire intramolecular dipolar coupling.
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Affiliation(s)
- Mahesh Aitha
- Department of Chemistry and Biochemistry, Miami University, 160 Hughes Hall, Oxford, OH 45056, United States
| | - Timothy K Richmond
- Department of Chemistry and Biochemistry, Miami University, 160 Hughes Hall, Oxford, OH 45056, United States
| | - Zhenxin Hu
- Department of Chemistry and Biochemistry, Miami University, 160 Hughes Hall, Oxford, OH 45056, United States
| | - Alyssa Hetrick
- Department of Chemistry and Biochemistry, Miami University, 160 Hughes Hall, Oxford, OH 45056, United States
| | - Raquel Reese
- Department of Chemistry and Biochemistry, Miami University, 160 Hughes Hall, Oxford, OH 45056, United States
| | - Althea Gunther
- Department of Chemistry and Biochemistry, Miami University, 160 Hughes Hall, Oxford, OH 45056, United States
| | - Robert McCarrick
- Department of Chemistry and Biochemistry, Miami University, 160 Hughes Hall, Oxford, OH 45056, United States
| | - Brian Bennett
- Department of Biophysics, National Biomedical EPR Center, Medical College of Wisconsin, Milwaukee, WI 53226, United States
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, 160 Hughes Hall, Oxford, OH 45056, United States.
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14
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Yang H, Aitha M, Marts AR, Hetrick A, Bennett B, Crowder MW, Tierney DL. Spectroscopic and mechanistic studies of heterodimetallic forms of metallo-β-lactamase NDM-1. J Am Chem Soc 2014; 136:7273-85. [PMID: 24754678 PMCID: PMC4046764 DOI: 10.1021/ja410376s] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
In
an effort to characterize the roles of each metal ion in metallo-β-lactamase
NDM-1, heterodimetallic analogues (CoCo-, ZnCo-, and CoCd-) of the
enzyme were generated and characterized. UV–vis, 1H NMR, EPR, and EXAFS spectroscopies were used to confirm the fidelity
of the metal substitutions, including the presence of a homogeneous,
heterodimetallic cluster, with a single-atom bridge. This marks the
first preparation of a metallo-β-lactamase selectively substituted
with a paramagnetic metal ion, Co(II), either in the Zn1 (CoCd-NDM-1) or in the Zn2 site (ZnCo-NDM-1), as well
as both (CoCo-NDM-1). We then used these metal-substituted forms of
the enzyme to probe the reaction mechanism, using steady-state and
stopped-flow kinetics, stopped-flow fluorescence, and rapid-freeze-quench
EPR. Both metal sites show significant effects on the kinetic constants,
and both paramagnetic variants (CoCd- and ZnCo-NDM-1) showed significant
structural changes on reaction with substrate. These changes are discussed
in terms of a minimal kinetic mechanism that incorporates all of the
data.
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Affiliation(s)
- Hao Yang
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
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Yang KW, Feng L, Yang SK, Aitha M, LaCuran AE, Oelschlaeger P, Crowder MW. New β-phospholactam as a carbapenem transition state analog: Synthesis of a broad-spectrum inhibitor of metallo-β-lactamases. Bioorg Med Chem Lett 2013; 23:5855-9. [PMID: 24064498 PMCID: PMC3833270 DOI: 10.1016/j.bmcl.2013.08.098] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 08/21/2013] [Accepted: 08/26/2013] [Indexed: 10/26/2022]
Abstract
In an effort to test whether a transition state analog is an inhibitor of the metallo-β-lactamases, a phospholactam analog of carbapenem has been synthesized and characterized. The phospholactam 1 proved to be a weak, time-dependent inhibitor of IMP-1 (70%), CcrA (70%), L1 (70%), NDM-1 (53%), and Bla2 (94%) at an inhibitor concentration of 100μM. The phospholactam 1 activated ImiS and BcII at the same concentration. Docking studies were used to explain binding and to offer suggestions for modifications to the phospholactam scaffold to improve binding affinities.
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Affiliation(s)
- Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710069, P. R. China
| | - Lei Feng
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710069, P. R. China
| | - Shao-Kang Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710069, P. R. China
| | - Mahesh Aitha
- Department of Chemistry and Biochemistry, Miami University, 160 Hughes Hall, Oxford, OH 45056, USA
| | - Alecander E. LaCuran
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, 309 E. Second St., Pomona, CA 91766, USA
| | - Peter Oelschlaeger
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, 309 E. Second St., Pomona, CA 91766, USA
| | - Michael W. Crowder
- Department of Chemistry and Biochemistry, Miami University, 160 Hughes Hall, Oxford, OH 45056, USA
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Yang H, Aitha M, Hetrick AM, Richmond TK, Tierney DL, Crowder MW. Mechanistic and spectroscopic studies of metallo-β-lactamase NDM-1. Biochemistry 2012; 51:3839-47. [PMID: 22482529 DOI: 10.1021/bi300056y] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In an effort to biochemically characterize metallo-β-lactamase NDM-1, we cloned, overexpressed, purified, and characterized several maltose binding protein (MBP)-NDM-1 fusion proteins with different N-termini (full-length, Δ6, Δ21, and Δ36). All MBP-NDM-1 fusion proteins were soluble; however, only one, MBP-NDM-1Δ36, exhibited high activity and bound 2 equiv of Zn(II). Thrombin cleavage of this fusion protein resulted in the truncated NDM-1Δ36 variant, which exhibited a k(cat) of 16 s(-1) and a K(m) of 1.1 μM when using nitrocefin as a substrate, bound 2 equiv of Zn(II), and was monomeric in solution. Extended X-ray absorption fine structure studies of the NDM-1Δ36 variant indicate the average metal binding site for Zn(II) in this variant consists of four N/O donors (two of which are histidines) and 0.5 sulfur donor per zinc, with a Zn-Zn distance of 3.38 Å. This metal binding site is very similar to those of other metallo-β-lactamases that belong to the B1 subclass. Pre-steady-state kinetic studies using nitrocefin and chromacef and the NDM-1Δ36 variant indicate that the enzyme utilizes a kinetic mechanism similar to that used by metallo-β-lactamases L1 and CcrA, in which a reactive nitrogen anion is stabilized and its protonation is rate-limiting. While they are very different in terms of amino acid sequence, these studies demonstrate that NDM-1 is structurally and mechanistically very similar to metallo-β-lactamase CcrA.
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Affiliation(s)
- Hao Yang
- Department of Chemistry and Biochemistry, 160 Hughes Hall, Miami University, Oxford, Ohio 45056, USA
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