1
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Karamitros CS, Murray K, Kumada Y, Johnson KA, D'Arcy S, Georgiou G. Mechanistic conformational and substrate selectivity profiles emerging in the evolution of enzymes via parallel trajectories. Nat Commun 2024; 15:7068. [PMID: 39152129 PMCID: PMC11329768 DOI: 10.1038/s41467-024-51133-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 07/30/2024] [Indexed: 08/19/2024] Open
Abstract
Laboratory evolution studies have demonstrated that parallel evolutionary trajectories can lead to genetically distinct enzymes with high activity towards a non-preferred substrate. However, it is unknown whether such enzymes have convergent conformational dynamics and mechanistic features. To address this question, we use as a model the wild-type Homo sapiens kynureninase (HsKYNase), which is of great interest for cancer immunotherapy. Earlier, we isolated HsKYNase_66 through an unusual evolutionary trajectory, having a 410-fold increase in the kcat/KM for kynurenine (KYN) and reverse substrate selectivity relative to HsKYNase. Here, by following a different evolutionary trajectory we generate a genetically distinct variant, HsKYNase_93D9, that exhibits KYN catalytic activity comparable to that of HsKYNase_66, but instead it is a "generalist" that accepts 3'-hydroxykynurenine (OH-KYN) with the same proficiency. Pre-steady-state kinetic analysis reveals that while the evolution of HsKYNase_66 is accompanied by a change in the rate-determining step of the reactions, HsKYNase_93D9 retains the same catalytic mechanism as HsKYNase. HDX-MS shows that the conformational dynamics of the two enzymes are markedly different and distinct from ortholog prokaryotic enzymes with high KYN activity. Our work provides a mechanistic framework for understanding the relationship between evolutionary mechanisms and phenotypic traits of evolved generalist and specialist enzyme species.
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Affiliation(s)
- Christos S Karamitros
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, TX, USA
- Research and Clinical Development, Nestlé Health Science, Lausanne, 1000, Switzerland
| | - Kyle Murray
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
- Trajan Scientific America's, Inc. Boston, Massachusetts, MA, USA
| | - Yoichi Kumada
- Department of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Kyoto, Japan
| | - Kenneth A Johnson
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, TX, USA
| | - Sheena D'Arcy
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, TX, USA.
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, TX, USA.
- Department of Biomedical Engineering, University of Texas at Austin (UT Austin), Austin, TX, USA.
- Institute for Cellular and Molecular Biology, The University of Texas at Austin (UT Austin), Austin, TX, USA.
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2
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Nakata M, Kosaka N, Kawauchi K, Miyoshi D. Quantitative Effects of the Loop Region on Topology, Thermodynamics, and Cation Binding of DNA G-quadruplexes. ACS OMEGA 2024; 9:35028-35036. [PMID: 39157113 PMCID: PMC11325513 DOI: 10.1021/acsomega.4c05008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 08/20/2024]
Abstract
The thermal stability of G-quadruplexes is important for their biological roles. G-quadruplexes are stable in the presence of cations such as K+ and Na+ because these cations coordinate in the G-quartet of four guanine bases. It is well known that the number of G-quartets and the configuration of the guanine bases affect the binding affinity of the cation. Recently, structures formed in the loop regions connecting the guanine stretches have attracted significant attention, because the loop region affects G-quadruplex properties, such as topology, thermal stability, and interactions with proteins and small molecules. Considering these effects, the loop region can also affect the binding affinity of the cations. Here, we designed a series of G-quadruplex-forming DNA sequences that contain a hairpin in a loop region and investigated the effects of the sequence and structure of the loop region on the cation binding affinity as well as the thermal stability of the G-quadruplex as a whole. First, structural analysis of the DNA sequences showed that the hairpin at the loop plays a key role in determining G4 topology (strand orientation). Second, in the case of the G-quadruplexes with the hairpin-forming loop region, it was found that a longer loop length led to a higher thermodynamic stability of the G-quadruplex as well as higher cation binding affinity. In contrast, an unstructured loop region did not lead to such effects. Interestingly, the cation binding affinity was correlated to the thermodynamic stability of the hairpin structure at the loop region. It was quantitatively demonstrated that the stable loop region stabilized the whole G-quadruplex structure, which induced higher cation binding affinity. These systematic and quantitative results showed that the loop region is one of the determinants of cation binding and expanded the possibilities of drug development targeting G4s by stabilizing the loop region.
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Affiliation(s)
- Minori Nakata
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Naoki Kosaka
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Keiko Kawauchi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
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3
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Pinto MF, Sirina J, Holliday ND, McWhirter CL. High-throughput kinetics in drug discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100170. [PMID: 38964171 DOI: 10.1016/j.slasd.2024.100170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/21/2024] [Accepted: 06/17/2024] [Indexed: 07/06/2024]
Abstract
The importance of a drug's kinetic profile and interplay of structure-kinetic activity with PK/PD has long been appreciated in drug discovery. However, technical challenges have often limited detailed kinetic characterization of compounds to the latter stages of projects. This review highlights the advances that have been made in recent years in techniques, instrumentation, and data analysis to increase the throughput of detailed kinetic and mechanistic characterization, enabling its application earlier in the drug discovery process.
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Affiliation(s)
- Maria Filipa Pinto
- Artios Pharma Ltd, B940, Babraham Research Campus, Cambridge CB22 3FH, United Kingdom
| | - Julija Sirina
- Excellerate Bioscience Ltd, 21 The Triangle, NG2 Business Park, Nottingham, NG2 1AE, United Kingdom
| | - Nicholas D Holliday
- Excellerate Bioscience Ltd, 21 The Triangle, NG2 Business Park, Nottingham, NG2 1AE, United Kingdom; School of Life Sciences, The Medical School, University of Nottingham, Nottingham, NG7 2UH, United Kingdom
| | - Claire L McWhirter
- Artios Pharma Ltd, B940, Babraham Research Campus, Cambridge CB22 3FH, United Kingdom.
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4
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Gao J, Proffitt D, Marecki J, Protacio R, Wahls W, Byrd A, Raney K. Two residues in the DNA binding site of Pif1 helicase are essential for nuclear functions but dispensable for mitochondrial respiratory growth. Nucleic Acids Res 2024; 52:6543-6557. [PMID: 38752483 PMCID: PMC11194084 DOI: 10.1093/nar/gkae403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 04/24/2024] [Accepted: 05/01/2024] [Indexed: 05/21/2024] Open
Abstract
Pif1 helicase functions in both the nucleus and mitochondria. Pif1 tightly couples ATP hydrolysis, single-stranded DNA translocation, and duplex DNA unwinding. We investigated two Pif1 variants (F723A and T464A) that have each lost one site of interaction of the protein with the DNA substrate. Both variants exhibit minor reductions in affinity for DNA and ATP hydrolysis but have impaired DNA unwinding activity. However, these variants translocate on single-stranded DNA faster than the wildtype enzyme and can slide on the DNA substrate in an ATP-independent manner. This suggests they have lost their grip on the DNA, interfering with coupling ATP hydrolysis to translocation and unwinding. Yeast expressing these variants have increased gross chromosomal rearrangements, increased telomere length, and can overcome the lethality of dna2Δ, similar to phenotypes of yeast lacking Pif1. However, unlike pif1Δ mutants, they are viable on glycerol containing media and maintain similar mitochondrial DNA copy numbers as Pif1 wildtype. Overall, our data indicate that a tight grip of the trailing edge of the Pif1 enzyme on the DNA couples ATP hydrolysis to DNA translocation and DNA unwinding. This tight grip appears to be essential for the Pif1 nuclear functions tested but is dispensable for mitochondrial respiratory growth.
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Affiliation(s)
- Jun Gao
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (Slot 516), Little Rock, AR 72205, USA
| | - David R Proffitt
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (Slot 516), Little Rock, AR 72205, USA
| | - John C Marecki
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (Slot 516), Little Rock, AR 72205, USA
| | - Reine U Protacio
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (Slot 516), Little Rock, AR 72205, USA
| | - Wayne P Wahls
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (Slot 516), Little Rock, AR 72205, USA
| | - Alicia K Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (Slot 516), Little Rock, AR 72205, USA
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (Slot 516), Little Rock, AR 72205, USA
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5
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Bravo JPK, Ramos DA, Fregoso Ocampo R, Ingram C, Taylor DW. Plasmid targeting and destruction by the DdmDE bacterial defence system. Nature 2024; 630:961-967. [PMID: 38740055 DOI: 10.1038/s41586-024-07515-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 05/03/2024] [Indexed: 05/16/2024]
Abstract
Although eukaryotic Argonautes have a pivotal role in post-transcriptional gene regulation through nucleic acid cleavage, some short prokaryotic Argonaute variants (pAgos) rely on auxiliary nuclease factors for efficient foreign DNA degradation1. Here we reveal the activation pathway of the DNA defence module DdmDE system, which rapidly eliminates small, multicopy plasmids from the Vibrio cholerae seventh pandemic strain (7PET)2. Through a combination of cryo-electron microscopy, biochemistry and in vivo plasmid clearance assays, we demonstrate that DdmE is a catalytically inactive, DNA-guided, DNA-targeting pAgo with a distinctive insertion domain. We observe that the helicase-nuclease DdmD transitions from an autoinhibited, dimeric complex to a monomeric state upon loading of single-stranded DNA targets. Furthermore, the complete structure of the DdmDE-guide-target handover complex provides a comprehensive view into how DNA recognition triggers processive plasmid destruction. Our work establishes a mechanistic foundation for how pAgos utilize ancillary factors to achieve plasmid clearance, and provides insights into anti-plasmid immunity in bacteria.
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Affiliation(s)
- Jack P K Bravo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
- Institute of Science and Technology Austria (ISTA), Klosterneuberg, Austria.
| | - Delisa A Ramos
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | | | - Caiden Ingram
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - David W Taylor
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
- Livestrong Cancer Institutes, Dell Medical School, Austin, TX, USA
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6
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Du Y. Binding Curve Viewer: Visualizing the Equilibrium and Kinetics of Protein-Ligand Binding and Competitive Binding. J Chem Inf Model 2024; 64:4180-4192. [PMID: 38720179 PMCID: PMC11134506 DOI: 10.1021/acs.jcim.4c00130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/21/2024] [Accepted: 04/25/2024] [Indexed: 05/28/2024]
Abstract
Understanding the thermodynamics and kinetics of the protein-ligand interaction is essential for biologists and pharmacologists. To visualize the equilibrium and kinetics of the binding reaction with 1:1 stoichiometry and no cooperativity, we obtained the exact relationship of the concentration of the protein-ligand complex and the time in the second-order binding process and numerically simulated the process of competitive binding. First, two common concerns in measuring protein-ligand interactions were focused on how to avoid the titration regime and how to establish the appropriate incubation time. Then, we gave examples of how the commonly used experimental conditions of [L]0 ≫ [P]0 and [I]0 ≫ [P]0 affected the estimation of the kinetic and thermodynamic properties. Theoretical inhibition curves were calculated, and the apparent IC50 and IC50 were estimated accordingly under predefined conditions. Using the estimated apparent IC50, we compared the apparent Ki and Ki calculated by using the Cheng-Prusoff equation, Lin-Riggs equation, and Wang's group equation. We also applied our tools to simulate high-throughput screening and compare the results of real experiments. The visualization tool for simulating the saturation experiment, kinetic experiments of binding and competitive binding, and inhibition curve, "Binding Curve Viewer," is available at www.eplatton.net/binding-curve-viewer.
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Affiliation(s)
- Yu Du
- Department
of Clinical Laboratory, The Second Affiliated
Hospital of Jiaxing University, Huancheng North Road 1518, Jiaxing, Zhejiang 314000, China
- The
Key Laboratory, The Second Affiliated Hospital
of Jiaxing University, Huancheng North Road 1518, Jiaxing, Zhejiang 314000, China
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7
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Ringenbach S, Yoza R, Jones PA, Du M, Klugh KL, Peterson LW, Colabroy KL. Discovery and characterization of l-DOPA 2,3-dioxygenase from Streptomyces hygroscopicus jingganensis. Arch Biochem Biophys 2024; 755:109967. [PMID: 38556098 DOI: 10.1016/j.abb.2024.109967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/19/2024] [Accepted: 03/21/2024] [Indexed: 04/02/2024]
Abstract
The largest natural reservoir of untapped carbon can be found in the cell-wall strengthening, plant woody-tissue polymer, lignin - a polymer of catechols or 1,2-dihydroxybenzene monomers. The catecholic carbon of lignin could be valorized into feedstocks and natural products by way of catabolic and biosynthetic transformations, including the oxygen-dependent cleavage reaction of extradiol dioxygenase (EDX) enzymes. The EDX l-DOPA 2,3-dioxygenase was first discovered as part of a biosynthetic gene cluster to the natural product antibiotic, lincomycin, and also contributes to the biosyntheses of anthramycin, sibiromycin, tomaymycin, porothramycin and hormaomycin. Using these l-DOPA 2,3-dioxygenases as a starting point, we searched sequence space in order to identify new sources of dioxygenase driven natural product diversity. A "vicinal-oxygen-chelate (VOC) family protein" from Streptomyces hygroscopicus jingganensis was identified using bioinformatic methods and biochemically investigated for dioxygenase activity against a suite of natural and synthetic catechols. Steady-state oxygen consumption assays were used to screen and identify substrates, and a steady-state kinetic model of oxygen consumption was developed to evaluate activity of the S. hygroscopicus jingganensis VOC-family-protein with respect to activity of l-DOPA 2,3-dioxygenases from Streptomyces lincolnensis and Streptomyces sclerotialus. Lastly, these data were integrated with steady-state kinetic methods to observe the formation of the EDX cleavage product with UV-visible spectroscopy. The genomic context and enzymatic activity of the S. hygroscopicus jingganensis VOC family protein are consistent with a l-DOPA 2,3-dioxygenase contained within a cryptic biosynthetic pathway.
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Affiliation(s)
- Sara Ringenbach
- Department of Chemistry, Muhlenberg College, 2400 Chew St, Allentown, PA, 18104, USA
| | - Riri Yoza
- Department of Chemistry, Muhlenberg College, 2400 Chew St, Allentown, PA, 18104, USA
| | - Paige A Jones
- Department of Chemistry, Muhlenberg College, 2400 Chew St, Allentown, PA, 18104, USA
| | - Muxue Du
- Department of Chemistry, Muhlenberg College, 2400 Chew St, Allentown, PA, 18104, USA
| | - Kameron L Klugh
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, TN, 38112, USA
| | - Larryn W Peterson
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, TN, 38112, USA
| | - Keri L Colabroy
- Department of Chemistry, Muhlenberg College, 2400 Chew St, Allentown, PA, 18104, USA.
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8
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Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW. Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. Nat Commun 2024; 15:3663. [PMID: 38688943 PMCID: PMC11061278 DOI: 10.1038/s41467-024-47830-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
CRISPR-Cas9 is a powerful tool for genome editing, but the strict requirement for an NGG protospacer-adjacent motif (PAM) sequence immediately next to the DNA target limits the number of editable genes. Recently developed Cas9 variants have been engineered with relaxed PAM requirements, including SpG-Cas9 (SpG) and the nearly PAM-less SpRY-Cas9 (SpRY). However, the molecular mechanisms of how SpRY recognizes all potential PAM sequences remains unclear. Here, we combine structural and biochemical approaches to determine how SpRY interrogates DNA and recognizes target sites. Divergent PAM sequences can be accommodated through conformational flexibility within the PAM-interacting region, which facilitates tight binding to off-target DNA sequences. Nuclease activation occurs ~1000-fold slower than for Streptococcus pyogenes Cas9, enabling us to directly visualize multiple on-pathway intermediate states. Experiments with SpG position it as an intermediate enzyme between Cas9 and SpRY. Our findings shed light on the molecular mechanisms of PAMless genome editing.
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Affiliation(s)
- Grace N Hibshman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Interdisciplinary Life Sciences Graduate Programs, Austin, TX, 78712, USA
| | - Jack P K Bravo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria.
| | - Matthew M Hooper
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Interdisciplinary Life Sciences Graduate Programs, Austin, TX, 78712, USA
| | - Tyler L Dangerfield
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Hongshan Zhang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Kenneth A Johnson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Interdisciplinary Life Sciences Graduate Programs, Austin, TX, 78712, USA
| | - David W Taylor
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
- Interdisciplinary Life Sciences Graduate Programs, Austin, TX, 78712, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA.
- LIVESTRONG Cancer Institutes, Dell Medical School, Austin, TX, 78712, USA.
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9
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Valentín-Goyco J, Im SC, Auchus RJ. Kinetics of Intermediate Release Enhances P450 11B2-Catalyzed Aldosterone Synthesis. Biochemistry 2024; 63:1026-1037. [PMID: 38564530 PMCID: PMC11259377 DOI: 10.1021/acs.biochem.3c00725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The mitochondrial enzyme cytochrome P450 11B2 (aldosterone synthase) catalyzes the 3 terminal transformations in the biosynthesis of aldosterone from 11-deoxycorticosterone (DOC): 11β-hydroxylation to corticosterone, 18-hydroxylation, and 18-oxidation. Prior studies have shown that P450 11B2 produces more aldosterone from DOC than from the intermediate corticosterone and that the reaction sequence is processive, with intermediates remaining bound to the active site between oxygenation reactions. In contrast, P450 11B1 (11β-hydroxylase), which catalyzes the terminal step in cortisol biosynthesis, shares a 93% amino acid sequence identity with P450 11B2, converts DOC to corticosterone, but cannot synthesize aldosterone from DOC. The biochemical and biophysical properties of P450 11B2, which enable its unique 18-oxygenation activity and processivity, yet are not also represented in P450 11B1, remain unknown. To understand the mechanism of aldosterone biosynthesis, we introduced point mutations at residue 320, which partially exchange the activities of P450 11B1 and P450 11B2 (V320A and A320V, respectively). We then investigated NADPH coupling efficiencies, binding kinetics and affinities, and product formation of purified P450 11B1 and P450 11B2, wild-type, and residue 320 mutations in phospholipid vesicles and nanodiscs. Coupling efficiencies for the 18-hydroxylase reaction with corticosterone as the substrate failed to correlate with aldosterone synthesis, ruling out uncoupling as a relevant mechanism. Conversely, corticosterone dissociation rates correlated inversely with aldosterone production. We conclude that intermediate dissociation kinetics, not coupling efficiency, enable P450 11B2 to synthesize aldosterone via a processive mechanism. Our kinetic data also suggest that the binding of DOC to P450 11B enzymes occurs in at least two distinct steps, favoring an induced-fit mechanism.
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Affiliation(s)
- Juan Valentín-Goyco
- Division of Metabolism, Endocrinology, & Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, United States
- LTC Charles S. Kettles Veterans Affairs Medical Center, 2215 Fuller Road, Ann Arbor, MI 48105, United States
| | - Sang-Choul Im
- Division of Metabolism, Endocrinology, & Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, United States
- LTC Charles S. Kettles Veterans Affairs Medical Center, 2215 Fuller Road, Ann Arbor, MI 48105, United States
| | - Richard J. Auchus
- Division of Metabolism, Endocrinology, & Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, United States
- LTC Charles S. Kettles Veterans Affairs Medical Center, 2215 Fuller Road, Ann Arbor, MI 48105, United States
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10
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Keijzer N, Priyanka A, Stijf-Bultsma Y, Fish A, Gersch M, Sixma TK. Variety in the USP deubiquitinase catalytic mechanism. Life Sci Alliance 2024; 7:e202302533. [PMID: 38355287 PMCID: PMC10867860 DOI: 10.26508/lsa.202302533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
The ubiquitin-specific protease (USP) family of deubiquitinases (DUBs) controls cellular ubiquitin-dependent signaling events. This generates therapeutic potential, with active-site inhibitors in preclinical and clinical studies. Understanding of the USP active site is primarily guided by USP7 data, where the catalytic triad consists of cysteine, histidine, and a third residue (third critical residue), which polarizes the histidine through a hydrogen bond. A conserved aspartate (fourth critical residue) is directly adjacent to this third critical residue. Although both critical residues accommodate catalysis in USP2, these residues have not been comprehensively investigated in other USPs. Here, we quantitatively investigate their roles in five USPs. Although USP7 relies on the third critical residue for catalysis, this residue is dispensable in USP1, USP15, USP40, and USP48, where the fourth critical residue is vital instead. Furthermore, these residues vary in importance for nucleophilic attack. The diverging catalytic mechanisms of USP1 and USP7 are independent of substrate and retained in cells for USP1. This unexpected variety of catalytic mechanisms in this well-conserved protein family may generate opportunities for selective targeting of individual USPs.
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Affiliation(s)
- Niels Keijzer
- https://ror.org/03xqtf034 Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Anu Priyanka
- https://ror.org/03xqtf034 Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Yvette Stijf-Bultsma
- https://ror.org/03xqtf034 Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Alexander Fish
- https://ror.org/03xqtf034 Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Malte Gersch
- Max Planck Institute of Molecular Physiology, Chemical Genomics Centre, Dortmund, Germany
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Titia K Sixma
- https://ror.org/03xqtf034 Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
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11
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Ghadirian N, Morgan RD, Horton NC. DNA Sequence Control of Enzyme Filamentation and Activation of the SgrAI Endonuclease. Biochemistry 2024; 63:326-338. [PMID: 38207281 DOI: 10.1021/acs.biochem.3c00313] [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: 01/13/2024]
Abstract
Enzyme polymerization (also known as filamentation) has emerged as a new layer of enzyme regulation. SgrAI is a sequence-dependent DNA endonuclease that forms polymeric filaments with enhanced DNA cleavage activity as well as altered DNA sequence specificity. To better understand this unusual regulatory mechanism, full global kinetic modeling of the reaction pathway, including the enzyme filamentation steps, has been undertaken. Prior work with the primary DNA recognition sequence cleaved by SgrAI has shown how the kinetic rate constants of each reaction step are tuned to maximize activation and DNA cleavage while minimizing the extent of DNA cleavage to the host genome. In the current work, we expand on our prior study by now including DNA cleavage of a secondary recognition sequence, to understand how the sequence of the bound DNA modulates filamentation and activation of SgrAI. The work shows that an allosteric equilibrium between low and high activity states is modulated by the sequence of bound DNA, with primary sequences more prone to activation and filament formation, while SgrAI bound to secondary recognition sequences favor the low (and nonfilamenting) state by up to 40-fold. In addition, the degree of methylation of secondary sequences in the host organism, Streptomyces griseus, is now reported for the first time and shows that as predicted, these sequences are left unprotected from the SgrAI endonuclease making sequence specificity critical in this unusual filament-forming enzyme.
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Affiliation(s)
- Niloofar Ghadirian
- Department of Chemistry & Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Richard D Morgan
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, United States
| | - Nancy C Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, United States
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12
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Johnson KA. You get what you screen for: Standards for experimental design and data fitting in drug discovery. Methods Enzymol 2023; 690:131-157. [PMID: 37858528 DOI: 10.1016/bs.mie.2023.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
A common mantra in drug discovery is that "You get what you screen for." This is not a promise that you will always get an effective drug candidate, but rather a warning that inaccuracies in your protocol for screening will more likely produce a compound that fails to be an effective candidate because it matches the properties of your screen, not the desired features of an ideal lead compound. It is with this in mind that we examine the current protocols for evaluating drug candidates and highlight some deficiencies while pointing the way to better methods. Many of the errors in data fitting can be rectified by abandoning the traditional equation-based data fitting methods and adopting the more rigorous mechanism-based fitting afforded by computer simulation based on numerical integration of rate equations. Using these methods bypasses the errors in judgement in choosing the appropriate equation for data fitting and the approximations required to derive those equations. In this chapter we outline the limitations and systematic errors in conventional methods of data fitting and illustrate the advantages of computer simulation and introduce the methods of analysis.
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Affiliation(s)
- Kenneth A Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.
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13
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Melkonian TR, Vuksanovic N, Silvaggi NR. Probing mechanistic questions in the PLP- and O 2-dependent l-Arg oxidases. Methods Enzymol 2023; 685:493-529. [PMID: 37245913 DOI: 10.1016/bs.mie.2023.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The pyridoxal-5'-phosphate-dependent l-Arg oxidases are unusual in that they are able to catalyze 4-electron oxidations of arginine using only the PLP cofactor. No metals or other accessory cosubstrates are involved; only arginine, dioxygen, and PLP. The catalytic cycles of these enzymes are replete with colored intermediates whose accumulation and decay can be monitored spectrophotometrically. This makes the l-Arg oxidases excellent subjects for detailed mechanistic investigations. They are worth studying, because they can teach us much about how PLP-dependent enzymes modulate the cofactor (structure-function-dynamics) and how new activities can arise from existing enzyme scaffolds. Herein we describe a series of experiments that can be used to probe the mechanisms of l-Arg oxidases. These methods by no means originated in our lab but were learned from talented researchers in other enzyme fields (flavoenzymes and Fe(II)-dependent oxygenases) and have been adapted to fit the requirements of our system. We present practical information for expressing and purifying the l-Arg oxidases, protocols for running stopped-flow experiments to examine the reactions with l-Arg and with dioxygen, and a tandem mass spectrometry-based quench-flow assay to follow the accumulation of the products of the hydroxylating l-Arg oxidases.
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Affiliation(s)
- Trevor R Melkonian
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
| | | | - Nicholas R Silvaggi
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI, United States.
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14
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Pitsawong W, Pádua RAP, Grant T, Hoemberger M, Otten R, Bradshaw N, Grigorieff N, Kern D. From primordial clocks to circadian oscillators. Nature 2023; 616:183-189. [PMID: 36949197 PMCID: PMC10076222 DOI: 10.1038/s41586-023-05836-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 02/13/2023] [Indexed: 03/24/2023]
Abstract
Circadian rhythms play an essential part in many biological processes, and only three prokaryotic proteins are required to constitute a true post-translational circadian oscillator1. The evolutionary history of the three Kai proteins indicates that KaiC is the oldest member and a central component of the clock2. Subsequent additions of KaiB and KaiA regulate the phosphorylation state of KaiC for time synchronization. The canonical KaiABC system in cyanobacteria is well understood3-6, but little is known about more ancient systems that only possess KaiBC. However, there are reports that they might exhibit a basic, hourglass-like timekeeping mechanism7-9. Here we investigate the primordial circadian clock in Rhodobacter sphaeroides, which contains only KaiBC, to elucidate its inner workings despite missing KaiA. Using a combination of X-ray crystallography and cryogenic electron microscopy, we find a new dodecameric fold for KaiC, in which two hexamers are held together by a coiled-coil bundle of 12 helices. This interaction is formed by the carboxy-terminal extension of KaiC and serves as an ancient regulatory moiety that is later superseded by KaiA. A coiled-coil register shift between daytime and night-time conformations is connected to phosphorylation sites through a long-range allosteric network that spans over 140 Å. Our kinetic data identify the difference in the ATP-to-ADP ratio between day and night as the environmental cue that drives the clock. They also unravel mechanistic details that shed light on the evolution of self-sustained oscillators.
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Affiliation(s)
- Warintra Pitsawong
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA, USA
- Biomolecular Discovery, Relay Therapeutics, Cambridge, MA, USA
| | - Ricardo A P Pádua
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA, USA
| | - Timothy Grant
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Madison, WI, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Marc Hoemberger
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA, USA
- Treeline Biosciences, Watertown, MA, USA
| | - Renee Otten
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA, USA
- Treeline Biosciences, Watertown, MA, USA
| | - Niels Bradshaw
- Department of Biochemistry, Brandeis University, Waltham, MA, USA
| | - Nikolaus Grigorieff
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Howard Hughes Medical Institute, RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Dorothee Kern
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA, USA.
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15
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Trastoy B, Du JJ, Cifuente JO, Rudolph L, García-Alija M, Klontz EH, Deredge D, Sultana N, Huynh CG, Flowers MW, Li C, Sastre DE, Wang LX, Corzana F, Mallagaray A, Sundberg EJ, Guerin ME. Mechanism of antibody-specific deglycosylation and immune evasion by Streptococcal IgG-specific endoglycosidases. Nat Commun 2023; 14:1705. [PMID: 36973249 PMCID: PMC10042849 DOI: 10.1038/s41467-023-37215-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 03/03/2023] [Indexed: 03/29/2023] Open
Abstract
Bacterial pathogens have evolved intricate mechanisms to evade the human immune system, including the production of immunomodulatory enzymes. Streptococcus pyogenes serotypes secrete two multi-modular endo-β-N-acetylglucosaminidases, EndoS and EndoS2, that specifically deglycosylate the conserved N-glycan at Asn297 on IgG Fc, disabling antibody-mediated effector functions. Amongst thousands of known carbohydrate-active enzymes, EndoS and EndoS2 represent just a handful of enzymes that are specific to the protein portion of the glycoprotein substrate, not just the glycan component. Here, we present the cryoEM structure of EndoS in complex with the IgG1 Fc fragment. In combination with small-angle X-ray scattering, alanine scanning mutagenesis, hydrolytic activity measurements, enzyme kinetics, nuclear magnetic resonance and molecular dynamics analyses, we establish the mechanisms of recognition and specific deglycosylation of IgG antibodies by EndoS and EndoS2. Our results provide a rational basis from which to engineer novel enzymes with antibody and glycan selectivity for clinical and biotechnological applications.
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Affiliation(s)
- Beatriz Trastoy
- Structural Glycobiology Laboratory, Biocruces Health Research Institute, Barakaldo, Bizkaia, 48903, Spain.
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
- Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain.
| | - Jonathan J Du
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Javier O Cifuente
- Structural Glycobiology Laboratory, Biocruces Health Research Institute, Barakaldo, Bizkaia, 48903, Spain
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Lorena Rudolph
- University of Lübeck, Center of Structural and Cell Biology in Medicine (CSCM), Institute of Chemistry and Metabolomics, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Mikel García-Alija
- Structural Glycobiology Laboratory, Biocruces Health Research Institute, Barakaldo, Bizkaia, 48903, Spain
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Erik H Klontz
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Nazneen Sultana
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Chau G Huynh
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Maria W Flowers
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Chao Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Diego E Sastre
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Francisco Corzana
- Departamento Química and Centro de Investigación en Síntesis Quı́mica, Universidad de La Rioja, 26006, Rioja, Spain
| | - Alvaro Mallagaray
- University of Lübeck, Center of Structural and Cell Biology in Medicine (CSCM), Institute of Chemistry and Metabolomics, Ratzeburger Allee 160, 23562, Lübeck, Germany.
| | - Eric J Sundberg
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Marcelo E Guerin
- Structural Glycobiology Laboratory, Biocruces Health Research Institute, Barakaldo, Bizkaia, 48903, Spain.
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
- Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain.
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16
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Manesis AC, Slater JW, Cantave K, Martin Bollinger J, Krebs C, Rosenzweig AC. Capturing a bis-Fe(IV) State in Methylosinus trichosporium OB3b MbnH. Biochemistry 2023; 62:1082-1092. [PMID: 36812111 PMCID: PMC10083075 DOI: 10.1021/acs.biochem.3c00021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The diheme bacterial cytochrome c peroxidase (bCcP)/MauG superfamily is a diverse set of enzymes that remains largely uncharacterized. One recently discovered member, MbnH, converts a tryptophan residue in its substrate protein, MbnP, to kynurenine. Here we show that upon reaction with H2O2, MbnH forms a bis-Fe(IV) intermediate, a state previously detected in just two other enzymes, MauG and BthA. Using absorption, Mössbauer, and electron paramagnetic resonance (EPR) spectroscopies coupled with kinetic analysis, we characterized the bis-Fe(IV) state of MbnH and determined that this intermediate decays back to the diferric state in the absence of MbnP substrate. In the absence of MbnP substrate, MbnH can also detoxify H2O2 to prevent oxidative self damage, unlike MauG, which has long been viewed as the prototype for bis-Fe(IV) forming enzymes. MbnH performs a different reaction from MauG, while the role of BthA remains unclear. All three enzymes can form a bis-Fe(IV) intermediate but within distinct kinetic regimes. The study of MbnH significantly expands our knowledge of enzymes that form this species. Computational and structural analyses indicate that electron transfer between the two heme groups in MbnH and between MbnH and the target tryptophan in MbnP likely occurs via a hole-hopping mechanism involving intervening tryptophan residues. These findings set the stage for discovery of additional functional and mechanistic diversity within the bCcP/MauG superfamily.
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Affiliation(s)
- Anastasia C Manesis
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Jeffrey W Slater
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Kenny Cantave
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - J Martin Bollinger
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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17
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Cebula M, Morgenstern R. Enzymology of reactive intermediate protection: kinetic analysis and temperature dependence of the mesophilic membrane protein catalyst MGST1. FEBS J 2023. [PMID: 36808476 DOI: 10.1111/febs.16754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/25/2023] [Accepted: 02/16/2023] [Indexed: 02/23/2023]
Abstract
Glutathione transferases (GSTs) are a class of phase II detoxifying enzymes catalysing the conjugation of glutathione (GSH) to endogenous and exogenous electrophilic molecules, with microsomal glutathione transferase 1 (MGST1) being one of its key members. MGST1 forms a homotrimer displaying third-of-the-sites-reactivity and up to 30-fold activation through modification of its Cys-49 residue. It has been shown that the steady-state behaviour of the enzyme at 5 °C can be accounted for by its pre-steady-state behaviour if the presence of a natively activated subpopulation (~ 10%) is assumed. Low temperature was used as the ligand-free enzyme is unstable at higher temperatures. Here, we overcame enzyme lability through stop-flow limited turnover analysis, whereby kinetic parameters at 30 °C were obtained. The acquired data are more physiologically relevant and enable confirmation of the previously established enzyme mechanism (at 5 °C), yielding parameters relevant for in vivo modelling. Interestingly, the kinetic parameter defining toxicant metabolism, kcat /KM , is strongly dependent on substrate reactivity (Hammett value 4.2), underscoring that glutathione transferases function as efficient and responsive interception catalysts. The temperature behaviour of the enzyme was also analysed. Both the KM and KD values decreased with increasing temperature, while the chemical step k3 displayed modest temperature dependence (Q10 : 1.1-1.2), mirrored in that of the nonenzymatic reaction (Q10 : 1.1-1.7). Unusually high Q10 values for GSH thiolate anion formation (k2 : 3.9), kcat (2.7-5.6) and kcat /KM (3.4-5.9) support that large structural transitions govern GSH binding and deprotonation, which limits steady-state catalysis.
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Affiliation(s)
- Marcus Cebula
- Division of Biochemical Toxicology, Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden
| | - Ralf Morgenstern
- Division of Biochemical Toxicology, Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden
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18
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The Binding of Different Substrate Molecules at the Docking Site and the Active Site of γ-Secretase Can Trigger Toxic Events in Sporadic and Familial Alzheimer's Disease. Int J Mol Sci 2023; 24:ijms24031835. [PMID: 36768156 PMCID: PMC9915333 DOI: 10.3390/ijms24031835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
Pathogenic changes in γ-secretase activity, along with its response to different drugs, can be affected by changes in the saturation of γ-secretase with its substrate. We analyze the saturation of γ-secretase with its substrate using multiscale molecular dynamics studies. We found that an increase in the saturation of γ-secretase with its substrate could result in the parallel binding of different substrate molecules at the docking site and the active site. The C-terminal domain of the substrate bound at the docking site can interact with the most dynamic presenilin sites at the cytosolic end of the active site tunnel. Such interactions can inhibit the ongoing catalytic activity and increase the production of the longer, more hydrophobic, and more toxic Aβ proteins. Similar disruptions in dynamic presenilin structures can be observed with different drugs and disease-causing mutations. Both, C99-βCTF-APP substrate and its different Aβ products, can support the toxic aggregation. The aggregation depends on the substrate N-terminal domain. Thus, the C99-βCTF-APP substrate and β-secretase path can be more toxic than the C83-αCTF-APP substrate and α-secretase path. Nicastrin can control the toxic aggregation in the closed conformation. The binding of the C99-βCTF-APP substrate to γ-secretase can be controlled by substrate channeling between the nicastrin and β-secretase. We conclude that the presented two-substrate mechanism could explain the pathogenic changes in γ-secretase activity and Aβ metabolism in different sporadic and familial cases of Alzheimer's disease. Future drug-development efforts should target different cellular mechanisms that regulate the optimal balance between γ-secretase activity and amyloid metabolism.
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19
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Du JJ, Sastre D, Trastoy B, Roberts B, Deredge D, Klontz EH, Flowers MW, Sultana N, Guerin ME, Sundberg EJ. Mass Spectrometry-Based Methods to Determine the Substrate Specificities and Kinetics of N-Linked Glycan Hydrolysis by Endo-β-N-Acetylglucosaminidases. Methods Mol Biol 2023; 2674:147-167. [PMID: 37258966 PMCID: PMC10988651 DOI: 10.1007/978-1-0716-3243-7_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Glycosylation is a common posttranslational modification of proteins and refers to the covalent addition of glycans, chains of polysaccharides, onto proteins producing glycoproteins. The glycans influence the structure, function, and stability of proteins. They also play an integral role in the immune system, and aberrantly glycosylated proteins have wide ranging effects, including leading to diseases such as autoimmune conditions and cancer. Carbohydrate-active enzymes (CAZymes) are produced in bacteria, fungi, and humans and are enzymes which modify glycans via the addition or subtraction of individual or multiple saccharides from glycans. One of the hurdles in studying these enzymes is determining the types of substrates each enzyme is specific for and the kinetics of enzymatic activity. In this chapter, we discuss methods which are currently used to study the substrate specificity and kinetics of CAZymes and introduce a novel mass spectrometry-based technique which enables the specificity and kinetics of CAZymes to be determined accurately and efficiently.
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Affiliation(s)
- Jonathan J Du
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA.
| | - Diego Sastre
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Beatriz Trastoy
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
| | - Blaine Roberts
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, USA
| | - Erik H Klontz
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Maria W Flowers
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Nazneen Sultana
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Marcelo E Guerin
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Eric J Sundberg
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA.
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20
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Dangerfield T, Johnson KA. Substrate Specificity and Kinetics of RNA Hydrolysis by SARS-CoV-2 NSP10/14 Exonuclease. ACS BIO & MED CHEM AU 2022; 2:600-606. [PMID: 36570070 PMCID: PMC9718090 DOI: 10.1021/acsbiomedchemau.2c00046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 11/18/2022]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the virus that causes COVID-19, continues to evolve resistance to vaccines and existing antiviral therapies at an alarming rate, increasing the need for new direct-acting antiviral drugs. Despite significant advances in our fundamental understanding of the kinetics and mechanism of viral RNA replication, there are still open questions regarding how the proofreading exonuclease (NSP10/NSP14 complex) contributes to replication fidelity and resistance to nucleoside analogs. Through single turnover kinetic analysis, we show that the preferred substrate for the exonuclease is double-stranded RNA without any mismatches. Double-stranded RNA containing a 3'-terminal remdesivir was hydrolyzed at a rate similar to a correctly base-paired cognate nucleotide. Surprisingly, single-stranded RNA or duplex RNA containing a 3'-terminal mismatch was hydrolyzed at rates 125- and 45-fold slower, respectively, compared to the correctly base-paired double-stranded RNA. These results define the substrate specificity and rate of removal of remdesivir for the exonuclease and outline rigorous kinetic assays that could help in finding next-generation exonuclease inhibitors or nucleoside analogs that are able to evade excision. These results also raise important questions about the role of the polymerase/exonuclease complex in proofreading during viral replication. Addressing these questions through rigorous kinetic analysis will facilitate the search for desperately needed antiviral drugs to combat COVID-19.
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21
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The role of filamentation in activation and DNA sequence specificity of the sequence-specific endonuclease SgrAI. Biochem Soc Trans 2022; 50:1703-1714. [PMID: 36398769 PMCID: PMC9788392 DOI: 10.1042/bst20220547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/09/2022] [Accepted: 10/12/2022] [Indexed: 11/19/2022]
Abstract
Filament formation by metabolic, biosynthetic, and other enzymes has recently come into focus as a mechanism to fine-tune enzyme activity in the cell. Filamentation is key to the function of SgrAI, a sequence-specific DNA endonuclease that has served as a model system to provide some of the deepest insights into the biophysical characteristics of filamentation and its functional consequences. Structure-function analyses reveal that, in the filamentous state, SgrAI stabilizes an activated enzyme conformation that leads to accelerated DNA cleavage activity and expanded DNA sequence specificity. The latter is thought to be mediated by sequence-specific DNA structure, protein-DNA interactions, and a disorder-to-order transition in the protein, which collectively affect the relative stabilities of the inactive, non-filamentous conformation and the active, filamentous conformation of SgrAI bound to DNA. Full global kinetic modeling of the DNA cleavage pathway reveals a slow, rate-limiting, second-order association rate constant for filament assembly, and simulations of in vivo activity predict that filamentation is superior to non-filamenting mechanisms in ensuring rapid activation and sequestration of SgrAI's DNA cleavage activity on phage DNA and away from the host chromosome. In vivo studies demonstrate the critical requirement for accelerated DNA cleavage by SgrAI in its biological role to safeguard the bacterial host. Collectively, these data have advanced our understanding of how filamentation can regulate enzyme structure and function, while the experimental strategies used for SgrAI can be applied to other enzymatic systems to identify novel functional roles for filamentation.
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22
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Kinetics of DNA strand transfer between polymerase and proofreading exonuclease active sites regulates error correction during high-fidelity replication. J Biol Chem 2022; 299:102744. [PMID: 36436560 PMCID: PMC9800556 DOI: 10.1016/j.jbc.2022.102744] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/18/2022] [Accepted: 11/20/2022] [Indexed: 11/25/2022] Open
Abstract
We show that T7 DNA polymerase (pol) and exonuclease (exo) domains contribute to selective error correction during DNA replication by regulating bidirectional strand transfer between the two active sites. To explore the kinetic basis for selective removal of mismatches, we used a fluorescent cytosine analog (1,3-diaza-2-oxophenoxazine) to monitor the kinetics of DNA transfer between the exo and pol sites. We globally fit stopped-flow fluorescence and base excision kinetic data and compared results obtained with ssDNA versus duplex DNA to resolve how DNA transfer governs exo specificity. We performed parallel studies using hydrolysis-resistant phosphorothioate oligonucleotides to monitor DNA transfer to the exo site without hydrolysis. ssDNA binds to the exo site at the diffusion limit (109 M-1 s-1, Kd = 40 nM) followed by fast hydrolysis of the 3'-terminal nucleotide (>5000 s-1). Analysis using duplex DNA with a 3'-terminal mismatch or a buried mismatch exposed a unique intermediate state between pol and exo active sites and revealed that transfer via the intermediate to the exo site is stimulated by free nucleoside triphosphates. Transfer from the exo site back to the pol site after cleavage is fast and efficient. We propose a model to explain why buried mismatches are removed faster than single 3'-terminal mismatches and thereby provide an additional opportunity for error correction. Our data provide the first comprehensive model to explain how DNA transfer from pol to exo active sites and back again after base excision allow efficient selective mismatch removal during DNA replication to improve fidelity by more than 1000-fold.
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23
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Kumari A, Yadav A, Lahiri I. Transient State Kinetics of Plasmodium falciparum Apicoplast DNA Polymerase Suggests the Involvement of Accessory Factors for Efficient and Accurate DNA Synthesis. Biochemistry 2022; 61:2319-2333. [PMID: 36251801 DOI: 10.1021/acs.biochem.2c00446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plasmodium, the causative agent of malaria, belongs to the phylum Apicomplexa. Most apicomplexans, including Plasmodium, contain an essential nonphotosynthetic plastid called the apicoplast that harbors its own genome that is replicated by a dedicated organellar replisome. This replisome employs a single DNA polymerase (apPol), which is expected to perform both replicative and translesion synthesis. Unlike other replicative polymerases, no processivity factor for apPol has been identified. While preliminary structural and biochemical studies have provided an overall characterization of apPol, the kinetic mechanism of apPol's activity remains unknown. We have used transient state methods to determine the kinetics of replicative and translesion synthesis by apPol and show that apPol has low processivity and efficiency while copying undamaged DNA. Moreover, while apPol can bypass oxidatively damaged lesions, the bypass is error-prone. Taken together, our results raise the following question─how does a polymerase with low processivity, efficiency, and fidelity (for translesion synthesis) faithfully replicate the apicoplast organellar DNA within the hostile environment of the human host? We hypothesize that interactions with putative components of the apicoplast replisome and/or an as-yet-undiscovered processivity factor transform apPol into an efficient and accurate enzyme.
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Affiliation(s)
- Anamika Kumari
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Punjab 140306, India
| | - Anjali Yadav
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Punjab 140306, India
| | - Indrajit Lahiri
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Punjab 140306, India.,Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, U.K
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24
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Vang JY, Breceda C, Her C, Krishnan VV. Enzyme kinetics by real-time quantitative NMR (qNMR) spectroscopy with progress curve analysis. Anal Biochem 2022; 658:114919. [PMID: 36154835 DOI: 10.1016/j.ab.2022.114919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/26/2022]
Abstract
This review article summarizes how the experimental data obtained using quantitative nuclear magnetic resonance (qNMR) spectroscopy can be combined with progress curve analysis to determine enzyme kinetic parameters. The qNMR approach enables following the enzymatic conversion of the substrate to the product in real-time by a continuous collection of spectra. The Lambert-W function, a closed-form solution to the time-dependent substrate/product kinetics of the rate equation, can estimate the Michaelis-Menten constant (KM.) and the maximum velocity (Vmax) from a single experiment. This article highlights how the qNMR data is well suited for analysis using the Lambert-W function with three different applications. Results from studies on acetylcholinesterase (acetylcholine to acetic acid and choline), β-Galactosidase (lactose to glucose and galactose), and invertase (sucrose to glucose and fructose) are presented. Furthermore, an additional example of how the progress curve analysis is applied to understand the inhibitory role of the artificial sweetener sucralose on sucrose's enzymatic conversion by invertase is discussed. With the wide availability of NMR spectrometers in academia and industries, including bench-top systems with permanent magnets, and the potential to enhance sensitivity using dynamic nuclear polarization in combination with ultrafast methods, the NMR-based enzyme kinetics could be considered a valuable tool for broader applications in the field of enzyme kinetics.
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Affiliation(s)
- Justin Y Vang
- Department of Chemistry & Biochemistry, California State University, Fresno, CA, 93740, USA
| | - Candido Breceda
- Department of Chemistry & Biochemistry, California State University, Fresno, CA, 93740, USA
| | - Cheenou Her
- Department of Chemistry & Biochemistry, California State University, Fresno, CA, 93740, USA
| | - V V Krishnan
- Department of Chemistry & Biochemistry, California State University, Fresno, CA, 93740, USA; Department of Medical Pathology & Laboratory Medicine, University of California Davis School of Medicine, Davis, CA, 95616, USA.
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25
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Basak S, Li Y, Tao S, Daryaee F, Merino J, Gu C, Delker SL, Phan JN, Edwards TE, Walker SG, Tonge PJ. Structure-Kinetic Relationship Studies for the Development of Long Residence Time LpxC Inhibitors. J Med Chem 2022; 65:11854-11875. [PMID: 36037447 PMCID: PMC10182817 DOI: 10.1021/acs.jmedchem.2c00974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is a promising drug target in Gram-negative bacteria. Previously, we described a correlation between the residence time of inhibitors on Pseudomonas aeruginosa LpxC (paLpxC) and the post-antibiotic effect (PAE) caused by the inhibitors on the growth of P. aeruginosa. Given that drugs with prolonged activity following compound removal may have advantages in dosing regimens, we have explored the structure-kinetic relationship for paLpxC inhibition by analogues of the pyridone methylsulfone PF5081090 (1) originally developed by Pfizer. Several analogues have longer residence times on paLpxC than 1 (41 min) including PT913, which has a residence time of 124 min. PT913 also has a PAE of 4 h, extending the original correlation observed between residence time and PAE. Collectively, the studies provide a platform for the rational modulation of paLpxC inhibitor residence time and the potential development of antibacterial agents that cause prolonged suppression of bacterial growth.
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Affiliation(s)
- Sneha Basak
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Yong Li
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Suyuan Tao
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Fereidoon Daryaee
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Jonathan Merino
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Chendi Gu
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | | | - Jenny N. Phan
- McGill University Montreal, Quebec H3A 0G4, Canada Canada
| | | | - Stephen G. Walker
- Department of Oral Biology and Pathology, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Peter J. Tonge
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Radiology, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
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26
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Graham JE, Niks D, Zane GM, Gui Q, Hom K, Hille R, Wall JD, Raman CS. How a Formate Dehydrogenase Responds to Oxygen: Unexpected O 2 Insensitivity of an Enzyme Harboring Tungstopterin, Selenocysteine, and [4Fe–4S] Clusters. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joel E. Graham
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland21201, United States
| | - Dimitri Niks
- Department of Biochemistry, University of California, Riverside, California92521, United States
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, Missouri65211, United States
| | - Qin Gui
- Department of Biochemistry, University of Missouri, Columbia, Missouri65211, United States
| | - Kellie Hom
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland21201, United States
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, California92521, United States
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri, Columbia, Missouri65211, United States
| | - C. S. Raman
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland21201, United States
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27
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Johnson CM, Fast W. On the kinetic mechanism of dimethylarginine dimethylaminohydrolase. Bioorg Med Chem 2022; 66:116816. [PMID: 35598478 DOI: 10.1016/j.bmc.2022.116816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 11/28/2022]
Abstract
Dimethylarginine dimethylaminohydrolase (DDAH, EC 3.5.3.18) catalyzes the hydrolysis of asymmetric Nω,Nω-dimethyl-l-arginine (ADMA), an endogenous inhibitor of human nitric oxide synthases. The active-site cysteine residue has been proposed to serve as the catalytic nucleophile, forming an S-alkylthiourea reaction intermediate, and serving as a target for covalent inhibitors. Inhibition can lead to ADMA accumulation and downstream inhibition of nitric oxide production. Prior studies have provided experimental evidence for formation of this covalent adduct but have not characterized it kinetically. Here, rapid quench-flow is used with ADMA and the DDAH from Pseudomonas aeruginosa to determine the rate constants for formation (k2 = 17 ± 2 s-1) and decay (k3 = 1.5 ± 0.1 s-1) of the covalent S-alkylthiourea adduct. A minimal kinetic mechanism for DDAH is proposed that supports the kinetic competence of this species as a covalent reaction intermediate and assigns the rate-limiting step in substrate turnover as hydrolysis of this intermediate. This work helps elucidate the different reactivities of S-alkylthiourea intermediates found among the mechanistically diverse pentein superfamily of guanidine-modifying enzymes and provides information useful for inhibitor development.
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Affiliation(s)
- Corey M Johnson
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712, USA; Department of Chemistry and Biochemistry, Howard College of Arts and Sciences, Samford University, Birmingham, AL 35229, USA
| | - Walter Fast
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712, USA.
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28
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Kisgeropoulos EC, Gan YJ, Greer SM, Hazel JM, Shafaat HS. Pulsed Multifrequency Electron Paramagnetic Resonance Spectroscopy Reveals Key Branch Points for One- vs Two-Electron Reactivity in Mn/Fe Proteins. J Am Chem Soc 2022; 144:11991-12006. [PMID: 35786920 DOI: 10.1021/jacs.1c13738] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Traditionally, the ferritin-like superfamily of proteins was thought to exclusively use a diiron active site in catalyzing a diverse array of oxygen-dependent reactions. In recent years, novel redox-active cofactors featuring heterobimetallic Mn/Fe active sites have been discovered in both the radical-generating R2 subunit of class Ic (R2c) ribonucleotide reductases (RNRs) and the related R2-like ligand-binding oxidases (R2lox). However, the protein-specific factors that differentiate the radical reactivity of R2c from the C-H activation reactions of R2lox remain unknown. In this work, multifrequency pulsed electron paramagnetic resonance (EPR) spectroscopy and ligand hyperfine techniques in conjunction with broken-symmetry density functional theory calculations are used to characterize the molecular and electronic structures of two EPR-active intermediates trapped during aerobic assembly of the R2lox Mn/Fe cofactor. A MnIII(μ-O)(μ-OH)FeIII species is identified as the first EPR-active species and represents a common state between the two classes of redox-active Mn/Fe proteins. The species downstream from the MnIII(μ-O)(μ-OH)FeIII state exhibits unique EPR properties, including unprecedented spectral breadth and isotope-dependent g-tensors, which are attributed to a weakly coupled, hydrogen-bonded MnIII(μ-OH)FeIII species. This final intermediate precedes formation of the MnIII/FeIII resting state and is suggested to be relevant to understanding the endogenous reactivity of R2lox.
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Affiliation(s)
- Effie C Kisgeropoulos
- The Ohio State Biochemistry Program, The Ohio State University, 100 W 18th Avenue, Columbus, Ohio 43210, United States
| | - Yunqiao J Gan
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W 18th Avenue, Columbus, Ohio 43210, United States
| | - Samuel M Greer
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States.,Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Joseph M Hazel
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W 18th Avenue, Columbus, Ohio 43210, United States
| | - Hannah S Shafaat
- The Ohio State Biochemistry Program, The Ohio State University, 100 W 18th Avenue, Columbus, Ohio 43210, United States.,Department of Chemistry and Biochemistry, The Ohio State University, 100 W 18th Avenue, Columbus, Ohio 43210, United States
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29
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Aledo JC. renz: An R package for the analysis of enzyme kinetic data. BMC Bioinformatics 2022; 23:182. [PMID: 35578161 PMCID: PMC9112463 DOI: 10.1186/s12859-022-04729-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/11/2022] [Indexed: 12/04/2022] Open
Abstract
Background Complex enzymatic models are required for analyzing kinetic data derived under conditions that may not satisfy the assumptions associated with Michaelis–Menten kinetics. To analyze these data, several software packages have been developed. However, the complexity introduced by these programs is often dispensable when analyzing data conforming to the canonical Michaelis–Menten model. In these cases, the sophisticated routines of these packages become inefficient and unnecessarily intricated for the intended purpose, reason for which most users resort to general-purpose graphing programs. However, this approach, in addition of being time-consuming, is prone to human error, and can lead to misleading estimates of kinetic parameters, particularly when unweighted regression analyses of transformed kinetic data are performed. Results To fill the existing gap between highly specialized and general-purpose software, we have developed an easy-to-use R package, renz, designed for accurate and efficient estimation of enzyme kinetic parameters. The package provides different methods that can be clustered into four categories, depending on whether they are based on data fitting to a single progress curve (evolution of substrate concentration over time) or, alternatively, based on the dependency of initial rates on substrate concentration (differential rate equation). A second criterion to be considered is whether the experimental data need to be manipulated to obtain linear functions or, alternatively, data are directly fitted using non-linear regression analysis. The current program is a cross-platform, free and open-source software that can be obtained from the CRAN repository. The package is accompanied by five vignettes, which are intended to guide users to choose the appropriate method in each case, as well as providing the basic theoretical foundations of each method. These vignettes use real experimental data to illustrate the use of the package utilities. Conclusions renz is a rigorous and yet easy-to-use software devoted to the analysis of kinetic data. This application has been designed to meet the needs of users who are not practicing enzymologists, but who need to accurately estimate the kinetic parameters of enzymes. The current software saves time and minimizes the risk of making mistakes or introducing biases due to uncorrected error propagation effects.
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Affiliation(s)
- Juan Carlos Aledo
- Departamento de Biología Molecular Y Bioquímica, Universidad de Málaga, 29071, Málaga, Spain.
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30
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Venus S, Jankowsky E. Measuring the impact of cofactors on RNA helicase activities. Methods 2022; 204:376-385. [PMID: 35429628 PMCID: PMC9306305 DOI: 10.1016/j.ymeth.2022.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/03/2022] [Accepted: 04/12/2022] [Indexed: 12/25/2022] Open
Abstract
RNA helicases are the largest class of enzymes in eukaryotic RNA metabolism. In cells, protein cofactors regulate RNA helicase functions and impact biochemical helicase activities. Understanding how cofactors affect enzymatic activities of RNA helicases is thus critical for delineating physical roles and regulation of RNA helicases in cells. Here, we discuss approaches and conceptual considerations for the design of experiments to interrogate cofactor effects on RNA helicase activities in vitro. We outline the mechanistic frame for helicase reactions, discuss optimization of experimental setup and reaction parameters for measuring cofactor effects on RNA helicase activities, and provide basic guides to data analysis and interpretation. The described approaches are also instructive for determining the impact of small molecule inhibitors of RNA helicases.
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31
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Borsari C, Keles E, McPhail JA, Schaefer A, Sriramaratnam R, Goch W, Schaefer T, De Pascale M, Bal W, Gstaiger M, Burke JE, Wymann MP. Covalent Proximity Scanning of a Distal Cysteine to Target PI3Kα. J Am Chem Soc 2022; 144:6326-6342. [PMID: 35353516 PMCID: PMC9011356 DOI: 10.1021/jacs.1c13568] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Covalent protein
kinase inhibitors exploit currently noncatalytic
cysteines in the adenosine 5′-triphosphate (ATP)-binding site
via electrophiles directly appended to a reversible-inhibitor scaffold.
Here, we delineate a path to target solvent-exposed cysteines at a
distance >10 Å from an ATP-site-directed core module and produce
potent covalent phosphoinositide 3-kinase α (PI3Kα) inhibitors.
First, reactive warheads are used to reach out to Cys862 on PI3Kα,
and second, enones are replaced with druglike warheads while linkers
are optimized. The systematic investigation of intrinsic warhead reactivity
(kchem), rate of covalent bond formation
and proximity (kinact and reaction space
volume Vr), and integration of structure
data, kinetic and structural modeling, led to the guided identification
of high-quality, covalent chemical probes. A novel stochastic approach
provided direct access to the calculation of overall reaction rates
as a function of kchem, kinact, Ki, and Vr, which was validated with compounds with varied linker
lengths. X-ray crystallography, protein mass spectrometry (MS), and
NanoBRET assays confirmed covalent bond formation of the acrylamide
warhead and Cys862. In rat liver microsomes, compounds 19 and 22 outperformed the rapidly metabolized CNX-1351,
the only known PI3Kα irreversible inhibitor. Washout experiments
in cancer cell lines with mutated, constitutively activated PI3Kα
showed a long-lasting inhibition of PI3Kα. In SKOV3 cells, compounds 19 and 22 revealed PI3Kβ-dependent signaling,
which was sensitive to TGX221. Compounds 19 and 22 thus qualify as specific chemical probes to explore PI3Kα-selective
signaling branches. The proposed approach is generally suited to develop
covalent tools targeting distal, unexplored Cys residues in biologically
active enzymes.
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Affiliation(s)
- Chiara Borsari
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Erhan Keles
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Jacob A McPhail
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Alexander Schaefer
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Rohitha Sriramaratnam
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Wojciech Goch
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Thorsten Schaefer
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Martina De Pascale
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Wojciech Bal
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Matthias P Wymann
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
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32
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Nikitin D, Mican J, Toul M, Bednar D, Peskova M, Kittova P, Thalerova S, Vitecek J, Damborsky J, Mikulik R, Fleishman SJ, Prokop Z, Marek M. Computer-aided engineering of staphylokinase toward enhanced affinity and selectivity for plasmin. Comput Struct Biotechnol J 2022; 20:1366-1377. [PMID: 35386102 PMCID: PMC8941168 DOI: 10.1016/j.csbj.2022.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/02/2022] [Accepted: 03/05/2022] [Indexed: 11/15/2022] Open
Abstract
Cardio- and cerebrovascular diseases are leading causes of death and disability, resulting in one of the highest socio-economic burdens of any disease type. The discovery of bacterial and human plasminogen activators and their use as thrombolytic drugs have revolutionized treatment of these pathologies. Fibrin-specific agents have an advantage over non-specific factors because of lower rates of deleterious side effects. Specifically, staphylokinase (SAK) is a pharmacologically attractive indirect plasminogen activator protein of bacterial origin that forms stoichiometric noncovalent complexes with plasmin, promoting the conversion of plasminogen into plasmin. Here we report a computer-assisted re-design of the molecular surface of SAK to increase its affinity for plasmin. A set of computationally designed SAK mutants was produced recombinantly and biochemically characterized. Screening revealed a pharmacologically interesting SAK mutant with ∼7-fold enhanced affinity toward plasmin, ∼10-fold improved plasmin selectivity and moderately higher plasmin-generating efficiency in vitro. Collectively, the results obtained provide a framework for SAK engineering using computational affinity-design that could pave the way to next-generation of effective, highly selective, and less toxic thrombolytics.
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Affiliation(s)
- Dmitri Nikitin
- International Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jan Mican
- International Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- Neurology Department, St. Anne's University Hospital and Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Martin Toul
- International Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - David Bednar
- International Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Michaela Peskova
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
- Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Patricia Kittova
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
- Department of Biochemistry, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Sandra Thalerova
- International Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
- Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jan Vitecek
- International Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
- Neurology Department, St. Anne's University Hospital and Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jiri Damborsky
- International Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Robert Mikulik
- International Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
- Neurology Department, St. Anne's University Hospital and Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | | | - Zbynek Prokop
- International Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Martin Marek
- International Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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Mechanism of cooperative N-glycan processing by the multi-modular endoglycosidase EndoE. Nat Commun 2022; 13:1137. [PMID: 35241669 PMCID: PMC8894350 DOI: 10.1038/s41467-022-28722-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 02/04/2022] [Indexed: 11/29/2022] Open
Abstract
Bacteria produce a remarkably diverse range of glycoside hydrolases to metabolize glycans from the environment as a primary source of nutrients, and to promote the colonization and infection of a host. Here we focus on EndoE, a multi-modular glycoside hydrolase secreted by Enterococcus faecalis, one of the leading causes of healthcare-associated infections. We provide X-ray crystal structures of EndoE, which show an architecture composed of four domains, including GH18 and GH20 glycoside hydrolases connected by two consecutive three α-helical bundles. We determine that the GH20 domain is an exo-β-1,2-N-acetylglucosaminidase, whereas the GH18 domain is an endo-β-1,4-N-acetylglucosaminidase that exclusively processes the central core of complex-type or high-mannose-type N-glycans. Both glycoside hydrolase domains act in a concerted manner to process diverse N-glycans on glycoproteins, including therapeutic IgG antibodies. EndoE combines two enzyme domains with distinct functions and glycan specificities to play a dual role in glycan metabolism and immune evasion. EndoE is a multi-domain glycoside hydrolase of the human pathogen Enterococcus faecalis. Here, the authors present crystal structures of EndoE and provide biochemical insights into the molecular basis of EndoE’s substrate specificity and catalytic mechanism.
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34
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Srinivasan B. A guide to enzyme kinetics in early drug discovery. FEBS J 2022; 290:2292-2305. [PMID: 35175693 DOI: 10.1111/febs.16404] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/10/2022] [Accepted: 02/15/2022] [Indexed: 12/28/2022]
Abstract
Drugs interact with their target of interest to bring about the desired phenotypic outcome that results in disease alleviation. Traditionally, most lead optimization exercises were driven by affinity measures (like IC50 ) to inform structure-activity relationship (SAR)-guided medicinal chemistry. However, an IC50 value is a thermodynamic estimate measured under equilibrium conditions that can vary as a function of substrate concentration and/or time (the latter especially for nonequilibrium modalities). Further, like other thermodynamic estimates, it is a state-function that is indifferent to the path traversed from the initial state to the final state. This can be a cause for concern in drug discovery given the predominance of nonequilibrium interactions and the open thermodynamic nature of the human system. Under such situations, employing rates along with equilibrium constants (or IC50 values) would be far more relevant to capture the time evolution of the small molecule's interaction with the target of interest. These rates are generally typified by the rate of association, rate of dissociation and the residence time of the small molecule on the target (target occupancy). These parameters, when combined with the concept of target vulnerability, therapeutic window, pharmacokinetic profile of the small molecule, estimates of endogenous ligand and target turnover, will shed critical insights into the kinetics and dynamics of a small molecule's interaction with the protein, and allow realistic modelling of the system to enable optimizations and dosing decisions. With that aim, this guide will attempt to introduce the traditional role of mechanistic enzymology within drug discovery and emphasize the importance of kinetics in guiding SAR-based optimizations. It will also present initial ideas on how kinetic investigation should be positioned relative to the temporal span of a drug-discovery pipeline to leverage maximal utility from the investment in time and effort.
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Affiliation(s)
- Bharath Srinivasan
- Mechanistic and Structural Biology Discovery Sciences R&D AstraZeneca Cambridge UK
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35
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Regularization and concave loss functions for estimation of chemical kinetic models. Appl Soft Comput 2022. [DOI: 10.1016/j.asoc.2021.108286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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36
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Dangerfield TL, Kirmizialtin S, Johnson KA. Substrate specificity and proposed structure of the proofreading complex of T7 DNA polymerase. J Biol Chem 2022; 298:101627. [PMID: 35074426 PMCID: PMC8867116 DOI: 10.1016/j.jbc.2022.101627] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/25/2022] Open
Abstract
Faithful replication of genomic DNA by high-fidelity DNA polymerases is crucial for the survival of most living organisms. While high-fidelity DNA polymerases favor canonical base pairs over mismatches by a factor of ∼1 × 105, fidelity is further enhanced several orders of magnitude by a 3′–5′ proofreading exonuclease that selectively removes mispaired bases in the primer strand. Despite the importance of proofreading to maintaining genome stability, it remains much less studied than the fidelity mechanisms employed at the polymerase active site. Here we characterize the substrate specificity for the proofreading exonuclease of a high-fidelity DNA polymerase by investigating the proofreading kinetics on various DNA substrates. The contribution of the exonuclease to net fidelity is a function of the kinetic partitioning between extension and excision. We show that while proofreading of a terminal mismatch is efficient, proofreading a mismatch buried by one or two correct bases is even more efficient. Because the polymerase stalls after incorporation of a mismatch and after incorporation of one or two correct bases on top of a mismatch, the net contribution of the exonuclease is a function of multiple opportunities to correct mistakes. We also characterize the exonuclease stereospecificity using phosphorothioate-modified DNA, provide a homology model for the DNA primer strand in the exonuclease active site, and propose a dynamic structural model for the transfer of DNA from the polymerase to the exonuclease active site based on MD simulations.
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Affiliation(s)
- Tyler L Dangerfield
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas, USA
| | - Serdal Kirmizialtin
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
| | - Kenneth A Johnson
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas, USA.
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37
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Read BJ, Fisher G, Wissett OLR, Machado TFG, Nicholson J, Mitchell JBO, da Silva RG. Allosteric Inhibition of Acinetobacter baumannii ATP Phosphoribosyltransferase by Protein:Dipeptide and Protein:Protein Interactions. ACS Infect Dis 2022; 8:197-209. [PMID: 34928596 DOI: 10.1021/acsinfecdis.1c00539] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
ATP phosphoribosyltransferase (ATPPRT) catalyzes the first step of histidine biosynthesis in bacteria, namely, the condensation of ATP and 5-phospho-α-d-ribosyl-1-pyrophosphate (PRPP) to generate N1-(5-phospho-β-d-ribosyl)-ATP (PRATP) and pyrophosphate. Catalytic (HisGS) and regulatory (HisZ) subunits assemble in a hetero-octamer where HisZ activates HisGS and mediates allosteric inhibition by histidine. In Acinetobacter baumannnii, HisGS is necessary for the bacterium to persist in the lung during pneumonia. Inhibition of ATPPRT is thus a promising strategy for specific antibiotic development. Here, A. baumannii ATPPRT is shown to follow a rapid equilibrium random kinetic mechanism, unlike any other ATPPRT. Histidine noncompetitively inhibits ATPPRT. Binding kinetics indicates histidine binds to free ATPPRT and to ATPPRT:PRPP and ATPPRT:ATP binary complexes with similar affinity following a two-step binding mechanism, but with distinct kinetic partition of the initial enzyme:inhibitor complex. The dipeptide histidine-proline inhibits ATPPRT competitively and likely uncompetitively, respectively, against PRPP and ATP. Rapid kinetics analysis shows His-Pro binds to the ATPPRT:ATP complex via a two-step binding mechanism. A related HisZ that shares 43% sequence identity with A. baumannii HisZ is a tight-binding allosteric inhibitor of A. baumannii HisGS. These findings lay the foundation for inhibitor design against A. baumannii ATPPRT.
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Affiliation(s)
- Benjamin J. Read
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - Gemma Fisher
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - Oliver L. R. Wissett
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - Teresa F. G. Machado
- School of Chemistry, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - John Nicholson
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - John B. O. Mitchell
- School of Chemistry, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - Rafael G. da Silva
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
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38
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Singh A, Patel SS. Quantitative methods to study helicase, DNA polymerase, and exonuclease coupling during DNA replication. Methods Enzymol 2022; 672:75-102. [PMID: 35934486 PMCID: PMC9933136 DOI: 10.1016/bs.mie.2022.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Genome replication is accomplished by highly regulated activities of enzymes in a multi-protein complex called the replisome. Two major enzymes, DNA polymerase and helicase, catalyze continuous DNA synthesis on the leading strand of the parental DNA duplex while the lagging strand is synthesized discontinuously. The helicase and DNA polymerase on their own are catalytically inefficient and weak motors for unwinding/replicating double-stranded DNA. However, when a helicase and DNA polymerase are functionally and physically coupled, they catalyze fast and highly processive leading strand DNA synthesis. DNA polymerase has a 3'-5' exonuclease activity, which removes nucleotides misincorporated in the nascent DNA. DNA synthesis kinetics, processivity, and accuracy are governed by the interplay of the helicase, DNA polymerase, and exonuclease activities within the replisome. This chapter describes quantitative biochemical and biophysical methods to study the coupling of these three critical activities during DNA replication. The methods include real-time quantitation of kinetics of DNA unwinding-synthesis by a coupled helicase-DNA polymerase complex, a 2-aminopurine fluorescence-based assay to map the precise positions of helicase and DNA polymerase with respect to the replication fork junction, and a radiometric assay to study the coupling of DNA polymerase, exonuclease, and helicase activities during processive leading strand DNA synthesis. These methods are presented here with bacteriophage T7 replication proteins as an example but can be applied to other systems with appropriate modifications.
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39
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Analysis of the conformational space and dynamics of RNA helicases by single-molecule FRET in solution and on surfaces. Methods Enzymol 2022; 673:251-310. [DOI: 10.1016/bs.mie.2022.03.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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40
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Püschmann J, Mahor D, de Geus DC, Strampraad MJF, Srour B, Hagen WR, Todorovic S, Hagedoorn PL. Unique Biradical Intermediate in the Mechanism of the Heme Enzyme Chlorite Dismutase. ACS Catal 2021; 11:14533-14544. [PMID: 34888122 PMCID: PMC8650003 DOI: 10.1021/acscatal.1c03432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/04/2021] [Indexed: 11/30/2022]
Abstract
![]()
The heme enzyme chlorite
dismutase (Cld) catalyzes O–O bond
formation as part of the conversion of the toxic chlorite (ClO2–) to chloride (Cl–) and
molecular oxygen (O2). Enzymatic O–O bond formation
is rare in nature, and therefore, the reaction mechanism of Cld is
of great interest. Microsecond timescale pre-steady-state kinetic
experiments employing Cld from Azospira oryzae (AoCld), the natural substrate chlorite, and the
model substrate peracetic acid (PAA) reveal the formation of distinct
intermediates. AoCld forms a complex with PAA rapidly,
which is cleaved heterolytically to yield Compound I, which is sequentially
converted to Compound II. In the presence of chlorite, AoCld forms an initial intermediate with spectroscopic characteristics
of a 6-coordinate high-spin ferric substrate adduct, which subsequently
transforms at kobs = 2–5 ×
104 s–1 to an intermediate 5-coordinated
high-spin ferric species. Microsecond-timescale freeze-hyperquench
experiments uncovered the presence of a transient low-spin ferric
species and a triplet species attributed to two weakly coupled amino
acid cation radicals. The intermediates of the chlorite reaction were
not observed with the model substrate PAA. These findings demonstrate
the nature of physiologically relevant catalytic intermediates and
show that the commonly used model substrate may not behave as expected,
which demands a revision of the currently proposed mechanism of Clds.
The transient triplet-state biradical species that we designate as
Compound T is, to the best of our knowledge, unique in heme enzymology.
The results highlight electron paramagnetic resonance spectroscopic
evidence for transient intermediate formation during the reaction
of AoCld with its natural substrate chlorite. In
the proposed mechanism, the heme iron remains ferric throughout the
catalytic cycle, which may minimize the heme moiety’s reorganization
and thereby maximize the enzyme’s catalytic efficiency.
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Affiliation(s)
- Julia Püschmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Durga Mahor
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Daniël C. de Geus
- Janssen Vaccines & Prevention, Archimedesweg 4-6, 2333 CN Leiden, The Netherlands
| | - Marc J. F. Strampraad
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Batoul Srour
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Wilfred R. Hagen
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Peter-Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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41
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Wang Z, Paragas EM, Nagar S, Korzekwa K. Complex Cytochrome P450 Kinetics Due to Multisubstrate Binding and Sequential Metabolism. Part 1. Theoretical Considerations. Drug Metab Dispos 2021; 49:1090-1099. [PMID: 34503952 PMCID: PMC11022900 DOI: 10.1124/dmd.121.000553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/06/2021] [Indexed: 11/22/2022] Open
Abstract
Complexities in P450-mediated metabolism kinetics include multisubstrate binding, multiple-product formation, and sequential metabolism. Saturation curves and intrinsic clearances were simulated for single-substrate and multisubstrate models using derived velocity equations and numerical solutions of ordinary differential equations (ODEs). Multisubstrate models focused on sigmoidal kinetics because of their dramatic impact on clearance predictions. These models were combined with multiple-product formation and sequential metabolism, and simulations were performed with random error. Use of single-substrate models to characterize multisubstrate data can result in inaccurate kinetic parameters and poor clearance predictions. Comparing results for use of standard velocity equations with ODEs clearly shows that ODEs are more versatile and provide better parameter estimates. It would be difficult to derive concentration-velocity relationships for complex models, but these relationships can be easily modeled using numerical methods and ODEs. SIGNIFICANCE STATEMENT: The impact of multisubstrate binding, multiple-product formation, and sequential metabolism on the P450 kinetics was investigated. Numerical methods are capable of characterizing complicated P450 kinetics.
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Affiliation(s)
- Zeyuan Wang
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, Pennsylvania
| | - Erickson M Paragas
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, Pennsylvania
| | - Swati Nagar
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, Pennsylvania
| | - Ken Korzekwa
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, Pennsylvania
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42
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Dangerfield TL, Huang NZ, Johnson KA. High throughput quantification of short nucleic acid samples by capillary electrophoresis with automated data processing. Anal Biochem 2021; 629:114239. [PMID: 33979658 PMCID: PMC8384658 DOI: 10.1016/j.ab.2021.114239] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/14/2021] [Accepted: 04/28/2021] [Indexed: 01/29/2023]
Abstract
Analysis of catalytic activity of nucleic acid enzymes is crucial for many applications, ranging from biotechnology to the search for antiviral drugs. Commonly used analytical methods for quantifying DNA and RNA reaction products based on slab-gel electrophoresis are limited in throughput, speed, and accuracy. Here we report the optimization of high throughput methods to separate and quantify short nucleic acid reaction products using DNA sequencing instruments based on capillary electrophoresis with fluorescence detection. These methods afford single base resolution without requiring extensive sample preparation. Additionally, we show that the utility of our system extends to quantifying RNA products. The efficiency and reliability of modern instruments offers a large increase in throughput but complications due to variations in migration times between capillaries required us to develop a computer program to normalize the data and quantify the products for automated kinetic analysis. The methods presented here greatly increase sample throughput and accuracy and should be applicable to many nucleic acid enzymes.
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Affiliation(s)
- Tyler L Dangerfield
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas, 2500 Speedway, Austin, TX, 78712, USA
| | - Nathan Z Huang
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas, 2500 Speedway, Austin, TX, 78712, USA
| | - Kenneth A Johnson
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas, 2500 Speedway, Austin, TX, 78712, USA.
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43
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Goldberg AM, Robinson MK, Starr ES, Marasco RN, Alana AC, Cochrane CS, Klugh KL, Strzeminski DJ, Du M, Colabroy KL, Peterson LW. L-DOPA Dioxygenase Activity on 6-Substituted Dopamine Analogues. Biochemistry 2021; 60:2492-2507. [PMID: 34324302 DOI: 10.1021/acs.biochem.1c00310] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dioxygenase enzymes are essential protein catalysts for the breakdown of catecholic rings, structural components of plant woody tissue. This powerful chemistry is used in nature to make antibiotics and other bioactive materials or degrade plant material, but we have a limited understanding of the breadth and depth of substrate space for these potent catalysts. Here we report steady-state and pre-steady-state kinetic analysis of dopamine derivatives substituted at the 6-position as substrates of L-DOPA dioxygenase, and an analysis of that activity as a function of the electron-withdrawing nature of the substituent. Steady-state and pre-steady-state kinetic data demonstrate the dopamines are impaired in binding and catalysis with respect to the cosubstrate molecular oxygen, which likely afforded spectroscopic observation of an early reaction intermediate, the semiquinone of dopamine. The reaction pathway of dopamine in the pre-steady state is consistent with a nonproductive mode of binding of oxygen at the active site. Despite these limitations, L-DOPA dioxygenase is capable of binding all of the dopamine derivatives and catalyzing multiple turnovers of ring cleavage for dopamine, 6-bromodopamine, 6-carboxydopamine, and 6-cyanodopamine. 6-Nitrodopamine was a single-turnover substrate. The variety of substrates accepted by the enzyme is consistent with an interplay of factors, including the capacity of the active site to bind large, negatively charged groups at the 6-position and the overall oxidizability of each catecholamine, and is indicative of the utility of extradiol cleavage in semisynthetic and bioremediation applications.
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Affiliation(s)
- Alexander M Goldberg
- Department of Chemistry, Muhlenberg College, 2400 Chew Street, Allentown, Pennsylvania 18104, United States
| | - Miranda K Robinson
- Department of Chemistry, Muhlenberg College, 2400 Chew Street, Allentown, Pennsylvania 18104, United States
| | - Erykah S Starr
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, United States
| | - Ryan N Marasco
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, United States
| | - Alexa C Alana
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, United States
| | - C Skyler Cochrane
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, United States
| | - Kameron L Klugh
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, United States
| | - David J Strzeminski
- Department of Chemistry, Muhlenberg College, 2400 Chew Street, Allentown, Pennsylvania 18104, United States
| | - Muxue Du
- Department of Chemistry, Muhlenberg College, 2400 Chew Street, Allentown, Pennsylvania 18104, United States
| | - Keri L Colabroy
- Department of Chemistry, Muhlenberg College, 2400 Chew Street, Allentown, Pennsylvania 18104, United States
| | - Larryn W Peterson
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, United States
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44
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Srinivasan B. A guide to the Michaelis-Menten equation: steady state and beyond. FEBS J 2021; 289:6086-6098. [PMID: 34270860 DOI: 10.1111/febs.16124] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/01/2021] [Accepted: 07/15/2021] [Indexed: 01/25/2023]
Abstract
The modern definition of enzymology is synonymous with the Michaelis-Menten equation instituted by Leonor Michaelis and Maud Menten. Most textbooks, or chapters within, discussing enzymology start with the derivation of the equation under the assumption of rapid equilibrium (as done by Michaelis-Menten) or steady state (as modified by Briggs and Haldane) conditions to highlight the importance of this equation as the bedrock on which interpretation of enzyme kinetic results is dependent. However, few textbooks or monographs take the effort of placing the equation within its right historical context and discuss the assumptions that have gone into its institution. This guide will dwell on these in substantial detail. Further, this guide will attempt to instil a sense of appreciation for the mathematical curve rectangular hyperbola, its unique attributes and how ubiquitous the curve is in biological systems. To conclude, this guide will discuss the limitations of the equation, and the method it embodies, and trace the journey of how investigators are attempting to move beyond the steady-state approach and the Michaelis-Menten equation into full progress curve, pre-steady state and single-turnover kinetic analysis to obtain greater insights into enzyme kinetics and catalysis.
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Affiliation(s)
- Bharath Srinivasan
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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45
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Sigg A, Klimacek M, Nidetzky B. Three-level hybrid modeling for systematic optimization of biocatalytic synthesis: α-glucosyl glycerol production by enzymatic trans-glycosylation from sucrose. Biotechnol Bioeng 2021; 118:4028-4040. [PMID: 34232503 PMCID: PMC8518044 DOI: 10.1002/bit.27878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/28/2021] [Accepted: 07/04/2021] [Indexed: 11/07/2022]
Abstract
Mechanism-based kinetic models are rigorous tools to analyze enzymatic reactions, but their extension to actual conditions of the biocatalytic synthesis can be difficult. Here, we demonstrate (mechanistic-empirical) hybrid modeling for systematic optimization of the sucrose phosphorylase-catalyzed glycosylation of glycerol from sucrose, to synthesize the cosmetic ingredient α-glucosyl glycerol (GG). The empirical model part was developed to capture nonspecific effects of high sucrose concentrations (up to 1.5 M) on microscopic steps of the enzymatic trans-glycosylation mechanism. Based on verified predictions of the enzyme performance under initial rate conditions (Level 1), the hybrid model was expanded by microscopic terms of the reverse reaction to account for the full-time course of GG synthesis (Level 2). Lastly (Level 3), the application of the hybrid model for comprehensive window-of-operation analysis and constrained optimization of the GG production (~250 g/L) was demonstrated. Using two candidate sucrose phosphorylases (from Leuconostoc mesenteroides and Bifidobacterium adolescentis), we reveal the hybrid model as a powerful tool of "process decision making" to guide rational selection of the best-suited enzyme catalyst. Our study exemplifies a closing of the gap between enzyme kinetic models considered for mechanistic research and applicable in technologically relevant reaction conditions; and it highlights the important benefit thus realizable for biocatalytic process development.
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Affiliation(s)
- Alexander Sigg
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Mario Klimacek
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
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46
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Glanowski M, Wójcik P, Procner M, Borowski T, Lupa D, Mielczarek P, Oszajca M, Świderek K, Moliner V, Bojarski AJ, Szaleniec M. Enzymatic Δ 1-Dehydrogenation of 3-Ketosteroids—Reconciliation of Kinetic Isotope Effects with the Reaction Mechanism. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01479] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michał Glanowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Patrycja Wójcik
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Magdalena Procner
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Dawid Lupa
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Przemysław Mielczarek
- Laboratory of Proteomics and Mass Spectrometry, Maj Institute of Pharmacology, Polish Academy of Sciences, 31-343 Krakow, Poland
| | - Maria Oszajca
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Katarzyna Świderek
- Department of Physical and Analytical Chemistry, Universitat Jaume I, 12071 Castellón, Spain
| | - Vicent Moliner
- Department of Physical and Analytical Chemistry, Universitat Jaume I, 12071 Castellón, Spain
| | - Andrzej J. Bojarski
- Department of Medicinal Chemistry, Maj Institute of Pharmacology, Polish Academy of Sciences, Smetna 12, 31-343 Krakow, Poland
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
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47
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Measuring the Complex Effects of the Single-Stranded DNA-Binding Protein gp2.5 on Primer Synthesis and Extension by the Bacteriophage T7 Replisome. Methods Mol Biol 2021; 2281:323-332. [PMID: 33847969 DOI: 10.1007/978-1-0716-1290-3_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The single-stranded DNA-binding protein gp2.5 of bacteriophage T7 plays myriad functions in the replication of phage genomes. In addition to interacting with ssDNA, gp2.5 binds to the T7 DNA polymerase and primase/helicase proteins, regulating their enzymatic activities. Here we describe in vitro methods to examine the effects of gp2.5 on primer synthesis and extension by the T7 replisome.
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48
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Schenkmayerova A, Pinto GP, Toul M, Marek M, Hernychova L, Planas-Iglesias J, Daniel Liskova V, Pluskal D, Vasina M, Emond S, Dörr M, Chaloupkova R, Bednar D, Prokop Z, Hollfelder F, Bornscheuer UT, Damborsky J. Engineering the protein dynamics of an ancestral luciferase. Nat Commun 2021; 12:3616. [PMID: 34127663 PMCID: PMC8203615 DOI: 10.1038/s41467-021-23450-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 04/27/2021] [Indexed: 01/06/2023] Open
Abstract
Protein dynamics are often invoked in explanations of enzyme catalysis, but their design has proven elusive. Here we track the role of dynamics in evolution, starting from the evolvable and thermostable ancestral protein AncHLD-RLuc which catalyses both dehalogenase and luciferase reactions. Insertion-deletion (InDel) backbone mutagenesis of AncHLD-RLuc challenged the scaffold dynamics. Screening for both activities reveals InDel mutations localized in three distinct regions that lead to altered protein dynamics (based on crystallographic B-factors, hydrogen exchange, and molecular dynamics simulations). An anisotropic network model highlights the importance of the conformational flexibility of a loop-helix fragment of Renilla luciferases for ligand binding. Transplantation of this dynamic fragment leads to lower product inhibition and highly stable glow-type bioluminescence. The success of our approach suggests that a strategy comprising (i) constructing a stable and evolvable template, (ii) mapping functional regions by backbone mutagenesis, and (iii) transplantation of dynamic features, can lead to functionally innovative proteins.
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Affiliation(s)
- Andrea Schenkmayerova
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Gaspar P Pinto
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Martin Toul
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Martin Marek
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lenka Hernychova
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Joan Planas-Iglesias
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Veronika Daniel Liskova
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Daniel Pluskal
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michal Vasina
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Stephane Emond
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Mark Dörr
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Radka Chaloupkova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - David Bednar
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zbynek Prokop
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | | | - Uwe T Bornscheuer
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Greifswald, Germany.
| | - Jiri Damborsky
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic.
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic.
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49
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Mäkinen JJ, Shin Y, Vieras E, Virta P, Metsä-Ketelä M, Murakami KS, Belogurov GA. The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases. Nat Commun 2021; 12:796. [PMID: 33542236 PMCID: PMC7862312 DOI: 10.1038/s41467-021-21005-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 01/06/2021] [Indexed: 01/18/2023] Open
Abstract
RNA polymerases (RNAPs) synthesize RNA from NTPs, whereas DNA polymerases synthesize DNA from 2'dNTPs. DNA polymerases select against NTPs by using steric gates to exclude the 2'OH, but RNAPs have to employ alternative selection strategies. In single-subunit RNAPs, a conserved Tyr residue discriminates against 2'dNTPs, whereas selectivity mechanisms of multi-subunit RNAPs remain hitherto unknown. Here, we show that a conserved Arg residue uses a two-pronged strategy to select against 2'dNTPs in multi-subunit RNAPs. The conserved Arg interacts with the 2'OH group to promote NTP binding, but selectively inhibits incorporation of 2'dNTPs by interacting with their 3'OH group to favor the catalytically-inert 2'-endo conformation of the deoxyribose moiety. This deformative action is an elegant example of an active selection against a substrate that is a substructure of the correct substrate. Our findings provide important insights into the evolutionary origins of biopolymers and the design of selective inhibitors of viral RNAPs.
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Affiliation(s)
- Janne J Mäkinen
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Yeonoh Shin
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Eeva Vieras
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Pasi Virta
- Department of Chemistry, University of Turku, Turku, Finland
| | | | - Katsuhiko S Murakami
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
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50
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Strom A, Shah R, Wagner CR. "Switching On" Enzyme Substrate Specificity Analysis with a Fluorescent Competitive Inhibitor. Biochemistry 2021; 60:440-450. [PMID: 33513008 DOI: 10.1021/acs.biochem.0c00954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymatically driven change to the spectroscopic properties of a chemical substrate or product has been a linchpin in the development of continuous enzyme kinetics assays. These assays inherently necessitate substrates or products that naturally comply with the constraints of the spectroscopic technique being used, or they require structural changes to the molecules involved to make them observable. Here we demonstrate a new analytical kinetics approach with enzyme histidine triad nucleotide binding protein 1 (HINT1) that allows us to extract both useful kcat values and a rank-ordered list of substrate specificities without the need to track substrates or products directly. Instead, this is accomplished indirectly using a "switch on" competitive inhibitor that fluoresces maximally only when bound to the HINT1 enzyme active site. Kinetic information is extracted from the duration of the diminished fluorescence when the monitorable inhibitor-bound enzyme is challenged with saturating concentrations of a nonfluorescent substrate. We refer to the loss of fluorescence, while the substrate competes for the fluorescent probe in the active site, as the substrate's residence transit time (RTT). The ability to assess kcat values and substrate specificity by monitoring the RTTs for a set of substrates with a competitive "switch on" inhibitor should be broadly applicable to other enzymatic reactions in which the "switch on" inhibitor has sufficient binding affinity over the enzymatic product.
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Affiliation(s)
- Alexander Strom
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Rachit Shah
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Carston R Wagner
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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