1
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Kretsch AM, Gadgil MG, DiCaprio AJ, Barrett SE, Kille BL, Si Y, Zhu L, Mitchell DA. Peptidase Activation by a Leader Peptide-Bound RiPP Recognition Element. Biochemistry 2023; 62:956-967. [PMID: 36734655 PMCID: PMC10126823 DOI: 10.1021/acs.biochem.2c00700] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The RiPP precursor recognition element (RRE) is a conserved domain found in many prokaryotic ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthetic gene clusters (BGCs). RREs bind with high specificity and affinity to a recognition sequence within the N-terminal leader region of RiPP precursor peptides. Lasso peptide biosynthesis involves an RRE-dependent leader peptidase, which is discretely encoded or fused to the RRE as a di-domain protein. Here we leveraged thousands of predicted BGCs to define the RRE:leader peptidase interaction through evolutionary covariance analysis. Each interacting domain contributes a three-stranded β-sheet to form a hydrophobic β-sandwich-like interface. The bioinformatics-guided predictions were experimentally confirmed using proteins from discrete and fused lasso peptide BGC architectures. Support for the domain-domain interface derived from chemical shift perturbation, paramagnetic relaxation enhancement experiments, and rapid variant activity screening using cell-free biosynthesis. Further validation of selected variants was performed with purified proteins. We developed a p-nitroanilide-based leader peptidase assay to illuminate the role of RRE domains. Our data show that RRE domains play a dual function. RRE domains deliver the precursor peptide to the leader peptidase, and the rate is saturable as expected for a substrate. RRE domains also partially compose the elusive S2 proteolytic pocket that binds the penultimate threonine of lasso leader peptides. Because the RRE domain is required to form the active site, leader peptidase activity is greatly diminished when the RRE domain is supplied at substoichiometric levels. Full proteolytic activation requires RRE engagement with the recognition sequence-containing portion of the leader peptide. Together, our observations define a new mechanism for protease activity regulation.
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Affiliation(s)
- Ashley M. Kretsch
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Chemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Mayuresh G. Gadgil
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Chemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Adam J. DiCaprio
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Chemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Susanna E. Barrett
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Chemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Bryce L. Kille
- Department of Computer Science, Rice University, Houston, Texas, United States of America
| | - Yuanyuan Si
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Chemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Lingyang Zhu
- School of Chemical Sciences, NMR Laboratory, University of Illinois, Urbana, Illinois, United States of America
| | - Douglas A. Mitchell
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Chemistry, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
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2
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Aspelin V, Lidskog A, Solano Arribas C, Hervø-Hansen S, Stenqvist B, Chudoba R, Wärnmark K, Lund M. Counterintuitive Electrostatics upon Metal Ion Coordination to a Receptor with Two Homotopic Binding Sites. J Am Chem Soc 2022; 144:2921-2932. [PMID: 35142499 PMCID: PMC8874967 DOI: 10.1021/jacs.1c08507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
![]()
The consecutive binding
of two potassium ions to a bis(18-crown-6)
analogue of Tröger’s base (BCETB) in water was studied
by isothermal titration calorimetry using four different salts, KCl,
KI, KSCN, and K2SO4. A counterintuitive result
was observed: the enthalpy change associated with the binding of the
second ion is more negative than that of the first (ΔHbind,2° < ΔHbind,1°). This remarkable finding is supported
by continuum electrostatic theory as well as by atomic scale replica
exchange molecular dynamics simulations, where the latter robustly
reproduces experimental trends for all simulated salts, KCl, KI, and
KSCN, using multiple force fields. While an enthalpic K+–K+attraction in water poses
a small, but fundamentally important, contribution to the overall
interaction, the probability of the collapsed conformation (COL) of
BCETB, where both crown ether moieties (CEs) of BCETB are bent in
toward the cavity, was found to increase successively upon binding
of the first and second potassium ions. The promotion of the COL conformation
reveals favorable intrinsic interactions between the potassium coordinated
CEs, which further contribute to the observation that ΔHbind,2° < ΔHbind,1°. While the observed trend is independent
of the counterion, the origin of the significantly larger magnitude
of the difference ΔHbind,2° – ΔHbind,1° observed experimentally for KSCN was studied in light of the weaker
hydration of the thiocyanate anion, resulting in an enrichment of
thiocyanate ions close to BCETB compared to the other studied counterions.
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Affiliation(s)
- Vidar Aspelin
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, Lund SE 221 00, Sweden
| | - Anna Lidskog
- Center for Analysis and Synthesis (CAS), Department of Chemistry, Lund University, Lund SE 221 00, Sweden
| | - Carlos Solano Arribas
- Center for Analysis and Synthesis (CAS), Department of Chemistry, Lund University, Lund SE 221 00, Sweden
| | - Stefan Hervø-Hansen
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, Lund SE 221 00, Sweden
| | - Björn Stenqvist
- Division of Physical Chemistry, Department of Chemistry, Lund University, Lund SE 221 00, Sweden
| | - Richard Chudoba
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, Lund SE 221 00, Sweden
| | - Kenneth Wärnmark
- Center for Analysis and Synthesis (CAS), Department of Chemistry, Lund University, Lund SE 221 00, Sweden
| | - Mikael Lund
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, Lund SE 221 00, Sweden.,Lund Institute of Advanced Neutron and X-ray Science (LINXS), Scheelevägen 19, Lund SE 223 70, Sweden
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3
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Abstract
Enzymatic reactions and noncovalent (i.e., supramolecular) interactions are two fundamental nongenetic attributes of life. Enzymatic noncovalent synthesis (ENS) refers to a process where enzymatic reactions control intermolecular noncovalent interactions for spatial organization of higher-order molecular assemblies that exhibit emergent properties and functions. Like enzymatic covalent synthesis (ECS), in which an enzyme catalyzes the formation of covalent bonds to generate individual molecules, ENS is a unifying theme for understanding the functions, morphologies, and locations of molecular ensembles in cellular environments. This review intends to provide a summary of the works of ENS within the past decade and emphasize ENS for functions. After comparing ECS and ENS, we describe a few representative examples where nature uses ENS, as a rule of life, to create the ensembles of biomacromolecules for emergent properties/functions in a myriad of cellular processes. Then, we focus on ENS of man-made (synthetic) molecules in cell-free conditions, classified by the types of enzymes. After that, we introduce the exploration of ENS of man-made molecules in the context of cells by discussing intercellular, peri/intracellular, and subcellular ENS for cell morphogenesis, molecular imaging, cancer therapy, and other applications. Finally, we provide a perspective on the promises of ENS for developing molecular assemblies/processes for functions. This review aims to be an updated introduction for researchers who are interested in exploring noncovalent synthesis for developing molecular science and technologies to address societal needs.
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Affiliation(s)
- Hongjian He
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Weiyi Tan
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Jiaqi Guo
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Meihui Yi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Adrianna N Shy
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
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4
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Robertsson C, Svensäter G, Blum Z, Wickström C. Intracellular Ser/Thr/Tyr phosphoproteome of the oral commensal Streptococcus gordonii DL1. BMC Microbiol 2020; 20:280. [PMID: 32928109 PMCID: PMC7488673 DOI: 10.1186/s12866-020-01944-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/11/2020] [Indexed: 12/28/2022] Open
Abstract
Background To respond and adapt to environmental challenges, prokaryotes regulate cellular processes rapidly and reversibly through protein phosphorylation and dephosphorylation. This study investigates the intracellular proteome and Ser/Thr/Tyr phosphoproteome of the oral commensal Streptococcus gordonii. Intracellular proteins from planktonic cells of S. gordonii DL1 were extracted and subjected to 2D-gel electrophoresis. Proteins in general were visualized using Coomassie Brilliant Blue and T-Rex staining. Phosphorylated proteins were visualized with Pro-Q Diamond Phosphoprotein Gel Stain. Proteins were identified by LC-MS/MS and sequence analysis. Results In total, sixty-one intracellular proteins were identified in S. gordonii DL1, many of which occurred at multiple isoelectric points. Nineteen of these proteins were present as one or more Ser/Thr/Tyr phosphorylated form. The identified phosphoproteins turned out to be involved in a variety of cellular processes. Conclusion Nineteen phosphoproteins involved in various cellular functions were identified in S. gordonii. This is the first time the global intracellular Ser/Thr/Tyr phosphorylation profile has been analysed in an oral streptococcus. Comparison with phosphoproteomes of other species from previous studies showed many similarities. Proteins that are consistently found in a phosphorylated state across several species and growth conditions may represent a core phosphoproteome profile shared by many bacteria.
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Affiliation(s)
- Carolina Robertsson
- Department of Oral Biology and Pathology, Faculty of Odontology, Malmö University, 20506, Malmö, Sweden.
| | - Gunnel Svensäter
- Department of Oral Biology and Pathology, Faculty of Odontology, Malmö University, 20506, Malmö, Sweden
| | - Zoltan Blum
- Department of Biomedical Science, Malmö University, 20506, Malmö, Sweden
| | - Claes Wickström
- Department of Oral Biology and Pathology, Faculty of Odontology, Malmö University, 20506, Malmö, Sweden
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5
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Artz JH, Tokmina-Lukaszewska M, Mulder DW, Lubner CE, Gutekunst K, Appel J, Bothner B, Boehm M, King PW. The structure and reactivity of the HoxEFU complex from the cyanobacterium Synechocystis sp. PCC 6803. J Biol Chem 2020; 295:9445-9454. [PMID: 32409585 PMCID: PMC7363133 DOI: 10.1074/jbc.ra120.013136] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/11/2020] [Indexed: 11/19/2022] Open
Abstract
Cyanobacterial Hox is a [NiFe] hydrogenase that consists of the hydrogen (H2)-activating subunits HoxYH, which form a complex with the HoxEFU assembly to mediate reactions with soluble electron carriers like NAD(P)H and ferredoxin (Fdx), thereby coupling photosynthetic electron transfer to energy-transforming catalytic reactions. Researchers studying the HoxEFUYH complex have observed that HoxEFU can be isolated independently of HoxYH, leading to the hypothesis that HoxEFU is a distinct functional subcomplex rather than an artifact of Hox complex isolation. Moreover, outstanding questions about the reactivity of Hox with natural substrates and the site(s) of substrate interactions and coupling of H2, NAD(P)H, and Fdx remain to be resolved. To address these questions, here we analyzed recombinantly produced HoxEFU by electron paramagnetic resonance spectroscopy and kinetic assays with natural substrates. The purified HoxEFU subcomplex catalyzed electron transfer reactions among NAD(P)H, flavodoxin, and several ferredoxins, thus functioning in vitro as a shuttle among different cyanobacterial pools of reducing equivalents. Both Fdx1-dependent reductions of NAD+ and NADP+ were cooperative. HoxEFU also catalyzed the flavodoxin-dependent reduction of NAD(P)+, Fdx2-dependent oxidation of NADH and Fdx4- and Fdx11-dependent reduction of NAD+. MS-based mapping identified an Fdx1-binding site at the junction of HoxE and HoxF, adjacent to iron-sulfur (FeS) clusters in both subunits. Overall, the reactivity of HoxEFU observed here suggests that it functions in managing peripheral electron flow from photosynthetic electron transfer, findings that reveal detailed insights into how ubiquitous cellular components may be used to allocate energy flow into specific bioenergetic products.
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Affiliation(s)
- Jacob H Artz
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | | | - David W Mulder
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Carolyn E Lubner
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | | | - Jens Appel
- Botanical Institute, Christian-Albrechts-University, Kiel, Germany
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Marko Boehm
- Botanical Institute, Christian-Albrechts-University, Kiel, Germany
| | - Paul W King
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
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6
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Khanppnavar B, Chatterjee R, Choudhury GB, Datta S. Genome-wide survey and crystallographic analysis suggests a role for both horizontal gene transfer and duplication in pantothenate biosynthesis pathways. Biochim Biophys Acta Gen Subj 2019; 1863:1547-1559. [DOI: 10.1016/j.bbagen.2019.05.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 05/21/2019] [Accepted: 05/24/2019] [Indexed: 01/13/2023]
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7
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Tsyrulneva I, Alagappan P, Liedberg B. Colorimetric Detection of Salivary α-Amylase Using Maltose as a Noncompetitive Inhibitor for Polysaccharide Cleavage. ACS Sens 2019; 4:865-873. [PMID: 30895774 DOI: 10.1021/acssensors.8b01343] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This paper describes an approach for colorimetric detection of salivary α-amylase, one of the potential biomarkers of autonomic nervous system (ANS) activity, for enabling assessment of fatigue. The ability of α-amylase to cleave α-bonds of polysaccharides is utilized for developing a colorimetric assay. In the proposed approach, 2-chloro-4-nitrophenyl-α-d-maltotrioside as substrate releases a colored byproduct upon cleavage by salivary α-amylase. Introduction of maltose as a noncompetitive inhibitor yields desirable linear responses in the physiologically relevant concentration range (20-500 μg/mL) with a limit of detection (LOD) of 8 μg/mL (in aqueous solution). The concentrations of substrate and noncompetitive inhibitor are subsequently optimized for colorimetric detection of salivary α-amylase. A facile paper-based "strip" assay is proposed for analysis of human saliva samples with marginal interference from saliva components. The proposed assay is rapid, specific, and easy-to-implement for colorimetric detection of salivary α-amylase between 20 and 500 μg/mL. Complementary RGB (red, green, blue components) analysis offers quantitative detection with a LOD of 11 μg/mL. The two assay formats are benchmarked against the Phadebas test, a state of the art method for spectrophotometric detection of α-amylase. The reported paper-based methodology possesses a high potential for estimation of altered ANS responses toward stressors that possibly could find applications in assessment of fatigue and for monitoring onset of fatigue.
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Affiliation(s)
- Iuna Tsyrulneva
- Institute for Sports Research, School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore, 637460
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798
| | - Palaniappan Alagappan
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798
| | - Bo Liedberg
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798
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8
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Sea K, Lee J, To D, Chen B, Sazinsky MH, Crane EJ. A broader active site in Pyrococcus horikoshii CoA disulfide reductase accommodates larger substrates and reveals evidence of subunit asymmetry. FEBS Open Bio 2018; 8:1083-1092. [PMID: 29988575 PMCID: PMC6026696 DOI: 10.1002/2211-5463.12439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 02/07/2018] [Accepted: 04/25/2018] [Indexed: 12/03/2022] Open
Abstract
Within the family of pyridine nucleotide disulfide oxidoreductase (PNDOR), enzymes are a group of single‐cysteine containing FAD‐dependent reductases that utilize a tightly bound coenzyme A to assist in the NAD(P)H‐dependent reduction of di‐, per‐, and polysulfide substrates in bacteria and archaea. For many of these homodimeric enzymes, it has proved difficult to determine the substrate specificity and metabolic function based on sequence and genome analysis alone. Coenzyme A‐disulfide reductase (CoADR) isolated from Pyrococcus horikoshii (phCoADR) reduces Co‐A per‐ and polysulfides, but, unlike other highly homologous members of this group, is a poor CoA disulfide reductase. The phCoADR structure has a narrower access channel for CoA substrates, which suggested that this restriction might be responsible for the enzyme's poor activity toward the bulky CoA disulfide substrate. To test this hypothesis, the substrate channel was widened by making four mutations along the channel wall (Y65A, Y66A, P67G, and H367G). The structure of the quadruple mutant shows a widened substrate channel, which is supported by a fourfold increase in kcat for the NAD(P)H‐dependent reduction of CoA disulfide and enhanced activity toward the substrate at lower temperatures. Anaerobic titrations of the enzyme with NADH revealed a half‐site reactivity not observed with the wild‐type enzyme in which one subunit of the enzyme could be fully reduced to an EH4 state, while the other remained in an EH2 or EH2·NADH state. These results suggest that for these closely related enzymes, substrate channel morphology is an important determinant of substrate specificity, and homology modeling will be the preferred technique for predicting function among PNDORs.
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Affiliation(s)
- Kevin Sea
- Department of Chemistry Pomona College Claremont CA USA.,Department of Wine Studies Santa Rosa Junior College CA USA
| | - Jerry Lee
- Department of Biology Pomona College Claremont CA USA
| | - Daniel To
- Department of Chemistry Pomona College Claremont CA USA
| | - Berniece Chen
- Department of Chemistry Pomona College Claremont CA USA
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9
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Salazar H, Eibl C, Chebli M, Plested A. Mechanism of partial agonism in AMPA-type glutamate receptors. Nat Commun 2017; 8:14327. [PMID: 28211453 PMCID: PMC5321683 DOI: 10.1038/ncomms14327] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 12/19/2016] [Indexed: 02/04/2023] Open
Abstract
Neurotransmitters trigger synaptic currents by activating ligand-gated ion channel receptors. Whereas most neurotransmitters are efficacious agonists, molecules that activate receptors more weakly-partial agonists-also exist. Whether these partial agonists have weak activity because they stabilize less active forms, sustain active states for a lesser fraction of the time or both, remains an open question. Here we describe the crystal structure of an α-amino-3-hydroxy-5-methyl-4-isoxazolepropionate receptor (AMPAR) ligand binding domain (LBD) tetramer in complex with the partial agonist 5-fluorowillardiine (FW). We validate this structure, and others of different geometry, using engineered intersubunit bridges. We establish an inverse relation between the efficacy of an agonist and its promiscuity to drive the LBD layer into different conformations. These results suggest that partial agonists of the AMPAR are weak activators of the receptor because they stabilize multiple non-conducting conformations, indicating that agonism is a function of both the space and time domains.
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Affiliation(s)
- Hector Salazar
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
- Cluster of Excellence NeuroCure, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Clarissa Eibl
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
- Cluster of Excellence NeuroCure, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Miriam Chebli
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
- Cluster of Excellence NeuroCure, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Andrew Plested
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
- Cluster of Excellence NeuroCure, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
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10
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LaMattina JW, Delrossi M, Uy KG, Keul ND, Nix DB, Neelam AR, Lanzilotta WN. Anaerobic Heme Degradation: ChuY Is an Anaerobilin Reductase That Exhibits Kinetic Cooperativity. Biochemistry 2017; 56:845-855. [PMID: 28045510 DOI: 10.1021/acs.biochem.6b01099] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heme catabolism is an important biochemical process that many bacterial pathogens utilize to acquire iron. However, tetrapyrrole catabolites can be reactive and often require further processing for transport out of the cell or conversion to another useful cofactor. In previous work, we presented in vitro evidence of an anaerobic heme degradation pathway in Escherichia coli O157:H7. Consistent with reactions that have been reported for other radical S-adenosyl-l-methionine methyltransferases, ChuW transfers a methyl group to heme by a radical-mediated mechanism and catalyzes the β-scission of the porphyrin macrocycle. This facilitates iron release and the production of a new linear tetrapyrrole termed "anaerobilin". In this work, we describe the structure and function of ChuY, an enzyme expressed downstream from chuW within the same heme utilization operon. ChuY is structurally similar to biliverdin reductase and forms a dimeric complex in solution that reduces anaerobilin to the product we have termed anaerorubin. Steady state analysis of ChuY exhibits kinetic cooperativity that is best explained by a random addition mechanism with a kinetically preferred path for initial reduced nicotinamide adenine dinucleotide phosphate binding.
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Affiliation(s)
- Joseph W LaMattina
- Department of Biochemistry and Molecular Biology and ‡The Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - Michael Delrossi
- Department of Biochemistry and Molecular Biology and ‡The Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - Katherine G Uy
- Department of Biochemistry and Molecular Biology and ‡The Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - Nicholas D Keul
- Department of Biochemistry and Molecular Biology and ‡The Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - David B Nix
- Department of Biochemistry and Molecular Biology and ‡The Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - Anudeep R Neelam
- Department of Biochemistry and Molecular Biology and ‡The Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - William N Lanzilotta
- Department of Biochemistry and Molecular Biology and ‡The Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
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11
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Xu H, Shaw DE. A Simple Model of Multivalent Adhesion and Its Application to Influenza Infection. Biophys J 2016; 110:218-33. [PMID: 26745425 PMCID: PMC4805874 DOI: 10.1016/j.bpj.2015.10.045] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 10/12/2015] [Accepted: 10/29/2015] [Indexed: 01/06/2023] Open
Abstract
Adhesion between biological surfaces, which is typically the result of molecular binding between receptors on one surface and ligands on another, plays a fundamental role in biology and is key to the infection mechanisms of certain viruses, including influenza. The physiological outcome of adhesion depends on both the number of bound cells (or viruses, or other biological particles) and the properties of the adhesion interface that is formed, including the equilibrium number of receptor-ligand connections. Here, we introduce a quantitative model for biological adhesion by adapting thermodynamic models developed for the related problem of multivalent molecular binding. In our model, adhesion affinity is approximated by a simple, analytical expression involving the numbers of ligands and receptors at the interface. Our model contains only two fitting parameters and is simple to interpret. When applied to the adhesion between the hemagglutinin ligands on influenza viruses and the sialic acid receptors on biosensors or on host cells, our model generates adhesion affinities consistent with experimental measurements performed over a range of numbers of receptors, and provides a semiquantitative estimate of the affinity range of the hemagglutinin-sialic acid interaction necessary for the influenza virus to successfully infect host cells. The model also provides a quantitative explanation for the experimental finding that a mutant avian virus gained transmissibility in mammals despite the mutations conferring only a less than twofold increase in the affinity of its hemagglutinin for mammalian receptors: the model predicts an order-of-magnitude improvement in adhesion to mammalian cells. We also extend our model to describe the competitive inhibition of adhesion: the model predicts that hemagglutinin inhibitors of relatively modest affinity can dramatically reduce influenza virus adhesion to host cells, suggesting that such inhibitors, if discovered, may be viable therapeutic agents against influenza.
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Affiliation(s)
- Huafeng Xu
- D. E. Shaw Research, New York, New York.
| | - David E Shaw
- D. E. Shaw Research, New York, New York; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York.
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12
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Oyugi MA, Bashiri G, Baker EN, Johnson-Winters K. Investigating the Reaction Mechanism of F 420-Dependent Glucose-6-phosphate Dehydrogenase from Mycobacterium tuberculosis: Kinetic Analysis of the Wild-Type and Mutant Enzymes. Biochemistry 2016; 55:5566-5577. [PMID: 27603793 DOI: 10.1021/acs.biochem.6b00638] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
F420-dependent glucose-6-phosphate dehydrogenase (FGD) catalyzes the conversion of glucose-6-phosphate (G6P) to 6-phosphogluconolactone, using F420 cofactor as the hydride transfer acceptor, within mycobacteria. A previous crystal structure of wild-type FGD led to a proposed mechanism suggesting that the active site residues His40, Trp44, and Glu109 could be involved in catalysis. We have characterized the wild-type FGD and five FGD variants (H40A, W44F, W44Y, W44A, and E109Q) by fluorescence binding assays and steady-state and pre-steady-state kinetic experiments. Compared to wild-type FGD, all the variants had lower binding affinities for F420, thus suggesting that Trp44, His40, and Glu109 aid in F420 binding. While all the variants had decreased catalytic efficiencies, FGD H40A and W44A were the least efficient, having lost ∼1000- and ∼2000-fold activity, respectively. This confirms a crucial catalytic role for His40 in the FGD reaction and suggests that aromaticity at residue 44 aids catalysis. To investigate the proposed roles of Glu109 and His40 in acid-base catalysis, the pH dependence of kinetic parameters has been determined for the E109Q and H40A mutants and compared to those of the wild-type enzyme. The log kcat-pH profile of wild-type FGD and E109Q revealed two ionizable residues in the enzyme-substrate complex, while H40A displayed only one ionization event. The FGD E109Q variant displayed pH-dependent kinetic cooperativity with respect to the F420 cofactor. The multiple-turnover pre-steady-state kinetics were biphasic for wild-type FGD, W44F, W44Y, and E109Q, while the H40A and W44A variants displayed only a single phase because of their reduced catalytic efficiency.
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Affiliation(s)
- Mercy A Oyugi
- Department of Chemistry and Biochemistry, The University of Texas at Arlington , Arlington, Texas 76019-0065, United States
| | - Ghader Bashiri
- Laboratory of Structural Biology and Maurice Wilkins Center for Molecular Biodiscovery, School of Biological Sciences, The University of Auckland , Auckland 1010, New Zealand
| | - Edward N Baker
- Laboratory of Structural Biology and Maurice Wilkins Center for Molecular Biodiscovery, School of Biological Sciences, The University of Auckland , Auckland 1010, New Zealand
| | - Kayunta Johnson-Winters
- Department of Chemistry and Biochemistry, The University of Texas at Arlington , Arlington, Texas 76019-0065, United States
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13
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Michel D. Conformational selection or induced fit? New insights from old principles. Biochimie 2016; 128-129:48-54. [DOI: 10.1016/j.biochi.2016.06.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 06/21/2016] [Indexed: 02/03/2023]
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14
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Sherman E, Barr VA, Merrill RK, Regan CK, Sommers CL, Samelson LE. Hierarchical nanostructure and synergy of multimolecular signalling complexes. Nat Commun 2016; 7:12161. [PMID: 27396911 PMCID: PMC4942584 DOI: 10.1038/ncomms12161] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 06/07/2016] [Indexed: 01/15/2023] Open
Abstract
Signalling complexes are dynamic, multimolecular structures and sites for intracellular signal transduction. Although they play a crucial role in cellular activation, current research techniques fail to resolve their structure in intact cells. Here we present a multicolour, photoactivated localization microscopy approach for imaging multiple types of single molecules in fixed and live cells and statistical tools to determine the nanoscale organization, topology and synergy of molecular interactions in signalling complexes downstream of the T-cell antigen receptor. We observe that signalling complexes nucleated at the key adapter LAT show a hierarchical topology. The critical enzymes PLCγ1 and VAV1 localize to the centre of LAT-based complexes, and the adapter SLP-76 and actin molecules localize to the periphery. Conditional second-order statistics reveal a hierarchical network of synergic interactions between these molecules. Our results extend our understanding of the nanostructure of signalling complexes and are relevant to studying a wide range of multimolecular complexes.
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Affiliation(s)
- Eilon Sherman
- Racah Institute of Physics, The Hebrew University,
Jerusalem
91904, Israel
| | - Valarie A. Barr
- Laboratory of Cellular and Molecular Biology, CCR, NCI,
NIH, Bethesda, Maryland
20892, USA
| | - Robert K. Merrill
- Laboratory of Cellular and Molecular Biology, CCR, NCI,
NIH, Bethesda, Maryland
20892, USA
| | - Carole K. Regan
- Laboratory of Cellular and Molecular Biology, CCR, NCI,
NIH, Bethesda, Maryland
20892, USA
| | - Connie L. Sommers
- Laboratory of Cellular and Molecular Biology, CCR, NCI,
NIH, Bethesda, Maryland
20892, USA
| | - Lawrence E. Samelson
- Laboratory of Cellular and Molecular Biology, CCR, NCI,
NIH, Bethesda, Maryland
20892, USA
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15
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Abstract
The functions of many proteins are regulated through allostery, whereby effector binding at a distal site changes the functional activity (e.g., substrate binding affinity or catalytic efficiency) at the active site. Most allosteric studies have focused on thermodynamic properties, in particular, substrate binding affinity. Changes in substrate binding affinity by allosteric effectors have generally been thought to be mediated by conformational transitions of the proteins or, alternatively, by changes in the broadness of the free energy basin of the protein conformational state without shifting the basin minimum position. When effector binding changes the free energy landscape of a protein in conformational space, the change affects not only thermodynamic properties but also dynamic properties, including the amplitudes of motions on different time scales and rates of conformational transitions. Here we assess the roles of conformational dynamics in allosteric regulation. Two cases are highlighted where NMR spectroscopy and molecular dynamics simulation have been used as complementary approaches to identify residues possibly involved in allosteric communication. Perspectives on contentious issues, for example, the relationship between picosecond-nanosecond local and microsecond-millisecond conformational exchange dynamics, are presented.
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Affiliation(s)
- Jingjing Guo
- School of Chemistry and Chemical Engineering, Henan Normal University , Xinxiang, Henan 453007, People's Republic of China
| | - Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
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16
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Biochemical studies on Francisella tularensis RelA in (p)ppGpp biosynthesis. Biosci Rep 2015; 35:BSR20150229. [PMID: 26450927 PMCID: PMC4708007 DOI: 10.1042/bsr20150229] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 09/16/2015] [Indexed: 12/19/2022] Open
Abstract
Francisella tularensis RelA shows significant sequence differences from other members of the RelA family of enzymes. In the present study, we describe the functional similarities and differences between F. tularensis RelA and the model RelA from Escherichia coli. The bacterial stringent response is induced by nutrient deprivation and is mediated by enzymes of the RSH (RelA/SpoT homologue; RelA, (p)ppGpp synthetase I; SpoT, (p)ppGpp synthetase II) superfamily that control concentrations of the ‘alarmones’ (p)ppGpp (guanosine penta- or tetra-phosphate). This regulatory pathway is present in the vast majority of pathogens and has been proposed as a potential anti-bacterial target. Current understanding of RelA-mediated responses is based on biochemical studies using Escherichia coli as a model. In comparison, the Francisella tularensis RelA sequence contains a truncated regulatory C-terminal region and an unusual synthetase motif (EXSD). Biochemical analysis of F. tularensis RelA showed the similarities and differences of this enzyme compared with the model RelA from Escherichia coli. Purification of the enzyme yielded a stable dimer capable of reaching concentrations of 10 mg/ml. In contrast with other enzymes from the RelA/SpoT homologue superfamily, activity assays with F. tularensis RelA demonstrate a high degree of specificity for GTP as a pyrophosphate acceptor, with no measurable turnover for GDP. Steady state kinetic analysis of F. tularensis RelA gave saturation activity curves that best fitted a sigmoidal function. This kinetic profile can result from allosteric regulation and further measurements with potential allosteric regulators demonstrated activation by ppGpp (5′,3′-dibisphosphate guanosine) with an EC50 of 60±1.9 μM. Activation of F. tularensis RelA by stalled ribosomal complexes formed with ribosomes purified from E. coli MRE600 was observed, but interestingly, significantly weaker activation with ribosomes isolated from Francisella philomiragia.
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17
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Sanchez JE, Gross PG, Goetze RW, Walsh RM, Peeples WB, Wood ZA. Evidence of Kinetic Cooperativity in Dimeric Ketopantoate Reductase from Staphylococcus aureus. Biochemistry 2015; 54:3360-3369. [PMID: 25946571 DOI: 10.1021/acs.biochem.5b00174] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ketopantoate reductase (KPR) catalyzes the NADPH-dependent production of pantoate, an essential precursor in the biosynthesis of coenzyme A. Previous structural studies have been limited to Escherichia coli KPR, a monomeric enzyme that follows a sequential ordered mechanism. Here we report the crystal structure of the Staphylococcus aureus enzyme at 1.8 Å resolution, the first description of a dimeric KPR. Using sedimentation velocity analysis, we show that the S. aureus KPR dimer is stable in solution. In fact, our structural analysis shows that the dimeric assembly we identify is present in the majority of KPR crystal structures. Steady state analysis of S. aureus KPR reveals strong positive cooperativity with respect to NADPH (Hill coefficient of 2.5). In contrast, high concentrations of the substrate ketopantoate (KP) inhibit the activity of the enzyme. These observations are consistent with a random addition mechanism in which the initial binding of NADPH is the kinetically preferred path. In fact, Förster resonance energy transfer studies of the equilibrium binding of NADPH show only a small degree of cooperativity between subunits (Hill coefficient of 1.3). Thus, the apparently strong cooperativity observed in substrate saturation curves is due to a kinetic process that favors NADPH binding first. This interpretation is consistent with our analysis of the A181L substitution, which increases the Km of ketopantoate 844-fold, without affecting kcat. The crystal structure of KPRA181L shows that the substitution displaces Ser239, which is known to be important for the binding affinity of KP. The decrease in KP affinity would enhance the already kinetically preferred NADPH binding path, making the random mechanism appear to be sequentially ordered and reducing the kinetic cooperativity. Consistent with this interpretation, the NADPH saturation curve for KPRA181L is hyperbolic.
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Affiliation(s)
- Joseph E Sanchez
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Phillip G Gross
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Russell W Goetze
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Richard M Walsh
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - William B Peeples
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Zachary A Wood
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
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18
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Banerjee K, Das B, Gangopadhyay G. On the estimation of cooperativity in ion channel kinetics: activation free energy and kinetic mechanism of Shaker K+ channel. J Chem Phys 2013; 138:165102. [PMID: 23635173 DOI: 10.1063/1.4801999] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In this paper, we have explored generic criteria of cooperative behavior in ion channel kinetics treating it on the same footing with multistate receptor-ligand binding in a compact theoretical framework. We have shown that the characterization of cooperativity of ion channels in terms of the Hill coefficient violates the standard Hill criteria defined for allosteric cooperativity of ligand binding. To resolve the issue, an alternative measure of cooperativity is proposed here in terms of the cooperativity index that sets a unified criteria for both the systems. More importantly, for ion channel this index can be very useful to describe the cooperative kinetics as it can be readily determined from the experimentally measured ionic current combined with theoretical modelling. We have analyzed the correlation between the voltage value and slope of the voltage-activation curve at the half-activation point and consequently determined the standard free energy of activation of the ion channel using two well-established mechanisms of cooperativity, namely, Koshland-Nemethy-Filmer (KNF) and Monod-Wyman-Changeux (MWC) models. Comparison of the theoretical results for both the models with appropriate experimental data of mutational perturbation of Shaker K(+) channel supports the experimental fact that the KNF model is more suitable to describe the cooperative behavior of this class of ion channels, whereas the performance of the MWC model is unsatisfactory. We have also estimated the mechanistic performance through standard free energy of channel activation for both the models and proposed a possible functional disadvantage in the MWC scheme.
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Affiliation(s)
- Kinshuk Banerjee
- S N Bose National Centre For Basic Sciences, Salt Lake, Kolkata 700098, India
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19
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20
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Veith N, Feldman-Salit A, Cojocaru V, Henrich S, Kummer U, Wade RC. Organism-adapted specificity of the allosteric regulation of pyruvate kinase in lactic acid bacteria. PLoS Comput Biol 2013; 9:e1003159. [PMID: 23946717 PMCID: PMC3738050 DOI: 10.1371/journal.pcbi.1003159] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 06/11/2013] [Indexed: 11/19/2022] Open
Abstract
Pyruvate kinase (PYK) is a critical allosterically regulated enzyme that links glycolysis, the primary energy metabolism, to cellular metabolism. Lactic acid bacteria rely almost exclusively on glycolysis for their energy production under anaerobic conditions, which reinforces the key role of PYK in their metabolism. These organisms are closely related, but have adapted to a huge variety of native environments. They include food-fermenting organisms, important symbionts in the human gut, and antibiotic-resistant pathogens. In contrast to the rather conserved inhibition of PYK by inorganic phosphate, the activation of PYK shows high variability in the type of activating compound between different lactic acid bacteria. System-wide comparative studies of the metabolism of lactic acid bacteria are required to understand the reasons for the diversity of these closely related microorganisms. These require knowledge of the identities of the enzyme modifiers. Here, we predict potential allosteric activators of PYKs from three lactic acid bacteria which are adapted to different native environments. We used protein structure-based molecular modeling and enzyme kinetic modeling to predict and validate potential activators of PYK. Specifically, we compared the electrostatic potential and the binding of phosphate moieties at the allosteric binding sites, and predicted potential allosteric activators by docking. We then made a kinetic model of Lactococcus lactis PYK to relate the activator predictions to the intracellular sugar-phosphate conditions in lactic acid bacteria. This strategy enabled us to predict fructose 1,6-bisphosphate as the sole activator of the Enterococcus faecalis PYK, and to predict that the PYKs from Streptococcus pyogenes and Lactobacillus plantarum show weaker specificity for their allosteric activators, while still having fructose 1,6-bisphosphate play the main activator role in vivo. These differences in the specificity of allosteric activation may reflect adaptation to different environments with different concentrations of activating compounds. The combined computational approach employed can readily be applied to other enzymes.
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Affiliation(s)
- Nadine Veith
- Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
- Department of Modelling Biological Processes, Centre for Organismal Studies (COS)/BIOQUANT, Heidelberg University, Heidelberg, Germany
| | - Anna Feldman-Salit
- Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
- Department of Modelling Biological Processes, Centre for Organismal Studies (COS)/BIOQUANT, Heidelberg University, Heidelberg, Germany
- Center for Modelling and Simulation in the Biosciences (BIOMS), Heidelberg, Germany
| | - Vlad Cojocaru
- Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Stefan Henrich
- Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Ursula Kummer
- Department of Modelling Biological Processes, Centre for Organismal Studies (COS)/BIOQUANT, Heidelberg University, Heidelberg, Germany
| | - Rebecca C. Wade
- Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
- Center for Molecular Biology (ZMBH), Heidelberg University, Heidelberg, Germany
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21
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Computer simulation of assembly and co-operativity of hexameric AAA ATPases. PLoS One 2013; 8:e67815. [PMID: 23869207 PMCID: PMC3711915 DOI: 10.1371/journal.pone.0067815] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 05/22/2013] [Indexed: 11/19/2022] Open
Abstract
AAA ATPases form a functionally diverse superfamily of proteins. Most members form homo-hexameric ring complexes, are catalytically active only in the fully assembled state, and show co-operativity among the six subunits. The mutual dependence among the subunits is clearly evidenced by the fact that incorporation of mutated, inactive subunits can decrease the activity of the remaining wild type subunits. For the first time, we develop here models to describe this form of allostery, evaluate them in a simulation study, and test them on experimental data. We show that it is important to consider the assembly reactions in the kinetic model, and to define a formal inhibition scheme. We simulate three inhibition scenarios explicitly, and demonstrate that they result in differing outcomes. Finally, we deduce fitting formulas, and test them on real and simulated data. A non-competitive inhibition formula fitted experimental and simulated data best. To our knowledge, our study is the first one that derives and tests formal allosteric schemes to explain the inhibitory effects of mutant subunits on oligomeric enzymes.
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22
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Banerjee K, Das B, Gangopadhyay G. Entropic estimate of cooperative binding of substrate on a single oligomeric enzyme: An index of cooperativity. J Chem Phys 2012; 136:154502. [DOI: 10.1063/1.3703505] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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23
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Bosello M, Mielcarek A, Giessen TW, Marahiel MA. An enzymatic pathway for the biosynthesis of the formylhydroxyornithine required for rhodochelin iron coordination. Biochemistry 2012; 51:3059-66. [PMID: 22439765 DOI: 10.1021/bi201837f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhodochelin, a mixed catecholate-hydroxamate type siderophore isolated from Rhodococcus jostii RHA1, holds two L-δ-N-formyl-δ-N-hydroxyornithine (L-fhOrn) moieties essential for proper iron coordination. Previously, bioinformatic and genetic analysis proposed rmo and rft as the genes required for the tailoring of the L-ornithine (L-Orn) precursor [Bosello, M. (2011) J. Am. Chem. Soc.133, 4587-4595]. In order to investigate if both Rmo and Rft constitute a pathway for L-fhOrn biosynthesis, the enzymes were heterologously produced and assayed in vitro. In the presence of molecular oxygen, NADPH and FAD, Rmo monooxygenase was able to convert L-Orn into L-δ-N-hydroxyornithine (L-hOrn). As confirmed in a coupled reaction assay, this hydroxylated intermediate serves as a substrate for the subsequent N(10)-formyl-tetrahydrofolate-dependent (N(10)-fH(4)F) Rtf-catalyzed formylation reaction, establishing a route for the L-fhOrn biosynthesis, prior to its incorporation by the NRPS assembly line. It is of particular interest that a major improvement to this study has been reached with the use of an alternative approach to the chemoenzymatic FolD-dependent N(10)-fH(4)F conversion, also rescuing the previously inactive CchA, the Rft-homologue in coelichelin assembly line [Buchenau, B. (2004) Arch. Microbiol.182, 313-325; Pohlmann, V. (2008) Org. Biomol. Chem.6, 1843-1848].
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Affiliation(s)
- Mattia Bosello
- Biochemistry, Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Strasse, D-35043 Marburg, Germany
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24
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Jiao W, Hutton RD, Cross PJ, Jameson GB, Parker EJ. Dynamic Cross-Talk among Remote Binding Sites: The Molecular Basis for Unusual Synergistic Allostery. J Mol Biol 2012; 415:716-26. [DOI: 10.1016/j.jmb.2011.11.037] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2011] [Revised: 11/16/2011] [Accepted: 11/20/2011] [Indexed: 10/14/2022]
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25
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Lefurgy ST, Leyh TS. Analytical expressions for the homotropic binding of ligand to protein dimers and trimers. Anal Biochem 2011; 421:433-8. [PMID: 22230282 DOI: 10.1016/j.ab.2011.12.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 11/28/2011] [Accepted: 12/05/2011] [Indexed: 11/16/2022]
Abstract
Cooperative binding of a ligand to multiple subsites on a protein is a common theme among enzymes and receptors. The analysis of cooperative binding data (either positive or negative) often relies on the assumption that free ligand concentration, L, can be approximated by the total ligand concentration, L(T). When this approximation does not hold, such analyses result in inaccurate estimates of dissociation constants. Presented here are exact analytical expressions for equilibrium concentrations of all enzyme and ligand species (in terms of K(d) values and total concentrations of protein and ligand) for homotropic dimeric and trimeric protein-ligand systems. These equations circumvent the need to approximate L and are provided in Excel worksheets suitable for simulation and least-squares fitting. The equations and worksheets are expanded to treat cases where binding signals vary with distinct site occupancy.
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Affiliation(s)
- Scott T Lefurgy
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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26
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Katsuyama Y, Kita T, Funa N, Horinouchi S. Curcuminoid biosynthesis by two type III polyketide synthases in the herb Curcuma longa. J Biol Chem 2009; 284:11160-70. [PMID: 19258320 DOI: 10.1074/jbc.m900070200] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Curcuminoids found in the rhizome of turmeric, Curcuma longa, possess various biological activities. Despite much attention regarding the biosynthesis of curcuminoids because of their pharmaceutically important properties and biosynthetically intriguing structures, no enzyme systems have been elucidated. Here we propose a pathway for curcuminoid biosynthesis in the herb C. longa, which includes two novel type III polyketide synthases. One of the type III polyketide synthases, named diketide-CoA synthase (DCS), catalyzed the formation of feruloyldiketide-CoA by condensing feruloyl-CoA and malonyl-CoA. The other, named curcumin synthase (CURS), catalyzed the in vitro formation of curcuminoids from cinnamoyldiketide-N-acetylcysteamine (a mimic of the CoA ester) and feruloyl-CoA. Co-incubation of DCS and CURS in the presence of feruloyl-CoA and malonyl-CoA yielded curcumin at high efficiency, although CURS itself possessed low activity for the synthesis of curcumin from feruloyl-CoA and malonyl-CoA. These findings thus revealed the curcumin biosynthetic route in turmeric, in which DCS synthesizes feruloyldiketide-CoA, and CURS then converts the diketide-CoA esters into a curcuminoid scaffold.
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Affiliation(s)
- Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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27
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28
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Yerkes N, Wu JX, McCoy E, Galan MC, Chen S, O'Connor SE. Substrate specificity and diastereoselectivity of strictosidine glucosidase, a key enzyme in monoterpene indole alkaloid biosynthesis. Bioorg Med Chem Lett 2007; 18:3095-8. [PMID: 18061449 DOI: 10.1016/j.bmcl.2007.11.063] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Revised: 11/14/2007] [Accepted: 11/15/2007] [Indexed: 11/29/2022]
Abstract
Strictosidine glucosidase (SGD) from Catharanthus roseus catalyzes the deglycosylation of strictosidine, an intermediate from which thousands of monoterpene indole alkaloids are derived. The steady-state kinetics of SGD with a variety of strictosidine analogs revealed the substrate preferences of this enzyme at two key positions of the strictosidine substrate. Additionally, SGD from C. roseus turns over both strictosidine and its stereoisomer vincoside, indicating that although this enzyme prefers the naturally occurring diastereomer, the enzyme is not completely diastereoselective. The implications of the substrate specificity of SGD in metabolic engineering efforts of C. roseus are highlighted.
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Affiliation(s)
- Nancy Yerkes
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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29
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Allosteric bindings of thiacalix[4]arene-based receptors with 1,3-alternate conformation having two different side arms. J INCL PHENOM MACRO 2007. [DOI: 10.1007/s10847-007-9367-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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30
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Pérez-Casas C, Rahman S, Begum N, Xi Z, Yamato T. Synthesis and Inclusion Properties of 1,3-alternate-bis[(ethoxycarbonyl) Methoxy]thiacalix[4]arene-mono(crown-4) Ether. JOURNAL OF CHEMICAL RESEARCH 2007. [DOI: 10.3184/030823407x198159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A novel ditopic receptor possessing two complexation sites such as crown ether and (ethoxycarbonyl) methoxy groups bearing 1,3-alternate conformation based on thiacalix[4]arene was prepared. The binding behaviours with alkali metals have been examined by 1H NMR titration experiment. The exclusive formation of the heterogeneous dinuclear complexes of 1,3-alternate-3 with Li+ and K+ was observed.
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Affiliation(s)
- Carol Pérez-Casas
- Department of Applied Chemistry, Faculty of Science and Engineering, Saga University, Honjo-machi 1, Saga-shi, Saga 840-8502, Japan
| | - Shofiur Rahman
- Department of Applied Chemistry, Faculty of Science and Engineering, Saga University, Honjo-machi 1, Saga-shi, Saga 840-8502, Japan
| | - Nazneen Begum
- Department of Applied Chemistry, Faculty of Science and Engineering, Saga University, Honjo-machi 1, Saga-shi, Saga 840-8502, Japan
| | - Zeng Xi
- Department of Applied Chemistry, Faculty of Science and Engineering, Saga University, Honjo-machi 1, Saga-shi, Saga 840-8502, Japan
| | - Takehiko Yamato
- Department of Applied Chemistry, Faculty of Science and Engineering, Saga University, Honjo-machi 1, Saga-shi, Saga 840-8502, Japan
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31
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Abel-Santos E, Dodatko T. Differential nucleoside recognition during Bacillus cereus 569 (ATCC 10876) spore germination. NEW J CHEM 2007. [DOI: 10.1039/b616695d] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Li Z, Lukasik SM, Liu Y, Grembecka J, Bielnicka I, Bushweller JH, Speck NA. A mutation in the S-switch region of the Runt domain alters the dynamics of an allosteric network responsible for CBFbeta regulation. J Mol Biol 2006; 364:1073-83. [PMID: 17059830 PMCID: PMC1783549 DOI: 10.1016/j.jmb.2006.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2006] [Revised: 08/26/2006] [Accepted: 10/02/2006] [Indexed: 02/03/2023]
Abstract
The Runt domain is the DNA binding domain of the core binding factor (CBF) Runx subunits. The CBFs are transcription factors that play critical roles in hematopoiesis, bone, and neuron development in mammals. A common non-DNA binding CBFbeta subunit heterodimerizes with the Runt domain of the Runx proteins and allosterically regulates its affinity for DNA. Previous NMR dynamics studies suggested a model whereby CBFbeta allosterically regulates DNA binding by quenching conformational exchange in the Runt domain, particularly in the S-switch region and the betaE'-F loop. We sought to test this model, and to this end introduced all possible single amino acid substitutions into the S-switch region and the betaE'-F loop, and screened for mutations that enhanced DNA-binding. We demonstrate that one Runt domain mutant, R164N, binds both DNA and CBFbeta with higher affinity, but it is less sensitive to allosteric regulation by CBFbeta. Analysis of NMR relaxation data shows that the chemical exchange exhibited by the wild-type Runt domain is largely quenched by the R164N substitution. These data support a model in which the dynamic behavior of a network of residues connecting the CBFbeta and DNA binding sites on the Runt domain plays a critical role in the mechanism of allosteric regulation. This study provides an important functional link between dynamic behavior and protein allosteric function, consistent with results on other allosterically regulated proteins.
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Affiliation(s)
- Zhe Li
- Department of Biochemistry, Dartmouth Medical School, Hanover,
New Hampshire 03755
| | - Steven M. Lukasik
- Department of Molecular Physiology and Biological Physics,
University of Virginia, Charlottesville, Virginia 22906-0011
| | - Yizhou Liu
- Department of Molecular Physiology and Biological Physics,
University of Virginia, Charlottesville, Virginia 22906-0011
| | - Jolanta Grembecka
- Department of Molecular Physiology and Biological Physics,
University of Virginia, Charlottesville, Virginia 22906-0011
| | - Izabela Bielnicka
- Department of Molecular Physiology and Biological Physics,
University of Virginia, Charlottesville, Virginia 22906-0011
| | - John H. Bushweller
- Department of Molecular Physiology and Biological Physics,
University of Virginia, Charlottesville, Virginia 22906-0011
- Corresponding authors: Nancy A. Speck, Phone:
603-650-1159, Fax: 603-650-1128, , John
H. Bushweller, Phone: 434-243-6409, Fax: 434-982-1616,
| | - Nancy A. Speck
- Department of Biochemistry, Dartmouth Medical School, Hanover,
New Hampshire 03755
- Corresponding authors: Nancy A. Speck, Phone:
603-650-1159, Fax: 603-650-1128, , John
H. Bushweller, Phone: 434-243-6409, Fax: 434-982-1616,
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33
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Synthesis and Inclusion Properties of a Novel Thiacalix[4]arene-Based Hard–Soft Receptor with 1,3-Alternate Conformation. J INCL PHENOM MACRO 2006. [DOI: 10.1007/s10847-005-9014-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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34
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Changeux JP, Edelstein SJ. Allosteric receptors after 30 years. RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI 2006. [DOI: 10.1007/bf02904502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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35
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Salhany JM. Slow transitions between two conformational states of band 3 (AE1) modulate divalent anion transport and DBDS binding to a second site on band 3 which is activated by lowering the pH (pK approximately 5.0). Blood Cells Mol Dis 2005; 32:372-8. [PMID: 15121094 DOI: 10.1016/j.bcmd.2004.01.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2004] [Indexed: 10/26/2022]
Abstract
Evidence is emerging which indicates that the anion transport activity of band 3 may be regulated. I review the molecular basis for regulation of the anion transport function of band 3 in terms of evidence showing that divalent anion transport involves a slow "hysteretic" transition between two functional states, mediated by interactions between subunits within band 3 oligomers. In addition, I briefly describe recent work from my laboratory where we have discovered a novel manifestation of slow conformational changes in band 3. This involves 4,4'-dibenzamido-2,2'-stilbenedisulfonate (DBDS) binding to a second, proton-activated site distinct from the primary stilbenedisulfonate site. This site is exposed on the outer aspect of band 3 when the pH is lowered (pK approximately 5.0). This is the same pK as the protonation site on band 3 involved in divalent anion-proton co-transport (APCT) [J. Gen. Physiol. 79 (1982) 87]. Significantly, we have found that DBDS binding to this proton-activated site has unusually slow kinetics, and increasing DBDS concentration causes a decrease in the apparent pseudo-first-order rate constant. These results suggest that a slow conformational pre-equilibrium is the rate limiting step in DBDS binding to the proton-activated site on band 3 observed at low pH. Our results support an allosteric two-state model for regulation of divalent anion transport by band 3 oligomers involving a slow conformational transition and interactions between subunits [Biochemistry 31 (1992) 7301].
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Affiliation(s)
- James M Salhany
- The Veterans Administration Medical Center and Departments of Internal Medicine and Biochemistry and Molecular Biology, University of Nebraska Medical Center, 984510 Nebraska Medical Center, Omaha, NE 68198-4510, USA.
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36
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Yan J, Liu Y, Lukasik SM, Speck NA, Bushweller JH. CBFbeta allosterically regulates the Runx1 Runt domain via a dynamic conformational equilibrium. Nat Struct Mol Biol 2004; 11:901-6. [PMID: 15322525 DOI: 10.1038/nsmb819] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2004] [Accepted: 06/18/2004] [Indexed: 11/09/2022]
Abstract
Core binding factors (CBFs) are heterodimeric transcription factors consisting of a DNA-binding CBFalpha subunit and non-DNA-binding CBFbeta subunit. The CBFbeta subunit increases the affinity of the DNA-binding Runt domain of CBFalpha for DNA while making no direct contacts to the DNA. We present evidence for conformational exchange in the S-switch region in a Runt domain-DNA complex that is quenched upon CBFbeta binding. Analysis of (15)N backbone relaxation parameters shows that binding of CBFbeta reduces the backbone dynamics in the microsecond-to-millisecond time frame for several regions of the Runt domain that make energetically important contacts with the DNA. The DNA also undergoes conformational exchange in the Runt domain-DNA complex that is quenched in the presence of CBFbeta. Our results indicate that allosteric regulation by the CBFbeta subunit is mediated by a shift in an existing dynamic conformational equilibrium of both the Runt domain and DNA.
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Affiliation(s)
- Jiangli Yan
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22906, USA
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37
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Galletto R, Bujalowski W. The E. coli replication factor DnaC protein exists in two conformations with different nucleotide binding capabilities. I. Determination of the binding mechanism using ATP and ADP fluorescent analogues. Biochemistry 2002; 41:8907-20. [PMID: 12102633 DOI: 10.1021/bi0201264] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The kinetic mechanism of binding of ATP and ADP fluorescent analogues to the E. coli replicative factor DnaC protein has been studied using the fluorescence stopped-flow technique. The experiments have been performed under pseudo-first-order conditions with respect to the nucleotide cofactor or the DnaC concentration. Three relaxation processes are observed at a large excess of the nucleotide, while only two relaxation processes are detected in the excess of the protein. Such behavior of the kinetic system is a diagnostic indication of the presence of the protein conformational equilibrium prior to the ligand binding. The obtained data indicate that the minimum mechanism that describes the observed kinetics includes the conformational transition of the DnaC protein, prior to nucleotide binding, followed by the two-step, sequential association of the cofactor to only one of the protein conformations, as defined by In the examined solution conditions, the conformation of the DnaC protein is shifted toward the state (DnaC)(2) that binds the nucleotide. The lack of any cofactor binding to the (DnaC)(1) state points to the existence of a stringent locking mechanism of the nucleotide binding-site in the protein. Binding of ATP and ADP analogues obeys the same mechanism, with similar rate constants, indicating that ATP and ADP analogues bind to the same protein conformation. The (C)(1) intermediate dominates the distribution of the DnaC protein population in the presence of cofactors. The formation of (C)(1) is accompanied by a low nucleotide fluorescence increase, indicating a hydrophilic environment around the ribose of bound cofactors. Transition to (C)(2) places the ribose region in a highly hydrophobic environment with relative molar fluorescence intensity approximately 8-fold higher than that of the free cofactor. The significance of these results for the functioning of the DnaC protein is discussed.
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Affiliation(s)
- Roberto Galletto
- Department of Human Biological Chemistry & Genetics, Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555-1053, USA
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38
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Abstract
Understanding the molecular mechanisms of enzyme catalysis and allosteric regulation has been a primary goal of biochemistry for many years. The dynamics of these processes, approached through a variety of kinetic methods, are discussed. The results obtained for many different enzymes suggest that multiple intermediates and conformations are general characteristics of the catalytic process and allosteric regulation. Ribonuclease, dihydrofolate reductase, chymotrypsin, aspartate aminotransferase, and aspartate transcarbamoylase are considered as specific examples. Typical and maximum rates of conformational changes and catalysis are also discussed, based on results obtained from model systems. The nature and rates of interconversion of the intermediates, along with structural information, can be used as the bases for understanding the incredible catalytic efficiency of enzymes. Potential roles of conformational changes in the catalytic process are discussed in terms of static and environmental effects, and in terms of dynamic coupling within the enzyme-substrate complex.
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Affiliation(s)
- Gordon G Hammes
- Department of Biochemistry, Box 3711, Duke University Medical Center, Durham, North Carolina 27710, USA
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39
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Affiliation(s)
- J P Changeux
- Neurobiologie Moléculaire Institut Pasteur, Paris, France.
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40
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Raghavan KS, Chang RK, Pang J, Figuly GD, Hussain MA. Physical and chemical properties of DMP 504, a polyalkylammonium-based bile acid sequestrant. Pharm Dev Technol 1997; 2:233-41. [PMID: 9552451 DOI: 10.3109/10837459709031443] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The purpose of this study was to characterize the physicochemical properties of DMP 504 and lay the foundation for formulation development. Thermal properties were characterized by DSC and TGA and moisture sorption and desorption by TGA. The association rate and equilibrium binding capacity of the polymer for a prototype bile acid was evaluated using cholic acid, and solid state stability was examined at 25 degrees C, 40 degrees C (with and without 5% added water), 60 degrees C, and 600 foot candles/25 degrees C. The solid state excipient compatibility of binary mixtures of DMP 504 and several commonly used pharmaceutical excipients was also evaluated. Thermal analysis of the polymer showed a glass transition temperature at approximately 95 degrees C and no melting point, indicating a highly amorphous macromolecular structure with thermal stability up to 250 degrees C. Moisture sorption and desorption isotherms at controlled humidity ranging from 11% to 97% RH did not display hysteresis. Cholic acid associated with DMP 504 extremely rapidly so that binding was essentially complete within 5 min. Scatchard analysis of the equilibrium binding of cholic acid to DMP 504 was unconventional, and indicated that the system was exhibiting positive cooperative behavior. Modeling the binding curve for a system exhibiting cooperative behavior indicated a maximum binding capacity of DMP 504 for cholic acid in phosphate buffered saline (pH 7.0) of 4.9 mumol/mg, and a cooperativity value, P, of 2.2 implying that binding of one molecule promotes the binding of additional molecules. DMP 504, a hygroscopic, amorphous cross-linked polymer with a tendency to gain or lose moisture with ease, is stable in the solid state, either drug substance alone or in presence of excipients, at normal storage temperatures and light, and under controlled conditions of humidity.
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Affiliation(s)
- K S Raghavan
- DuPont Merck Pharmaceutical Company, Experimental Station, Wilmington, Delaware 19880-0400, USA
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41
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Blanc S, Yakirevitch P, Leize E, Meyer M, Libman J, Van Dorsselaer A, Albrecht-Gary AM, Shanzer A. Allosteric Effects in Polynuclear Triple-Stranded Ferric Complexes. J Am Chem Soc 1997. [DOI: 10.1021/ja962472c] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sylvie Blanc
- Contribution from the Laboratoire de Physico-Chimie Bioinorganique, CNRS URA 405, ECPM, 1 rue Blaise Pascal, 67000 Strasbourg, France, Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israël, and Laboratoire de Spectrométrie de Masse Bio-Organique, CNRS URA 31, Faculté de Chimie, 1 rue Blaise Pascal, 67000 Strasbourg, France
| | - Pnina Yakirevitch
- Contribution from the Laboratoire de Physico-Chimie Bioinorganique, CNRS URA 405, ECPM, 1 rue Blaise Pascal, 67000 Strasbourg, France, Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israël, and Laboratoire de Spectrométrie de Masse Bio-Organique, CNRS URA 31, Faculté de Chimie, 1 rue Blaise Pascal, 67000 Strasbourg, France
| | - Emmanuelle Leize
- Contribution from the Laboratoire de Physico-Chimie Bioinorganique, CNRS URA 405, ECPM, 1 rue Blaise Pascal, 67000 Strasbourg, France, Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israël, and Laboratoire de Spectrométrie de Masse Bio-Organique, CNRS URA 31, Faculté de Chimie, 1 rue Blaise Pascal, 67000 Strasbourg, France
| | - Michel Meyer
- Contribution from the Laboratoire de Physico-Chimie Bioinorganique, CNRS URA 405, ECPM, 1 rue Blaise Pascal, 67000 Strasbourg, France, Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israël, and Laboratoire de Spectrométrie de Masse Bio-Organique, CNRS URA 31, Faculté de Chimie, 1 rue Blaise Pascal, 67000 Strasbourg, France
| | - Jacqueline Libman
- Contribution from the Laboratoire de Physico-Chimie Bioinorganique, CNRS URA 405, ECPM, 1 rue Blaise Pascal, 67000 Strasbourg, France, Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israël, and Laboratoire de Spectrométrie de Masse Bio-Organique, CNRS URA 31, Faculté de Chimie, 1 rue Blaise Pascal, 67000 Strasbourg, France
| | - Alain Van Dorsselaer
- Contribution from the Laboratoire de Physico-Chimie Bioinorganique, CNRS URA 405, ECPM, 1 rue Blaise Pascal, 67000 Strasbourg, France, Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israël, and Laboratoire de Spectrométrie de Masse Bio-Organique, CNRS URA 31, Faculté de Chimie, 1 rue Blaise Pascal, 67000 Strasbourg, France
| | - Anne-Marie Albrecht-Gary
- Contribution from the Laboratoire de Physico-Chimie Bioinorganique, CNRS URA 405, ECPM, 1 rue Blaise Pascal, 67000 Strasbourg, France, Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israël, and Laboratoire de Spectrométrie de Masse Bio-Organique, CNRS URA 31, Faculté de Chimie, 1 rue Blaise Pascal, 67000 Strasbourg, France
| | - Abraham Shanzer
- Contribution from the Laboratoire de Physico-Chimie Bioinorganique, CNRS URA 405, ECPM, 1 rue Blaise Pascal, 67000 Strasbourg, France, Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israël, and Laboratoire de Spectrométrie de Masse Bio-Organique, CNRS URA 31, Faculté de Chimie, 1 rue Blaise Pascal, 67000 Strasbourg, France
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42
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Serfozo P, Cash DJ. Effect of a benzodiazepine (chlordiazepoxide) on a GABAA receptor from rat brain. Requirement of only one bound GABA molecule for channel opening. FEBS Lett 1992; 310:55-9. [PMID: 1382022 DOI: 10.1016/0014-5793(92)81145-c] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Chlordiazepoxide (CDPX) enhanced the rate of chloride exchange mediated by the major GABAA receptor found on sealed native membrane vesicles from rat cerebral cortex. The initial rate constant for chloride exchange for this receptor, (JA), a measure of open channel, was determined from the progress of GABA-mediated influx of 36Cl-. The dependence of JA on GABA concentration was hyperbolic in the presence of CDPX (150 microM, sufficient to give maximum enhancement of chloride exchange rate) but sigmoid in its absence. Enhancement of channel opening (10-fold at 0.3 microM GABA) decreased with increasing GABA concentration. The maximal response, above 1,000 microM GABA, was unaltered. The half-response concentration was reduced from 80 microM to 50 microM. CDPX alone caused no measurable 36Cl- exchange. In the presence of CDPX, channel opening occurred with only one bound GABA molecule, whereas in its absence, channel opening with two bound GABA molecules was much more favorable. This could not be direct allosteric modulation of the channel opening conformational change by binding of CDPX at effector sites, but could be explained by an additional change of the receptor on binding CDPX to give a closed state which gave channel opening mediated by a single GABA binding site. Another possibility is that CDPX could act at one of the channel opening binding sites without a postulated, second closed conformational state.
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Affiliation(s)
- P Serfozo
- Department of Biochemistry, University of Missouri, Columbia 65211
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43
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Segarra RA, Booth MC, Morales DA, Huycke MM, Gilmore MS. Molecular characterization of the Enterococcus faecalis cytolysin activator. Infect Immun 1991; 59:1239-46. [PMID: 1900808 PMCID: PMC257833 DOI: 10.1128/iai.59.4.1239-1246.1991] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The gene encoding component A (cylA), the activator protein of the Enterococcus faecalis cytolysin, has been localized on pAD1, and the nucleotide sequence was determined. cylA consists of a 1,236-bp open reading frame encoding a 412-amino-acid polypeptide. A search of the National Biomedical Research Foundation data base revealed significant homology between the inferred amino acid sequence of component A and subtilisin BPN'. Component A activation of the cytolysin precursor (component L) was observed to be inhibited by the serine protease inhibitor diisopropylfluorophosphate. Mature component A exhibits a molecular weight of approximately 30,000 and an isoelectric point of 4.5. Differences between the size of the primary translation product (45,625 daltons) and the mature enzyme suggest that, as for subtilisin, component A is secreted as a proenzyme. These results provide the basis for a model of component A activation of component L and a role for component A in protecting the cytolysin-producing cell from lysis.
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Affiliation(s)
- R A Segarra
- Department of Microbiology and Immunology, University of Oklahoma College of Medicine, Oklahoma City 73190
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44
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Cooperativity of ligand binding as a function of monomer-dimer equilibrium parameters and acceptor concentration. ACTA ACUST UNITED AC 1987. [DOI: 10.1007/bf02343341] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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45
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Nissani E, Perlmutter-Hayman B. Drug-binding to biological macromolecules. A kinetic study of the system chlorodiazepoxide (librium) and bovine serum albumin. INT J CHEM KINET 1986. [DOI: 10.1002/kin.550181003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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46
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47
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Structural characterization and the determination of negative cooperativity in the tight binding of 2-carboxyarabinitol bisphosphate to higher plant ribulose bisphosphate carboxylase. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(17)39320-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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48
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Nissani E, Perlmutter-Hayman B. Bovine serum albumin and alizarin yellow G ? a model system for positive cooperative binding to macromolecules. INT J CHEM KINET 1985. [DOI: 10.1002/kin.550170605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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49
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Acetylcholine-receptor-mediated ion fluxes in Electrophorus electricus and Torpedo california membrane vesicles. Rev Physiol Biochem Pharmacol 1985; 102:73-117. [PMID: 2412273 DOI: 10.1007/bfb0034085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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50
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Hess GP, Kolb HA, Läuger P, Schoffeniels E, Schwarze W. Acetylcholine receptor (from Electrophorus electricus): a comparison of single-channel current recordings and chemical kinetic measurements. Proc Natl Acad Sci U S A 1984; 81:5281-5. [PMID: 6089188 PMCID: PMC391687 DOI: 10.1073/pnas.81.17.5281] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
We report a direct comparison between two types of measurements of the dynamic properties of the acetylcholine receptor: single-channel currents recorded using the patch-clamp technique and chemical kinetic measurements. Electrophorus electricus electroplax cells, and membrane vesicles prepared from these cells, were used. Such a comparison, and single-channel currents recorded from these cells, have not previously been reported. We first give the theoretical basis for the comparison and define the conditions under which the comparisons are elegantly simple. We relate (i) measurements of currents through receptor channels in the cell membranes to measurements of the rates of ion translocation through the receptor channels in vesicles and (ii) measurements of the lifetimes of receptor states (for instance, the lifetime of the active state of the receptor--i.e., the state in which it can form open channels) to rate coefficients obtained in chemical kinetic measurements (for instance, those for the interconversions between different states of the receptor). In eel Ringer's solution we have found the single-channel conductance (gamma) of the receptor in E. electricus electroplax cells to be 53 pS. From this value, a specific reaction rate for ion translocation, J, of 5 X 10(7) M-1 X sec-1 was calculated. When membrane vesicles prepared from the electroplax cells and the same solution compositions were used, chemical kinetic measurements gave a J value of 3 X 10(7) M-1 X sec-1. The agreement between the two measurements is important because (i) they reflect different experimental conditions, which require different assumptions in interpreting the results, and (ii) it indicates that the two techniques can be used to obtain complementary information: the methods have different time resolutions and can be used in different ranges of acetylcholine concentrations.
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