1
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Manson MD, Nan B, Lele PP, Liu J, Duncan TM. Editorial: Biological rotary nanomotors. Front Microbiol 2022; 13:1012681. [PMID: 36212881 PMCID: PMC9532838 DOI: 10.3389/fmicb.2022.1012681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/29/2022] [Indexed: 01/28/2023] Open
Affiliation(s)
- Michael D. Manson
- Department of Biology, Texas A&M University, College Station, TX, United States,*Correspondence: Michael D. Manson
| | - Beiyan Nan
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Pushkar P. Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - Jun Liu
- Microbial Sciences Institute, Department of Microbial Pathogenesis, Yale University, New Haven, CT, United States
| | - Thomas M. Duncan
- Department of Biochemistry & Molecular Biology, Upstate Medical University, Syracuse, NY, United States
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2
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Imran A, Moyer BS, Kalina D, Duncan TM, Moody KJ, Wolfe AJ, Cosgrove MS, Movileanu L. Convergent Alterations of a Protein Hub Produce Divergent Effects within a Binding Site. ACS Chem Biol 2022; 17:1586-1597. [PMID: 35613319 PMCID: PMC9207812 DOI: 10.1021/acschembio.2c00273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Progress in tumor
sequencing and cancer databases has created an
enormous amount of information that scientists struggle to sift through.
While several research groups have created computational methods to
analyze these databases, much work still remains in distinguishing
key implications of pathogenic mutations. Here, we describe an approach
to identify and evaluate somatic cancer mutations of WD40 repeat protein
5 (WDR5), a chromatin-associated protein hub. This multitasking protein
maintains the functional integrity of large multi-subunit enzymatic
complexes of the six human SET1 methyltransferases. Remarkably, the
somatic cancer mutations of WDR5 preferentially distribute within
and around an essential cavity, which hosts the WDR5 interaction (Win)
binding site. Hence, we assessed the real-time binding kinetics of
the interactions of key clustered WDR5 mutants with the Win motif
peptide ligands of the SET1 family members (SET1Win). Our
measurements highlight that this subset of mutants exhibits divergent
perturbations in the kinetics and strength of interactions not only
relative to those of the native WDR5 but also among various SET1Win ligands. These outcomes could form a fundamental basis
for future drug discovery and other developments in medical biotechnology.
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Affiliation(s)
- Ali Imran
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
| | - Brandon S. Moyer
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
| | - Dan Kalina
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, United States
| | - Thomas M. Duncan
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, United States
| | - Kelsey J. Moody
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, United States
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
| | - Aaron J. Wolfe
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, United States
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
| | - Michael S. Cosgrove
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, United States
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United States
- The BioInspired Institute, Syracuse University, Syracuse, New York 13244, United States
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3
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Milgrom YM, Duncan TM. F-ATP-ase of Escherichia coli membranes: The ubiquitous MgADP-inhibited state and the inhibited state induced by the ε-subunit's C-terminal domain are mutually exclusive. Biochim Biophys Acta Bioenerg 2020; 1861:148189. [PMID: 32194063 DOI: 10.1016/j.bbabio.2020.148189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/10/2020] [Accepted: 03/13/2020] [Indexed: 12/21/2022]
Abstract
ATP synthases are important energy-coupling, rotary motor enzymes in all kingdoms of life. In all F-type ATP synthases, the central rotor of the catalytic F1 complex is composed of the γ subunit and the N-terminal domain (NTD) of the ε subunit. In the enzymes of diverse bacteria, the C-terminal domain of ε (εCTD) can undergo a dramatic conformational change to trap the enzyme in a transiently inactive state. This inhibitory mechanism is absent in the mitochondrial enzyme, so the εCTD could provide a means to selectively target ATP synthases of pathogenic bacteria for antibiotic development. For Escherichia coli and other bacterial model systems, it has been difficult to dissect the relationship between ε inhibition and a MgADP-inhibited state that is ubiquitous for FOF1 from bacteria and eukaryotes. A prior study with the isolated catalytic complex from E. coli, EcF1, showed that these two modes of inhibition are mutually exclusive, but it has long been known that interactions of F1 with the membrane-embedded FO complex modulate inhibition by the εCTD. Here, we study membranes containing EcFOF1 with wild-type ε, ε lacking the full εCTD, or ε with a small deletion at the C-terminus. By using compounds with distinct activating effects on F-ATP-ase activity, we confirm that εCTD inhibition and ubiquitous MgADP inhibition are mutually exclusive for membrane-bound E. coli F-ATP-ase. We determine that most of the enzyme complexes in wild-type membranes are in the ε-inhibited state (>50%) or in the MgADP-inhibited state (30%).
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Affiliation(s)
- Yakov M Milgrom
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, 750 E Adams St, Syracuse, NY 13210, USA.
| | - Thomas M Duncan
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, 750 E Adams St, Syracuse, NY 13210, USA.
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4
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Jin Y, Zheng H, Ibanez ACS, Patil PD, Lv S, Luo M, Duncan TM, Luk YY. Cell-Wall-Targeting Antibiotics Cause Lag-Phase Bacteria to Form Surface-Mediated Filaments Promoting the Formation of Biofilms and Aggregates. Chembiochem 2019; 21:825-835. [PMID: 31553819 DOI: 10.1002/cbic.201900508] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Indexed: 01/01/2023]
Abstract
Antibiotics are known to promote bacterial formation of enhanced biofilms, the mechanism of which is not well understood. Here, using biolayer interferometry, we have shown that bacterial cultures containing antibiotics that target cell walls cause biomass deposition on surfaces over time with a linear profile rather than the Langmuir-like profiles exhibited by bacterial adherence in the absence of antibiotics. We observed about three times the initial rate and 12 times the final biomass deposition on surfaces for cultures containing carbenicillin than without. Unexpectedly, in the presence of antibiotics, the rate of biomass deposition inversely correlated with bacterial densities from different stages of a culture. Detailed studies revealed that carbenicillin caused faster growth of filaments that were seeded on surfaces from young bacteria (from lag phase) than those from high-density fast-growing bacteria, with rates of filament elongation of about 0.58 and 0.13 μm min-1 , respectively. With surfaces that do not support bacterial adherence, few filaments were observed even in solution. These filaments aggregated in solution and formed increased amounts of biofilms on surfaces. These results reveal the lifestyle of antibiotic-induced filamentous bacteria, as well as one way in which the antibiotics promote biofilm formation.
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Affiliation(s)
- Yuchen Jin
- Department of Chemistry, Syracuse University, 1-014 Center of Science and Technology, Syracuse, NY, 13244-4100, USA
| | - Hewen Zheng
- Department of Chemistry, Syracuse University, 1-014 Center of Science and Technology, Syracuse, NY, 13244-4100, USA
| | - Arizza Chiara S Ibanez
- Department of Chemistry, Syracuse University, 1-014 Center of Science and Technology, Syracuse, NY, 13244-4100, USA
| | - Pankaj D Patil
- Department of Chemistry, Syracuse University, 1-014 Center of Science and Technology, Syracuse, NY, 13244-4100, USA
| | - Suqi Lv
- Department of Chemistry, Syracuse University, 1-014 Center of Science and Technology, Syracuse, NY, 13244-4100, USA
| | - Minrui Luo
- Department of Chemistry, Syracuse University, 1-014 Center of Science and Technology, Syracuse, NY, 13244-4100, USA
| | - Thomas M Duncan
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 E. Adams St., Syracuse, NY, 13210, USA
| | - Yan-Yeung Luk
- Department of Chemistry, Syracuse University, 1-014 Center of Science and Technology, Syracuse, NY, 13244-4100, USA
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5
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Wang L, Shi C, Wang X, Guo D, Duncan TM, Luo J. Zwitterionic Janus Dendrimer with distinct functional disparity for enhanced protein delivery. Biomaterials 2019; 215:119233. [PMID: 31176068 PMCID: PMC6585461 DOI: 10.1016/j.biomaterials.2019.119233] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 05/22/2019] [Accepted: 05/28/2019] [Indexed: 02/07/2023]
Abstract
The development of a facile protein delivery vehicle is challenging and remains an unmet demand for clinical applications. The well-defined structure and functionality of a nanocarrier are highly desirable for the reproducibility and regulatory compliance. Herein, we report for the first time a novel Janus dendrimer (JD) system, comprised of two distinct dendrons with superior protein binding and protein repelling properties, respectively, for efficient spontaneous protein loading and enhanced in vivo protein delivery. Core-forming dendron is tethered with a combination of charged and hydrophobic moieties, which coat protein surface efficiently via the multivalent and synergistic interactions. Zwitterionic peripheries on the counter dendron endow the nanoparticle (<20 nm) with a highly hydrophilic and antifouling surface, which efficiently prevents serum protein adsorption and exchange as demonstrated in biolayer interferometry assay, therefore, reducing premature protein release. Surprisingly, JD nanocarriers containing biomimicking glycerylphosphorylcholine (GPC) surface significantly enhanced the intracellular uptake of protein therapeutics specifically in cancer cells, compared with zwitterionic carboxybetain (CB)-JD and PEGylated nanocarriers. The zwitterionic JD nanocarriers greatly prolonged the in vivo pharmacokinetic profiles of payloads relative to the PEGylated nanocarriers. Janus nanocarrier controlled the in vivo release of insulin and improved the blood sugar control in mice.
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Affiliation(s)
- Lili Wang
- Department of Pharmacology, State University of New York Upstate Medical University, Syracuse, NY, 13210, United States
| | - Changying Shi
- Department of Pharmacology, State University of New York Upstate Medical University, Syracuse, NY, 13210, United States
| | - Xu Wang
- Department of Pharmacology, State University of New York Upstate Medical University, Syracuse, NY, 13210, United States; National Engineering Research Center for Colloidal Materials, School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, PR China
| | - Dandan Guo
- Department of Pharmacology, State University of New York Upstate Medical University, Syracuse, NY, 13210, United States
| | - Thomas M Duncan
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY, 13210, United States
| | - Juntao Luo
- Department of Pharmacology, State University of New York Upstate Medical University, Syracuse, NY, 13210, United States; Department of Surgery, State University of New York Upstate Medical University, Syracuse, NY, 13210, United States; Upstate Cancer Center, State University of New York Upstate Medical University, Syracuse, NY, 13210, United States.
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6
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Sobti M, Ishmukhametov R, Bouwer JC, Ayer A, Suarna C, Smith NJ, Christie M, Stocker R, Duncan TM, Stewart AG. Cryo-EM reveals distinct conformations of E. coli ATP synthase on exposure to ATP. eLife 2019; 8:e43864. [PMID: 30912741 PMCID: PMC6449082 DOI: 10.7554/elife.43864] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/25/2019] [Indexed: 12/13/2022] Open
Abstract
ATP synthase produces the majority of cellular energy in most cells. We have previously reported cryo-EM maps of autoinhibited E. coli ATP synthase imaged without addition of nucleotide (Sobti et al. 2016), indicating that the subunit ε engages the α, β and γ subunits to lock the enzyme and prevent functional rotation. Here we present multiple cryo-EM reconstructions of the enzyme frozen after the addition of MgATP to identify the changes that occur when this ε inhibition is removed. The maps generated show that, after exposure to MgATP, E. coli ATP synthase adopts a different conformation with a catalytic subunit changing conformation substantially and the ε C-terminal domain transitioning via an intermediate 'half-up' state to a condensed 'down' state. This work provides direct evidence for unique conformational states that occur in E. coli ATP synthase when ATP binding prevents the ε C-terminal domain from entering the inhibitory 'up' state.
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Affiliation(s)
- Meghna Sobti
- Molecular, Structural and Computational Biology DivisionThe Victor Chang Cardiac Research InstituteDarlinghurstAustralia
- St Vincent’s Clinical School, Faculty of MedicineUNSW SydneySydneyAustralia
| | - Robert Ishmukhametov
- Department of Physics, Clarendon LaboratoryUniversity of OxfordOxfordUnited Kingdom
| | - James C Bouwer
- Molecular HorizonsThe University of WollongongWollongongAustralia
| | - Anita Ayer
- St Vincent’s Clinical School, Faculty of MedicineUNSW SydneySydneyAustralia
- Vascular Biology DivisionVictor Chang Cardiac Research InstituteDarlinghurstAustralia
| | - Cacang Suarna
- Vascular Biology DivisionVictor Chang Cardiac Research InstituteDarlinghurstAustralia
| | - Nicola J Smith
- St Vincent’s Clinical School, Faculty of MedicineUNSW SydneySydneyAustralia
- Molecular Cardiology and Biophysics DivisionVictor Chang Cardiac Research InstituteDarlinghurstAustralia
| | - Mary Christie
- Molecular, Structural and Computational Biology DivisionThe Victor Chang Cardiac Research InstituteDarlinghurstAustralia
- St Vincent’s Clinical School, Faculty of MedicineUNSW SydneySydneyAustralia
| | - Roland Stocker
- St Vincent’s Clinical School, Faculty of MedicineUNSW SydneySydneyAustralia
- Vascular Biology DivisionVictor Chang Cardiac Research InstituteDarlinghurstAustralia
| | - Thomas M Duncan
- Department of Biochemistry & Molecular BiologySUNY Upstate Medical UniversitySyracuse, NYUnited States
| | - Alastair G Stewart
- Molecular, Structural and Computational Biology DivisionThe Victor Chang Cardiac Research InstituteDarlinghurstAustralia
- St Vincent’s Clinical School, Faculty of MedicineUNSW SydneySydneyAustralia
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7
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Sielaff H, Duncan TM, Börsch M. The regulatory subunit ε in Escherichia coli F OF 1-ATP synthase. Biochim Biophys Acta Bioenerg 2018; 1859:775-788. [PMID: 29932911 DOI: 10.1016/j.bbabio.2018.06.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/13/2018] [Accepted: 06/14/2018] [Indexed: 11/16/2022]
Abstract
F-type ATP synthases are extraordinary multisubunit proteins that operate as nanomotors. The Escherichia coli (E. coli) enzyme uses the proton motive force (pmf) across the bacterial plasma membrane to drive rotation of the central rotor subunits within a stator subunit complex. Through this mechanical rotation, the rotor coordinates three nucleotide binding sites that sequentially catalyze the synthesis of ATP. Moreover, the enzyme can hydrolyze ATP to turn the rotor in the opposite direction and generate pmf. The direction of net catalysis, i.e. synthesis or hydrolysis of ATP, depends on the cell's bioenergetic conditions. Different control mechanisms have been found for ATP synthases in mitochondria, chloroplasts and bacteria. This review discusses the auto-inhibitory behavior of subunit ε found in FOF1-ATP synthases of many bacteria. We focus on E. coli FOF1-ATP synthase, with insights into the regulatory mechanism of subunit ε arising from structural and biochemical studies complemented by single-molecule microscopy experiments.
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Affiliation(s)
- Hendrik Sielaff
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Thomas M Duncan
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany.
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8
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Krishnamurthy S, Li J, Shen Y, Duncan TM, Jenrow KA, Haacke EM. Normal macromolecular clearance out of the ventricles is delayed in hydrocephalus. Brain Res 2017; 1678:337-355. [PMID: 29066366 DOI: 10.1016/j.brainres.2017.10.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 10/04/2017] [Accepted: 10/12/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Satish Krishnamurthy
- Department of Neurosurgery, Upstate Medical University, Syracuse, NY 13210, USA.
| | - Jie Li
- Department of Neurosurgery, Upstate Medical University, Syracuse, NY 13210, USA
| | - Yimin Shen
- Department of Radiology, Wayne State University, Detroit, MI 48201, USA
| | - Thomas M Duncan
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Kenneth A Jenrow
- Department of Psychology, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - E Mark Haacke
- Department of Radiology, Wayne State University, Detroit, MI 48201, USA
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9
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Abstract
Structure-based nanocarrier design for protein delivery remains challenging and has rarely been documented in the literature. We herein present a facile computer-aided approach for rational and customized design of a unique linear-dendritic telodendrimer that self-assembles into a nanocarrier for therapeutic protein delivery, e.g., insulin. Virtual screening of a small-molecule library was performed to identify optimal protein binding moieties, which were conjugated precisely in the telodendrimer backbone preinstalled with charged moieties. We systematically tested our hypothesis and obtained significant correlations between the computational predictions and experimental results. The d-α-tocopherol (vitamin E)-containing nanocarrier showed strong binding affinity for insulin in both computational prediction and experiments, which led to improved blood glucose control. This study affirms the concept and validates the approach of structure-based nanocarrier design for protein delivery.
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Affiliation(s)
| | | | - Li Zhang
- Department
of Applied Chemistry, China Agricultural University, Beijing 100193, P. R. China
| | | | | | | | - Yan Yang
- College
of Marine Life Sciences, Ocean University of China, Qingdao 266003, P. R. China
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10
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Shah NB, Duncan TM. Aerobic Growth of Escherichia coli Is Reduced, and ATP Synthesis Is Selectively Inhibited when Five C-terminal Residues Are Deleted from the ϵ Subunit of ATP Synthase. J Biol Chem 2015; 290:21032-21041. [PMID: 26160173 PMCID: PMC4543661 DOI: 10.1074/jbc.m115.665059] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 06/19/2015] [Indexed: 11/06/2022] Open
Abstract
F-type ATP synthases are rotary nanomotor enzymes involved in cellular energy metabolism in eukaryotes and eubacteria. The ATP synthase from Gram-positive and -negative model bacteria can be autoinhibited by the C-terminal domain of its ϵ subunit (ϵCTD), but the importance of ϵ inhibition in vivo is unclear. Functional rotation is thought to be blocked by insertion of the latter half of the ϵCTD into the central cavity of the catalytic complex (F1). In the inhibited state of the Escherichia coli enzyme, the final segment of ϵCTD is deeply buried but has few specific interactions with other subunits. This region of the ϵCTD is variable or absent in other bacteria that exhibit strong ϵ-inhibition in vitro. Here, genetically deleting the last five residues of the ϵCTD (ϵΔ5) caused a greater defect in respiratory growth than did the complete absence of the ϵCTD. Isolated membranes with ϵΔ5 generated proton-motive force by respiration as effectively as with wild-type ϵ but showed a nearly 3-fold decrease in ATP synthesis rate. In contrast, the ϵΔ5 truncation did not change the intrinsic rate of ATP hydrolysis with membranes. Further, the ϵΔ5 subunit retained high affinity for isolated F1 but reduced the maximal inhibition of F1-ATPase by ϵ from >90% to ∼20%. The results suggest that the ϵCTD has distinct regulatory interactions with F1 when rotary catalysis operates in opposite directions for the hydrolysis or synthesis of ATP.
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Affiliation(s)
- Naman B Shah
- Department of Biochemistry and Molecular Biology, State University of New York, Upstate Medical University, Syracuse, New York 13210
| | - Thomas M Duncan
- Department of Biochemistry and Molecular Biology, State University of New York, Upstate Medical University, Syracuse, New York 13210.
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11
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Bockenhauer SD, Duncan TM, Moerner WE, Börsch M. The regulatory switch of F 1-ATPase studied by single-molecule FRET in the ABEL Trap. Proc SPIE Int Soc Opt Eng 2014; 8950:89500H. [PMID: 25309100 DOI: 10.1117/12.2042688] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
F1-ATPase is the soluble portion of the membrane-embedded enzyme FoF1-ATP synthase that catalyzes the production of adenosine triphosphate in eukaryotic and eubacterial cells. In reverse, the F1 part can also hydrolyze ATP quickly at three catalytic binding sites. Therefore, catalysis of 'non-productive' ATP hydrolysis by F1 (or FoF1) must be minimized in the cell. In bacteria, the ε subunit is thought to control and block ATP hydrolysis by mechanically inserting its C-terminus into the rotary motor region of F1. We investigate this proposed mechanism by labeling F1 specifically with two fluorophores to monitor the C-terminus of the ε subunit by Förster resonance energy transfer. Single F1 molecules are trapped in solution by an Anti-Brownian electrokinetic trap which keeps the FRET-labeled F1 in place for extended observation times of several hundreds of milliseconds, limited by photobleaching. FRET changes in single F1 and FRET histograms for different biochemical conditions are compared to evaluate the proposed regulatory mechanism.
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Affiliation(s)
- Samuel D Bockenhauer
- Department of Chemistry, Stanford University, Stanford, CA, USA ; Department of Physics, Stanford University, Stanford, CA, USA
| | - Thomas M Duncan
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany
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12
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Duncan TM, Düser MG, Heitkamp T, McMillan DGG, Börsch M. Regulatory conformational changes of the ε subunit in single FRET-labeled F oF 1-ATP synthase. Proc SPIE Int Soc Opt Eng 2014; 8948:89481J. [PMID: 25076824 DOI: 10.1117/12.2040463] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Subunit ε is an intrinsic regulator of the bacterial FoF1-ATP synthase, the ubiquitous membrane-embedded enzyme that utilizes a proton motive force in most organisms to synthesize adenosine triphosphate (ATP). The C-terminal domain of ε can extend into the central cavity formed by the α and β subunits, as revealed by the recent X-ray structure of the F1 portion of the Escherichia coli enzyme. This insertion blocks the rotation of the central γ subunit and, thereby, prevents wasteful ATP hydrolysis. Here we aim to develop an experimental system that can reveal conditions under which ε inhibits the holoenzyme FoF1-ATP synthase in vitro. Labeling the C-terminal domain of ε and the γ subunit specifically with two different fluorophores for single-molecule Förster resonance energy transfer (smFRET) allowed monitoring of the conformation of ε in the reconstituted enzyme in real time. New mutants were made for future three-color smFRET experiments to unravel the details of regulatory conformational changes in ε.
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Affiliation(s)
- Thomas M Duncan
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Monika G Düser
- 3 Institute of Physics, Stuttgart University, Stuttgart, Germany
| | - Thomas Heitkamp
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Duncan G G McMillan
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany
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13
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Shah NB, Duncan TM. Bio-layer interferometry for measuring kinetics of protein-protein interactions and allosteric ligand effects. J Vis Exp 2014:e51383. [PMID: 24638157 DOI: 10.3791/51383] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
We describe the use of Bio-layer Interferometry to study inhibitory interactions of subunit ε with the catalytic complex of Escherichia coli ATP synthase. Bacterial F-type ATP synthase is the target of a new, FDA-approved antibiotic to combat drug-resistant tuberculosis. Understanding bacteria-specific auto-inhibition of ATP synthase by the C-terminal domain of subunit ε could provide a new means to target the enzyme for discovery of antibacterial drugs. The C-terminal domain of ε undergoes a dramatic conformational change when the enzyme transitions between the active and inactive states, and catalytic-site ligands can influence which of ε's conformations is predominant. The assay measures kinetics of ε's binding/dissociation with the catalytic complex, and indirectly measures the shift of enzyme-bound ε to and from the apparently nondissociable inhibitory conformation. The Bio-layer Interferometry signal is not overly sensitive to solution composition, so it can also be used to monitor allosteric effects of catalytic-site ligands on ε's conformational changes.
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Affiliation(s)
- Naman B Shah
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University
| | - Thomas M Duncan
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University;
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14
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Shah NB, Hutcheon ML, Haarer BK, Duncan TM. F1-ATPase of Escherichia coli: the ε- inhibited state forms after ATP hydrolysis, is distinct from the ADP-inhibited state, and responds dynamically to catalytic site ligands. J Biol Chem 2013; 288:9383-95. [PMID: 23400782 DOI: 10.1074/jbc.m113.451583] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
F1-ATPase is the catalytic complex of rotary nanomotor ATP synthases. Bacterial ATP synthases can be autoinhibited by the C-terminal domain of subunit ε, which partially inserts into the enzyme's central rotor cavity to block functional subunit rotation. Using a kinetic, optical assay of F1·ε binding and dissociation, we show that formation of the extended, inhibitory conformation of ε (εX) initiates after ATP hydrolysis at the catalytic dwell step. Prehydrolysis conditions prevent formation of the εX state, and post-hydrolysis conditions stabilize it. We also show that ε inhibition and ADP inhibition are distinct, competing processes that can follow the catalytic dwell. We show that the N-terminal domain of ε is responsible for initial binding to F1 and provides most of the binding energy. Without the C-terminal domain, partial inhibition by the ε N-terminal domain is due to enhanced ADP inhibition. The rapid effects of catalytic site ligands on conformational changes of F1-bound ε suggest dynamic conformational and rotational mobility in F1 that is paused near the catalytic dwell position.
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Affiliation(s)
- Naman B Shah
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210, USA
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15
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Roy A, Hutcheon ML, Duncan TM, Cingolani G. Improved crystallization of Escherichia coli ATP synthase catalytic complex (F1) by introducing a phosphomimetic mutation in subunit ε. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1229-33. [PMID: 23027754 DOI: 10.1107/s1744309112036718] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Accepted: 08/23/2012] [Indexed: 11/10/2022]
Abstract
The bacterial ATP synthase (F(O)F(1)) of Escherichia coli has been the prominent model system for genetics, biochemical and more recently single-molecule studies on F-type ATP synthases. With 22 total polypeptide chains (total mass of ∼529 kDa), E. coli F(O)F(1) represents nature's smallest rotary motor, composed of a membrane-embedded proton transporter (F(O)) and a peripheral catalytic complex (F(1)). The ATPase activity of isolated F(1) is fully expressed by the α(3)β(3)γ 'core', whereas single δ and ε subunits are required for structural and functional coupling of E. coli F(1) to F(O). In contrast to mitochondrial F(1)-ATPases that have been determined to atomic resolution, the bacterial homologues have proven very difficult to crystallize. In this paper, we describe a biochemical strategy that led us to improve the crystallogenesis of the E. coli F(1)-ATPase catalytic core. Destabilizing the compact conformation of ε's C-terminal domain with a phosphomimetic mutation (εS65D) dramatically increased crystallization success and reproducibility, yielding crystals of E. coli F(1) that diffract to ∼3.15 Å resolution.
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Affiliation(s)
- Ankoor Roy
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
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16
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Duncan TM, Cingolani G. A unique conformation of the inhibitory ε subunit in a crystal structure of the
Escherichia coli
F
1
‐ATPase. FASEB J 2009. [DOI: 10.1096/fasebj.23.1_supplement.504.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Thomas M Duncan
- Biochemistry & Molecular BiologySUNY Upstate Medical UniversitySyracuseNY
| | - Gino Cingolani
- Biochemistry & Molecular BiologySUNY Upstate Medical UniversitySyracuseNY
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17
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Peneva K, Mihov G, Herrmann A, Zarrabi N, Börsch M, Duncan TM, Müllen K. Exploiting the Nitrilotriacetic Acid Moiety for Biolabeling with Ultrastable Perylene Dyes. J Am Chem Soc 2008; 130:5398-9. [DOI: 10.1021/ja711322g] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kalina Peneva
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany, Zernike Institute for Advanced Materials, Department of Polymer Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, Physikalisches Institut, Universität Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart, Germany, and Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210
| | - Gueorgui Mihov
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany, Zernike Institute for Advanced Materials, Department of Polymer Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, Physikalisches Institut, Universität Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart, Germany, and Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210
| | - Andreas Herrmann
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany, Zernike Institute for Advanced Materials, Department of Polymer Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, Physikalisches Institut, Universität Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart, Germany, and Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210
| | - Nawid Zarrabi
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany, Zernike Institute for Advanced Materials, Department of Polymer Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, Physikalisches Institut, Universität Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart, Germany, and Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210
| | - Michael Börsch
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany, Zernike Institute for Advanced Materials, Department of Polymer Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, Physikalisches Institut, Universität Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart, Germany, and Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210
| | - Thomas M. Duncan
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany, Zernike Institute for Advanced Materials, Department of Polymer Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, Physikalisches Institut, Universität Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart, Germany, and Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210
| | - Klaus Müllen
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany, Zernike Institute for Advanced Materials, Department of Polymer Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, Physikalisches Institut, Universität Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart, Germany, and Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210
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18
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Bulygin VV, Duncan TM, Cross RL. Rotor/Stator interactions of the epsilon subunit in Escherichia coli ATP synthase and implications for enzyme regulation. J Biol Chem 2004; 279:35616-21. [PMID: 15199054 DOI: 10.1074/jbc.m405012200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The H(+)-translocating F(0)F(1)-ATP synthase of Escherichia coli functions as a rotary motor, coupling the transmembrane movement of protons through F(0) to the synthesis of ATP by F(1). Although the epsilon subunit appears to be tightly associated with the gamma subunit in the central stalk region of the rotor assembly, several studies suggest that the C-terminal domain of epsilon can undergo significant conformational change as part of a regulatory process. Here we use disulfide cross-linking of substituted cysteines on functionally coupled ATP synthase to characterize interactions of epsilon with an F(0) component of the rotor (subunit c) and with an F(1) component of the stator (subunit beta). Oxidation of the engineered F(0)F(1) causes formation of two disulfide bonds, betaD380C-S108C epsilon and epsilonE31C-cQ42C, to give a beta-epsilon-c cross-linked product in high yield. The results demonstrate the ability of epsilon to span the central stalk region from the surface of the membrane (epsilon-c) to the bottom of F(1) (beta-epsilon) and suggest that the conformation detected here is distinct from both the "closed" state seen with isolated epsilon (Uhlin, U., Cox, G. B., and Guss, J. M. (1997) Structure 5, 1219-1230) and the "open" state seen in a complex with a truncated form of the gamma subunit (Rodgers, A. J., and Wilce, M. C. (2000) Nat. Struct. Biol. 7, 1051-1054). The kinetics of beta-epsilon and epsilon-c cross-linking were studied separately using F(0)F(1) containing one or the other matched cysteine pair. The rate of cross-linking at the epsilon/c (rotor/rotor) interface is not influenced by the type of nucleotide added. In contrast, the rate of beta-epsilon cross-linking is fastest under ATP hydrolysis conditions, intermediate with MgADP, and slowest with MgAMP-PNP. This is consistent with a regulatory role for a reversible beta/epsilon (stator/rotor) interaction that blocks rotation and inhibits catalysis. Furthermore, the rate of beta-epsilon cross-linking is much faster than that indicated by previous studies, allowing for the possibility of a rapid response to regulatory signals.
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Affiliation(s)
- Vladimir V Bulygin
- Department of Biochemistry and Molecular Biology, State University of New York, Upstate Medical University, Syracuse, New York 13210, USA
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19
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Hutcheon ML, Duncan TM, Ngai H, Cross RL. Energy-driven subunit rotation at the interface between subunit a and the c oligomer in the F(O) sector of Escherichia coli ATP synthase. Proc Natl Acad Sci U S A 2001; 98:8519-24. [PMID: 11438702 PMCID: PMC37468 DOI: 10.1073/pnas.151236798] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2001] [Accepted: 05/14/2001] [Indexed: 11/18/2022] Open
Abstract
Subunit rotation within the F(1) catalytic sector of the ATP synthase has been well documented, identifying the synthase as the smallest known rotary motor. In the membrane-embedded F(O) sector, it is thought that proton transport occurs at a rotor/stator interface between the oligomeric ring of c subunits (rotor) and the single-copy a subunit (stator). Here we report evidence for an energy-dependent rotation at this interface. F(O)F(1) was expressed with a pair of substituted cysteines positioned to allow an intersubunit disulfide crosslink between subunit a and a c subunit [aN214C/cM65C; Jiang, W. & Fillingame, R. H. (1998) Proc. Natl. Acad. Sci. USA 95, 6607--6612]. Membranes were treated with N,N'-dicyclohexyl-[(14)C]carbodiimide to radiolabel the D61 residue on less than 20% of the c subunits. After oxidation to form an a--c crosslink, the c subunit properly aligned to crosslink to subunit a was found to contain very little (14)C label relative to other members of the c ring. However, exposure to MgATP before oxidation significantly increased the radiolabel in the a-c crosslink, indicating that a different c subunit was now aligned with subunit a. This increase was not induced by exposure to MgADP/P(i). Furthermore, preincubation with MgADP and azide to inhibit F(1) or with high concentrations of N,N'-dicyclohexylcarbodiimide to label most c subunits prevented the ATP effect. These results provide evidence for an energy-dependent rotation of the c ring relative to subunit a.
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Affiliation(s)
- M L Hutcheon
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210, USA
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20
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Abstract
We report evidence for catalysis-dependent rotation of the single epsilon subunit relative to the three catalytic beta subunits of functionally coupled, membrane-bound FOF1-ATP synthase. Cysteines substituted at beta380 and epsilon108 allowed rapid formation of a specific beta-epsilon disulfide cross-link upon oxidation. Consistent with a need for epsilon to rotate during catalysis, tethering epsilon to one of the beta subunits resulted in the inhibition of both ATP synthesis and hydrolysis. These activities were fully restored upon reduction of the beta-epsilon cross-link. As a more critical test for rotation, a subunit dissociation/reassociation procedure was used to prepare a beta-epsilon cross-linked hybrid F1 having epitope-tagged betaD380C subunits (betaflag) exclusively in the two noncross-linked positions. This allowed the beta subunit originally aligned with epsilon to form the cross-link to be distinguished from the other two betas. The cross-linked hybrid was reconstituted with FO in F1-depleted membranes. After reduction of the beta-epsilon cross-link and a brief period of catalytic turnover, reoxidation resulted in a significant amount of betaflag in the beta-epsilon cross-linked product. In contrast, exposure to ligands that bind to the catalytic site but do not allow catalysis resulted in the subsequent cross-linking of epsilon to the original untagged beta. Furthermore, catalysis-dependent rotation of epsilon was prevented by prior treatment of membranes with N,N'-dicyclohexylcarbodiimide to block proton translocation through FO. From these results, we conclude that epsilon is part of the rotor that couples proton transport to ATP synthesis.
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Affiliation(s)
- V V Bulygin
- Department of Biochemistry and Molecular Biology, State University of New York Health Science Center, Syracuse, New York 13210, USA
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21
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Abstract
We report evidence for proton-driven subunit rotation in membrane-bound FoF1-ATP synthase during oxidative phosphorylation. A betaD380C/gammaC87 crosslinked hybrid F1 having epitope-tagged betaD380C subunits (betaflag) exclusively in the two noncrosslinked positions was bound to Fo in F1-depleted membranes. After reduction of the beta-gamma crosslink, a brief exposure to conditions for ATP synthesis followed by reoxidation resulted in a significant amount of betaflag appearing in the beta-gamma crosslinked product. Such a reorientation of gammaC87 relative to the three beta subunits can only occur through subunit rotation. Rotation was inhibited when proton transport through Fo was blocked or when ADP and Pi were omitted. These results establish FoF1 as the second example in nature where proton transport is coupled to subunit rotation.
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Affiliation(s)
- Y Zhou
- Department of Biochemistry and Molecular Biology, State University of New York Health Science Center, 750 East Adams Street, Syracuse, NY 13210, USA
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22
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Cross RL, Duncan TM. Subunit rotation in F0F1-ATP synthases as a means of coupling proton transport through F0 to the binding changes in F1. J Bioenerg Biomembr 1996; 28:403-8. [PMID: 8951086 DOI: 10.1007/bf02113981] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The rotation of an asymmetric core of subunits in F0F1-ATP synthases has been proposed as a means of coupling the exergonic transport of protons through F0 to the endergonic conformational changes in F1 required for substrate binding and produce release. Here we review earlier evidence both for and against subunit rotation and then discuss our most recent studies using reversible intersubunit disulfide cross-links to test for rotation. We conclude that the gamma subunit of F1 rotates relative to the surrounding catalytic subunits during catalytic turnover by both soluble F1 and membrane-bound F0F1. Furthermore, the inhibition of this rotation by the modification of F0 with DCCD suggests that rotation in F1 is obligatorily coupled to rotation in F0 as an integral part of the coupling mechanism.
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Affiliation(s)
- R L Cross
- Department of Biochemistry and Molecular Biology, State University of New York Health Science Center, Syracuse 13210, USA
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23
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Zhou Y, Duncan TM, Bulygin VV, Hutcheon ML, Cross RL. ATP hydrolysis by membrane-bound Escherichia coli F0F1 causes rotation of the gamma subunit relative to the beta subunits. Biochim Biophys Acta 1996; 1275:96-100. [PMID: 8688454 DOI: 10.1016/0005-2728(96)00056-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We recently demonstrated that the gamma subunit in soluble F1-ATPase from Escherichia coli rotates relative to surrounding beta subunits during catalytic turnover (Duncan et al. (1995) Proc. Natl. Acad. Sci. USA 92, 10964-10968). Here, we extend our studies to the more physiologically relevant membrane-bound F0F1 complex. It is shown that beta D380C-F1, containing a beta-gamma intersubunit disulfide bond, can bind to F1-depleted membranes and can restore coupled membrane activities upon reduction of the disulfide. Using a dissociation/reconstitution approach with crosslinked beta D380C-F1, beta subunits containing an N-terminal Flag epitope (beta flag) were incorporated into the two non-crosslinked beta positions and the hybrid F1 was reconstituted with membrane-bound F0. Following reduction and ATP hydrolysis, reoxidation resulted in a significant amount of crosslinking of beta flag to the gamma subunit. This demonstrates that gamma rotates within F1 during catalytic turnover by membrane-bound F0-F1. Furthermore, the rotation of gamma is functionally coupled to F0, since preincubation with DCCD to modify F0 blocked rotation.
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Affiliation(s)
- Y Zhou
- Department of Biochemistry and Molecular Biology, State University of New York Health Science Center, Syracuse 13210, USA
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24
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Abstract
During oxidative and photo-phosphorylation, F0F1-ATP synthases couple the movement of protons down an electrochemical gradient to the synthesis of ATP. One proposed mechanistic feature that has remained speculative is that this coupling process requires the rotation of subunits within F0F1. Guided by a recent, high-resolution structure for bovine F1 [Abrahams, J. P., Leslie, A. G., Lutter, R. & Walker, J. E. (1994) Nature (London) 370, 621-628], we have developed a critical test for rotation of the central gamma subunit relative to the three catalytic beta subunits in soluble F1 from Escherichia coli. In the bovine F1 structure, a specific point of contact between the gamma subunit and one of the three catalytic beta subunits includes positioning of the homolog of E. coli gamma-subunit C87 (gamma C87) close to the beta-subunit 380DELSEED386 sequence. A beta D380C mutation allowed us to induce formation of a specific disulfide bond between beta and gamma C87 in soluble E. coli F1. Formation of the crosslink inactivated beta D380C-F1, and reduction restored full activity. Using a dissociation/reassembly approach with crosslinked beta D380C-F1, we incorporated radiolabeled beta subunits into the two noncrosslinked beta-subunit positions of F1. After reduction of the initial nonradioactive beta-gamma crosslink, only exposure to conditions for catalytic turnover results in similar reactivities of unlabeled and radiolabeled beta subunits with gamma C87 upon reoxidation. The results demonstrate that gamma subunit rotates relative to the beta subunits during catalysis.
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Affiliation(s)
- T M Duncan
- Department of Biochemistry and Molecular Biology, State University of New York Health Science Center, Syracuse 13210, USA
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25
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Duncan TM, Zhou Y, Bulygin VV, Hutcheon ML, Cross RL. Probing interactions of the Escherichia coli F0F1 ATP synthase beta and gamma subunits with disulphide cross-links. Biochem Soc Trans 1995; 23:736-41. [PMID: 8654828 DOI: 10.1042/bst0230736] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- T M Duncan
- Department of Biochemistry & Molecular Biology, SUNY Health Science Center, Syracuse, USA
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26
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Adami P, Duncan TM, McIntyre JO, Carter CE, Fu C, Melin M, Latruffe N, Fleischer S. Monoclonal antibodies for structure-function studies of (R)-3-hydroxybutyrate dehydrogenase, a lipid-dependent membrane-bound enzyme. Biochem J 1993; 292 ( Pt 3):863-72. [PMID: 7686368 PMCID: PMC1134194 DOI: 10.1042/bj2920863] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Monoclonal antibodies (mAbs) have been used to study structure-function relationships of (R)-3-hydroxybutyrate dehydrogenase (BDH) (EC 1.1.1.30), a lipid-requiring mitochondrial membrane enzyme with an absolute and specific requirement for phosphatidylcholine (PC) for enzymic activity. The purified enzyme (apoBDH, devoid of phospholipid and thereby inactive) can be re-activated with preformed phospholipid vesicles containing PC or by short-chain soluble PC. Five of six mAbs cross-react with BDH from bovine heart and rat liver, including two mAbs to conformational epitopes. One mAb was found to be specific for the C-terminal sequence of BDH and served to: (1) map endopeptidase cleavage and epitope sites on BDH; and (2) demonstrate that the C-terminus is essential for the activity of BDH. Carboxypeptidase cleavage of only a few (< or = 14) C-terminal amino acids from apoBDH (as detected by the loss of C-terminal epitope for mAb 3-10A) prevents activation by either bilayer or soluble PC. Further, for BDH in bilayers containing PC, the C-terminus is protected from carboxy-peptidase cleavage, whereas in bilayers devoid of PC the C-terminus is cleaved, and subsequent activation by PC is precluded. We conclude that: (1) the C-terminus of BDH is essential for enzymic activity, consistent with the prediction, from primary sequence analysis, that the PC-binding site is in the C-terminal domain of BDH; and (2) the allosteric activation of BDH by PC in bilayers protects the C-terminus from carboxypeptidase cleavage, indicative of a PC-induced conformational change in the enzyme.
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Affiliation(s)
- P Adami
- Department of Molecular Biology, Vanderbilt University, Nashville, TN 37235
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27
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Abstract
An updated topological model is constructed for the catalytic nucleotide-binding site of the F1-ATPase. The model is based on analogies to the known structures of the MgATP site on adenylate kinase and the guanine nucleotide sites on elongation factor Tu (Ef-Tu) and the ras p21 protein. Recent studies of these known nucleotide-binding domains have revealed several common functional features and similar alignment of nucleotide in their binding folds, and these are used as a framework for evaluating results of affinity labeling and mutagenesis studies of the beta subunit of F1. Several potentially important residues on beta are noted that have not yet been studied by mutagenesis or affinity labeling.
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Affiliation(s)
- T M Duncan
- Department of Biochemistry and Molecular Biology, SUNY Health Science Center, Syracuse 13210
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28
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Marks AR, McIntyre JO, Duncan TM, Erdjument-Bromage H, Tempst P, Fleischer S. Molecular cloning and characterization of (R)-3-hydroxybutyrate dehydrogenase from human heart. J Biol Chem 1992; 267:15459-63. [PMID: 1639787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The complete amino acid sequence of human heart (R)-3-hydroxybutyrate dehydrogenase (EC 1.1.1.30) has been deduced from the nucleotide sequence of cDNA clones. This mitochondrial enzyme has an absolute and specific requirement of phosphatidylcholine for enzymic activity (allosteric activator) and is an important prototype of lipid-requiring enzymes. Despite extensive studies, the primary sequence has not been available and is now reported. The mature form of the enzyme consists of 297 amino acids (predicted M(r) of 33,117), does not appear to contain any transmembrane helices, and is homologous with the family of short-chain alcohol dehydrogenases (SC-ADH) (Persson, B., Krook, M., and Jörnvall, H. (1991) Eur. J. Biochem. 200, 537-543) (30% residue identity with human 17 beta-hydroxysteroid dehydrogenase). The first two-thirds of the enzyme includes both putative coenzyme binding and active site conserved residues and exhibits a predicted secondary structure motif (alternating alpha-helices and beta-sheet) characteristic of SC-ADH. Bovine heart peptide sequences (174 residues in nine sequences determined by microsequencing) have extensive homology (89% identical residues) with the deduced human heart sequence. The C-terminal third (Asn-194 to Arg-297) shows little sequence homology with the SC-ADH and likely contains elements that determine the substrate specificity for the enzyme including the phospholipid (phosphatidylcholine) binding site(s). Northern blot analysis identifies a 1.3-kilobase mRNA encoding the enzyme in heart tissue.
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Affiliation(s)
- A R Marks
- Brookdale Center for Molecular Biology, Mount Sinai School of Medicine, New York, New York 10029
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29
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Sandermann H, Duncan TM. Lipid-dependent membrane enzymes. Kinetic modelling of the activation of protein kinase C by phosphatidylserine. Biochim Biophys Acta 1991; 1069:235-40. [PMID: 1932063 DOI: 10.1016/0005-2736(91)90130-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A previously developed kinetic theory for lipid-dependent membrane enzymes (Sandermann, H. (1982) Eur. J. Biochem. 127, 123-128) is used to examine the activation of protein kinase C by phosphatidylserine. Hill-coefficients ranging up to 11 have been reported for activation in mixed micelles with Triton X-100. On the basis of this uniquely high degree of cooperativity, protein kinase C has been postulated to represent a new class of lipid-dependent membrane enzymes (Newton, A. and Koshland, D.E., Jr. (1989) J. Biol. Chem. 264, 14909-14915). In contrast, activation in the absence of Triton X-100 has led to Hill-coefficients of only less than or equal to 2.6. In order to resolve the apparent discrepancy, activation is now considered to involve binding of PS monomers to interacting sites on the enzyme, a non-activating PS trapping process also occurring in the presence of Triton X-100. Estimates for trapping are made for several sets of published data for micellar activation. The kinetic model developed here successfully fits each data set using a Hill-coefficient of only 3.0. An influence of Ca2+/ions or of a two-step mechanism of lipid-protein interaction are considered as possible molecular explanations. It is concluded (i) that lipid activation of protein kinase C may proceed without unique cooperativity and (ii) that ligand trapping could provide another means for 'threshold-type' kinetic regulation of membrane enzyme and receptor systems.
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Affiliation(s)
- H Sandermann
- Institut für Biochemische Pflanzenpathologie, GSF München, Neuherberg, Germany
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32
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Cortese JD, McIntyre JO, Duncan TM, Fleischer S. Cooperativity in lipid activation of 3-hydroxybutyrate dehydrogenase: role of lecithin as an essential allosteric activator. Biochemistry 1989; 28:3000-8. [PMID: 2742824 DOI: 10.1021/bi00433a040] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
3-Hydroxybutyrate dehydrogenase (BDH) is a lecithin-requiring mitochondrial enzyme which catalyzes the interconversion of 3-hydroxybutyrate and acetoacetate with NAD(H) as coenzyme. The purified enzyme devoid of lipid (i.e., the apodehydrogenase or apoBDH) can be reactivated with soluble lecithin or by insertion into phospholipid vesicles containing lecithin. Two different models have been proposed to explain the sigmoidal lipid activation curves. For both models, activation of BDH is assumed to require the binding of two lecithin molecules per functional unit. Activation of soluble enzyme (dimeric form) by short-chain (soluble) lecithin is consistent with a model in which lecithin binding is noncooperative, whereas activation of the membrane-bound enzyme (tetrameric form) indicates cooperativity between the lecithin binding sites. A new comprehensive model is presented in which lecithin is considered to be an essential allosteric activator that shifts the equilibrium between conformational states of the enzyme. Resonance energy transfer data, reflecting NADH binding to membrane-bound and soluble apoBDH, are consistent with such a lecithin-induced conformational change. Apparent dissociation constants for binding of NADH to BDH are approximately 10 microM and approximately 37 microM for BDH activated by bilayer and soluble lecithin, respectively. The maximal fluorescence resonance energy transfer (delta F max) increases with higher mole fraction of lecithin in the bilayer. The largest changes occur between mole fractions 0 and 0.13, thereby correlating with enzymic function. Essentially no binding of NADH is observed in the absence of lecithin.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- J D Cortese
- Department of Molecular Biology, Vanderbilt University, Nashville, Tennessee 37235
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Parsonage D, Duncan TM, Wilke-Mounts S, Kironde FA, Hatch L, Senior AE. The defective proton-ATPase of uncD mutants of Escherichia coli. Identification by DNA sequencing of residues in the beta-subunit which are essential for catalysis or normal assembly. J Biol Chem 1987; 262:6301-7. [PMID: 2883184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Six mutant uncD alleles, affecting essential residues of the beta-subunit of Escherichia coli proton-ATPase, have been identified by intragenic complementation mapping, cloning, and DNA sequencing. Five of the mutations impair catalysis but do not cause structural perturbation of F1-ATPase. The amino acid substitutions found were as follows: uncD412, Gly-142----Ser; uncD430 and uncD431, both Arg-246----Cys; uncD478, Ser-174----Phe; and uncD484, Met-209----Ile. Kinetic characteristics of each corresponding mutant F1-ATPase are described or reviewed. In each case, the major determinant of impaired catalysis appears to be an attenuation of positive catalytic site cooperativity. Additionally, each mutation affects intrinsic properties of the catalytic site, including affinity for ATP, the ratio between unisite-bound substrate and products, and the rate of release of product inorganic phosphate under unisite ATP hydrolysis conditions. These effects are discussed in terms of a structural model of the catalytic nucleotide-binding domain of beta-subunit proposed recently (Duncan, T.M., Parsonage, D., and Senior, A.E. (1986) FEBS Lett. 208, 1-6). Each of the mutations lies within that domain. The uncD409 allele abolishes normal assembly of F1-ATPase. The amino acid substitution is Gly-214----Arg, which is suggested to affect a beta-turn connecting a beta-strand and an alpha-helix in the predicted nucleotide-binding domain of the beta-subunit.
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Abstract
We propose a working model for the tertiary structure of the nucleotide-binding domain of the beta-subunit of E. coli F1-ATPase, derived from secondary structure prediction and from comparison of the amino acid sequence with the sequences of other nucleotide-binding proteins of known three-dimensional structure. The model is consistent with previously published results of specific chemical modification studies and of analyses of mutations in the beta-subunit and its implications for subunit interactions and catalytic mechanism in F1-ATPases are discussed.
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Duncan TM, Senior AE. The defective proton-ATPase of uncD mutants of Escherichia coli. Two mutations which affect the catalytic mechanism. J Biol Chem 1985; 260:4901-7. [PMID: 2859284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The catalytic characteristics of F1-ATPases from uncD412 and uncD484 mutant strains of Escherichia coli were studied in order to understand how these beta-subunit mutations cause defective catalysis. Both mutant enzymes showed reduced affinity for ATP at the first catalytic site. While uncD412 F1 was similar to normal in other aspects of single site catalysis, uncD484 F1 showed a Keq of bound reactants greatly biased toward bound substrate ATP and an abnormally fast rate of Pi release. Impairment of productive catalytic cooperativity was the major cause of the reduced steady state ("multisite") catalytic rate in both mutant enzymes. Addition of excess ATP to saturate second and/or third catalytic sites did promote ATP hydrolysis and product release at the first catalytic site of uncD412 F1, but the multisite turnover rate was significantly slower than normal. In contrast, with uncD484 F1, addition of excess ATP induced rapid release of ATP from the first catalytic site and so productive catalytic cooperativity was almost completely absent. The results show that both mutations affect properties of the catalytic site and catalytic site cooperativity and further that the relatively more severe uncD484 mutation affects a residue which acts as a determinant of the fate of bound substrate ATP during promotion of catalysis. Taken together with previous studies of uncA mutant F1-ATPases (Wise, J. G., Latchney, L. R., Ferguson, A. M., and Senior, A. E. (1984) Biochemistry 23, 1426-1432) the results indicate that catalytic site cooperativity in F1-ATPases involves concerted beta-alpha-beta intersubunit communication between catalytic sites on the beta-subunits.
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Duncan TM, Senior AE. The defective proton-ATPase of uncD mutants of Escherichia coli. Two mutations which affect the catalytic mechanism. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(18)89157-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Abstract
Properties of purified F1-ATPase from Escherichia coli mutant strain AN484 (uncD412) have been studied in an attempt to understand why the amino acid substitution in the beta-subunit of this enzyme causes a tenfold reduction from normal MgATP hydrolysis rate. In most properties that were studied, uncD412 F1-ATPase resembled normal E. coli F1-ATPase. Both enzymes were found to contain a total of six adenine-nucleotide-binding sites, of which three were found to be non-exchangeable and three were exchangeable (catalytic) sites. Binding of the non-hydrolysable substrate analogue adenosine 5'-[beta gamma-imido]triphosphate (p[NH]ppA) to the three exchangeable sites showed apparent negative co-operativity. The binding affinities for p[NH]ppA, and also ADP, at the exchangeable sites were similar in the two enzymes. Both enzymes were inhibited by efrapeptin, aurovertin and p[NH]ppA, and were inactivated by dicyclohexylcarbodi-imide, 4-chloro-7-nitrobenzofurazan and p-fluorosulphonyl-benzoyl-5'-adenosine. Km values for CaATP and MgATP were similar in the two enzymes. uncD412 F1-ATPase was abnormally unstable at high pH, and dissociated into subunits readily with consequent loss of activity. The reason for the impairment of catalysis in uncD412 F1-ATPase cannot be stated with certainty from these studies. However we discuss the possibility that the mutation interrupts subunit interaction, thereby causing a partial impairment in the site-site co-operativity which is required for 'promotion' of catalysis in this enzyme.
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