1
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Bohr F, Bohr SSR, Mishra NK, González-Foutel NS, Pinholt HD, Wu S, Nielsen EM, Zhang M, Kjaergaard M, Jensen KJ, Hatzakis NS. Enhanced hexamerization of insulin via assembly pathway rerouting revealed by single particle studies. Commun Biol 2023; 6:178. [PMID: 36792809 PMCID: PMC9932072 DOI: 10.1038/s42003-022-04386-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 12/20/2022] [Indexed: 02/17/2023] Open
Abstract
Insulin formulations with diverse oligomerization states are the hallmark of interventions for the treatment of diabetes. Here using single-molecule recordings we firstly reveal that insulin oligomerization can operate via monomeric additions and secondly quantify the existence, abundance and kinetic characterization of diverse insulin assembly and disassembly pathways involving addition of monomeric, dimeric or tetrameric insulin species. We propose and experimentally validate a model where the insulin self-assembly pathway is rerouted, favoring monomeric or oligomeric assembly, by solution concentration, additives and formulations. Combining our practically complete kinetic characterization with rate simulations, we calculate the abundance of each oligomeric species from nM to mM offering mechanistic insights and the relative abundance of all oligomeric forms at concentrations relevant both for secreted and administrated insulin. These reveal a high abundance of all oligomers and a significant fraction of hexamer resulting in practically halved bioavailable monomer concentration. In addition to providing fundamental new insights, the results and toolbox presented here can be universally applied, contributing to the development of optimal insulin formulations and the deciphering of oligomerization mechanisms for additional proteins.
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Affiliation(s)
- Freja Bohr
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren S-R Bohr
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Narendra Kumar Mishra
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark
| | - Nicolás Sebastian González-Foutel
- Department of Molecular Biology and Genetics, The Danish Research Institute for Translational Neuroscience (DANDRITE), Nordic EMBL Partnership for Molecular Medicine, and Center for Proteins in Memory PROMEMO, Danish National Research Foundation, Aarhus University, Aarhus, Denmark
| | - Henrik Dahl Pinholt
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Physics Department, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Shunliang Wu
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark
| | - Emilie Milan Nielsen
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Min Zhang
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Magnus Kjaergaard
- Department of Molecular Biology and Genetics, The Danish Research Institute for Translational Neuroscience (DANDRITE), Nordic EMBL Partnership for Molecular Medicine, and Center for Proteins in Memory PROMEMO, Danish National Research Foundation, Aarhus University, Aarhus, Denmark
| | - Knud J Jensen
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark.
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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2
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Baek S, Han D, Kwon SR, Sundaresan V, Bohn PW. Electrochemical Zero-Mode Waveguide Potential-Dependent Fluorescence of Glutathione Reductase at Single-Molecule Occupancy. Anal Chem 2022; 94:3970-3977. [PMID: 35213143 PMCID: PMC8904319 DOI: 10.1021/acs.analchem.1c05091] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Understanding functional states of individual redox enzymes is important because electron-transfer reactions are fundamental to life, and single-enzyme molecules exhibit molecule-to-molecule heterogeneity in their properties, such as catalytic activity. Zero-mode waveguides (ZMW) constitute a powerful tool for single-molecule studies, enabling investigations of binding reactions up to the micromolar range due to the ability to trap electromagnetic radiation in zeptoliter-scale observation volumes. Here, we report the potential-dependent fluorescence dynamics of single glutathione reductase (GR) molecules using a bimodal electrochemical ZMW (E-ZMW), where a single-ring electrode embedded in each of the nanopores of an E-ZMW array simultaneously serves to control electrochemical potential and to confine optical radiation within the nanopores. Here, the redox state of GR is manipulated using an external potential control of the Au electrode in the presence of a redox mediator, methyl viologen (MV). Redox-state transitions in GR are monitored by correlating electrochemical and spectroscopic signals from freely diffusing MV/GR in 60 zL effective observation volumes at single GR molecule average pore occupancy, ⟨n⟩ ∼ 0.8. Fluorescence intensities decrease (increase) at reducing (oxidizing) potentials for MV due to the MV-mediated control of the GR redox state. The spectroelectrochemical response of GR to the enzyme substrate, i.e., glutathione disulfide (GSSG), shows that GSSG promotes GR oxidation via enzymatic reduction. The capabilities of E-ZMWs to probe spectroelectrochemical phenomena in zL-scale-confined environments show great promise for the study of single-enzyme reactions and can be extended to important technological applications, such as those in molecular diagnostics.
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Affiliation(s)
- Seol Baek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Donghoon Han
- Department of Chemistry, The Catholic University of Korea, Bucheon, Gyeonggi-do 14662, South Korea
| | - Seung-Ryong Kwon
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, South Korea
| | - Vignesh Sundaresan
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Paul W Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States.,Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
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3
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Laursen T, Lam HYM, Sørensen KK, Tian P, Hansen CC, Groves JT, Jensen KJ, Christensen SM. Membrane anchoring facilitates colocalization of enzymes in plant cytochrome P450 redox systems. Commun Biol 2021; 4:1057. [PMID: 34504298 PMCID: PMC8429664 DOI: 10.1038/s42003-021-02604-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 08/25/2021] [Indexed: 01/03/2023] Open
Abstract
Plant metabolism depends on cascade reactions mediated by dynamic enzyme assemblies known as metabolons. In this context, the cytochrome P450 (P450) superfamily catalyze key reactions underpinning the unique diversity of bioactive compounds. In contrast to their soluble bacterial counterparts, eukaryotic P450s are anchored to the endoplasmic reticulum membrane and serve as metabolon nucleation sites. Hence, membrane anchoring appears to play a pivotal role in the evolution of complex biosynthetic pathways. Here, a model membrane assay enabled characterization of membrane anchor dynamics by single molecule microscopy. As a model system, we reconstituted the membrane anchor of cytochrome P450 oxidoreductase (POR), the ubiquitous electron donor to all microsomal P450s. The transmembrane segment in the membrane anchor of POR is relatively conserved, corroborating its functional importance. We observe dynamic colocalization of the POR anchors in our assay suggesting that membrane anchoring might promote intermolecular interactions and in this way impact assembly of metabolic multienzyme complexes.
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Affiliation(s)
- Tomas Laursen
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Cecilie Cetti Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jay T Groves
- Department of Chemistry, University of California, Berkeley, CA, USA
| | | | - Sune M Christensen
- Department of Chemistry, University of California, Berkeley, CA, USA. .,Enzyme Research, Lyngby, Denmark.
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4
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Sørensen M, Møller BL. Metabolic Engineering of Photosynthetic Cells – in Collaboration with Nature. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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5
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Moses ME, Lund PM, Bohr SSR, Iversen JF, Kæstel-Hansen J, Kallenbach AS, Iversen L, Christensen SM, Hatzakis NS. Single-Molecule Study of Thermomyces lanuginosus Lipase in a Detergency Application System Reveals Diffusion Pattern Remodeling by Surfactants and Calcium. ACS APPLIED MATERIALS & INTERFACES 2021; 13:33704-33712. [PMID: 34235926 DOI: 10.1021/acsami.1c08809] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Lipases comprise one of the major enzyme classes in biotechnology with applications within, e.g., baking, brewing, biocatalysis, and the detergent industry. Understanding the mechanisms of lipase function and regulation is therefore important to facilitate the optimization of their function by protein engineering. Advances in single-molecule studies in model systems have provided deep mechanistic insights on lipase function, such as the existence of functional states, their dependence on regulatory cues, and their correlation to activity. However, it is unclear how these observations translate to enzyme behavior in applied settings. Here, single-molecule tracking of individual Thermomyces lanuginosus lipase (TLL) enzymes in a detergency application system allowed real-time direct observation of spatiotemporal localization, and thus diffusional behavior, of TLL enzymes on a lard substrate. Parallelized imaging of thousands of individual enzymes allowed us to observe directly the existence and quantify the abundance and interconversion kinetics between three diffusional states that we recently provided evidence to correlate with function. We observe redistribution of the enzyme's diffusional pattern at the lipid-water interface as well as variations in binding efficiency in response to surfactants and calcium, demonstrating that detergency effectors can drive the sampling of lipase functional states. Our single-molecule results combined with ensemble activity assays and enzyme surface binding efficiency readouts allowed us to deconvolute how application conditions can significantly alter protein functional dynamics and/or surface binding, both of which underpin enzyme performance. We anticipate that our results will inspire further efforts to decipher and integrate the dynamic nature of lipases, and other enzymes, in the design of new biotechnological solutions.
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Affiliation(s)
- Matias E Moses
- Novozymes A/S, Biologiens Vej 2, DK-2800 Kgs. Lyngby, Denmark
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Philip M Lund
- Novozymes A/S, Biologiens Vej 2, DK-2800 Kgs. Lyngby, Denmark
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Søren S-R Bohr
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Josephine F Iversen
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Jacob Kæstel-Hansen
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Amalie S Kallenbach
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Lars Iversen
- Novozymes A/S, Biologiens Vej 2, DK-2800 Kgs. Lyngby, Denmark
| | | | - Nikos S Hatzakis
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
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6
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Ducharme J, Sevrioukova IF, Thibodeaux CJ, Auclair K. Structural Dynamics of Cytochrome P450 3A4 in the Presence of Substrates and Cytochrome P450 Reductase. Biochemistry 2021; 60:2259-2271. [PMID: 34196520 DOI: 10.1021/acs.biochem.1c00178] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome P450 3A4 (CYP3A4) is the most important drug-metabolizing enzyme in humans and has been associated with harmful drug interactions. The activity of CYP3A4 is known to be modulated by several compounds and by the electron transfer partner, cytochrome P450 reductase (CPR). The underlying mechanism of these effects, however, is poorly understood. We have used hydrogen-deuterium exchange mass spectrometry to investigate the impact of binding of CPR and of three different substrates (7-benzyloxy-4-trifluoromethyl-coumarin, testosterone, and progesterone) on the conformational dynamics of CYP3A4. Here, we report that interaction of CYP3A4 with substrates or with the oxidized or reduced forms of CPR leads to a global rigidification of the CYP3A4 structure. This was evident from the suppression of deuterium exchange in several regions of CYP3A4, including regions known to be involved in protein-protein interactions (helix C) and substrate binding and specificity (helices B' and E, and loop K/β1). Furthermore, the bimodal isotopic distributions observed for some CYP3A4-derived peptides were drastically impacted upon binding to CPR and/or substrates, suggesting the existence of stable CYP3A4 conformational populations that are perturbed by ligand/CPR binding. The results have implications for understanding the mechanisms of ligand binding, allostery, and catalysis in CYP enzymes.
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Affiliation(s)
- Julie Ducharme
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Irina F Sevrioukova
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
| | - Christopher J Thibodeaux
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Karine Auclair
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
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7
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Biased cytochrome P450-mediated metabolism via small-molecule ligands binding P450 oxidoreductase. Nat Commun 2021; 12:2260. [PMID: 33859207 PMCID: PMC8050233 DOI: 10.1038/s41467-021-22562-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/15/2021] [Indexed: 02/02/2023] Open
Abstract
Metabolic control is mediated by the dynamic assemblies and function of multiple redox enzymes. A key element in these assemblies, the P450 oxidoreductase (POR), donates electrons and selectively activates numerous (>50 in humans and >300 in plants) cytochromes P450 (CYPs) controlling metabolism of drugs, steroids and xenobiotics in humans and natural product biosynthesis in plants. The mechanisms underlying POR-mediated CYP metabolism remain poorly understood and to date no ligand binding has been described to regulate the specificity of POR. Here, using a combination of computational modeling and functional assays, we identify ligands that dock on POR and bias its specificity towards CYP redox partners, across mammal and plant kingdom. Single molecule FRET studies reveal ligand binding to alter POR conformational sampling, which results in biased activation of metabolic cascades in whole cell assays. We propose the model of biased metabolism, a mechanism akin to biased signaling of GPCRs, where ligand binding on POR stabilizes different conformational states that are linked to distinct metabolic outcomes. Biased metabolism may allow designing pathway-specific therapeutics or personalized food suppressing undesired, disease-related, metabolic pathways.
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8
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Monoclonal antibody stability can be usefully monitored using the excitation-energy-dependent fluorescence edge-shift. Biochem J 2021; 477:3599-3612. [PMID: 32869839 PMCID: PMC7527260 DOI: 10.1042/bcj20200580] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/27/2020] [Accepted: 09/01/2020] [Indexed: 11/17/2022]
Abstract
Among the major challenges in the development of biopharmaceuticals are structural heterogeneity and aggregation. The development of a successful therapeutic monoclonal antibody (mAb) requires both a highly active and also stable molecule. Whilst a range of experimental (biophysical) approaches exist to track changes in stability of proteins, routine prediction of stability remains challenging. The fluorescence red edge excitation shift (REES) phenomenon is sensitive to a range of changes in protein structure. Based on recent work, we have found that quantifying the REES effect is extremely sensitive to changes in protein conformational state and dynamics. Given the extreme sensitivity, potentially this tool could provide a ‘fingerprint’ of the structure and stability of a protein. Such a tool would be useful in the discovery and development of biopharamceuticals and so we have explored our hypothesis with a panel of therapeutic mAbs. We demonstrate that the quantified REES data show remarkable sensitivity, being able to discern between structurally identical antibodies and showing sensitivity to unfolding and aggregation. The approach works across a broad concentration range (µg–mg/ml) and is highly consistent. We show that the approach can be applied alongside traditional characterisation testing within the context of a forced degradation study (FDS). Most importantly, we demonstrate the approach is able to predict the stability of mAbs both in the short (hours), medium (days) and long-term (months). The quantified REES data will find immediate use in the biopharmaceutical industry in quality assurance, formulation and development. The approach benefits from low technical complexity, is rapid and uses instrumentation which exists in most biochemistry laboratories without modification.
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9
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Mukherjee P, Chandra Singh P. Experimental insight into enzyme catalysis and dynamics: A review on applications of state of art spectroscopic methods. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 122:33-62. [PMID: 32951815 DOI: 10.1016/bs.apcsb.2020.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymes are dynamic in nature and understanding their activity depends on exploring their overall structural fluctuation as well as transformation at the active site in free state as well as turnover conditions. In this chapter, the application of several different spectroscopy techniques viz. single molecule spectroscopy, ultrafast spectroscopy and Raman spectroscopy in the context of enzyme dynamics and catalysis are discussed. The importance of such studies are significant in the understanding of new discoveries of drugs, cure for some lethal diseases, gene modification as well as in industrial applications.
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Affiliation(s)
- Puspal Mukherjee
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
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10
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Sligar SG, Denisov IG. Nanodiscs: A toolkit for membrane protein science. Protein Sci 2020; 30:297-315. [PMID: 33165998 DOI: 10.1002/pro.3994] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 10/30/2020] [Accepted: 10/30/2020] [Indexed: 12/25/2022]
Abstract
Membrane proteins are involved in numerous vital biological processes, including transport, signal transduction and the enzymes in a variety of metabolic pathways. Integral membrane proteins account for up to 30% of the human proteome and they make up more than half of all currently marketed therapeutic targets. Unfortunately, membrane proteins are inherently recalcitrant to study using the normal toolkit available to scientists, and one is most often left with the challenge of finding inhibitors, activators and specific antibodies using a denatured or detergent solubilized aggregate. The Nanodisc platform circumvents these challenges by providing a self-assembled system that renders typically insoluble, yet biologically and pharmacologically significant, targets such as receptors, transporters, enzymes, and viral antigens soluble in aqueous media in a native-like bilayer environment that maintain a target's functional activity. By providing a bilayer surface of defined composition and structure, Nanodiscs have found great utility in the study of cellular signaling complexes that assemble on a membrane surface. Nanodiscs provide a nanometer scale vehicle for the in vivo delivery of amphipathic drugs, therapeutic lipids, tethered nucleic acids, imaging agents and active protein complexes. This means for generating nanoscale lipid bilayers has spawned the successful use of numerous other polymer and peptide amphipathic systems. This review, in celebration of the Anfinsen Award, summarizes some recent results and provides an inroad into the current and historical literature.
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Affiliation(s)
- Stephen G Sligar
- Departments of Biochemistry Chemistry, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
| | - Ilia G Denisov
- Departments of Biochemistry Chemistry, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
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11
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Thodberg S, Sørensen M, Bellucci M, Crocoll C, Bendtsen AK, Nelson DR, Motawia MS, Møller BL, Neilson EHJ. A flavin-dependent monooxygenase catalyzes the initial step in cyanogenic glycoside synthesis in ferns. Commun Biol 2020; 3:507. [PMID: 32917937 PMCID: PMC7486406 DOI: 10.1038/s42003-020-01224-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 08/12/2020] [Indexed: 12/21/2022] Open
Abstract
Cyanogenic glycosides form part of a binary plant defense system that, upon catabolism, detonates a toxic hydrogen cyanide bomb. In seed plants, the initial step of cyanogenic glycoside biosynthesis-the conversion of an amino acid to the corresponding aldoxime-is catalyzed by a cytochrome P450 from the CYP79 family. An evolutionary conundrum arises, as no CYP79s have been identified in ferns, despite cyanogenic glycoside occurrence in several fern species. Here, we report that a flavin-dependent monooxygenase (fern oxime synthase; FOS1), catalyzes the first step of cyanogenic glycoside biosynthesis in two fern species (Phlebodium aureum and Pteridium aquilinum), demonstrating convergent evolution of biosynthesis across the plant kingdom. The FOS1 sequence from the two species is near identical (98%), despite diversifying 140 MYA. Recombinant FOS1 was isolated as a catalytic active dimer, and in planta, catalyzes formation of an N-hydroxylated primary amino acid; a class of metabolite not previously observed in plants.
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Affiliation(s)
- Sara Thodberg
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Copenhagen, Denmark
- VILLUM Center for Plant Plasticity, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Copenhagen, Denmark
| | - Mette Sørensen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Copenhagen, Denmark
- VILLUM Center for Plant Plasticity, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Copenhagen, Denmark
| | - Matteo Bellucci
- Novo Nordisk Foundation Center for Protein Research, Protein Production and Characterization Platform, University of Copenhagen, Blegdamsvej 3, 2200, Copenhagen N, Denmark
| | - Christoph Crocoll
- Section for Plant Molecular Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Copenhagen, Denmark
| | - Amalie Kofoed Bendtsen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Copenhagen, Denmark
- VILLUM Center for Plant Plasticity, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Copenhagen, Denmark
| | - David Ralph Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee, 858 Madison Ave. Suite G01, Memphis, TN, 38163, USA
| | - Mohammed Saddik Motawia
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Copenhagen, Denmark
- VILLUM Center for Plant Plasticity, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Copenhagen, Denmark
- Center for Synthetic Biology, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Copenhagen, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Copenhagen, Denmark
- VILLUM Center for Plant Plasticity, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Copenhagen, Denmark
- Center for Synthetic Biology, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Copenhagen, Denmark
| | - Elizabeth Heather Jakobsen Neilson
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Copenhagen, Denmark.
- VILLUM Center for Plant Plasticity, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Copenhagen, Denmark.
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12
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Bohr SSR, Thorlaksen C, Kühnel RM, Günther-Pomorski T, Hatzakis NS. Label-Free Fluorescence Quantification of Hydrolytic Enzyme Activity on Native Substrates Reveals How Lipase Function Depends on Membrane Curvature. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:6473-6481. [PMID: 32437165 DOI: 10.1021/acs.langmuir.0c00787] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Lipases are important hydrolytic enzymes used in a spectrum of technological applications, such as the pharmaceutical and detergent industries. Because of their versatile nature and ability to accept a broad range of substrates, they have been extensively used for biotechnological and industrial applications. Current assays to measure lipase activity primarily rely on low-sensitivity measurements of pH variations or visible changes of material properties, like hydration, and often require high amounts of proteins. Fluorescent readouts, on the other hand, offer high contrast and even single-molecule sensitivity, albeit they are reliant on fluorogenic substrates that structurally resemble the native ones. Here we present a method that combines the highly sensitive readout of fluorescent techniques while reporting enzymatic lipase function on native substrates. The method relies on embedding the environmentally sensitive fluorescent dye pHrodo and native substrates into the bilayer of liposomes. The charged products of the enzymatic hydrolysis alter the local membrane environment and thus the fluorescence intensity of pHrodo. The fluorescence can be accurately quantified and directly assigned to product formation and thus enzymatic activity. We illustrated the capacity of the assay to report the function of diverse lipases and phospholipases both in a microplate setup and at the single-particle level on individual nanoscale liposomes using total internal reflection fluorescence (TIRF). The parallelized sensitive readout of microscopy combined with the inherent polydispersity in sizes of liposomes allowed us to screen the effect of membrane curvature on lipase function and identify how mutations in the lid region control the membrane curvature-dependent activity. We anticipate this methodology to be applicable for sensitive activity readouts for a spectrum of enzymes where the product of the enzymatic reaction is charged.
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Affiliation(s)
- Søren S-R Bohr
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
- Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Camilla Thorlaksen
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
- Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
- Biophysics, Novo Nordisk A/S, Novo Nordisk Park 1, Maaloev 2760, Denmark
- Drug Delivery and Biophysics of Biopharmaceuticals, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen 2100, Denmark
| | - Ronja Marie Kühnel
- Faculty of Chemistry and Biochemistry, Department of Molecular Biochemistry, Ruhr University Bochum, Universitätstrasse 150, D-44780 Bochum, Germany
| | - Thomas Günther-Pomorski
- Faculty of Chemistry and Biochemistry, Department of Molecular Biochemistry, Ruhr University Bochum, Universitätstrasse 150, D-44780 Bochum, Germany
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
- Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
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13
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Knudsen C, Bavishi K, Viborg KM, Drew DP, Simonsen HT, Motawia MS, Møller BL, Laursen T. Stabilization of dhurrin biosynthetic enzymes from Sorghum bicolor using a natural deep eutectic solvent. PHYTOCHEMISTRY 2020; 170:112214. [PMID: 31794881 DOI: 10.1016/j.phytochem.2019.112214] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/14/2019] [Accepted: 11/16/2019] [Indexed: 06/10/2023]
Abstract
In recent years, ionic liquids and deep eutectic solvents (DESs) have gained increasing attention due to their ability to extract and solubilize metabolites and biopolymers in quantities far beyond their solubility in oil and water. The hypothesis that naturally occurring metabolites are able to form a natural deep eutectic solvent (NADES), thereby constituting a third intracellular phase in addition to the aqueous and lipid phases, has prompted researchers to study the role of NADES in living systems. As an excellent solvent for specialized metabolites, formation of NADES in response to dehydration of plant cells could provide an appropriate environment for the functional storage of enzymes during drought. Using the enzymes catalyzing the biosynthesis of the defense compound dhurrin as an experimental model system, we demonstrate that enzymes involved in this pathway exhibit increased stability in NADES compared with aqueous buffer solutions, and that enzyme activity is restored upon rehydration. Inspired by nature, application of NADES provides a biotechnological approach for long-term storage of entire biosynthetic pathways including membrane-anchored enzymes.
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Affiliation(s)
- Camilla Knudsen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Copenhagen, Denmark; Center for Synthetic Biology "bioSYNergy", Thorvaldsensvej 40, DK-1871, Frederiksberg C, Copenhagen, Denmark; VILLUM Research Center "Plant Plasticity", Thorvaldsensvej 40, DK-1871, Frederiksberg C, Copenhagen, Denmark
| | - Krutika Bavishi
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Copenhagen, Denmark; Center for Synthetic Biology "bioSYNergy", Thorvaldsensvej 40, DK-1871, Frederiksberg C, Copenhagen, Denmark; VILLUM Research Center "Plant Plasticity", Thorvaldsensvej 40, DK-1871, Frederiksberg C, Copenhagen, Denmark; Department of Molecular Biology and Genetics, Structural Biology, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
| | - Ketil Mathiasen Viborg
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Copenhagen, Denmark; Center for Synthetic Biology "bioSYNergy", Thorvaldsensvej 40, DK-1871, Frederiksberg C, Copenhagen, Denmark; VILLUM Research Center "Plant Plasticity", Thorvaldsensvej 40, DK-1871, Frederiksberg C, Copenhagen, Denmark
| | - Damian Paul Drew
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Copenhagen, Denmark; Lyell McEwin Hospital, Elizabeth Vale, SA 5112, Australia
| | - Henrik Toft Simonsen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Copenhagen, Denmark; Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, DK-2800, Kgs. Lyngby, Denmark
| | - Mohammed Saddik Motawia
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Copenhagen, Denmark; Center for Synthetic Biology "bioSYNergy", Thorvaldsensvej 40, DK-1871, Frederiksberg C, Copenhagen, Denmark; VILLUM Research Center "Plant Plasticity", Thorvaldsensvej 40, DK-1871, Frederiksberg C, Copenhagen, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Copenhagen, Denmark; Center for Synthetic Biology "bioSYNergy", Thorvaldsensvej 40, DK-1871, Frederiksberg C, Copenhagen, Denmark; VILLUM Research Center "Plant Plasticity", Thorvaldsensvej 40, DK-1871, Frederiksberg C, Copenhagen, Denmark; Carlsberg Research Laboratory, J. C. Jacobsen Gade, DK-1799, Copenhagen V, Denmark.
| | - Tomas Laursen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Copenhagen, Denmark; Center for Synthetic Biology "bioSYNergy", Thorvaldsensvej 40, DK-1871, Frederiksberg C, Copenhagen, Denmark; VILLUM Research Center "Plant Plasticity", Thorvaldsensvej 40, DK-1871, Frederiksberg C, Copenhagen, Denmark.
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14
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Bohr SSR, Lund PM, Kallenbach AS, Pinholt H, Thomsen J, Iversen L, Svendsen A, Christensen SM, Hatzakis NS. Direct observation of Thermomyces lanuginosus lipase diffusional states by Single Particle Tracking and their remodeling by mutations and inhibition. Sci Rep 2019; 9:16169. [PMID: 31700110 PMCID: PMC6838188 DOI: 10.1038/s41598-019-52539-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/08/2019] [Indexed: 12/11/2022] Open
Abstract
Lipases are interfacially activated enzymes that catalyze the hydrolysis of ester bonds and constitute prime candidates for industrial and biotechnological applications ranging from detergent industry, to chiral organic synthesis. As a result, there is an incentive to understand the mechanisms underlying lipase activity at the molecular level, so as to be able to design new lipase variants with tailor-made functionalities. Our understanding of lipase function primarily relies on bulk assay averaging the behavior of a high number of enzymes masking structural dynamics and functional heterogeneities. Recent advances in single molecule techniques based on fluorogenic substrate analogues revealed the existence of lipase functional states, and furthermore so how they are remodeled by regulatory cues. Single particle studies of lipases on the other hand directly observed diffusional heterogeneities and suggested lipases to operate in two different modes. Here to decipher how mutations in the lid region controls Thermomyces lanuginosus lipase (TLL) diffusion and function we employed a Single Particle Tracking (SPT) assay to directly observe the spatiotemporal localization of TLL and rationally designed mutants on native substrate surfaces. Parallel imaging of thousands of individual TLL enzymes and HMM analysis allowed us to observe and quantify the diffusion, abundance and microscopic transition rates between three linearly interconverting diffusional states for each lipase. We proposed a model that correlate diffusion with function that allowed us to predict that lipase regulation, via mutations in lid region or product inhibition, primarily operates via biasing transitions to the active states.
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Affiliation(s)
- Søren S-R Bohr
- Department of Chemistry & Nanoscience Center, Thorvaldsensvej 40, University of Copenhagen, Frederiksberg C, 1871, Denmark
- NovoNordisk center for protein research, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Philip M Lund
- Department of Chemistry & Nanoscience Center, Thorvaldsensvej 40, University of Copenhagen, Frederiksberg C, 1871, Denmark
- NovoNordisk center for protein research, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Amalie S Kallenbach
- Department of Chemistry & Nanoscience Center, Thorvaldsensvej 40, University of Copenhagen, Frederiksberg C, 1871, Denmark
- NovoNordisk center for protein research, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Henrik Pinholt
- Department of Chemistry & Nanoscience Center, Thorvaldsensvej 40, University of Copenhagen, Frederiksberg C, 1871, Denmark
- NovoNordisk center for protein research, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Johannes Thomsen
- Department of Chemistry & Nanoscience Center, Thorvaldsensvej 40, University of Copenhagen, Frederiksberg C, 1871, Denmark
- NovoNordisk center for protein research, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Lars Iversen
- Novozymes A/S, Krogshøjsvej 36, DK 2880, Bagværd, Denmark
| | - Allan Svendsen
- Novozymes A/S, Krogshøjsvej 36, DK 2880, Bagværd, Denmark
| | | | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Center, Thorvaldsensvej 40, University of Copenhagen, Frederiksberg C, 1871, Denmark.
- NovoNordisk center for protein research, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
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15
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Conrard L, Tyteca D. Regulation of Membrane Calcium Transport Proteins by the Surrounding Lipid Environment. Biomolecules 2019; 9:E513. [PMID: 31547139 PMCID: PMC6843150 DOI: 10.3390/biom9100513] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 12/11/2022] Open
Abstract
Calcium ions (Ca2+) are major messengers in cell signaling, impacting nearly every aspect of cellular life. Those signals are generated within a wide spatial and temporal range through a large variety of Ca2+ channels, pumps, and exchangers. More and more evidences suggest that Ca2+ exchanges are regulated by their surrounding lipid environment. In this review, we point out the technical challenges that are currently being overcome and those that still need to be defeated to analyze the Ca2+ transport protein-lipid interactions. We then provide evidences for the modulation of Ca2+ transport proteins by lipids, including cholesterol, acidic phospholipids, sphingolipids, and their metabolites. We also integrate documented mechanisms involved in the regulation of Ca2+ transport proteins by the lipid environment. Those include: (i) Direct interaction inside the protein with non-annular lipids; (ii) close interaction with the first shell of annular lipids; (iii) regulation of membrane biophysical properties (e.g., membrane lipid packing, thickness, and curvature) directly around the protein through annular lipids; and (iv) gathering and downstream signaling of several proteins inside lipid domains. We finally discuss recent reports supporting the related alteration of Ca2+ and lipids in different pathophysiological events and the possibility to target lipids in Ca2+-related diseases.
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Affiliation(s)
- Louise Conrard
- CELL Unit, de Duve Institute and Université catholique de Louvain, UCL B1.75.05, avenue Hippocrate, 75, B-1200 Brussels, Belgium
| | - Donatienne Tyteca
- CELL Unit, de Duve Institute and Université catholique de Louvain, UCL B1.75.05, avenue Hippocrate, 75, B-1200 Brussels, Belgium.
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16
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Mellor SB, Vinde MH, Nielsen AZ, Hanke GT, Abdiaziz K, Roessler MM, Burow M, Motawia MS, Møller BL, Jensen PE. Defining optimal electron transfer partners for light-driven cytochrome P450 reactions. Metab Eng 2019; 55:33-43. [PMID: 31091467 DOI: 10.1016/j.ymben.2019.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/02/2019] [Accepted: 05/04/2019] [Indexed: 12/16/2022]
Abstract
Plants and cyanobacteria are promising heterologous hosts for metabolic engineering, and particularly suited for expression of cytochrome P450 (P450s), enzymes that catalyse key steps in biosynthetic pathways leading to valuable natural products such as alkaloids, terpenoids and phenylpropanoids. P450s are often difficult to express and require a membrane-bound NADPH-dependent reductase, complicating their use in metabolic engineering and bio-production. We previously demonstrated targeting of heterologous P450s to thylakoid membranes both in N. benthamiana chloroplasts and cyanobacteria, and functional substitution of their native reductases with the photosynthetic apparatus via the endogenous soluble electron carrier ferredoxin. However, because ferredoxin acts as a sorting hub for photosynthetic reducing power, there is fierce competition for reducing equivalents, which limits photosynthesis-driven P450 output. This study compares the ability of four electron carriers to increase photosynthesis-driven P450 activity. These carriers, three plant ferredoxins and a flavodoxin-like engineered protein derived from cytochrome P450 reductase, show only modest differences in their electron transfer to our model P450, CYP79A1 in vitro. However, only the flavodoxin-like carrier supplies appreciable reducing power in the presence of competition for reduced ferredoxin, because it possesses a redox potential that renders delivery of reducing equivalents to endogenous processes inefficient. We further investigate the efficacy of these electron carrier proteins in vivo by expressing them transiently in N. benthamiana fused to CYP79A1. All but one of the fusion enzymes show improved sequestration of photosynthetic reducing power. Fusion with the flavodoxin-like carrier offers the greatest improvement in this comparison - nearly 25-fold on a per protein basis. Thus, this study demonstrates that synthetic electron transfer pathways with optimal redox potentials can alleviate the problem of endogenous competition for reduced ferredoxin and sets out a new metabolic engineering strategy useful for producing valuable natural products.
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Affiliation(s)
- Silas Busck Mellor
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Marcos Hamborg Vinde
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Agnieszka Zygadlo Nielsen
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Guy Thomas Hanke
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, United Kingdom
| | - Kaltum Abdiaziz
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, United Kingdom
| | - Maxie M Roessler
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, United Kingdom
| | - Meike Burow
- DyNaMo Center of Excellence, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Mohammed Saddik Motawia
- Villum Research Center for Plant Plasticity, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Birger Lindberg Møller
- Villum Research Center for Plant Plasticity, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Poul Erik Jensen
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
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17
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Davydov RM, Jennings G, Hoffman BM, Podust LM. Short-lived neutral FMN and FAD semiquinones are transient intermediates in cryo-reduced yeast NADPH-cytochrome P450 reductase. Arch Biochem Biophys 2019; 673:108080. [PMID: 31445894 DOI: 10.1016/j.abb.2019.108080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 08/14/2019] [Accepted: 08/20/2019] [Indexed: 11/28/2022]
Abstract
The electron configuration of flavin cofactors, FMN and FAD, is a critical factor governing the reactivity of NADPH-cytochrome P450 reductase (CPR). The current view of electron transfer by the mammalian CPR, based on equilibrium redox potentials of the flavin cofactors, is that the two electron-reduced FMN hydroquinone (FMNH2), rather than one electron-reduced FMN semiquinone, serves as electron donor to the terminal protein acceptors. However, kinetic and thermodynamic studies on the CPR species originated from different organisms have shown that redox potentials measured at distinct electron transfer steps differ from redox potentials determined by equilibrium titration. Collectively, previous observations suggest that the short-lived transient semiquinone species may carry electrons in diflavin reductases. In this work, we have investigated spectroscopic properties of the CPR-bound FAD and FMN reduced at 77 K by radiolytically-generated thermalized electrons. Using UV-vis spectroscopy, we demonstrated that upon cryo-reduction of oxidized yeast CPR (yCPR) containing an equimolar ratio of both FAD and FMN, or FAD alone, neutral semiquinones were trapped at 77 K. During annealing at the elevated temperatures, unstable short-lived neutral semiquinones relaxed to spectroscopically distinct air-stable neutral semiquinones. This transition was independent of pH within the 6.0-10.7 range. Our data on yeast CPR are in line with the previous observations of others that the flavin short-lived transient semiquinone intermediates may have a role in the electron transfer by CPR at physiological conditions.
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Affiliation(s)
- Roman M Davydov
- The Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Gareth Jennings
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Brian M Hoffman
- The Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Larissa M Podust
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
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18
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Knudsen C, Gallage NJ, Hansen CC, Møller BL, Laursen T. Dynamic metabolic solutions to the sessile life style of plants. Nat Prod Rep 2019; 35:1140-1155. [PMID: 30324199 PMCID: PMC6254060 DOI: 10.1039/c8np00037a] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Plants are sessile organisms. To compensate for not being able to escape when challenged by unfavorable growth conditions, pests or herbivores, plants have perfected their metabolic plasticity by having developed the capacity for on demand dynamic biosynthesis and storage of a plethora of phytochemicals.
Covering: up to 2018 Plants are sessile organisms. To compensate for not being able to escape when challenged by unfavorable growth conditions, pests or herbivores, plants have perfected their metabolic plasticity by having developed the capacity for on demand synthesis of a plethora of phytochemicals to specifically respond to the challenges arising during plant ontogeny. Key steps in the biosynthesis of phytochemicals are catalyzed by membrane-bound cytochrome P450 enzymes which in plants constitute a superfamily. In planta, the P450s may be organized in dynamic enzyme clusters (metabolons) and the genes encoding the P450s and other enzymes in a specific pathway may be clustered. Metabolon formation facilitates transfer of substrates between sequential enzymes and therefore enables the plant to channel the flux of general metabolites towards biosynthesis of specific phytochemicals. In the plant cell, compartmentalization of the operation of specific biosynthetic pathways in specialized plastids serves to avoid undesired metabolic cross-talk and offers distinct storage sites for molar concentrations of specific phytochemicals. Liquid–liquid phase separation may lead to formation of dense biomolecular condensates within the cytoplasm or vacuole allowing swift activation of the stored phytochemicals as required upon pest or herbivore attack. The molecular grid behind plant plasticity offers an endless reservoir of functional modules, which may be utilized as a synthetic biology tool-box for engineering of novel biological systems based on rational design principles. In this review, we highlight some of the concepts used by plants to coordinate biosynthesis and storage of phytochemicals.
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Affiliation(s)
- Camilla Knudsen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark.
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19
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Hedison TM, Scrutton NS. Tripping the light fantastic in membrane redox biology: linking dynamic structures to function in ER electron transfer chains. FEBS J 2019; 286:2004-2017. [PMID: 30657259 PMCID: PMC6563164 DOI: 10.1111/febs.14757] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 12/16/2018] [Accepted: 01/15/2019] [Indexed: 12/19/2022]
Abstract
How the dynamics of proteins assist catalysis is a contemporary issue in enzymology. In particular, this holds true for membrane‐bound enzymes, where multiple structural, spectroscopic and biochemical approaches are needed to build up a comprehensive picture of how dynamics influence enzyme reaction cycles. Of note are the recent studies of cytochrome P450 reductases (CPR)–P450 (CYP) endoplasmic reticulum redox chains, showing the relationship between dynamics and electron flow through flavin and haem redox centres and the impact this has on monooxygenation chemistry. These studies have led to deeper understanding of mechanisms of electron flow, including the timing and control of electron delivery to protein‐bound cofactors needed to facilitate CYP‐catalysed reactions. Individual and multiple component systems have been used to capture biochemical behaviour and these have led to the emergence of more integrated models of catalysis. Crucially, the effects of membrane environment and composition on reaction cycle chemistry have also been probed, including effects on coenzyme binding/release, thermodynamic control of electron transfer, conformational coupling between partner proteins and vectorial versus ‘off pathway’ electron flow. Here, we review these studies and discuss evidence for the emergence of dynamic structural models of electron flow along human microsomal CPR–P450 redox chains.
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Affiliation(s)
- Tobias M Hedison
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, UK
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20
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Quast RB, Fatemi F, Kranendonk M, Margeat E, Truan G. Accurate Determination of Human CPR Conformational Equilibrium by smFRET Using Dual Orthogonal Noncanonical Amino Acid Labeling. Chembiochem 2019; 20:659-666. [DOI: 10.1002/cbic.201800607] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Robert B. Quast
- LISBP; Université de Toulouse; CNRS; INRA; INSA; 135 Avenue de Rangueil 31077 Toulouse France
| | - Fataneh Fatemi
- Protein Research Center; Shahid Beheshti University, G.C.; Evin 1983969411 Tehran Iran
| | - Michel Kranendonk
- Center for Toxicogenomics and Human Health (ToxOmics); Genetics, Oncology and Human Toxicology; NOVA Medical School; Faculdade de Ciências Médicas; Universidade Nova de Lisboa; Rua Câmara Pestana, no. 6 1150-082 Lisboa Portugal
| | - Emmanuel Margeat
- BS; CNRS; CINSERM; Université de Montpellier; Montpellier France
| | - Gilles Truan
- LISBP; Université de Toulouse; CNRS; INRA; INSA; 135 Avenue de Rangueil 31077 Toulouse France
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21
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Abstract
Numerous biosynthetic pathways have been shown to assemble at the surface of cellular membranes into efficient dynamic supramolecular assemblies termed metabolons. In response to environmental stimuli, metabolons assemble on-demand making them highly dynamic and fragile. This transient nature has previously hampered isolation and molecular characterization of dynamic metabolons. In contrast to conventional detergents, which tend to disrupt weak protein-protein interactions and remove lipids, the competence of a styrene maleic acid copolymer to carve out discrete lipid nanodisc from membranes offers immense potential for isolation of intact protein assemblies. Here, we present a method to extract the entire membrane-bound dhurrin pathway directly from microsomal fractions of the cereal Sorghum bicolor. This detergent-free nanodisc approach may be generally transposed for isolation of entire plant biosynthetic metabolons. This method provides a simple practical toolkit for the study of membrane protein complexes.
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22
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Flayhan A, Mertens HDT, Ural-Blimke Y, Martinez Molledo M, Svergun DI, Löw C. Saposin Lipid Nanoparticles: A Highly Versatile and Modular Tool for Membrane Protein Research. Structure 2018; 26:345-355.e5. [PMID: 29413323 PMCID: PMC5807053 DOI: 10.1016/j.str.2018.01.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/27/2017] [Accepted: 01/10/2018] [Indexed: 11/30/2022]
Abstract
Saposin-derived lipid nanoparticles (SapNPs) are a new alternative tool for membrane protein reconstitution. Here we demonstrate the potential and advantages of SapNPs. We show that SapA has the lowest lipid specificity for SapNP formation. These nanoparticles are modular and offer a tunable range of size and composition depending on the stoichiometric ratio of lipid and saposin components. They are stable and exhibit features typical of lipid-bilayer systems. Our data suggest that SapNPs are versatile and can adapt to membrane proteins of various sizes and architectures. Using SapA and various types of lipids we could reconstitute membrane proteins of different transmembrane cross-sectional areas (from 14 to 56 transmembrane α helices). SapNP-reconstituted proteins bound their respective ligands and were more heat stable compared with the detergent-solubilized form. Moreover, SapNPs encircle membrane proteins in a compact way, allowing structural investigations of small membrane proteins in a detergent-free environment using small-angle X-ray scattering. SapA shows the lowest lipid specificity for SapNP formation SapNPs are versatile and can adapt to MPs of various sizes and architectures SapNP-reconstituted MPs are more stable than in detergent SapNPs encapsulate MPs in a compact manner
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Affiliation(s)
- Ali Flayhan
- Centre for Structural Systems Biology (CSSB), DESY, Notkestrasse 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
| | - Haydyn D T Mertens
- European Molecular Biology Laboratory Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
| | - Yonca Ural-Blimke
- Centre for Structural Systems Biology (CSSB), DESY, Notkestrasse 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
| | - Maria Martinez Molledo
- Centre for Structural Systems Biology (CSSB), DESY, Notkestrasse 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB), DESY, Notkestrasse 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory Hamburg, Notkestrasse 85, 22607 Hamburg, Germany; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, 17177 Stockholm, Sweden.
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23
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Stella S, Mesa P, Thomsen J, Paul B, Alcón P, Jensen SB, Saligram B, Moses ME, Hatzakis NS, Montoya G. Conformational Activation Promotes CRISPR-Cas12a Catalysis and Resetting of the Endonuclease Activity. Cell 2018; 175:1856-1871.e21. [PMID: 30503205 DOI: 10.1016/j.cell.2018.10.045] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/27/2018] [Accepted: 10/22/2018] [Indexed: 02/07/2023]
Abstract
Cas12a, also known as Cpf1, is a type V-A CRISPR-Cas RNA-guided endonuclease that is used for genome editing based on its ability to generate specific dsDNA breaks. Here, we show cryo-EM structures of intermediates of the cleavage reaction, thus visualizing three protein regions that sense the crRNA-DNA hybrid assembly triggering the catalytic activation of Cas12a. Single-molecule FRET provides the thermodynamics and kinetics of the conformational activation leading to phosphodiester bond hydrolysis. These findings illustrate why Cas12a cuts its target DNA and unleashes unspecific cleavage activity, degrading ssDNA molecules after activation. In addition, we show that other crRNAs are able to displace the R-loop inside the protein after target DNA cleavage, terminating indiscriminate ssDNA degradation. We propose a model whereby the conformational activation of the enzyme results in indiscriminate ssDNA cleavage. The displacement of the R-loop by a new crRNA molecule will reset Cas12a specificity, targeting new DNAs.
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Affiliation(s)
- Stefano Stella
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Pablo Mesa
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Johannes Thomsen
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Bijoya Paul
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Pablo Alcón
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Simon B Jensen
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Bhargav Saligram
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Matias E Moses
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark.
| | - Guillermo Montoya
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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Molecular mechanism of metabolic NAD(P)H-dependent electron-transfer systems: The role of redox cofactors. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1860:233-258. [PMID: 30419202 DOI: 10.1016/j.bbabio.2018.11.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 10/30/2018] [Accepted: 11/07/2018] [Indexed: 12/14/2022]
Abstract
NAD(P)H-dependent electron-transfer (ET) systems require three functional components: a flavin-containing NAD(P)H-dehydrogenase, one-electron carrier and metal-containing redox center. In principle, these ET systems consist of one-, two- and three-components, and the electron flux from pyridine nucleotide cofactors, NADPH or NADH to final electron acceptor follows a linear pathway: NAD(P)H → flavin → one-electron carrier → metal containing redox center. In each step ET is primarily controlled by one- and two-electron midpoint reduction potentials of protein-bound redox cofactors in which the redox-linked conformational changes during the catalytic cycle are required for the domain-domain interactions. These interactions play an effective ET reactions in the multi-component ET systems. The microsomal and mitochondrial cytochrome P450 (cyt P450) ET systems, nitric oxide synthase (NOS) isozymes, cytochrome b5 (cyt b5) ET systems and methionine synthase (MS) ET system include a combination of multi-domain, and their organizations display similarities as well as differences in their components. However, these ET systems are sharing of a similar mechanism. More recent structural information obtained by X-ray and cryo-electron microscopy (cryo-EM) analysis provides more detail for the mechanisms associated with multi-domain ET systems. Therefore, this review summarizes the roles of redox cofactors in the metabolic ET systems on the basis of one-electron redox potentials. In final Section, evolutionary aspects of NAD(P)H-dependent multi-domain ET systems will be discussed.
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25
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Šrejber M, Navrátilová V, Paloncýová M, Bazgier V, Berka K, Anzenbacher P, Otyepka M. Membrane-attached mammalian cytochromes P450: An overview of the membrane's effects on structure, drug binding, and interactions with redox partners. J Inorg Biochem 2018; 183:117-136. [DOI: 10.1016/j.jinorgbio.2018.03.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/16/2018] [Accepted: 03/01/2018] [Indexed: 01/08/2023]
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26
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Direct observation of multiple conformational states in Cytochrome P450 oxidoreductase and their modulation by membrane environment and ionic strength. Sci Rep 2018; 8:6817. [PMID: 29717147 PMCID: PMC5931563 DOI: 10.1038/s41598-018-24922-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 04/03/2018] [Indexed: 12/20/2022] Open
Abstract
Cytochrome P450 oxidoreductase (POR) is the primary electron donor in eukaryotic cytochrome P450 (CYP) containing systems. A wealth of ensemble biophysical studies of Cytochrome P450 oxidoreductase (POR) has reported a binary model of the conformational equilibrium directing its catalytic efficiency and biomolecular recognition. In this study, full length POR from the crop plant Sorghum bicolor was site-specifically labeled with Cy3 (donor) and Cy5 (acceptor) fluorophores and reconstituted in nanodiscs. Our single molecule fluorescence resonance energy transfer (smFRET) burst analyses of POR allowed the direct observation and quantification of at least three dominant conformational sub-populations, their distribution and occupancies. Moreover, the state occupancies were remodeled significantly by ionic strength and the nature of reconstitution environment, i.e. phospholipid bilayers (nanodiscs) composed of different lipid head group charges vs. detergent micelles. The existence of conformational heterogeneity in POR may mediate selective activation of multiple downstream electron acceptors and association in complexes in the ER membrane.
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27
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Benítez-Mateos AI, Nidetzky B, Bolivar JM, López-Gallego F. Single-Particle Studies to Advance the Characterization of Heterogeneous Biocatalysts. ChemCatChem 2018. [DOI: 10.1002/cctc.201701590] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ana I. Benítez-Mateos
- Heterogeneous Biocatalysis Group; CIC BiomaGUNE; Paseo Miramon 182 San Sebastian-Donostia 20014 Spain
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering; Graz University of Technology, NAWI Graz; Petersgasse 12 8010 Graz Austria
- Austrian Centre of Industrial Biotechnology; Petersgasse 14 8010 Graz Austria
| | - Juan M. Bolivar
- Institute of Biotechnology and Biochemical Engineering; Graz University of Technology, NAWI Graz; Petersgasse 12 8010 Graz Austria
| | - Fernando López-Gallego
- Heterogeneous Biocatalysis Group; CIC BiomaGUNE; Paseo Miramon 182 San Sebastian-Donostia 20014 Spain
- IKERBASQUE; Basque Foundation for Science; Bilbao Spain
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28
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Abstract
Membrane proteins play a most important part in metabolism, signaling, cell motility, transport, development, and many other biochemical and biophysical processes which constitute fundamentals of life on the molecular level. Detailed understanding of these processes is necessary for the progress of life sciences and biomedical applications. Nanodiscs provide a new and powerful tool for a broad spectrum of biochemical and biophysical studies of membrane proteins and are commonly acknowledged as an optimal membrane mimetic system that provides control over size, composition, and specific functional modifications on the nanometer scale. In this review we attempted to combine a comprehensive list of various applications of nanodisc technology with systematic analysis of the most attractive features of this system and advantages provided by nanodiscs for structural and mechanistic studies of membrane proteins.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry and Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
| | - Stephen G Sligar
- Department of Biochemistry and Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
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29
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Abstract
Purpose of Review We provide an overview of the current knowledge on cytochrome P450-mediated metabolism organized as metabolons and factors that facilitate their stabilization. Essential parameters will be discussed including those that are commonly disregarded using the dhurrin metabolon from Sorghum bicolor as a case study. Recent Findings Sessile plants control their metabolism to prioritize their resources between growth and development, or defense. This requires fine-tuned complex dynamic regulation of the metabolic networks involved. Within the recent years, numerous studies point to the formation of dynamic metabolons playing a major role in controlling the metabolic fluxes within such networks. Summary We propose that P450s and their partners interact and associate dynamically with POR, which acts as a charging station possibly in concert with Cytb5. Solvent environment, lipid composition, and non-catalytic proteins guide metabolon formation and thereby activity, which have important implications for synthetic biology approaches aiming to produce high-value specialized metabolites in heterologous hosts.
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Affiliation(s)
- Jean-Etienne Bassard
- Plant Biochemistry Laboratory, Center for Synthetic Biology, VILLUM Research Center “Plant Plasticity,” Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Center for Synthetic Biology, VILLUM Research Center “Plant Plasticity,” Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen Denmark
- Carlsberg Research Laboratory, Gamle Carlsberg Vej 10, DK-1799 Copenhagen V, Denmark
| | - Tomas Laursen
- Plant Biochemistry Laboratory, Center for Synthetic Biology, VILLUM Research Center “Plant Plasticity,” Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen Denmark
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608 USA
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30
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Laursen T, Borch J, Knudsen C, Bavishi K, Torta F, Martens HJ, Silvestro D, Hatzakis NS, Wenk MR, Dafforn TR, Olsen CE, Motawia MS, Hamberger B, Møller BL, Bassard JE. Characterization of a dynamic metabolon producing the defense compound dhurrin in sorghum. Science 2016; 354:890-893. [PMID: 27856908 DOI: 10.1126/science.aag2347] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 10/04/2016] [Indexed: 12/16/2023]
Abstract
Metabolic highways may be orchestrated by the assembly of sequential enzymes into protein complexes, or metabolons, to facilitate efficient channeling of intermediates and to prevent undesired metabolic cross-talk while maintaining metabolic flexibility. Here we report the isolation of the dynamic metabolon that catalyzes the formation of the cyanogenic glucoside dhurrin, a defense compound produced in sorghum plants. The metabolon was reconstituted in liposomes, which demonstrated the importance of membrane surface charge and the presence of the glucosyltransferase for metabolic channeling. We used in planta fluorescence lifetime imaging microscopy and fluorescence correlation spectroscopy to study functional and structural characteristics of the metabolon. Understanding the regulation of biosynthetic metabolons offers opportunities to optimize synthetic biology approaches for efficient production of high-value products in heterologous hosts.
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Affiliation(s)
- Tomas Laursen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Center, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Jonas Borch
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- VILLUM Center For Bioanalytical Sciences, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Camilla Knudsen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Center, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Krutika Bavishi
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Center, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Federico Torta
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Helle Juel Martens
- Copenhagen Plant Science Center, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Daniele Silvestro
- Copenhagen Plant Science Center, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Nikos S Hatzakis
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- Department of Chemistry, Nano-Science Center, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Markus R Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
- Department of Biological Sciences, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
- Department of Business, Energy and Industrial Strategy, Her Majesty's Government, UK
| | - Carl Erik Olsen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871 Frederiksberg C, Denmark
| | - Mohammed Saddik Motawia
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Center, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Björn Hamberger
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Center, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- Carlsberg Research Laboratory, DK-1799 Copenhagen V, Denmark
| | - Jean-Etienne Bassard
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Center, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
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31
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Bavishi K, Laursen T, Martinez KL, Møller BL, Della Pia EA. Application of nanodisc technology for direct electrochemical investigation of plant cytochrome P450s and their NADPH P450 oxidoreductase. Sci Rep 2016; 6:29459. [PMID: 27386958 PMCID: PMC4937447 DOI: 10.1038/srep29459] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 05/18/2016] [Indexed: 11/15/2022] Open
Abstract
Direct electrochemistry of cytochrome P450 containing systems has primarily focused on investigating enzymes from microbes and animals for bio-sensing applications. Plant P450s receive electrons from NADPH P450 oxidoreductase (POR) to orchestrate the bio-synthesis of a plethora of commercially valuable compounds. In this report, full length CYP79A1, CYP71E1 and POR of the dhurrin pathway in Sorghum bicolor were reconstituted individually in nanoscale lipid patches, "nanodiscs", and directly immobilized on unmodified gold electrodes. Cyclic voltammograms of CYP79A1 and CYP71E1 revealed reversible redox peaks with average midpoint potentials of 80 ± 5 mV and 72 ± 5 mV vs. Ag/AgCl, respectively. POR yielded two pairs of redox peaks with midpoint potentials of 90 ± 5 mV and -300 ± 10 mV, respectively. The average heterogeneous electron transfer rate constant was calculated to be ~1.5 s(-1). POR was electro-catalytically active while the P450s generated hydrogen peroxide (H2O2). These nanodisc-based investigations lay the prospects and guidelines for construction of a simplified platform to perform mediator-free, direct electrochemistry of non-engineered cytochromes P450 under native-like conditions. It is also a prelude for driving plant P450 systems electronically for simplified and cost-effective screening of potential substrates/inhibitors and fabrication of nano-bioreactors for synthesis of high value natural products.
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Affiliation(s)
- Krutika Bavishi
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, Thorvaldsensvej 40, DK-1871 Frederiksberg C, University of Copenhagen, Denmark
- VILLUM Research Center for Plant Plasticity, Thorvaldsensvej 40, DK-1871 Frederiksberg C, University of Copenhagen, Denmark
- Center for Synthetic Biology ‘bioSYNergy’, Thorvaldsensvej 40, DK-1871 Frederiksberg C, University of Copenhagen, Denmark
| | - Tomas Laursen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, Thorvaldsensvej 40, DK-1871 Frederiksberg C, University of Copenhagen, Denmark
- VILLUM Research Center for Plant Plasticity, Thorvaldsensvej 40, DK-1871 Frederiksberg C, University of Copenhagen, Denmark
- Center for Synthetic Biology ‘bioSYNergy’, Thorvaldsensvej 40, DK-1871 Frederiksberg C, University of Copenhagen, Denmark
- Joint BioEnergy Institute, Feedstocks Division, Emeryville, CA 94608, USA
| | - Karen L. Martinez
- Center for Synthetic Biology ‘bioSYNergy’, Thorvaldsensvej 40, DK-1871 Frederiksberg C, University of Copenhagen, Denmark
- Bio-Nanotechnology Laboratory, Department of Chemistry & Nano-Science Center, Universitetparken 5, DK-2100, University of Copenhagen, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, Thorvaldsensvej 40, DK-1871 Frederiksberg C, University of Copenhagen, Denmark
- VILLUM Research Center for Plant Plasticity, Thorvaldsensvej 40, DK-1871 Frederiksberg C, University of Copenhagen, Denmark
- Center for Synthetic Biology ‘bioSYNergy’, Thorvaldsensvej 40, DK-1871 Frederiksberg C, University of Copenhagen, Denmark
| | - Eduardo Antonio Della Pia
- Bio-Nanotechnology Laboratory, Department of Chemistry & Nano-Science Center, Universitetparken 5, DK-2100, University of Copenhagen, Denmark
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32
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Catici DAM, Amos HE, Yang Y, van den Elsen JMH, Pudney CR. The red edge excitation shift phenomenon can be used to unmask protein structural ensembles: implications for NEMO-ubiquitin interactions. FEBS J 2016; 283:2272-84. [PMID: 27028374 DOI: 10.1111/febs.13724] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 03/29/2016] [Indexed: 02/02/2023]
Abstract
To understand complex molecular interactions, it is necessary to account for molecular flexibility and the available equilibrium of conformational states. Only a small number of experimental approaches can access such information. Potentially steady-state red edge excitation shift (REES) spectroscopy can act as a qualitative metric of changes to the protein free energy landscape (FEL) and the equilibrium of conformational states. First, we validate this hypothesis using a single Trp-containing protein, NF-κB essential modulator (NEMO). We provide detailed evidence from chemical denaturation studies, macromolecular crowding studies, and the first report of the pressure dependence of the REES effect. Combination of these data demonstrate that the REES effect can report on the 'ruggedness' of the FEL and we present a phenomenological model, based on realistic physical interpretations, for fitting steady-state REES data to allow quantification of this aspect of the REES effect. We test the conceptual framework we have developed by correlating findings from NEMO ligand-binding studies with the REES data in a range of NEMO-ligand binary complexes. Our findings shed light on the nature of the interaction between NEMO and poly-ubiquitin, suggesting that NEMO is differentially regulated by poly-ubiquitin chain length and that this regulation occurs via a modulation of the available equilibrium of conformational states, rather than gross structural change. This study therefore demonstrates the potential of REES as a powerful tool for tackling contemporary issues in structural biology and biophysics and elucidates novel information on the structure-function relationship of NEMO and key interaction partners.
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Affiliation(s)
- Dragana A M Catici
- Department of Biology and Biochemistry, Faculty of Science, University of Bath, UK
| | - Hope E Amos
- Department of Biology and Biochemistry, Faculty of Science, University of Bath, UK
| | - Yi Yang
- Department of Biology and Biochemistry, Faculty of Science, University of Bath, UK
| | | | - Christopher R Pudney
- Department of Biology and Biochemistry, Faculty of Science, University of Bath, UK
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33
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Nanodiscs for structural and functional studies of membrane proteins. Nat Struct Mol Biol 2016; 23:481-6. [PMID: 27273631 DOI: 10.1038/nsmb.3195] [Citation(s) in RCA: 332] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 02/24/2016] [Indexed: 12/12/2022]
Abstract
Membrane proteins have long presented a challenge to biochemical and functional studies. In the absence of a bilayer environment, individual proteins and critical macromolecular complexes may be insoluble and may display altered or absent activities. Nanodisc technology provides important advantages for the isolation, purification, structural resolution and functional characterization of membrane proteins. In addition, the ability to precisely control the nanodisc composition provides a nanoscale membrane surface for investigating molecular recognition events.
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34
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A well-balanced preexisting equilibrium governs electron flux efficiency of a multidomain diflavin reductase. Biophys J 2016; 108:1527-1536. [PMID: 25809265 DOI: 10.1016/j.bpj.2015.01.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/24/2014] [Accepted: 01/21/2015] [Indexed: 01/11/2023] Open
Abstract
Diflavin reductases are bidomain electron transfer proteins in which structural reorientation is necessary to account for the various intramolecular and intermolecular electron transfer steps. Using small-angle x-ray scattering and nuclear magnetic resonance data, we describe the conformational free-energy landscape of the NADPH-cytochrome P450 reductase (CPR), a typical bidomain redox enzyme composed of two covalently-bound flavin domains, under various experimental conditions. The CPR enzyme exists in a salt- and pH-dependent rapid equilibrium between a previously described rigid, locked state and a newly characterized, highly flexible, unlocked state. We further establish that maximal electron flux through CPR is conditioned by adjustable stability of the locked-state domain interface under resting conditions. This is rationalized by a kinetic scheme coupling rapid conformational sampling and slow chemical reaction rates. Regulated domain interface stability associated with fast stochastic domain contacts during the catalytic cycle thus provides, to our knowledge, a new paradigm for improving our understanding of multidomain enzyme function.
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35
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Evolution of NADPH-cytochrome P450 oxidoreductases (POR) in Apiales - POR 1 is missing. Mol Phylogenet Evol 2016; 98:21-8. [PMID: 26854662 DOI: 10.1016/j.ympev.2016.01.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 10/19/2015] [Accepted: 01/25/2016] [Indexed: 01/08/2023]
Abstract
The NADPH-dependent cytochrome P450 oxidoreductase (POR) is the obligate electron donor to eukaryotic microsomal cytochromes P450 enzymes. The number of PORs within plant species is limited to one to four isoforms, with the most common being two PORs per plant. These enzymes provide electrons to a huge number of different cytochromes P450s (from 50 to several hundred within one plant). Within the eudicotyledons, PORs can be divided into two major clades, POR 1 and POR 2. Based on our own sequencing analysis and publicly available data, we have identified 45 PORs from the angiosperm order Apiales. These were subjected to a phylogenetic analysis along with 237 other publicly available (NCBI and oneKP) POR sequences found within the clade Asterids. Here, we show that the order Apiales only harbor members of the POR 2 clade, which are further divided into two distinct subclades. This is in contrast to most other eudicotyledon orders that have both POR 1 and POR 2. This suggests that through gene duplications and one gene deletion, Apiales only contain members of the POR 2 clade. Three POR 2 isoforms from Thapsia garganica L., Apiaceae, were all full-length in an Illumina root transcriptome dataset (available from the SRA at NCBI). All three genes were shown to be functional upon reconstitution into nanodiscs, confirming that none of the isoforms are pseudogenes.
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36
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Moses M, Hedegård P, Hatzakis N. Quantification of Functional Dynamics of Membrane Proteins Reconstituted in Nanodiscs Membranes by Single Turnover Functional Readout. Methods Enzymol 2016; 581:227-256. [DOI: 10.1016/bs.mie.2016.08.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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37
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Bertram N, Laursen T, Barker R, Bavishi K, Møller B, Cárdenas M. Nanodisc Films for Membrane Protein Studies by Neutron Reflection: Effect of the Protein Scaffold Choice. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:8386-91. [PMID: 26172514 PMCID: PMC4528776 DOI: 10.1021/acs.langmuir.5b00936] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 07/05/2015] [Indexed: 06/04/2023]
Abstract
Nanodisc films are a promising approach to study the equilibrium conformation of membrane bound proteins in native-like environment. Here we compare nanodisc formation for NADPH-dependent cytochrome P450 oxidoreductase (POR) using two different scaffold proteins, MSP1D1 and MSP1E3D1. Despite the increased stability of POR loaded MSP1E3D1 based nanodiscs in comparison to MSP1D1 based nanodiscs, neutron reflection at the silicon-solution interface showed that POR loaded MSP1E3D1 based nanodisc films had poor surface coverage. This was the case, even when incubation was carried out under conditions that typically gave high coverage for empty nanodiscs. The low surface coverage affects the embedded POR coverage in the nanodisc film and limits the structural information that can be extracted from membrane bound proteins within them. Thus, nanodisc reconstitution on the smaller scaffold proteins is necessary for structural studies of membrane bound proteins in nanodisc films.
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Affiliation(s)
- Nicolas Bertram
- Nano-Science
Center and Department of Chemistry, Faculty of Science, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Tomas Laursen
- Plant Biochemistry Laboratory and VILLUM research
center of excellence “Plant
Plasticity”, Department of Plant
and Environmental Science, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- Center of
Synthetic Biology “bioSYNergy”, University of Copenhagen, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Denmark
| | - Robert Barker
- Institut
Laue Langevin, 71 Avenue
des Martyrs − CS 20156, 38042 Grenoble Cedex 9, France
| | - Krutika Bavishi
- Plant Biochemistry Laboratory and VILLUM research
center of excellence “Plant
Plasticity”, Department of Plant
and Environmental Science, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- Center of
Synthetic Biology “bioSYNergy”, University of Copenhagen, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Denmark
| | - Birger
Lindberg Møller
- Plant Biochemistry Laboratory and VILLUM research
center of excellence “Plant
Plasticity”, Department of Plant
and Environmental Science, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- Carlsberg
Laboratory, 10 Gamle
Carlsberg Vej, DK-1799 Copenhagen V, Denmark
- Center of
Synthetic Biology “bioSYNergy”, University of Copenhagen, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Denmark
| | - Marité Cárdenas
- Nano-Science
Center and Department of Chemistry, Faculty of Science, University of Copenhagen, DK-2200, Copenhagen, Denmark
- Malmo
University, Department of Biomedical Sciences
and Biofilm—Research Centre for Biointerfaces, Health &
Society, 20506 Malmo, Sweden
- Center of
Synthetic Biology “bioSYNergy”, University of Copenhagen, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Denmark
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38
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Malhotra K, Alder NN. Advances in the use of nanoscale bilayers to study membrane protein structure and function. Biotechnol Genet Eng Rev 2015; 30:79-93. [PMID: 25023464 DOI: 10.1080/02648725.2014.921502] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Within the last decade, nanoscale lipid bilayers have emerged as powerful experimental systems in the analysis of membrane proteins (MPs) for both basic and applied research. These discoidal lipid lamellae are stabilized by annuli of specially engineered amphipathic polypeptides (nanodiscs) or polymers (SMALPs/Lipodisqs®). As biomembrane mimetics, they are well suited for the reconstitution of MPs within a controlled lipid environment. Moreover, because they are water-soluble, they are amenable to solution-based biochemical and biophysical experimentation. Hence, due to their solubility, size, stability, and monodispersity, nanoscale lipid bilayers offer technical advantages over more traditional MP analytic approaches such as detergent solubilization and reconstitution into lipid vesicles. In this article, we review some of the most recent advances in the synthesis of polypeptide- and polymer-bound nanoscale lipid bilayers and their application in the study of MP structure and function.
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Affiliation(s)
- Ketan Malhotra
- a Department of Molecular and Cell Biology , University of Connecticut , Storrs , CT 06269 , USA
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Laursen T, Møller BL, Bassard JE. Plasticity of specialized metabolism as mediated by dynamic metabolons. TRENDS IN PLANT SCIENCE 2015; 20:20-32. [PMID: 25435320 DOI: 10.1016/j.tplants.2014.11.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 10/24/2014] [Accepted: 11/07/2014] [Indexed: 05/02/2023]
Abstract
The formation of specialized metabolites enables plants to respond to biotic and abiotic stresses, but requires the sequential action of multiple enzymes. To facilitate swift production and to avoid leakage of potentially toxic and labile intermediates, many of the biosynthetic pathways are thought to organize in multienzyme clusters termed metabolons. Dynamic assembly and disassembly enable the plant to rapidly switch the product profile and thereby prioritize its resources. The lifetime of metabolons is largely unknown mainly due to technological limitations. This review focuses on the factors that facilitate and stimulate the dynamic assembly of metabolons, including microenvironments, noncatalytic proteins, and allosteric regulation. Understanding how plants organize carbon fluxes within their metabolic grids would enable targeted bioengineering of high-value specialized metabolites.
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Affiliation(s)
- Tomas Laursen
- VILLUM Research Center for Plant Plasticity, Center for Synthetic Biology 'bioSYNergy', and Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Birger Lindberg Møller
- VILLUM Research Center for Plant Plasticity, Center for Synthetic Biology 'bioSYNergy', and Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark; Carlsberg Laboratory, 10 Gamle Carlsberg Vej, DK-1799 Copenhagen V, Denmark.
| | - Jean-Etienne Bassard
- VILLUM Research Center for Plant Plasticity, Center for Synthetic Biology 'bioSYNergy', and Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark
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Bavishi K, Hatzakis NS. Shedding light on protein folding, structural and functional dynamics by single molecule studies. Molecules 2014; 19:19407-34. [PMID: 25429564 PMCID: PMC6272019 DOI: 10.3390/molecules191219407] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 11/07/2014] [Accepted: 11/12/2014] [Indexed: 11/16/2022] Open
Abstract
The advent of advanced single molecule measurements unveiled a great wealth of dynamic information revolutionizing our understanding of protein dynamics and behavior in ways unattainable by conventional bulk assays. Equipped with the ability to record distribution of behaviors rather than the mean property of a population, single molecule measurements offer observation and quantification of the abundance, lifetime and function of multiple protein states. They also permit the direct observation of the transient and rarely populated intermediates in the energy landscape that are typically averaged out in non-synchronized ensemble measurements. Single molecule studies have thus provided novel insights about how the dynamic sampling of the free energy landscape dictates all aspects of protein behavior; from its folding to function. Here we will survey some of the state of the art contributions in deciphering mechanisms that underlie protein folding, structural and functional dynamics by single molecule fluorescence microscopy techniques. We will discuss a few selected examples highlighting the power of the emerging techniques and finally discuss the future improvements and directions.
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Affiliation(s)
- Krutika Bavishi
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, Center for Synthetic Biology "bioSYNergy", Villum Research Center "Plant Plasticity", University of Copenhagen, Thorvaldsenvej 40, DK-1871 Frederiksberg C, Denmark.
| | - Nikos S Hatzakis
- Bio-Nanotechnology Laboratory, Department of Chemistry, Nano-Science Center, Lundbeck Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, 2100 Copenhagen, Denmark.
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Kandel SE, Lampe JN. Role of protein-protein interactions in cytochrome P450-mediated drug metabolism and toxicity. Chem Res Toxicol 2014; 27:1474-86. [PMID: 25133307 PMCID: PMC4164225 DOI: 10.1021/tx500203s] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
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Through their unique oxidative chemistry,
cytochrome P450 monooxygenases
(CYPs) catalyze the elimination of most drugs and toxins from the
human body. Protein–protein interactions play a critical role
in this process. Historically, the study of CYP–protein interactions
has focused on their electron transfer partners and allosteric mediators,
cytochrome P450 reductase and cytochrome b5. However, CYPs can bind
other proteins that also affect CYP function. Some examples include
the progesterone receptor membrane component 1, damage resistance
protein 1, human and bovine serum albumin, and intestinal fatty acid
binding protein, in addition to other CYP isoforms. Furthermore, disruption
of these interactions can lead to altered paths of metabolism and
the production of toxic metabolites. In this review, we summarize
the available evidence for CYP protein–protein interactions
from the literature and offer a discussion of the potential impact
of future studies aimed at characterizing noncanonical protein–protein
interactions with CYP enzymes.
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Affiliation(s)
- Sylvie E Kandel
- XenoTech, LLC , 16825 West 116th Street, Lenexa, Kansas 66219, United States
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Turunen P, Rowan AE, Blank K. Single-enzyme kinetics with fluorogenic substrates: lessons learnt and future directions. FEBS Lett 2014; 588:3553-63. [DOI: 10.1016/j.febslet.2014.06.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/04/2014] [Accepted: 06/05/2014] [Indexed: 01/05/2023]
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