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Rivett ED, Heo L, Feig M, Hegg EL. Biosynthesis and trafficking of heme o and heme a: new structural insights and their implications for reaction mechanisms and prenylated heme transfer. Crit Rev Biochem Mol Biol 2021; 56:640-668. [PMID: 34428995 DOI: 10.1080/10409238.2021.1957668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Aerobic respiration is a key energy-producing pathway in many prokaryotes and virtually all eukaryotes. The final step of aerobic respiration is most commonly catalyzed by heme-copper oxidases embedded in the cytoplasmic or mitochondrial membrane. The majority of these terminal oxidases contain a prenylated heme (typically heme a or occasionally heme o) in the active site. In addition, many heme-copper oxidases, including mitochondrial cytochrome c oxidases, possess a second heme a cofactor. Despite the critical role of heme a in the electron transport chain, the details of the mechanism by which heme b, the prototypical cellular heme, is converted to heme o and then to heme a remain poorly understood. Recent structural investigations, however, have helped clarify some elements of heme a biosynthesis. In this review, we discuss the insight gained from these advances. In particular, we present a new structural model of heme o synthase (HOS) based on distance restraints from inferred coevolutionary relationships and refined by molecular dynamics simulations that are in good agreement with the experimentally determined structures of HOS homologs. We also analyze the two structures of heme a synthase (HAS) that have recently been solved by other groups. For both HOS and HAS, we discuss the proposed catalytic mechanisms and highlight how new insights into the heme-binding site locations shed light on previously obtained biochemical data. Finally, we explore the implications of the new structural data in the broader context of heme trafficking in the heme a biosynthetic pathway and heme-copper oxidase assembly.
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Affiliation(s)
- Elise D Rivett
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Lim Heo
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Eric L Hegg
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
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Olerinyova A, Sonn-Segev A, Gault J, Eichmann C, Schimpf J, Kopf AH, Rudden LSP, Ashkinadze D, Bomba R, Frey L, Greenwald J, Degiacomi MT, Steinhilper R, Killian JA, Friedrich T, Riek R, Struwe WB, Kukura P. Mass Photometry of Membrane Proteins. Chem 2021; 7:224-236. [PMID: 33511302 PMCID: PMC7815066 DOI: 10.1016/j.chempr.2020.11.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/20/2020] [Accepted: 11/11/2020] [Indexed: 02/07/2023]
Abstract
Integral membrane proteins (IMPs) are biologically highly significant but challenging to study because they require maintaining a cellular lipid-like environment. Here, we explore the application of mass photometry (MP) to IMPs and membrane-mimetic systems at the single-particle level. We apply MP to amphipathic vehicles, such as detergents and amphipols, as well as to lipid and native nanodiscs, characterizing the particle size, sample purity, and heterogeneity. Using methods established for cryogenic electron microscopy, we eliminate detergent background, enabling high-resolution studies of membrane-protein structure and interactions. We find evidence that, when extracted from native membranes using native styrene-maleic acid nanodiscs, the potassium channel KcsA is present as a dimer of tetramers—in contrast to results obtained using detergent purification. Finally, using lipid nanodiscs, we show that MP can help distinguish between functional and non-functional nanodisc assemblies, as well as determine the critical factors for lipid nanodisc formation. We introduce a label-free, single molecule approach for membrane-protein characterization Mass photometry quantifies membrane proteins in different membrane-mimetic systems MP reveals carrier and protein heterogeneity It helps distinguish different functional states of membrane proteins
Membrane proteins are some of the most important biological molecules, carrying out vital functions and being frequent drug targets. Yet, preferring lipid environments and so requiring solubilization, they are challenging to study. Here, we show that mass photometry can characterize the heterogeneity of membrane proteins and the carriers in which they are solubilized. It can also distinguish different functional states of membrane proteins. Our approach thus opens the door to more comprehensive studies of function, structure, and interaction of these critical proteins in their native membrane environment at the single-molecule level.
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Affiliation(s)
- Anna Olerinyova
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Adar Sonn-Segev
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Joseph Gault
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Cédric Eichmann
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Johannes Schimpf
- Institut für Biochemie, Albert-Ludwigs-Universität, Alberstraße 21, 79104 Freiburg im Breisgau, Germany
| | - Adrian H Kopf
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Lucas S P Rudden
- Department of Physics, Durham University, Lower Mountjoy, South Road, Durham DH1 3LE, UK
| | - Dzmitry Ashkinadze
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Radoslaw Bomba
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Lukas Frey
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Jason Greenwald
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Matteo T Degiacomi
- Department of Physics, Durham University, Lower Mountjoy, South Road, Durham DH1 3LE, UK
| | - Ralf Steinhilper
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - J Antoinette Killian
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität, Alberstraße 21, 79104 Freiburg im Breisgau, Germany
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Weston B Struwe
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
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