1
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Djurabekova A, Lasham J, Zdorevskyi O, Zickermann V, Sharma V. Long-range electron proton coupling in respiratory complex I - insights from molecular simulations of the quinone chamber and antiporter-like subunits. Biochem J 2024; 481:499-514. [PMID: 38572757 DOI: 10.1042/bcj20240009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 04/05/2024]
Abstract
Respiratory complex I is a redox-driven proton pump. Several high-resolution structures of complex I have been determined providing important information about the putative proton transfer paths and conformational transitions that may occur during catalysis. However, how redox energy is coupled to the pumping of protons remains unclear. In this article, we review biochemical, structural and molecular simulation data on complex I and discuss several coupling models, including the key unresolved mechanistic questions. Focusing both on the quinone-reductase domain as well as the proton-pumping membrane-bound domain of complex I, we discuss a molecular mechanism of proton pumping that satisfies most experimental and theoretical constraints. We suggest that protonation reactions play an important role not only in catalysis, but also in the physiologically-relevant active/deactive transition of complex I.
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Affiliation(s)
| | - Jonathan Lasham
- Department of Physics, University of Helsinki, Helsinki, Finland
| | | | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Vivek Sharma
- Department of Physics, University of Helsinki, Helsinki, Finland
- HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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2
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Kim H, Saura P, Pöverlein MC, Gamiz-Hernandez AP, Kaila VRI. Quinone Catalysis Modulates Proton Transfer Reactions in the Membrane Domain of Respiratory Complex I. J Am Chem Soc 2023; 145:17075-17086. [PMID: 37490414 PMCID: PMC10416309 DOI: 10.1021/jacs.3c03086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Indexed: 07/27/2023]
Abstract
Complex I is a redox-driven proton pump that drives electron transport chains and powers oxidative phosphorylation across all domains of life. Yet, despite recently resolved structures from multiple organisms, it still remains unclear how the redox reactions in Complex I trigger proton pumping up to 200 Å away from the active site. Here, we show that the proton-coupled electron transfer reactions during quinone reduction drive long-range conformational changes of conserved loops and trans-membrane (TM) helices in the membrane domain of Complex I from Yarrowia lipolytica. We find that the conformational switching triggers a π → α transition in a TM helix (TM3ND6) and establishes a proton pathway between the quinone chamber and the antiporter-like subunits, responsible for proton pumping. Our large-scale (>20 μs) atomistic molecular dynamics (MD) simulations in combination with quantum/classical (QM/MM) free energy calculations show that the helix transition controls the barrier for proton transfer reactions by wetting transitions and electrostatic effects. The conformational switching is enabled by re-arrangements of ion pairs that propagate from the quinone binding site to the membrane domain via an extended network of conserved residues. We find that these redox-driven changes create a conserved coupling network within the Complex I superfamily, with point mutations leading to drastic activity changes and mitochondrial disorders. On a general level, our findings illustrate how catalysis controls large-scale protein conformational changes and enables ion transport across biological membranes.
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Affiliation(s)
- Hyunho Kim
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Patricia Saura
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | | | - Ana P. Gamiz-Hernandez
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Ville R. I. Kaila
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
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3
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Zdorevskyi O, Djurabekova A, Lasham J, Sharma V. Horizontal proton transfer across the antiporter-like subunits in mitochondrial respiratory complex I. Chem Sci 2023; 14:6309-6318. [PMID: 37325138 PMCID: PMC10266447 DOI: 10.1039/d3sc01427d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
Respiratory complex I is a redox-driven proton pump contributing to about 40% of total proton motive force required for mitochondrial ATP generation. Recent high-resolution cryo-EM structural data revealed the positions of several water molecules in the membrane domain of the large enzyme complex. However, it remains unclear how protons flow in the membrane-bound antiporter-like subunits of complex I. Here, we performed multiscale computer simulations on high-resolution structural data to model explicit proton transfer processes in the ND2 subunit of complex I. Our results show protons can travel the entire width of antiporter-like subunits, including at the subunit-subunit interface, parallel to the membrane. We identify a previously unrecognized role of conserved tyrosine residues in catalyzing horizontal proton transfer, and that long-range electrostatic effects assist in reducing energetic barriers of proton transfer dynamics. Results from our simulations warrant a revision in several prevailing proton pumping models of respiratory complex I.
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Affiliation(s)
| | | | - Jonathan Lasham
- Department of Physics, University of Helsinki Helsinki Finland
| | - Vivek Sharma
- Department of Physics, University of Helsinki Helsinki Finland
- HiLIFE Institute of Biotechnology, University of Helsinki Helsinki Finland
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4
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Alkhaldi HA, Vik SB. Analysis of compound heterozygous and homozygous mutations found in peripheral subunits of human respiratory Complex I, NDUFS1, NDUFS2, NDUFS8 and NDUFV1, by modeling in the E. coli enzyme. Mitochondrion 2023; 68:87-104. [PMID: 36462614 PMCID: PMC9805526 DOI: 10.1016/j.mito.2022.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 11/14/2022] [Accepted: 11/26/2022] [Indexed: 12/05/2022]
Abstract
Respiratory Complex I (NADH:ubiquinone oxidoreductase) is composed of 45 subunits, seven mitochondrially-encoded and 38 imported. Mutations in the nuclearly-encoded subunits have been regularly discovered in humans in recent years, and many lead to cardiomyopathy, Leigh Syndrome, and early death. From the literature, we have identified mutations at 17 different sites and constructed 31 mutants in a bacterial model system. Many of these mutations, found in NDUFS1, NDUFS2, NDUFS8, and NDUFV1, map to subunit interfaces, and we hypothesized that they would disrupt assembly of Complex I. The mutations were constructed in the homologous E. coli genes, nuoG, nuoCD, nuoI and nuoF, respectively, and expressed from a plasmid containing all Complex I genes. Membrane vesicles were prepared and rates of deamino-NADH oxidase activity measured, which indicated a range of reduced activity. Some mutants were also analyzed using recently developed assays of assembly, time-delayed expression, and co-immunoprecipitation, which showed that assembly was disrupted. With compound heterozygotes, we determined which mutation was more deleterious. Construction of alanine mutations allowed us to distinguish between phenotypes that were caused by loss of the original amino acid or introduction of the mutant residue.
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Affiliation(s)
- Hind A Alkhaldi
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Steven B Vik
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA.
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5
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Wikström M, Djurabekova A, Sharma V. On the role of ubiquinone in the proton translocation mechanism of respiratory complex I. FEBS Lett 2023; 597:224-236. [PMID: 36180980 DOI: 10.1002/1873-3468.14506] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/23/2022] [Accepted: 09/23/2022] [Indexed: 01/26/2023]
Abstract
Complex I converts oxidoreduction energy into a proton electrochemical gradient across the inner mitochondrial or bacterial cell membrane. This gradient is the primary source of energy for aerobic synthesis of ATP. Oxidation of reduced nicotinamide adenine dinucleotide (NADH) by ubiquinone (Q) yields NAD+ and ubiquinol (QH2 ), which is tightly coupled to translocation of four protons from the negatively to the positively charged side of the membrane. Electrons from NADH oxidation reach the iron-sulfur centre N2 positioned near the bottom of a tunnel that extends circa 30 Å from the membrane domain into the hydrophilic domain of the complex. The tunnel is occupied by ubiquinone, which can take a distal position near the N2 centre or proximal positions closer to the membrane. Here, we review important structural, kinetic and thermodynamic properties of ubiquinone that define its role in complex I function. We suggest that this function exceeds that of a mere substrate or electron acceptor and propose that ubiquinone may be the redox element of complex I coupling electron transfer to proton translocation.
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Affiliation(s)
- Mårten Wikström
- HiLIFE Institute of Biotechnology, University of Helsinki, Finland
| | | | - Vivek Sharma
- HiLIFE Institute of Biotechnology, University of Helsinki, Finland.,Department of Physics, University of Helsinki, Finland
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6
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Alkhaldi HA, Phan DH, Vik SB. Analysis of Human Clinical Mutations of Mitochondrial ND1 in a Bacterial Model System for Complex I. Life (Basel) 2022; 12:1934. [PMID: 36431069 PMCID: PMC9696053 DOI: 10.3390/life12111934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/13/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
The most common causes of mitochondrial dysfunction and disease include mutations in subunits and assembly factors of Complex I. Numerous mutations in the mitochondrial gene ND1 have been identified in humans. Currently, a bacterial model system provides the only method for rapid construction and analysis of mutations in homologs of human ND1. In this report, we have identified nine mutations in human ND1 that are reported to be pathogenic and are located at subunit interfaces. Our hypothesis was that these mutations would disrupt Complex I assembly. Seventeen mutations were constructed in the homologous nuoH gene in an E. coli model system. In addition to the clinical mutations, alanine substitutions were constructed in order to distinguish between a deleterious effect from the introduction of the mutant residue and the loss of the original residue. The mutations were moved to an expression vector containing all thirteen genes of the E. coli nuo operon coding for Complex I. Membrane vesicles were prepared and rates of deamino-NADH oxidase activity and proton translocation were measured. Samples were also tested for assembly by native gel electrophoresis and for expression of NuoH by immunoblotting. A range of outcomes was observed: Mutations at four of the sites allow normal assembly with moderate activity (50−76% of wild type). Mutations at the other sites disrupt assembly and/or activity, and in some cases the outcomes depend upon the amino acid introduced. In general, the outcomes are consistent with the proposed pathogenicity in humans.
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Affiliation(s)
| | | | - Steven B. Vik
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275, USA
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7
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Alkhaldi HA, Vik SB. Subunits E-F-G of E. coli Complex I can form an active complex when expressed alone, but in time-delayed assembly co-expression of B-CD-E-F-G is optimal. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148593. [PMID: 35850264 PMCID: PMC9783743 DOI: 10.1016/j.bbabio.2022.148593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/15/2022] [Accepted: 07/11/2022] [Indexed: 12/27/2022]
Abstract
Respiratory Complex I from E. coli is a proto-type of the mitochondrial enzyme, consisting of a 6-subunit peripheral arm (B-CD-E-F-G-I) and a 7-subunit membrane arm. When subunits E-F-G (N-module), were expressed alone they formed an active complex as determined by co-immunoprecipitation and native gel electrophoresis. When co-expressed with subunits B and CD, only a complex of E-F-G was found. When these five subunits were co-expressed with subunit I and two membrane subunits, A and H, a complex of B-CD-E-F-G-I was membrane-bound, constituting the N- and Q-modules. Assembly of Complex I was also followed by splitting the genes between two plasmids, in three different groupings, and expressing them simultaneously, or with time-delay of expression from one plasmid. When the B-CD-E-F-G genes were co-expressed after a time-delay, assembly was over 90 % of that when the whole operon was expressed together. In summary, E-F-G was the only soluble subcomplex detected in these studies, but assembly was not optimal when these subunits were expressed either first or last. Co-expression of subunits B and CD with E-F-G provided a higher level of assembly, indicating that integrated assembly of N- and Q-modules provides a more efficient pathway.
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Affiliation(s)
- Hind A Alkhaldi
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Steven B Vik
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA.
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8
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Cloning and Organelle Expression of Bamboo Mitochondrial Complex I Subunits Nad1, Nad2, Nad4, and Nad5 in the Yeast Saccharomyces cerevisiae. Int J Mol Sci 2022; 23:ijms23074054. [PMID: 35409414 PMCID: PMC8999482 DOI: 10.3390/ijms23074054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/02/2022] [Accepted: 04/04/2022] [Indexed: 02/04/2023] Open
Abstract
Mitochondrial respiratory complex I catalyzes electron transfer from NADH to ubiquinone and pumps protons from the matrix into the intermembrane space. In particular, the complex I subunits Nad1, Nad2, Nad4, and Nad5, which are encoded by the nad1, nad2, nad4, and nad5 genes, reside at the mitochondrial inner membrane and possibly function as proton (H+) and ion translocators. To understand the individual functional roles of the Nad1, Nad2, Nad4, and Nad5 subunits in bamboo, each cDNA of these four genes was cloned into the pYES2 vector and expressed in the mitochondria of the yeast Saccharomyces cerevisiae. The mitochondrial targeting peptide mt gene (encoding MT) and the egfp marker gene (encoding enhanced green fluorescent protein, EGFP) were fused at the 5'-terminal and 3'-terminal ends, respectively. The constructed plasmids were then transformed into yeast. RNA transcripts and fusion protein expression were observed in the yeast transformants. Mitochondrial localizations of the MT-Nad1-EGFP, MT-Nad2-EGFP, MT-Nad4-EGFP, and MT-Nad5-EGFP fusion proteins were confirmed by fluorescence microscopy. The ectopically expressed bamboo subunits Nad1, Nad2, Nad4, and Nad5 may function in ion translocation, which was confirmed by growth phenotype assays with the addition of different concentrations of K+, Na+, or H+.
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9
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Zhang F, Dang QCL, Vik SB. Human clinical mutations in mitochondrially encoded subunits of Complex I can be successfully modeled in E. coli. Mitochondrion 2022; 64:59-72. [PMID: 35306226 PMCID: PMC9035099 DOI: 10.1016/j.mito.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/21/2022] [Accepted: 03/15/2022] [Indexed: 11/28/2022]
Abstract
Respiratory Complex I is the site of a large fraction of the mutations that appear to cause mitochondrial disease. Seven of its subunits are mitochondrially encoded, and therefore, such mutants are particularly difficult to construct in cell-culture model systems. We have selected 13 human clinical mutations found in ND2, ND3, ND4, ND4L, ND5 and ND6 that are generally found at subunit interfaces, and not in critical residues. These mutations have been modeled in E. coli subunits of Complex I, nuoN, nuoA, nuoM, nuoK, nuoL, and nuoJ, respectively. All mutants were expressed from a plasmid encoding the entire nuo operon, and membrane vesicles were analyzed for deamino-NADH oxidase activity, and proton translocation activity. ND5 mutants were also analyzed using a time-delayed expression system, recently described by this lab. Other mutants were analyzed for the ability to associate in subcomplexes, after expression of subsets of the genes. For most mutants there was a positive correlation between those that were previously determined to be pathogenic, or likely to be pathogenic, and those that we found with compromised Complex I activity or subunit interactions in E. coli. In conclusion, this approach provides another way to explore the deleterious effects of human mitochondrial mutations, and it can contribute to molecular understanding of such mutations.
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Affiliation(s)
- Fang Zhang
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Quynh-Chi L Dang
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Steven B Vik
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA.
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10
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Kaur D, Khaniya U, Zhang Y, Gunner MR. Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient. Front Chem 2021; 9:660954. [PMID: 34211960 PMCID: PMC8239185 DOI: 10.3389/fchem.2021.660954] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome c oxidase (CcO), are reviewed. These proteins all use water filled proton transfer paths. The proton pumps, that move protons uphill from low to high concentration compartments, also utilize Proton Loading Sites (PLS), that transiently load and unload protons and gates, which block backflow of protons. PLS and gates should be synchronized so PLS proton affinity is high when the gate opens to the side with few protons and low when the path is open to the high concentration side. Proton transfer paths in the proteins we describe have different design features. Linear paths are seen with a unique entry and exit and a relatively straight path between them. Alternatively, paths can be complex with a tangle of possible routes. Likewise, PLS can be a single residue that changes protonation state or a cluster of residues with multiple charge and tautomer states.
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Affiliation(s)
- Divya Kaur
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY, United States.,Department of Physics, City College of New York, New York, NY, United States
| | - Umesh Khaniya
- Department of Physics, City College of New York, New York, NY, United States.,Department of Physics, The Graduate Center, City University of New York, New York, NY, United States
| | - Yingying Zhang
- Department of Physics, City College of New York, New York, NY, United States.,Department of Physics, The Graduate Center, City University of New York, New York, NY, United States
| | - M R Gunner
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY, United States.,Department of Physics, City College of New York, New York, NY, United States.,Department of Physics, The Graduate Center, City University of New York, New York, NY, United States
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11
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Jarman OD, Biner O, Wright JJ, Hirst J. Paracoccus denitrificans: a genetically tractable model system for studying respiratory complex I. Sci Rep 2021; 11:10143. [PMID: 33980947 PMCID: PMC8115037 DOI: 10.1038/s41598-021-89575-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/27/2021] [Indexed: 02/03/2023] Open
Abstract
Mitochondrial complex I (NADH:ubiquinone oxidoreductase) is a crucial metabolic enzyme that couples the free energy released from NADH oxidation and ubiquinone reduction to the translocation of four protons across the inner mitochondrial membrane, creating the proton motive force for ATP synthesis. The mechanism by which the energy is captured, and the mechanism and pathways of proton pumping, remain elusive despite recent advances in structural knowledge. Progress has been limited by a lack of model systems able to combine functional and structural analyses with targeted mutagenic interrogation throughout the entire complex. Here, we develop and present the α-proteobacterium Paracoccus denitrificans as a suitable bacterial model system for mitochondrial complex I. First, we develop a robust purification protocol to isolate highly active complex I by introducing a His6-tag on the Nqo5 subunit. Then, we optimize the reconstitution of the enzyme into liposomes, demonstrating its proton pumping activity. Finally, we develop a strain of P. denitrificans that is amenable to complex I mutagenesis and create a catalytically inactive variant of the enzyme. Our model provides new opportunities to disentangle the mechanism of complex I by combining mutagenesis in every subunit with established interrogative biophysical measurements on both the soluble and membrane bound enzymes.
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Affiliation(s)
- Owen D. Jarman
- grid.5335.00000000121885934The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
| | - Olivier Biner
- grid.5335.00000000121885934The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
| | - John J. Wright
- grid.5335.00000000121885934The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
| | - Judy Hirst
- grid.5335.00000000121885934The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
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12
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Zhang F, Vik SB. Analysis of the assembly pathway for membrane subunits of Complex I reveals that subunit L (ND5) can assemble last in E. coli. BBA ADVANCES 2021; 1. [DOI: 10.1016/j.bbadva.2021.100027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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13
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Röpke M, Saura P, Riepl D, Pöverlein MC, Kaila VRI. Functional Water Wires Catalyze Long-Range Proton Pumping in the Mammalian Respiratory Complex I. J Am Chem Soc 2020; 142:21758-21766. [PMID: 33325238 PMCID: PMC7785131 DOI: 10.1021/jacs.0c09209] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The respiratory complex I is a gigantic
(1 MDa) redox-driven proton
pump that reduces the ubiquinone pool and generates proton motive
force to power ATP synthesis in mitochondria. Despite resolved molecular
structures and biochemical characterization of the enzyme from multiple
organisms, its long-range (∼300 Å) proton-coupled electron
transfer (PCET) mechanism remains unsolved. We employ here microsecond
molecular dynamics simulations to probe the dynamics of the mammalian
complex I in combination with hybrid quantum/classical (QM/MM) free
energy calculations to explore how proton pumping reactions are triggered
within its 200 Å wide membrane domain. Our simulations predict
extensive hydration dynamics of the antiporter-like subunits in complex
I that enable lateral proton transfer reactions on a microsecond time
scale. We further show how the coupling between conserved ion pairs
and charged residues modulate the proton transfer dynamics, and how
transmembrane helices and gating residues control the hydration process.
Our findings suggest that the mammalian complex I pumps protons by
tightly linked conformational and electrostatic coupling principles.
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Affiliation(s)
- Michael Röpke
- Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748 Garching, Germany
| | - Patricia Saura
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Daniel Riepl
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Maximilian C Pöverlein
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748 Garching, Germany
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14
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Mühlbauer ME, Saura P, Nuber F, Di Luca A, Friedrich T, Kaila VRI. Water-Gated Proton Transfer Dynamics in Respiratory Complex I. J Am Chem Soc 2020; 142:13718-13728. [PMID: 32643371 PMCID: PMC7659035 DOI: 10.1021/jacs.0c02789] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The respiratory complex I transduces
redox energy into an electrochemical
proton gradient in aerobic respiratory chains, powering energy-requiring
processes in the cell. However, despite recently resolved molecular
structures, the mechanism of this gigantic enzyme remains poorly understood.
By combining large-scale quantum and classical simulations with site-directed
mutagenesis and biophysical experiments, we show here how the conformational
state of buried ion-pairs and water molecules control the protonation
dynamics in the membrane domain of complex I and establish evolutionary
conserved long-range coupling elements. We suggest that an electrostatic
wave propagates in forward and reverse directions across the 200 Å
long membrane domain during enzyme turnover, without significant dissipation
of energy. Our findings demonstrate molecular principles that enable
efficient long-range proton–electron coupling (PCET) and how
perturbation of this PCET machinery may lead to development of mitochondrial
disease.
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Affiliation(s)
- Max E Mühlbauer
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748 Garching, Germany
| | - Patricia Saura
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748 Garching, Germany
| | - Franziska Nuber
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Andrea Di Luca
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748 Garching, Germany
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748 Garching, Germany
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15
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Khaniya U, Gupta C, Cai X, Mao J, Kaur D, Zhang Y, Singharoy A, Gunner MR. Hydrogen bond network analysis reveals the pathway for the proton transfer in the E-channel of T. thermophilus Complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148240. [PMID: 32531220 DOI: 10.1016/j.bbabio.2020.148240] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 05/19/2020] [Accepted: 06/03/2020] [Indexed: 10/24/2022]
Abstract
Complex I, NADH-ubiquinone oxidoreductase, is the first enzyme in the mitochondrial and bacterial aerobic respiratory chain. It pumps four protons through four transiently open pathways from the high pH, negative, N-side of the membrane to the positive, P-side driven by the exergonic transfer of electrons from NADH to a quinone. Three protons transfer through subunits descended from antiporters, while the fourth, E-channel is unique. The path through the E-channel is determined by a network analysis of hydrogen bonded pathways obtained by Monte Carlo sampling of protonation states, polar hydrogen orientation and water occupancy. Input coordinates are derived from molecular dynamics trajectories comparing oxidized, reduced (dihydro) and no menaquinone-8 (MQ). A complex proton transfer path from the N- to the P-side is found consisting of six clusters of highly connected hydrogen-bonded residues. The network connectivity depends on the presence of quinone and its redox state, supporting a role for this cofactor in coupling electron and proton transfers. The N-side is more organized with MQ-bound complex I facilitating proton entry, while the P-side is more connected in the apo-protein, facilitating proton exit. Subunit Nqo8 forms the core of the E channel; Nqo4 provides the N-side entry, Nqo7 and then Nqo10 join the pathway in the middle, while Nqo11 contributes to the P-side exit.
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Affiliation(s)
- Umesh Khaniya
- Department of Physics, City College of New York, New York 10031, USA; Department of Physics, The Graduate Center, City University of New York, New York 10016, USA
| | - Chitrak Gupta
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA; Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Xiuhong Cai
- Department of Physics, City College of New York, New York 10031, USA; Department of Physics, The Graduate Center, City University of New York, New York 10016, USA
| | - Junjun Mao
- Department of Physics, City College of New York, New York 10031, USA
| | - Divya Kaur
- Department of Physics, City College of New York, New York 10031, USA; Department of Chemistry, The Graduate Center, City University of New York, New York 10016, USA
| | - Yingying Zhang
- Department of Physics, City College of New York, New York 10031, USA; Department of Physics, The Graduate Center, City University of New York, New York 10016, USA
| | - Abhishek Singharoy
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA; Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - M R Gunner
- Department of Physics, City College of New York, New York 10031, USA; Department of Physics, The Graduate Center, City University of New York, New York 10016, USA; Department of Chemistry, The Graduate Center, City University of New York, New York 10016, USA.
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16
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Kaila VRI. Long-range proton-coupled electron transfer in biological energy conversion: towards mechanistic understanding of respiratory complex I. J R Soc Interface 2019; 15:rsif.2017.0916. [PMID: 29643224 PMCID: PMC5938582 DOI: 10.1098/rsif.2017.0916] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/13/2018] [Indexed: 12/20/2022] Open
Abstract
Biological energy conversion is driven by efficient enzymes that capture, store and transfer protons and electrons across large distances. Recent advances in structural biology have provided atomic-scale blueprints of these types of remarkable molecular machinery, which together with biochemical, biophysical and computational experiments allow us to derive detailed energy transduction mechanisms for the first time. Here, I present one of the most intricate and least understood types of biological energy conversion machinery, the respiratory complex I, and how its redox-driven proton-pump catalyses charge transfer across approximately 300 Å distances. After discussing the functional elements of complex I, a putative mechanistic model for its action-at-a-distance effect is presented, and functional parallels are drawn to other redox- and light-driven ion pumps.
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Affiliation(s)
- Ville R I Kaila
- Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, Garching, Germany
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17
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Haapanen O, Djurabekova A, Sharma V. Role of Second Quinone Binding Site in Proton Pumping by Respiratory Complex I. Front Chem 2019; 7:221. [PMID: 31024903 PMCID: PMC6465577 DOI: 10.3389/fchem.2019.00221] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 03/21/2019] [Indexed: 12/22/2022] Open
Abstract
Respiratory complex I performs the reduction of quinone (Q) to quinol (QH2) and pumps protons across the membrane. Structural data on complex I have provided spectacular insights into the electron and proton transfer paths, as well as into the long (~30 Å) and unique substrate binding channel. However, due to missing structural information on Q binding modes, it remains unclear how Q reduction drives long range (~20 nm) redox-coupled proton pumping in complex I. Here we applied multiscale computational approaches to study the dynamics and redox chemistry of Q and QH2. Based on tens of microseconds of atomistic molecular dynamics (MD) simulations of bacterial and mitochondrial complex I, we find that the dynamics of Q is remarkably rapid and it diffuses from the N2 binding site to another stable site near the entrance of the Q channel in microseconds. Analysis of simulation trajectories also reveal the presence of yet another Q binding site 25–30 Å from the N2 center, which is in remarkable agreement with the electron density observed in recent cryo electron microscopy structure of complex I from Yarrowia lipolytica. Quantum chemical computations on the two Q binding sites closer to the entrance of the Q tunnel reveal redox-coupled protonation reactions that may be important in driving the proton pump of complex I.
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Affiliation(s)
- Outi Haapanen
- Department of Physics, University of Helsinki, Helsinki, Finland
| | | | - Vivek Sharma
- Department of Physics, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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18
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A modeling and simulation perspective on the mechanism and function of respiratory complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:510-523. [DOI: 10.1016/j.bbabio.2018.04.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/03/2018] [Accepted: 04/10/2018] [Indexed: 12/12/2022]
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19
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Di Luca A, Mühlbauer ME, Saura P, Kaila VRI. How inter-subunit contacts in the membrane domain of complex I affect proton transfer energetics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:734-741. [PMID: 29883589 DOI: 10.1016/j.bbabio.2018.06.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 05/08/2018] [Accepted: 06/02/2018] [Indexed: 10/14/2022]
Abstract
The respiratory complex I is a redox-driven proton pump that employs the free energy released from quinone reduction to pump protons across its complete ca. 200 Å wide membrane domain. Despite recently resolved structures and molecular simulations, the exact mechanism for the proton transport process remains unclear. Here we combine large-scale molecular simulations with quantum chemical density functional theory (DFT) models to study how contacts between neighboring antiporter-like subunits in the membrane domain of complex I affect the proton transfer energetics. Our combined results suggest that opening of conserved Lys/Glu ion pairs within each antiporter-like subunit modulates the barrier for the lateral proton transfer reactions. Our work provides a mechanistic suggestion for key coupling effects in the long-range force propagation process of complex I.
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Affiliation(s)
- Andrea Di Luca
- Department Chemie, Technische Universität München, Lichtenbergstr. 4, Garching, D-85747, Germany
| | - Max E Mühlbauer
- Department Chemie, Technische Universität München, Lichtenbergstr. 4, Garching, D-85747, Germany
| | - Patricia Saura
- Department Chemie, Technische Universität München, Lichtenbergstr. 4, Garching, D-85747, Germany
| | - Ville R I Kaila
- Department Chemie, Technische Universität München, Lichtenbergstr. 4, Garching, D-85747, Germany.
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20
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Haapanen O, Sharma V. Role of water and protein dynamics in proton pumping by respiratory complex I. Sci Rep 2017; 7:7747. [PMID: 28798393 PMCID: PMC5552823 DOI: 10.1038/s41598-017-07930-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/05/2017] [Indexed: 11/29/2022] Open
Abstract
Membrane bound respiratory complex I is the key enzyme in the respiratory chains of bacteria and mitochondria, and couples the reduction of quinone to the pumping of protons across the membrane. Recently solved crystal or electron microscopy structures of bacterial and mitochondrial complexes have provided significant insights into the electron and proton transfer pathways. However, due to large spatial separation between the electron and proton transfer routes, the molecular mechanism of coupling remains unclear. Here, based on atomistic molecular dynamics simulations performed on the entire structure of complex I from Thermus thermophilus, we studied the hydration of the quinone-binding site and the membrane-bound subunits. The data from simulations show rapid diffusion of water molecules in the protein interior, and formation of hydrated regions in the three antiporter-type subunits. An unexpected water-protein based connectivity between the middle of the Q-tunnel and the fourth proton channel is also observed. The protonation-state dependent dynamics of key acidic residues in the Nqo8 subunit suggest that the latter may be linked to redox-coupled proton pumping in complex I. We propose that in complex I the proton and electron transfer paths are not entirely separate, instead the nature of coupling may in part be ‘direct’.
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Affiliation(s)
- Outi Haapanen
- Department of Physics, University of Helsinki, P. O. Box 64, FI-00014, Helsinki, Finland.,Department of Physics, Tampere University of Technology, P. O. Box 692, FI-33101, Tampere, Finland
| | - Vivek Sharma
- Department of Physics, University of Helsinki, P. O. Box 64, FI-00014, Helsinki, Finland. .,Department of Physics, Tampere University of Technology, P. O. Box 692, FI-33101, Tampere, Finland. .,Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
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21
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Abstract
Complex I functions as the initial electron acceptor in aerobic respiratory chains of most organisms. This gigantic redox-driven enzyme employs the energy from quinone reduction to pump protons across its complete approximately 200-Å membrane domain, thermodynamically driving synthesis of ATP. Despite recently resolved structures from several species, the molecular mechanism by which complex I catalyzes this long-range proton-coupled electron transfer process, however, still remains unclear. We perform here large-scale classical and quantum molecular simulations to study the function of the proton pump in complex I from Thermus thermophilus The simulations suggest that proton channels are established at symmetry-related locations in four subunits of the membrane domain. The channels open up by formation of quasi one-dimensional water chains that are sensitive to the protonation states of buried residues at structurally conserved broken helix elements. Our combined data provide mechanistic insight into long-range coupling effects and predictions for site-directed mutagenesis experiments.
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22
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Tursun A, Zhu S, Vik SB. Probing the proton channels in subunit N of Complex I from Escherichia coli through intra-subunit cross-linking. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1840-1848. [PMID: 27632419 DOI: 10.1016/j.bbabio.2016.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 08/19/2016] [Accepted: 09/09/2016] [Indexed: 10/21/2022]
Abstract
Respiratory Complex I appears to have 4 sites for proton translocation, which are coupled to the oxidation of NADH and reduction of coenzyme Q. The proton pathways are thought to be made of offset half-channels that connect to the membrane surfaces, and are connected by a horizontal path through the center of the membrane. In this study of the enzyme from Escherichia coli, subunit N, containing one of the sites, was targeted. Pairs of cysteine residues were introduced into neighboring α-helices along the proposed proton pathways. In an effort to constrain conformational changes that might occur during proton translocation, we attempted to form disulfide bonds or methanethiosulfonate bridges between two engineered cysteine residues. Cysteine modification was inferred by the inability of PEG-maleimide to shift the electrophoretic mobility of subunit N, which will occur upon reaction with free sulfhydryl groups. After the cross-linking treatment, NADH oxidase and NADH-driven proton translocation were measured. Ten different pairs of cysteine residues showed evidence of cross-linking. The most significant loss of enzyme activity was seen for residues near the essential Lys 395. This residue is positioned between the proposed proton half-channel to the periplasm and the horizontal connection through subunit N, and is also near the essential Glu 144 of subunit M. The results suggest important conformational changes in this region for the delivery of protons to the periplasm, or for coupling the actions of subunit N to subunit M.
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Affiliation(s)
- Ablat Tursun
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Shaotong Zhu
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Steven B Vik
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA.
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23
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Sperling E, Górecki K, Drakenberg T, Hägerhäll C. Functional Differentiation of Antiporter-Like Polypeptides in Complex I; a Site-Directed Mutagenesis Study of Residues Conserved in MrpA and NuoL but Not in MrpD, NuoM, and NuoN. PLoS One 2016; 11:e0158972. [PMID: 27391676 PMCID: PMC4938563 DOI: 10.1371/journal.pone.0158972] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/26/2016] [Indexed: 01/29/2023] Open
Abstract
It has long been known that the three largest subunits in the membrane domain (NuoL, NuoM and NuoN) of complex I are homologous to each other, as well as to two subunits (MrpA and MrpD) from a Na+/H+ antiporter, Mrp. MrpA and NuoL are more similar to each other and the same is true for MrpD and NuoN. This suggests a functional differentiation which was proven experimentally in a deletion strain model system, where NuoL could restore the loss of MrpA, but not that of MrpD and vice versa. The simplest explanation for these observations was that the MrpA and MrpD proteins are not antiporters, but rather single subunit ion channels that together form an antiporter. In this work our focus was on a set of amino acid residues in helix VIII, which are only conserved in NuoL and MrpA (but not in any of the other antiporter-like subunits.) and to compare their effect on the function of these two proteins. By combining complementation studies in B. subtilis and 23Na-NMR, response of mutants to high sodium levels were tested. All of the mutants were able to cope with high salt levels; however, all but one mutation (M258I/M225I) showed differences in the efficiency of cell growth and sodium efflux. Our findings showed that, although very similar in sequence, NuoL and MrpA seem to differ on the functional level. Nonetheless the studied mutations gave rise to interesting phenotypes which are of interest in complex I research.
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Affiliation(s)
- Eva Sperling
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Lund, Sweden
- * E-mail:
| | - Kamil Górecki
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Lund, Sweden
| | - Torbjörn Drakenberg
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, Lund, Sweden
| | - Cecilia Hägerhäll
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Lund, Sweden
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24
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Zhu S, Canales A, Bedair M, Vik SB. Loss of Complex I activity in the Escherichia coli enzyme results from truncating the C-terminus of subunit K, but not from cross-linking it to subunits N or L. J Bioenerg Biomembr 2016; 48:325-33. [PMID: 26931547 DOI: 10.1007/s10863-016-9655-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 02/25/2016] [Indexed: 12/16/2022]
Abstract
Complex I is a multi-subunit enzyme of the respiratory chain with seven core subunits in its membrane arm (A, H, J, K, L, M, and N). In the enzyme from Escherichia coli the C-terminal ten amino acids of subunit K lie along the lateral helix of subunit L, and contribute to a junction of subunits K, L and N on the cytoplasmic surface. Using double cysteine mutagenesis, the cross-linking of subunit K (R99C) to either subunit L (K581C) or subunit N (T292C) was attempted. A partial yield of cross-linked product had no effect on the activity of the enzyme, or on proton translocation, suggesting that the C-terminus of subunit K has no dynamic role in function. To further elucidate the role of subunit K genetic deletions were constructed at the C-terminus. Upon the serial deletion of the last 4 residues of the C-terminus of subunit K, various results were obtained. Deletion of one amino acid had little effect on the activity of Complex I, but deletions of 2 or more amino acids led to total loss of enzyme activity and diminished levels of subunits L, M, and N in preparations of membrane vesicles. Together these results suggest that while the C-terminus of subunit K has no dynamic role in energy transduction by Complex I, it is vital for the correct assembly of the enzyme.
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Affiliation(s)
- Shaotong Zhu
- Department of Biological Sciences, Southern Methodist University, Dallas, TX, 75275-0376, USA.,Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Alejandra Canales
- Department of Biological Sciences, Southern Methodist University, Dallas, TX, 75275-0376, USA.,Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA
| | - Mai Bedair
- Department of Biological Sciences, Southern Methodist University, Dallas, TX, 75275-0376, USA.,University of Texas Southwestern Medical School, Dallas, TX, 75390, USA
| | - Steven B Vik
- Department of Biological Sciences, Southern Methodist University, Dallas, TX, 75275-0376, USA.
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25
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Molecular simulation and modeling of complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:915-21. [PMID: 26780586 DOI: 10.1016/j.bbabio.2016.01.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/06/2016] [Accepted: 01/07/2016] [Indexed: 11/23/2022]
Abstract
Molecular modeling and molecular dynamics simulations play an important role in the functional characterization of complex I. With its large size and complicated function, linking quinone reduction to proton pumping across a membrane, complex I poses unique modeling challenges. Nonetheless, simulations have already helped in the identification of possible proton transfer pathways. Simulations have also shed light on the coupling between electron and proton transfer, thus pointing the way in the search for the mechanistic principles underlying the proton pump. In addition to reviewing what has already been achieved in complex I modeling, we aim here to identify pressing issues and to provide guidance for future research to harness the power of modeling in the functional characterization of complex I. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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26
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Adaptation of the Mitochondrial Genome in Cephalopods: Enhancing Proton Translocation Channels and the Subunit Interactions. PLoS One 2015; 10:e0135405. [PMID: 26285039 PMCID: PMC4540416 DOI: 10.1371/journal.pone.0135405] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/21/2015] [Indexed: 01/25/2023] Open
Abstract
Mitochondrial protein-coding genes (mt genes) encode subunits forming complexes of crucial cellular pathways, including those involved in the vital process of oxidative phosphorylation (OXPHOS). Despite the vital role of the mitochondrial genome (mt genome) in the survival of organisms, little is known with respect to its adaptive implications within marine invertebrates. The molluscan Class Cephalopoda is represented by a marine group of species known to occupy contrasting environments ranging from the intertidal to the deep sea, having distinct metabolic requirements, varied body shapes and highly advanced visual and nervous systems that make them highly competitive and successful worldwide predators. Thus, cephalopods are valuable models for testing natural selection acting on their mitochondrial subunits (mt subunits). Here, we used concatenated mt genes from 17 fully sequenced mt genomes of diverse cephalopod species to generate a robust mitochondrial phylogeny for the Class Cephalopoda. We followed an integrative approach considering several branches of interest–covering cephalopods with distinct morphologies, metabolic rates and habitats–to identify sites under positive selection and localize them in the respective protein alignment and/or tridimensional structure of the mt subunits. Our results revealed significant adaptive variation in several mt subunits involved in the energy production pathway of cephalopods: ND5 and ND6 from Complex I, CYTB from Complex III, COX2 and COX3 from Complex IV, and in ATP8 from Complex V. Furthermore, we identified relevant sites involved in protein-interactions, lining proton translocation channels, as well as disease/deficiencies related sites in the aforementioned complexes. A particular case, revealed by this study, is the involvement of some positively selected sites, found in Octopoda lineage in lining proton translocation channels (site 74 from ND5) and in interactions between subunits (site 507 from ND5) of Complex I.
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27
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Zhu S, Vik SB. Constraining the Lateral Helix of Respiratory Complex I by Cross-linking Does Not Impair Enzyme Activity or Proton Translocation. J Biol Chem 2015; 290:20761-20773. [PMID: 26134569 DOI: 10.1074/jbc.m115.660381] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Indexed: 12/19/2022] Open
Abstract
Complex I (NADH:ubiquinone oxidoreductase) is a multisubunit, membrane-bound enzyme of the respiratory chain. The energy from NADH oxidation in the peripheral region of the enzyme is used to drive proton translocation across the membrane. One of the integral membrane subunits, nuoL in Escherichia coli, has an unusual lateral helix of ∼75 residues that lies parallel to the membrane surface and has been proposed to play a mechanical role as a piston during proton translocation (Efremov, R. G., Baradaran, R., and Sazanov, L. A. (2010) Nature 465, 441-445). To test this hypothesis we have introduced 11 pairs of cysteine residues into Complex I; in each pair one is in the lateral helix, and the other is in a nearby region of subunit N, M, or L. The double mutants were treated with Cu(2+) ions or with bi-functional methanethiosulfonate reagents to catalyze cross-link formation in membrane vesicles. The yields of cross-linked products were typically 50-90%, as judged by immunoblotting, but in no case did the activity of Complex I decrease by >10-20%, as indicated by deamino-NADH oxidase activity or rates of proton translocation. In contrast, several pairs of cysteine residues introduced at other interfaces of N:M and M:L subunits led to significant loss of activity, in particular, in the region of residue Glu-144 of subunit M. The results do not support the hypothesis that the lateral helix of subunit L functions like a piston, but rather, they suggest that conformational changes might be transmitted more directly through the functional residues of the proton translocation apparatus.
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Affiliation(s)
- Shaotong Zhu
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
| | - Steven B Vik
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376.
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28
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Wikström M, Sharma V, Kaila VRI, Hosler JP, Hummer G. New Perspectives on Proton Pumping in Cellular Respiration. Chem Rev 2015; 115:2196-221. [DOI: 10.1021/cr500448t] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mårten Wikström
- Institute
of Biotechnology, University of Helsinki, Biocenter 3 (Viikinkaari 1), PB
65, Helsinki 00014, Finland
| | - Vivek Sharma
- Department
of Physics, Tampere University of Technology, Korkeakoulunkatu 3, Tampere 33720, Finland
| | - Ville R. I. Kaila
- Department
Chemie, Technische Universität München, Lichtenbergstraße 4, D-85748 Garching, Germany
| | - Jonathan P. Hosler
- Department
of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi 39216, United States
| | - Gerhard Hummer
- Department
of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße
3, 60438 Frankfurt
am Main, Germany
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29
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Schulte M, Mattay D, Kriegel S, Hellwig P, Friedrich T. Inhibition of Escherichia coli respiratory complex I by Zn(2+). Biochemistry 2014; 53:6332-9. [PMID: 25238255 DOI: 10.1021/bi5009276] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, couples NADH oxidation and quinone reduction with the translocation of protons across the membrane. Complex I exhibits a unique L shape with a peripheral arm extending in the aqueous phase and a membrane arm embedded in the lipid bilayer. Both arms have a length of ∼180 Å. The electron transfer reaction is catalyzed by a series of cofactors in the peripheral arm, while the membrane arm catalyzes proton translocation. We used the inhibition of complex I by zinc to shed light on the coupling of the two processes, which is not yet understood. Enzyme kinetics revealed the presence of two high-affinity binding sites for Zn(2+) that are attributed to the proton translocation pathways in the membrane arm. Electrochemically induced Fourier transform infrared difference spectroscopy demonstrated that zinc binding involves at least two protonated acidic residues. Electron paramagnetic resonance spectroscopy showed that one of the cofactors is only partially reduced by NADH in the presence of Zn(2+). We conclude that blocking the proton channels in the membrane arm leads to a partial block of the electron transfer in the peripheral arm, indicating the long-range coupling between both processes.
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Affiliation(s)
- Marius Schulte
- Institut für Biochemie, Albert-Ludwigs-Universität , 79104 Freiburg, Germany
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30
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Tan P, Feng Z, Zhang L, Hou T, Li Y. The mechanism of proton translocation in respiratory complex I from molecular dynamics. J Recept Signal Transduct Res 2014; 35:170-9. [PMID: 25055024 DOI: 10.3109/10799893.2014.942464] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Respiratory complex I, the biggest enzyme of respiratory chain, plays a key role in energy production by the mitochondrial respiratory chain and has been implicated in many human neurodegenerative diseases. Recently, the crystal structure of respiratory complex I is reported. We perform 50 ns molecular dynamics simulations on the membrane domain of respiratory complex I under two hypothetical states (oxidized state and reduced state). We find that the density of water molecules in the trans-membrane domain under reduced state is bigger than that under oxidized state. The connecting elements (helix HL and β-hairpins-helix element) fluctuate stronger under reduced state than that under oxidized state, causing more internal water molecules and facilitating the proton conduction. The conformational changes of helix HL and the crucial charged residue Glu in TM5 play key roles in the mechanism of proton translocation. Our results illustrate the dynamic behavior and the potential mechanism of respiratory complex I, which provides the structural basis for drug design of respiratory complex I.
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Affiliation(s)
- Pengli Tan
- Institute of Functional Nano & Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University , Suzhou , China and
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31
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Sato M, Torres-Bacete J, Sinha PK, Matsuno-Yagi A, Yagi T. Essential regions in the membrane domain of bacterial complex I (NDH-1): the machinery for proton translocation. J Bioenerg Biomembr 2014; 46:279-87. [PMID: 24973951 DOI: 10.1007/s10863-014-9558-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 06/18/2014] [Indexed: 01/09/2023]
Abstract
The proton-translocating NADH-quinone oxidoreductase (complex I/NDH-1) is the first and largest enzyme of the respiratory chain which has a central role in cellular energy production and is implicated in many human neurodegenerative diseases and aging. It is believed that the peripheral domain of complex I/NDH-1 transfers the electron from NADH to Quinone (Q) and the redox energy couples the proton translocation in the membrane domain. To investigate the mechanism of the proton translocation, in a series of works we have systematically studied all membrane subunits in the Escherichia coli NDH-1 by site-directed mutagenesis. In this mini-review, we have summarized our strategy and results of the mutagenesis by depicting residues essential for proton translocation, along with those for subunit connection. It is suggested that clues to understanding the driving forces of proton translocation lie in the similarities and differences of the membrane subunits, highlighting the communication of essential charged residues among the subunits. A possible proton translocation mechanism with all membrane subunits operating in unison is described.
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Affiliation(s)
- Motoaki Sato
- Department of Molecular and Experimental Medicine, MEM-256, The Scripps Research Institute, La Jolla, CA, 92037, USA,
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Sato M, Sinha PK, Torres-Bacete J, Matsuno-Yagi A, Yagi T. Energy transducing roles of antiporter-like subunits in Escherichia coli NDH-1 with main focus on subunit NuoN (ND2). J Biol Chem 2013; 288:24705-16. [PMID: 23864658 DOI: 10.1074/jbc.m113.482968] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The proton-translocating NADH-quinone oxidoreductase (complex I/NDH-1) contains a peripheral and a membrane domain. Three antiporter-like subunits in the membrane domain, NuoL, NuoM, and NuoN (ND5, ND4 and ND2, respectively), are structurally similar. We analyzed the role of NuoN in Escherichia coli NDH-1. The lysine residue at position 395 in NuoN (NLys(395)) is conserved in NuoL (LLys(399)) but is replaced by glutamic acid (MGlu(407)) in NuoM. Our mutation study on NLys(395) suggests that this residue participates in the proton translocation. Furthermore, we found that MGlu(407) is also essential and most likely interacts with conserved LArg(175). Glutamic acids, NGlu(133), MGlu(144), and LGlu(144), are corresponding residues. Unlike mutants of MGlu(144) and LGlu(144), mutation of NGlu(133) scarcely affected the energy-transducing activities. However, a double mutant of NGlu(133) and nearby KGlu(72) showed significant inhibition of these activities. This suggests that NGlu(133) bears a functional role similar to LGlu(144) and MGlu(144) but its mutation can be partially compensated by the nearby carboxyl residue. Conserved prolines located at loops of discontinuous transmembrane helices of NuoL, NuoM, and NuoN were shown to play a similar role in the energy-transducing activity. It seems likely that NuoL, NuoM, and NuoN pump protons by a similar mechanism. Our data also revealed that NLys(158) is one of the key interaction points with helix HL in NuoL. A truncation study indicated that the C-terminal amphipathic segments of NTM14 interacts with the Mβ sheet located on the opposite side of helix HL. Taken together, the mechanism of H(+) translocation in NDH-1 is discussed.
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Affiliation(s)
- Motoaki Sato
- Department of Molecular and Experimental Medicine, MEM-256, The Scripps Research Institute, La Jolla, California 92037, USA
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Torres-Bacete J, Sinha PK, Sato M, Patki G, Kao MC, Matsuno-Yagi A, Yagi T. Roles of subunit NuoK (ND4L) in the energy-transducing mechanism of Escherichia coli NDH-1 (NADH:quinone oxidoreductase). J Biol Chem 2012; 287:42763-72. [PMID: 23105119 DOI: 10.1074/jbc.m112.422824] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The bacterial H(+)-translocating NADH:quinone oxidoreductase (NDH-1) catalyzes electron transfer from NADH to quinone coupled with proton pumping across the cytoplasmic membrane. The NuoK subunit (counterpart of the mitochondrial ND4L subunit) is one of the seven hydrophobic subunits in the membrane domain and bears three transmembrane segments (TM1-3). Two glutamic residues located in the adjacent transmembrane helices of NuoK are important for the energy coupled activity of NDH-1. In particular, mutation of the highly conserved carboxyl residue ((K)Glu-36 in TM2) to Ala led to a complete loss of the NDH-1 activities. Mutation of the second conserved carboxyl residue ((K)Glu-72 in TM3) moderately reduced the activities. To clarify the contribution of NuoK to the mechanism of proton translocation, we relocated these two conserved residues. When we shifted (K)Glu-36 along TM2 to positions 32, 38, 39, and 40, the mutants largely retained energy transducing NDH-1 activities. According to the recent structural information, these positions are located in the vicinity of (K)Glu-36, present in the same helix phase, in an immediately before and after helix turn. In an earlier study, a double mutation of two arginine residues located in a short cytoplasmic loop between TM1 and TM2 (loop-1) showed a drastic effect on energy transducing activities. Therefore, the importance of this cytosolic loop of NuoK ((K)Arg-25, (K)Arg-26, and (K)Asn-27) for the energy transducing activities was extensively studied. The probable roles of subunit NuoK in the energy transducing mechanism of NDH-1 are discussed.
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Affiliation(s)
- Jesus Torres-Bacete
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
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Efremov RG, Sazanov LA. The coupling mechanism of respiratory complex I — A structural and evolutionary perspective. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1785-95. [DOI: 10.1016/j.bbabio.2012.02.015] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 02/09/2012] [Accepted: 02/14/2012] [Indexed: 11/27/2022]
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Verkhovskaya M, Bloch DA. Energy-converting respiratory Complex I: on the way to the molecular mechanism of the proton pump. Int J Biochem Cell Biol 2012; 45:491-511. [PMID: 22982742 DOI: 10.1016/j.biocel.2012.08.024] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 08/27/2012] [Accepted: 08/28/2012] [Indexed: 12/16/2022]
Abstract
In respiring organisms the major energy transduction flux employs the transmembrane electrochemical proton gradient as a physical link between exergonic redox reactions and endergonic ADP phosphorylation. Establishing the gradient involves electrogenic, transmembrane H(+) translocation by the membrane-embedded respiratory complexes. Among others, Complex I (NADH:ubiquinone oxidoreductase) is the most structurally complex and functionally enigmatic respiratory enzyme; its molecular mechanism is as yet unknown. Here we highlight recent progress and discuss the catalytic events during Complex I turnover in relation to their role in energy conversion and to the enzyme structure.
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Affiliation(s)
- Marina Verkhovskaya
- Helsinki Bioenergetics Group, Institute of Biotechnology, PO Box 65 (Viikinkaari 1) FIN-00014 University of Helsinki, Finland.
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Shiraishi Y, Murai M, Sakiyama N, Ifuku K, Miyoshi H. Fenpyroximate Binds to the Interface between PSST and 49 kDa Subunits in Mitochondrial NADH-Ubiquinone Oxidoreductase. Biochemistry 2012; 51:1953-63. [DOI: 10.1021/bi300047h] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yusuke Shiraishi
- Division
of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502,
Japan
| | - Masatoshi Murai
- Division
of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502,
Japan
| | - Naoto Sakiyama
- Division
of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502,
Japan
| | - Kentaro Ifuku
- Division
of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502,
Japan
| | - Hideto Miyoshi
- Division
of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502,
Japan
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Dröse S, Brandt U. Molecular mechanisms of superoxide production by the mitochondrial respiratory chain. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 748:145-69. [PMID: 22729857 DOI: 10.1007/978-1-4614-3573-0_6] [Citation(s) in RCA: 349] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The mitochondrial respiratory chain is a major source of reactive oxygen species (ROS) in eukaryotic cells. Mitochondrial ROS production associated with a dysfunction of respiratory chain complexes has been implicated in a number of degenerative diseases and biological aging. Recent findings suggest that mitochondrial ROS can be integral components of cellular signal transduction as well. Within the respiratory chain, complexes I (NADH:ubiquinone oxidoreductase) and III (ubiquinol:cytochrome c oxidoreductase; cytochrome bc (1) complex) are generally considered as the main producers of superoxide anions that are released into the mitochondrial matrix and the intermembrane space, respectively. The primary function of both respiratory chain complexes is to employ energy supplied by redox reactions to drive the vectorial transfer of protons into the mitochondrial intermembrane space. This process involves a set of distinct electron carriers designed to minimize the unwanted leak of electrons from reduced cofactors onto molecular oxygen and hence ROS generation under normal circumstances. Nevertheless, it seems plausible that superoxide is derived from intermediates of the normal catalytic cycles of complexes I and III. Therefore, a detailed understanding of the molecular mechanisms driving these enzymes is required to understand mitochondrial ROS production during oxidative stress and redox signalling. This review summarizes recent findings on the chemistry and control of the reactions within respiratory complexes I and III that result in increased superoxide generation. Regulatory contributions of other components of the respiratory chain, especially complex II (succinate:ubiquinone oxidoreductase) and the redox state of the ubiquinone pool (Q-pool) will be briefly discussed.
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Affiliation(s)
- Stefan Dröse
- Center for Membrane Proteomics, Johann Wolfgang Goethe-Universität, Frankfurt am Main, Germany.
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Abstract
Mitochondrial dysfunction often leads to cell death and disease. We can now draw correlations between the dysfunction of one of the most important mitochondrial enzymes, NADH:ubiquinone reductase or complex I, and its structural organization thanks to the recent advances in the X-ray structure of its bacterial homologs. The new structural information on bacterial complex I provide essential clues to finally understand how complex I may work. However, the same information remains difficult to interpret for many scientists working on mitochondrial complex I from different angles, especially in the field of cell death. Here, we present a novel way of interpreting the bacterial structural information in accessible terms. On the basis of the analogy to semi-automatic shotguns, we propose a novel functional model that incorporates recent structural information with previous evidence derived from studies on mitochondrial diseases, as well as functional bioenergetics.
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Structure of the membrane domain of respiratory complex I. Nature 2011; 476:414-20. [PMID: 21822288 DOI: 10.1038/nature10330] [Citation(s) in RCA: 306] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 06/24/2011] [Indexed: 01/30/2023]
Abstract
Complex I is the first and largest enzyme of the respiratory chain, coupling electron transfer between NADH and ubiquinone to the translocation of four protons across the membrane. It has a central role in cellular energy production and has been implicated in many human neurodegenerative diseases. The L-shaped enzyme consists of hydrophilic and membrane domains. Previously, we determined the structure of the hydrophilic domain. Here we report the crystal structure of the Esherichia coli complex I membrane domain at 3.0 Å resolution. It includes six subunits, NuoL, NuoM, NuoN, NuoA, NuoJ and NuoK, with 55 transmembrane helices. The fold of the homologous antiporter-like subunits L, M and N is novel, with two inverted structural repeats of five transmembrane helices arranged, unusually, face-to-back. Each repeat includes a discontinuous transmembrane helix and forms half of a channel across the membrane. A network of conserved polar residues connects the two half-channels, completing the proton translocation pathway. Unexpectedly, lysines rather than carboxylate residues act as the main elements of the proton pump in these subunits. The fourth probable proton-translocation channel is at the interface of subunits N, K, J and A. The structure indicates that proton translocation in complex I, uniquely, involves coordinated conformational changes in six symmetrical structural elements.
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Vik SB. The transmembrane helices of the L, M, and N subunits of Complex I from E. coli can be assigned on the basis of conservation and hydrophobic moment analysis. FEBS Lett 2011; 585:1180-4. [PMID: 21420404 DOI: 10.1016/j.febslet.2011.03.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2011] [Revised: 03/12/2011] [Accepted: 03/14/2011] [Indexed: 02/03/2023]
Abstract
An assignment of the transmembrane helices of subunits L, M, and N of the Escherichia coli Complex I has been made from the helices as determined in a recent crystal structure [Efromov et al., Nature (2010) 465, 441-446]. The amino acid sequences of the three subunits were evaluated for hydrophobicity, and hydrophobic moments, to identify the helices that are likely to be in contact with membrane lipids. Using 29 closely related species, a similar analysis of average conservation, and conservation moments was performed. In each subunit, transmembrane helices 9 and 12 are predicted to form the discontinuous helices, which are likely to play a key role in function.
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Affiliation(s)
- Steven B Vik
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA.
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