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Wan J, Zhou Y, Beardall J, Raven JA, Lin J, Huang J, Lu Y, Liang S, Ye M, Xiao M, Zhao JY, Dai X, Xia J, Jin P. DNA methylation and gene transcription act cooperatively in driving the adaptation of a marine diatom to global change. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad150. [PMID: 37100754 DOI: 10.1093/jxb/erad150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Indexed: 06/19/2023]
Abstract
Genetic changes together with epigenetic modifications such as DNA methylation have been demonstrated to regulate many biological processes and thereby govern the response of organisms to environmental changes. However, how DNA methylation might act cooperatively with gene transcription and thereby mediate the long-term adaptive responses of marine microalgae to global change is virtually unknown. Here we performed a transcriptomic analysis, and a whole-genome bisulfite sequencing, along with phenotypic analysis of a model marine diatom Phaeodactylum tricornutum adapted for two years to high CO2 and/or warming conditions. Our results show that the methylated islands (peaks of methylation) mCHH were positively correlated with expression of genes in the sub-region of the gene body when the populations were grown under high CO2 or its combination with warming for ~2 years. We further identified the differentially expressed genes (DEGs) and hence the metabolic pathways in which they function, at the transcriptomics level in differentially methylated regions (DMRs). Although DEGs in DMRs contributed only 18-24% of the total DEGs, we found that those DEGs acted cooperatively with DNA methylation and then regulated key processes such as central carbon metabolism, amino acid metabolism, ribosome biogenesis, terpenoid backbone biosynthesis, and degradation of misfolded proteins. Taken together, by integrating transcriptomic, epigenetic and phenotypic analysis, our study provides evidence for DNA methylation acting cooperatively with gene transcription to contribute to the adaptation of microalgae to global changes.
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Affiliation(s)
- Jiaofeng Wan
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Yunyue Zhou
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - John Beardall
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - John A Raven
- Division of Plant Science, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- School of Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
- Climate Change Cluster, University of Technology, Sydney, Ultimo, NSW 2007, Australia
| | - Jiamin Lin
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Jiali Huang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Yucong Lu
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Shiman Liang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Mengcheng Ye
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Mengting Xiao
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Jing Yuan Zhao
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Xiaoying Dai
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Jianrong Xia
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Peng Jin
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
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Cryo-EM structures of the Synechocystis sp. PCC 6803 cytochrome b6f complex with and without the regulatory PetP subunit. Biochem J 2022; 479:1487-1503. [PMID: 35726684 PMCID: PMC9342900 DOI: 10.1042/bcj20220124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 06/01/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022]
Abstract
In oxygenic photosynthesis, the cytochrome b6f (cytb6f) complex links the linear electron transfer (LET) reactions occurring at photosystems I and II and generates a transmembrane proton gradient via the Q-cycle. In addition to this central role in LET, cytb6f also participates in a range of processes including cyclic electron transfer (CET), state transitions and photosynthetic control. Many of the regulatory roles of cytb6f are facilitated by auxiliary proteins that differ depending upon the species, yet because of their weak and transient nature the structural details of these interactions remain unknown. An apparent key player in the regulatory balance between LET and CET in cyanobacteria is PetP, a ∼10 kDa protein that is also found in red algae but not in green algae and plants. Here, we used cryogenic electron microscopy to determine the structure of the Synechocystis sp. PCC 6803 cytb6f complex in the presence and absence of PetP. Our structures show that PetP interacts with the cytoplasmic side of cytb6f, displacing the C-terminus of the PetG subunit and shielding the C-terminus of cytochrome b6, which binds the heme cn cofactor that is suggested to mediate CET. The structures also highlight key differences in the mode of plastoquinone binding between cyanobacterial and plant cytb6f complexes, which we suggest may reflect the unique combination of photosynthetic and respiratory electron transfer in cyanobacterial thylakoid membranes. The structure of cytb6f from a model cyanobacterial species amenable to genetic engineering will enhance future site-directed mutagenesis studies of structure-function relationships in this crucial ET complex.
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Cramer WA. Structure-function of the cytochrome b 6f lipoprotein complex: a scientific odyssey and personal perspective. PHOTOSYNTHESIS RESEARCH 2019; 139:53-65. [PMID: 30311133 PMCID: PMC6510485 DOI: 10.1007/s11120-018-0585-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/15/2018] [Indexed: 05/04/2023]
Abstract
Structure-function studies of the cytochrome b6f complex, the central hetero-oligomeric membrane protein complex in the electron transport chain of oxygenic photosynthesis, which formed the basis for a high-resolution (2.5 Å) crystallographic solution of the complex, are described. Structure-function differences between the structure of subunits of the bc complexes, b6f, and bc1 from mitochondria and photosynthetic bacteria, which are often assumed to function identically, are discussed. Major differences which suggest that quinone-dependent electron transport pathways can vary in b6f and bc1 complexes are as follows: (a) an additional c-type heme, cn, and bound single copies of chlorophyll a and β-carotene in the b6f complex; and (b) a cyclic electron transport pathway that encompasses the b6f and PSI reaction center complexes. The importance of including lipid in crystallization of the cytochrome complex, or with any hetero-oligomeric membrane protein complex, is emphasized, and consequences to structure-function of b6f being a lipoprotein complex discussed, including intra-protein dielectric heterogeneity and resultant pathways of trans-membrane electron transport. The role of the b6f complex in trans-membrane signal transduction from reductant generated on the p-side of the electron transport chain to the regulation of light energy to the two photosystems by trans-side phosphorylation of the light-harvesting chlorophyll protein is presented. Regarding structure aspects relevant to plastoquinol-quinone entrance-egress: (i) modification of the p-side channel for plastoquinone access to the iron-sulfur protein would change the rate-limiting step in electron transport; (ii) the narrow niche for entry of plastoquinol into b6f from the PSII reaction center complex would seem to require close proximity between the complexes.
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Affiliation(s)
- William A Cramer
- Department of Biological Sciences, Purdue University, Hockmeyer Building for Structural Biology, West Lafayette, IN, 47907, USA.
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4
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Antoshvili M, Caspy I, Hippler M, Nelson N. Structure and function of photosystem I in Cyanidioschyzon merolae. PHOTOSYNTHESIS RESEARCH 2019; 139:499-508. [PMID: 29582227 DOI: 10.1007/s11120-018-0501-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 03/21/2018] [Indexed: 05/19/2023]
Abstract
The evolution of photosynthesis from primitive photosynthetic bacteria to higher plants has been driven by the need to adapt to a wide range of environmental conditions. The red alga Cyanidioschyzon merolae is a primitive organism, which is capable of performing photosynthesis in extreme acidic and hot environments. The study of its photosynthetic machinery may provide new insight on the evolutionary path of photosynthesis and on light harvesting and its regulation in eukaryotes. With that aim, the structural and functional properties of the PSI complex were investigated by biochemical characterization, mass spectrometry, and X-ray crystallography. PSI was purified from cells grown at 25 and 42 °C, crystallized and its crystal structure was solved at 4 Å resolution. The structure of C. merolae reveals a core complex with a crescent-shaped structure, formed by antenna proteins. In addition, the structural model shows the position of PsaO and PsaM. PsaG and PsaH are present in plant complex and are missing from the C. merolae model as expected. This paper sheds new light onto the evolution of photosynthesis, which gives a strong indication for the chimerical properties of red algae PSI. The subunit composition of the PSI core from C. merolae and its associated light-harvesting antennae suggests that it is an evolutionary and functional intermediate between cyanobacteria and plants.
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Affiliation(s)
- Maya Antoshvili
- Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Ido Caspy
- Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Michael Hippler
- Institute of Plant Biology and Biotechnology, University of Münster, 48143, Münster, Germany
| | - Nathan Nelson
- Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel.
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5
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Ren X, Liu Y, Jeong HK, Jeong BR. Supplementary Light Source Affects the Growth and Development of Codonopsis lanceolata Seedlings. Int J Mol Sci 2018; 19:ijms19103074. [PMID: 30297684 PMCID: PMC6212986 DOI: 10.3390/ijms19103074] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 10/03/2018] [Accepted: 10/06/2018] [Indexed: 11/19/2022] Open
Abstract
Codonopsis lanceolata is widely used in traditional medicine and diets. However, there is no optimal protocol for the commercial production of C. lanceolata seedlings. This study was carried out to find the optimum supplementary light source for the production of C. lanceolata seedlings. Seedlings were grown for four weeks in a glasshouse with an average daily light intensity of 490 μmol·m−2·s−1 photosynthetic photon flux density (PPFD) coming from the sun and a 16-h daily supplementary lighting at 120 μmol·m−2·s−1 PPFD from either high-pressure sodium (HPS), metal halide (MH), far-red (FR), white LED (LED-w), or mixed (white: red: blue = 1:2:1) LEDs (LED-mix). The results showed that the greatest total biomass, stem diameter, ratio of shoot weight to shoot length, root biomass, and ratio of root weight to shoot weight were found in seedlings grown under supplementary LED-mix. Meanwhile, the stomatal properties and soluble sugar contents were improved for seedlings in LED-mix. The contents of starch, total phenols, and flavonoids were the greatest for seedlings in LED-w and LED-mix. The expression of photosynthetic proteins and genes in seedlings was also enhanced by LED-mix. Overall, these results suggest that LED-mix is advantageous to the photosynthetic potential and the accumulation of biomass, carbohydrates and secondary metabolites in C. lanceolata.
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Affiliation(s)
- Xiuxia Ren
- Division of Applied Life Science (BK21 Plus Program), Graduate School, Gyeongsang National University, Jinju 52828, Korea.
| | - Ya Liu
- Division of Applied Life Science (BK21 Plus Program), Graduate School, Gyeongsang National University, Jinju 52828, Korea.
| | - Hai Kyoung Jeong
- Division of Applied Life Science (BK21 Plus Program), Graduate School, Gyeongsang National University, Jinju 52828, Korea.
| | - Byoung Ryong Jeong
- Division of Applied Life Science (BK21 Plus Program), Graduate School, Gyeongsang National University, Jinju 52828, Korea.
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Korea.
- Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea.
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Dey S, Levy ED. Inferring and Using Protein Quaternary Structure Information from Crystallographic Data. Methods Mol Biol 2018; 1764:357-375. [PMID: 29605927 DOI: 10.1007/978-1-4939-7759-8_23] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A precise knowledge of the quaternary structure of proteins is essential to illuminate both their function and their evolution. The major part of our knowledge on quaternary structure is inferred from X-ray crystallography data, but this inference process is hard and error-prone. The difficulty lies in discriminating fortuitous protein contacts, which make up the lattice of protein crystals, from biological protein contacts that exist in the native cellular environment. Here, we review methods devised to discriminate between both types of contacts and describe resources for downloading protein quaternary structure information and identifying high-confidence quaternary structures. The use of high-confidence datasets of quaternary structures will be critical for the analysis of structural, functional, and evolutionary properties of proteins.
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Affiliation(s)
- Sucharita Dey
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Emmanuel D Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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7
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Structure-Function of the Cytochrome b 6 f Lipoprotein Complex. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2016. [DOI: 10.1007/978-94-017-7481-9_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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8
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Mechanisms of Superoxide Generation and Signaling in Cytochrome bc Complexes. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2016. [DOI: 10.1007/978-94-017-7481-9_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Hasan SS, Proctor EA, Yamashita E, Dokholyan NV, Cramer WA. Traffic within the cytochrome b6f lipoprotein complex: gating of the quinone portal. Biophys J 2015; 107:1620-8. [PMID: 25296314 DOI: 10.1016/j.bpj.2014.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 07/29/2014] [Accepted: 08/05/2014] [Indexed: 12/24/2022] Open
Abstract
The cytochrome bc complexes b6f and bc1 catalyze proton-coupled quinol/quinone redox reactions to generate a transmembrane proton electrochemical gradient. Quinol oxidation on the electrochemically positive (p) interface of the complex occurs at the end of a narrow quinol/quinone entry/exit Qp portal, 11 Å long in bc complexes. Superoxide, which has multiple signaling functions, is a by-product of the p-side quinol oxidation. Although the transmembrane core and the chemistry of quinone redox reactions are conserved in bc complexes, the rate of superoxide generation is an order of magnitude greater in the b6f complex, implying that functionally significant differences in structure exist between the b6f and bc1 complexes on the p-side. A unique structure feature of the b6f p-side quinol oxidation site is the presence of a single chlorophyll-a molecule whose function is unrelated to light harvesting. This study describes a cocrystal structure of the cytochrome b6f complex with the quinol analog stigmatellin, which partitions in the Qp portal of the bc1 complex, but not effectively in b6f. It is inferred that the Qp portal is partially occluded in the b6f complex relative to bc1. Based on a discrete molecular-dynamics analysis, occlusion of the Qp portal is attributed to the presence of the chlorophyll phytyl tail, which increases the quinone residence time within the Qp portal and is inferred to be a cause of enhanced superoxide production. This study attributes a novel (to our knowledge), structure-linked function to the otherwise enigmatic chlorophyll-a in the b6f complex, which may also be relevant to intracellular redox signaling.
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Affiliation(s)
- S Saif Hasan
- Department of Biological Sciences, Hockmeyer Hall of Structural Biology, Purdue University, West Lafayette, Indiana
| | - Elizabeth A Proctor
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, North Carolina
| | - Eiki Yamashita
- Osaka University, Institute for Protein Research, Suita, Osaka, Japan
| | - Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina
| | - William A Cramer
- Department of Biological Sciences, Hockmeyer Hall of Structural Biology, Purdue University, West Lafayette, Indiana.
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10
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Agarwal R, Hasan SS, Jones LM, Stofleth JT, Ryan CM, Whitelegge JP, Kehoe DM, Cramer WA. Role of domain swapping in the hetero-oligomeric cytochrome b6f lipoprotein complex. Biochemistry 2015; 54:3151-63. [PMID: 25928281 DOI: 10.1021/acs.biochem.5b00279] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Domain swapping that contributes to the stability of biologically crucial multisubunit complexes has been implicated in protein oligomerization. In the case of membrane protein assemblies, domain swapping of the iron-sulfur protein (ISP) subunit occurs in the hetero-oligomeric cytochrome b6f and bc1 complexes, which are organized as symmetric dimers that generate the transmembrane proton electrochemical gradient utilized for ATP synthesis. In these complexes, the ISP C-terminal predominantly β-sheet extrinsic domain containing the redox-active [2Fe-2S] cluster resides on the electrochemically positive side of each monomer in the dimeric complex. This domain is bound to the membrane sector of the complex through an N-terminal transmembrane α-helix that is "swapped' to the other monomer of the complex where it spans the complex and the membrane. Detailed analysis of the function and structure of the b6f complex isolated from the cyanobacterium Fremyella diplosiphon SF33 shows that the domain-swapped ISP structure is necessary for function but is not necessarily essential for maintenance of the dimeric structure of the complex. On the basis of crystal structures of the cytochrome complex, the stability of the cytochrome dimer is attributed to specific intermonomer protein-protein and protein-lipid hydrophobic interactions. The geometry of the domain-swapped ISP structure is proposed to be a consequence of the requirement that the anchoring helix of the ISP not perturb the heme organization or quinone channel in the conserved core of each monomer.
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Affiliation(s)
- Rachna Agarwal
- †Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - S Saif Hasan
- †Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - LaDonna M Jones
- ‡Department of Biology, Indiana University, Bloomington, Indiana 47405, United States
| | - Jason T Stofleth
- †Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Christopher M Ryan
- §Pasarow Mass Spectrometry Laboratory, NPI-Semel Institute, University of California, Los Angeles, California 90095, United States
| | - Julian P Whitelegge
- §Pasarow Mass Spectrometry Laboratory, NPI-Semel Institute, University of California, Los Angeles, California 90095, United States
| | - David M Kehoe
- ‡Department of Biology, Indiana University, Bloomington, Indiana 47405, United States
| | - William A Cramer
- †Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
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12
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Meyer A, Dierks K, Hussein R, Brillet K, Brognaro H, Betzel C. Systematic analysis of protein-detergent complexes applying dynamic light scattering to optimize solutions for crystallization trials. Acta Crystallogr F Struct Biol Commun 2015; 71:75-81. [PMID: 25615974 PMCID: PMC4304753 DOI: 10.1107/s2053230x14027149] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 12/11/2014] [Indexed: 11/12/2022] Open
Abstract
Detergents are widely used for the isolation and solubilization of membrane proteins to support crystallization and structure determination. Detergents are amphiphilic molecules that form micelles once the characteristic critical micelle concentration (CMC) is achieved and can solubilize membrane proteins by the formation of micelles around them. The results are presented of a study of micelle formation observed by in situ dynamic light-scattering (DLS) analyses performed on selected detergent solutions using a newly designed advanced hardware device. DLS was initially applied in situ to detergent samples with a total volume of approximately 2 µl. When measured with DLS, pure detergents show a monodisperse radial distribution in water at concentrations exceeding the CMC. A series of all-trans n-alkyl-β-D-maltopyranosides, from n-hexyl to n-tetradecyl, were used in the investigations. The results obtained verify that the application of DLS in situ is capable of distinguishing differences in the hydrodynamic radii of micelles formed by detergents differing in length by only a single CH2 group in their aliphatic tails. Subsequently, DLS was applied to investigate the distribution of hydrodynamic radii of membrane proteins and selected water-insoluble proteins in presence of detergent micelles. The results confirm that stable protein-detergent complexes were prepared for (i) bacteriorhodopsin and (ii) FetA in complex with a ligand as examples of transmembrane proteins. A fusion of maltose-binding protein and the Duck hepatitis B virus X protein was added to this investigation as an example of a non-membrane-associated protein with low water solubility. The increased solubility of this protein in the presence of detergent could be monitored, as well as the progress of proteolytic cleavage to separate the fusion partners. This study demonstrates the potential of in situ DLS to optimize solutions of protein-detergent complexes for crystallization applications.
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Affiliation(s)
- Arne Meyer
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany
| | - Karsten Dierks
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany
- XtalConcepts, Marlowring 19, 22525 Hamburg, Germany
| | - Rana Hussein
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany
| | - Karl Brillet
- UMR 7242–IMPReSs Platform, ESBS, Pôle API, 300 Boulevard Sébastien Brant, CS10413, 67412 Illkirch CEDEX, France
| | - Hevila Brognaro
- Multi User Center for Biomolecular Innovation, Department of Physics, São Paulo State University, UNESP/IBILCE, Caixa Postal 136, São José do Rio Preto-SP, 15054, Brazil
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany
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13
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Rexroth S, Rexroth D, Veit S, Plohnke N, Cormann KU, Nowaczyk MM, Rögner M. Functional characterization of the small regulatory subunit PetP from the cytochrome b6f complex in Thermosynechococcus elongatus. THE PLANT CELL 2014; 26:3435-48. [PMID: 25139006 PMCID: PMC4176442 DOI: 10.1105/tpc.114.125930] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 07/10/2014] [Accepted: 07/29/2014] [Indexed: 05/24/2023]
Abstract
The cyanobacterial cytochrome b(6)f complex is central for the coordination of photosynthetic and respiratory electron transport and also for the balance between linear and cyclic electron transport. The development of a purification strategy for a highly active dimeric b(6)f complex from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 enabled characterization of the structural and functional role of the small subunit PetP in this complex. Moreover, the efficient transformability of this strain allowed the generation of a ΔpetP mutant. Analysis on the whole-cell level by growth curves, photosystem II light saturation curves, and P700(+) reduction kinetics indicate a strong decrease in the linear electron transport in the mutant strain versus the wild type, while the cyclic electron transport via photosystem I and cytochrome b(6)f is largely unaffected. This reduction in linear electron transport is accompanied by a strongly decreased stability and activity of the isolated ΔpetP complex in comparison with the dimeric wild-type complex, which binds two PetP subunits. The distinct behavior of linear and cyclic electron transport may suggest the presence of two distinguishable pools of cytochrome b(6)f complexes with different functions that might be correlated with supercomplex formation.
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Affiliation(s)
- Sascha Rexroth
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Dorothea Rexroth
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Sebastian Veit
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Nicole Plohnke
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Kai U Cormann
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Marc M Nowaczyk
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Matthias Rögner
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
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14
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Internal lipid architecture of the hetero-oligomeric cytochrome b6f complex. Structure 2014; 22:1008-15. [PMID: 24931468 DOI: 10.1016/j.str.2014.05.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 05/04/2014] [Accepted: 05/06/2014] [Indexed: 12/18/2022]
Abstract
The role of lipids in the assembly, structure, and function of hetero-oligomeric membrane protein complexes is poorly understood. The dimeric photosynthetic cytochrome b6f complex, a 16-mer of eight distinct subunits and 26 transmembrane helices, catalyzes transmembrane proton-coupled electron transfer for energy storage. Using a 2.5 Å crystal structure of the dimeric complex, we identified 23 distinct lipid-binding sites per monomer. Annular lipids are proposed to provide a connection for super-complex formation with the photosystem-I reaction center and the LHCII kinase enzyme for transmembrane signaling. Internal lipids mediate crosslinking to stabilize the domain-swapped iron-sulfur protein subunit, dielectric heterogeneity within intermonomer and intramonomer electron transfer pathways, and dimer stabilization through lipid-mediated intermonomer interactions. This study provides a complete structure analysis of lipid-mediated functions in a multi-subunit membrane protein complex and reveals lipid sites at positions essential for assembly and function.
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15
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Li D, Howe N, Dukkipati A, Shah ST, Bax BD, Edge C, Bridges A, Hardwicke P, Singh OMP, Giblin G, Pautsch A, Pfau R, Schnapp G, Wang M, Olieric V, Caffrey M. Crystallizing Membrane Proteins in the Lipidic Mesophase. Experience with Human Prostaglandin E2 Synthase 1 and an Evolving Strategy. CRYSTAL GROWTH & DESIGN 2014; 14:2034-2047. [PMID: 24803849 PMCID: PMC3983278 DOI: 10.1021/cg500157x] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/04/2014] [Indexed: 05/29/2023]
Abstract
The lipidic mesophase or in meso method for crystallizing membrane proteins has several high profile targets to its credit and is growing in popularity. Despite its success, the method is in its infancy as far as rational crystallogenesis is concerned. Consequently, significant time, effort, and resources are still required to generate structure-grade crystals, especially with a new target type. Therefore, a need exists for crystallogenesis protocols that are effective with a broad range of membrane protein types. Recently, a strategy for crystallizing a prokaryotic α-helical membrane protein, diacylglycerol kinase (DgkA), by the in meso method was reported (Cryst. Growth. Des.2013, 14, 2846-2857). Here, we describe its application to the human α-helical microsomal prostaglandin E2 synthase 1 (mPGES1). While the DgkA strategy proved useful, significant modifications were needed to generate structure-quality crystals of this important therapeutic target. These included protein engineering, using an additive phospholipid in the hosting mesophase, performing multiple rounds of salt screening, and carrying out trials at 4 °C in the presence of a tight binding ligand. The crystallization strategy detailed here should prove useful for generating structures of other integral membrane proteins by the in meso method.
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Affiliation(s)
- Dianfan Li
- Membrane Structural
and Functional Biology Group, School of Medicine and School of Biochemistry
and Immunology, Trinity College Dublin, Dublin
2, Ireland
| | - Nicole Howe
- Membrane Structural
and Functional Biology Group, School of Medicine and School of Biochemistry
and Immunology, Trinity College Dublin, Dublin
2, Ireland
| | - Abhiram Dukkipati
- Membrane Structural
and Functional Biology Group, School of Medicine and School of Biochemistry
and Immunology, Trinity College Dublin, Dublin
2, Ireland
| | - Syed T.
A. Shah
- Membrane Structural
and Functional Biology Group, School of Medicine and School of Biochemistry
and Immunology, Trinity College Dublin, Dublin
2, Ireland
| | - Benjamin D. Bax
- Molecular Discovery
Research, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2PA, U.K.
| | - Colin Edge
- Molecular Discovery
Research, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2PA, U.K.
| | - Angela Bridges
- Molecular Discovery
Research, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2PA, U.K.
| | - Phil Hardwicke
- Molecular Discovery
Research, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2PA, U.K.
| | - Onkar M. P. Singh
- Molecular Discovery
Research, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2PA, U.K.
| | - Ged Giblin
- Molecular Discovery
Research, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2PA, U.K.
| | - Alexander Pautsch
- Departments of Lead
Identification and Optimization Support, Boehringer Ingelheim Pharma
GmbH & Co. KG, 88400 Biberach an der Riss, Germany
| | - Roland Pfau
- Departments of Lead
Identification and Optimization Support, Boehringer Ingelheim Pharma
GmbH & Co. KG, 88400 Biberach an der Riss, Germany
| | - Gisela Schnapp
- Departments of Lead
Identification and Optimization Support, Boehringer Ingelheim Pharma
GmbH & Co. KG, 88400 Biberach an der Riss, Germany
| | - Meitian Wang
- Swiss
Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Vincent Olieric
- Swiss
Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Martin Caffrey
- Membrane Structural
and Functional Biology Group, School of Medicine and School of Biochemistry
and Immunology, Trinity College Dublin, Dublin
2, Ireland
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16
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Buschmann S, Richers S, Ermler U, Michel H. A decade of crystallization drops: crystallization of the cbb3 cytochrome c oxidase from Pseudomonas stutzeri. Protein Sci 2014; 23:411-22. [PMID: 24488923 DOI: 10.1002/pro.2423] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 01/08/2014] [Accepted: 01/09/2014] [Indexed: 11/11/2022]
Abstract
The cbb3 cytochrome c oxidases are distant members of the superfamily of heme copper oxidases. These terminal oxidases couple O2 reduction with proton transport across the plasma membrane and, as a part of the respiratory chain, contribute to the generation of an electrochemical proton gradient. Compared with other structurally characterized members of the heme copper oxidases, the recently determined cbb3 oxidase structure at 3.2 Å resolution revealed significant differences in the electron supply system, the proton conducting pathways and the coupling of O2 reduction to proton translocation. In this paper, we present a detailed report on the key steps for structure determination. Improvement of the protein quality was achieved by optimization of the number of lipids attached to the protein as well as the separation of two cbb3 oxidase isoenzymes. The exchange of n-dodecyl-β-D-maltoside for a precisely defined mixture of two α-maltosides and decanoylsucrose as well as the choice of the crystallization method had a most profound impact on crystal quality. This report highlights problems frequently encountered in membrane protein crystallization and offers meaningful approaches to improve crystal quality.
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Affiliation(s)
- Sabine Buschmann
- Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Max-von-Laue-Str.3, D-60438, Germany
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17
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Baniulis D, Hasan SS, Stofleth JT, Cramer WA. Mechanism of enhanced superoxide production in the cytochrome b(6)f complex of oxygenic photosynthesis. Biochemistry 2013; 52:8975-83. [PMID: 24298890 DOI: 10.1021/bi4013534] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The specific rate of superoxide (O2(•-)) production in the purified active crystallizable cytochrome b6f complex, normalized to the rate of electron transport, has been found to be more than an order of magnitude greater than that measured in isolated yeast respiratory bc1 complex. The biochemical and structural basis for the enhanced production of O2(•-) in the cytochrome b6f complex compared to that in the bc1 complex is discussed. The higher rate of superoxide production in the b6f complex could be a consequence of an increased residence time of plastosemiquinone/plastoquinol in its binding niche near the Rieske protein iron-sulfur cluster, resulting from (i) occlusion of the quinone portal by the phytyl chain of the unique bound chlorophyll, (ii) an altered environment of the proton-accepting glutamate believed to be a proton acceptor from semiquinone, or (iii) a more negative redox potential of the heme bp on the electrochemically positive side of the complex. The enhanced rate of superoxide production in the b6f complex is physiologically significant as the chloroplast-generated reactive oxygen species (ROS) functions in the regulation of excess excitation energy, is a source of oxidative damage inflicted during photosynthetic reactions, and is a major source of ROS in plant cells. Altered levels of ROS production are believed to convey redox signaling from the organelle to the cytosol and nucleus.
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Affiliation(s)
- Danas Baniulis
- Department of Biological Sciences, Hockmeyer Hall of Structural Biology, Purdue University , West Lafayette, Indiana 47907, United States
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18
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Saif Hasan S, Baniulis D, Yamashita E, Zhalnina MV, Zakharov SD, Stofleth JT, Cramer WA. Methods for studying interactions of detergents and lipids with α-helical and β-barrel integral membrane proteins. ACTA ACUST UNITED AC 2013; 74:29.7.1-29.7.30. [PMID: 24510648 DOI: 10.1002/0471140864.ps2907s74] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Methods for studying interactions of protein with lipids and detergents are described for representatives of two major classes of membrane proteins: (1) the α-helical hetero-oligomeric integral cytochrome b6 f complex of oxygenic photosynthesis from cyanobacteria, and (2) the outer membrane β-barrel proteins BtuB and OmpF from Gram-negative Escherichia coli bacteria. Details are presented on the use of detergents for purification and crystallization of the b6 f complex as well as a method for lipid exchange. The positions of detergent and lipid molecules, which define eight potential lipid-binding sites in the b6 f complex, are described. Differences in detergent strategies for isolation and crystallization of β-barrel proteins relative to those for oligomeric helical membrane proteins are discussed, and purification and assessment of protein quality by circular dichroism (CD) is presented.
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Affiliation(s)
- S Saif Hasan
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana
| | - Danas Baniulis
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana.,Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Babtai, Kaunas Region, Lithuania
| | - Eiki Yamashita
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Mariya V Zhalnina
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana
| | - Stanislav D Zakharov
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana.,Institute of Basic Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - Jason T Stofleth
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana.,Department of Chemistry and Biochemistry, University of California San Diego, San Diego, California
| | - William A Cramer
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana
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19
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Detergent quantification in membrane protein samples and its application to crystallization experiments. Amino Acids 2013; 45:1293-302. [PMID: 24105076 DOI: 10.1007/s00726-013-1600-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 09/19/2013] [Indexed: 10/26/2022]
Abstract
The structural characterization of membrane proteins remains a challenging field, largely because the use of stabilizing detergents is required. Researchers must first select a suitable detergent for the solubility and stability of their protein during in vitro studies. In addition, an appropriate concentration of detergent in membrane protein samples can be essential for protein solubility, stability, and experimental success. For example, in membrane protein crystallography, detergent concentration in the crystallization drop can be a critical parameter influencing crystal growth. Over the past decade, multiple techniques have been developed for the measurement of detergent concentration using a wide variety of strategies. These methods include colorimetric reactions, which target specific detergent classes, and analytical techniques applicable to a wide variety of detergents. This review will summarize and discuss the available options. It will be a useful resource to those selecting a strategy that best fits their experimental requirements and available instruments.
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20
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Cross TA, Murray DT, Watts A. Helical membrane protein conformations and their environment. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2013; 42:731-55. [PMID: 23996195 PMCID: PMC3818118 DOI: 10.1007/s00249-013-0925-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 07/25/2013] [Accepted: 08/12/2013] [Indexed: 02/02/2023]
Abstract
Evidence that membrane proteins respond conformationally and functionally to their environment is growing. Structural models, by necessity, have been characterized in preparations where the protein has been removed from its native environment. Different structural methods have used various membrane mimetics that have recently included lipid bilayers as a more native-like environment. Structural tools applied to lipid bilayer-embedded integral proteins are informing us about important generic characteristics of how membrane proteins respond to the lipid environment as compared with their response to other nonlipid environments. Here, we review the current status of the field, with specific reference to observations of some well-studied α-helical membrane proteins, as a starting point to aid the development of possible generic principles for model refinement.
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Affiliation(s)
- Timothy A. Cross
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Dylan T. Murray
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Anthony Watts
- Biomembrane structure Unit, Biochemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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21
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Barret LA, Barrot-Ivolot C, Raynal S, Jungas C, Polidori A, Bonneté F. Influence of Hydrophobic Micelle Structure on Crystallization of the Photosynthetic RC-LH1-PufX Complex from Rhodobacter blasticus. J Phys Chem B 2013; 117:8770-81. [DOI: 10.1021/jp403483q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Laurie-Anne Barret
- Institut des Biomolécules
Max Mousseron (IBMM) UMR 5247 CNRS-Universités Montpellier
1 et 2, Chimie Bioorganique et Systèmes Amphiphiles, Université d’Avignon et des Pays de Vaucluse, 33 rue Louis Pasteur, F-84000 Avignon, France
- CEA DSV IBEB Lab Bioenerget Cellulaire, CNRS UMR Biol Veget & Microbiol Environ, Aix-Marseille Université, Saint-Paul-lez-Durance, F-13108, France
| | - Cherone Barrot-Ivolot
- Institut des Biomolécules
Max Mousseron (IBMM) UMR 5247 CNRS-Universités Montpellier
1 et 2, Chimie Bioorganique et Systèmes Amphiphiles, Université d’Avignon et des Pays de Vaucluse, 33 rue Louis Pasteur, F-84000 Avignon, France
| | - Simon Raynal
- Institut des Biomolécules
Max Mousseron (IBMM) UMR 5247 CNRS-Universités Montpellier
1 et 2, Chimie Bioorganique et Systèmes Amphiphiles, Université d’Avignon et des Pays de Vaucluse, 33 rue Louis Pasteur, F-84000 Avignon, France
| | - Colette Jungas
- CEA DSV IBEB Lab Bioenerget Cellulaire, CNRS UMR Biol Veget & Microbiol Environ, Aix-Marseille Université, Saint-Paul-lez-Durance, F-13108, France
| | - Ange Polidori
- Institut des Biomolécules
Max Mousseron (IBMM) UMR 5247 CNRS-Universités Montpellier
1 et 2, Chimie Bioorganique et Systèmes Amphiphiles, Université d’Avignon et des Pays de Vaucluse, 33 rue Louis Pasteur, F-84000 Avignon, France
| | - Françoise Bonneté
- Institut des Biomolécules
Max Mousseron (IBMM) UMR 5247 CNRS-Universités Montpellier
1 et 2, Chimie Bioorganique et Systèmes Amphiphiles, Université d’Avignon et des Pays de Vaucluse, 33 rue Louis Pasteur, F-84000 Avignon, France
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22
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Hasan SS, Stofleth JT, Yamashita E, Cramer WA. Lipid-induced conformational changes within the cytochrome b6f complex of oxygenic photosynthesis. Biochemistry 2013; 52:2649-54. [PMID: 23514009 DOI: 10.1021/bi301638h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cytochrome b6f catalyzes quinone redox reactions within photosynthetic membranes to generate a transmembrane proton electrochemical gradient for ATP synthesis. A key step involves the transfer of an electron from the [2Fe-2S] cluster of the iron-sulfur protein (ISP) extrinsic domain to the cytochrome f heme across a distance of 26 Å, which is too large for competent electron transfer but could be bridged by translation-rotation of the ISP. Here we report the first crystallographic evidence of significant motion of the ISP extrinsic domain. It is inferred that extensive crystallographic disorder of the ISP extrinsic domain indicates conformational flexibility. The ISP disorder observed in this structure, in contrast to the largely ordered ISP structure observed in the b6f complex supplemented with neutral lipids, is attributed to electrostatic interactions arising from anionic lipids.
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Affiliation(s)
- S Saif Hasan
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
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23
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Transmembrane signaling and assembly of the cytochrome b6f-lipidic charge transfer complex. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1295-308. [PMID: 23507619 DOI: 10.1016/j.bbabio.2013.03.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 02/27/2013] [Accepted: 03/06/2013] [Indexed: 12/30/2022]
Abstract
Structure-function properties of the cytochrome b6f complex are sufficiently unique compared to those of the cytochrome bc1 complex that b6f should not be considered a trivially modified bc1 complex. A unique property of the dimeric b6f complex is its involvement in transmembrane signaling associated with the p-side oxidation of plastoquinol. Structure analysis of lipid binding sites in the cyanobacterial b6f complex prepared by hydrophobic chromatography shows that the space occupied by the H transmembrane helix in the cytochrome b subunit of the bc1 complex is mostly filled by a lipid in the b6f crystal structure. It is suggested that this space can be filled by the domain of a transmembrane signaling protein. The identification of lipid sites and likely function defines the intra-membrane conserved central core of the b6f complex, consisting of the seven trans-membrane helices of the cytochrome b and subunit IV polypeptides. The other six TM helices, contributed by cytochrome f, the iron-sulfur protein, and the four peripheral single span subunits, define a peripheral less conserved domain of the complex. The distribution of conserved and non-conserved domains of each monomer of the complex, and the position and inferred function of a number of the lipids, suggests a model for the sequential assembly in the membrane of the eight subunits of the b6f complex, in which the assembly is initiated by formation of the cytochrome b6-subunit IV core sub-complex in a monomer unit. Two conformations of the unique lipidic chlorophyll a, defined in crystal structures, are described, and functions of the outlying β-carotene, a possible 'latch' in supercomplex formation, are discussed. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
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24
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Hattori M, Hibbs RE, Gouaux E. A fluorescence-detection size-exclusion chromatography-based thermostability assay for membrane protein precrystallization screening. Structure 2012; 20:1293-9. [PMID: 22884106 DOI: 10.1016/j.str.2012.06.009] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 06/07/2012] [Accepted: 06/13/2012] [Indexed: 10/28/2022]
Abstract
Optimization of membrane protein stability under different solution conditions is essential for obtaining crystals that diffract to high resolution. Traditional methods that evaluate protein stability require large amounts of material and are, therefore, ill suited for medium- to high-throughput screening of membrane proteins. Here we present a rapid and efficient fluorescence-detection size-exclusion chromatography-based thermostability assay (FSEC-TS). In this method, the target protein is fused to GFP. Heated protein samples, treated with a panel of additives, are then analyzed by FSEC. FSEC-TS allows one to evaluate the thermostability of nanogram-to-microgram amounts of the target protein under a variety of conditions without purification. We applied this method to the Danio rerio P2X4 receptor and Caenorhabditis elegans GluCl to screen ligands, ions, and lipids, including newly designed cholesterol derivatives. In the case of GluCl, the screening results were used to obtain crystals of the receptor in the presence of lipids.
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Affiliation(s)
- Motoyuki Hattori
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
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25
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Caffrey M, Li D, Dukkipati A. Membrane protein structure determination using crystallography and lipidic mesophases: recent advances and successes. Biochemistry 2012; 51:6266-88. [PMID: 22783824 DOI: 10.1021/bi300010w] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The crystal structure of the β(2)-adrenergic receptor in complex with an agonist and its cognate G protein has just recently been determined. It is now possible to explore in molecular detail the means by which this paradigmatic transmembrane receptor binds agonist, communicates the impulse or signaling event across the membrane, and sets in motion a series of G protein-directed intracellular responses. The structure was determined using crystals of the ternary complex grown in a rationally designed lipidic mesophase by the so-called in meso method. The method is proving to be particularly useful in the G protein-coupled receptor field where the structures of 13 distinct receptor types have been determined in the past 5 years. In addition to receptors, the method has proven to be useful with a wide variety of integral membrane protein classes that include bacterial and eukaryotic rhodopsins, light-harvesting complex II (LHII), photosynthetic reaction centers, cytochrome oxidases, β-barrels, an exchanger, and an integral membrane peptide. This attests to the versatility and range of the method and supports the view that the in meso method should be included in the arsenal of the serious membrane structural biologist. For this to happen, however, the reluctance to adopt it attributable, in part, to the anticipated difficulties associated with handling the sticky, viscous cubic mesophase in which crystals grow must be overcome. Harvesting and collecting diffraction data with the mesophase-grown crystals are also viewed with some trepidation. It is acknowledged that there are challenges associated with the method. Over the years, we have endeavored to establish how the method works at a molecular level and to make it user-friendly. To these ends, tools for handling the mesophase in the pico- to nanoliter volume range have been developed for highly efficient crystallization screening in manual and robotic modes. Methods have been implemented for evaluating the functional activity of membrane proteins reconstituted into the bilayer of the cubic phase as a prelude to crystallogenesis. Glass crystallization plates that provide unparalleled optical quality and sensitivity to nascent crystals have been built. Lipid and precipitant screens have been designed for a more rational approach to crystallogenesis such that the method can now be applied to an even wider variety of membrane protein types. In this work, these assorted advances are outlined along with a summary of the membrane proteins that have yielded to the method. The prospects for and the challenges that must be overcome to further develop the method are described.
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Affiliation(s)
- Martin Caffrey
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland.
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26
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Bolla JR, Su CC, Yu EW. Biomolecular membrane protein crystallization. PHILOSOPHICAL MAGAZINE (ABINGDON, ENGLAND) 2012; 92:2648-2661. [PMID: 23869195 PMCID: PMC3712538 DOI: 10.1080/14786435.2012.670734] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Integral membrane proteins comprise approximately 30% of the sequenced genomes, and there is an immediate need for their high-resolution structural information. Currently, the most reliable approach to obtain these structures is x-ray crystallography. However, obtaining crystals of membrane proteins that diffract to high resolution appears to be quite challenging, and remains a major obstacle in structural determination. This brief review summarizes a variety of methodologies for use in crystallizing these membrane proteins. Hopefully, by introducing the available methods, techniques, and providing a general understanding of membrane proteins, a rational decision can be made about now to crystallize these complex materials.
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Affiliation(s)
- Jani Reddy Bolla
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
| | - Chih-Chia Su
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
| | - Edward W. Yu
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
- Department of Physics and Astronomy, Iowa State University, Ames, IA 50011, USA
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27
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Kallas T. Cytochrome b 6 f Complex at the Heart of Energy Transduction and Redox Signaling. PHOTOSYNTHESIS 2012. [DOI: 10.1007/978-94-007-1579-0_21] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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28
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Cramer WA, Zakharov SD, Saif Hasan S, Zhang H, Baniulis D, Zhalnina MV, Soriano GM, Sharma O, Rochet JC, Ryan C, Whitelegge J, Kurisu G, Yamashita E. Membrane proteins in four acts: function precedes structure determination. Methods 2011; 55:415-20. [PMID: 22079407 DOI: 10.1016/j.ymeth.2011.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 09/30/2011] [Accepted: 11/01/2011] [Indexed: 10/15/2022] Open
Abstract
Studies on four membrane protein systems, which combine information derived from crystal structures and biophysical studies have emphasized, as a precursor to crystallization, demonstration of functional activity. These assays have relied on sensitive spectrophotometric, electrophysiological, and microbiological assays of activity to select purification procedures that lead to functional complexes and with greater likelihood to successful crystallization: (I), Hetero-oligomeric proteins involved in electron transport/proton translocation. (1) Crystal structures of the eight subunit hetero-oligomeric trans-membrane dimeric cytochrome b(6)f complex were obtained from cyanobacteria using a protocol that allowed an analysis of the structure and function of internal lipids at specific intra-membrane, intra-protein sites. Proteolysis and monomerization that inactivated the complex and prevented crystallization was minimized through the use of filamentous cyanobacterial strains that seem to have a different set of membrane-active proteases. (2) An NADPH-quinone oxido-reductase isolated from cyanobacteria contains an expanded set of 17 monotopic and polytopic hetero-subunits. (II) β-Barrel outer membrane proteins (OMPs). High resolution structures of the vitamin B(12) binding protein, BtuB, solved in meso and in surfo, provide the best example of the differences in such structures that were anticipated in the first application of the lipid cubic phase to membrane proteins [1]. A structure of the complex of BtuB with the colicin E3 and E2 receptor binding domain established a "fishing pole" model for outer membrane receptor function in cellular import of nuclease colicins. (III) A modified faster purification procedure contributed to significantly improved resolution (1.83Å) of the universal porin, OmpF, the first membrane protein for which meaningful 3D crystals have been obtained [2]. A crystal structure of the N-terminal translocation domain of colicin E3 complexed to OmpF established the role of OmpF as an import channel for colicin nuclease cytotoxins. (IV) α-Synuclein, associated with the etiology of Parkinson's Disease, is an example of a protein, which is soluble and disordered in solution, but which can assume an ordered predominantly α-helical conformation upon binding to membranes. When subjected in its membrane-bound form to a trans-membrane electrical potential, α-synuclein can form voltage-gated ion channels. Summary of methods to assay functions/activities: (i) sensitive spectrophotometric assay to measure electron transfer activities; (ii) hydrophobic chromatography to deplete lipids, allowing reconstitution with specific lipids for studies on lipid-protein interactions; (iii) microbiological screen to assay high affinity binding of colicin receptor domains to Escherichia coli outer membrane receptors; (iv) electrophysiology/channel analysis (a) to select channel-occluding ligands for co-crystallization with ion channels of OmpF, and (b) to provide a unique description of voltage-gated ion channels of α-synuclein.
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Affiliation(s)
- W A Cramer
- Department of Biological Sciences, Purdue University, Hall of Structural Biology, 240 Hockmeyer Hall, West Lafayette, IN 47907-1354, USA.
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29
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Affiliation(s)
- Julian Whitelegge
- NPI-Semel Institute for Neuroscience and Human Behavior, University of California at Los Angeles, Los Angeles, CA 90024-1759, USA.
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Hasan SS, Yamashita E, Ryan CM, Whitelegge JP, Cramer WA. Conservation of lipid functions in cytochrome bc complexes. J Mol Biol 2011; 414:145-62. [PMID: 21978667 DOI: 10.1016/j.jmb.2011.09.023] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 09/05/2011] [Accepted: 09/14/2011] [Indexed: 11/24/2022]
Abstract
Lipid binding sites and properties are compared in two sub-families of hetero-oligomeric membrane protein complexes known to have similar functions in order to gain further understanding of the role of lipid in the function, dynamics, and assembly of these complexes. Using the crystal structure information for both complexes, we compared the lipid binding properties of the cytochrome b(6)f and bc(1) complexes that function in photosynthetic and respiratory membrane energy transduction. Comparison of lipid and detergent binding sites in the b(6)f complex with those in bc(1) shows significant conservation of lipid positions. Seven lipid binding sites in the cyanobacterial b(6)f complex overlap three natural sites in the Chlamydomonas reinhardtii algal complex and four sites in the yeast mitochondrial bc(1) complex. The specific identity of lipids is different in b(6)f and bc(1) complexes: b(6)f contains sulfoquinovosyldiacylglycerol, phosphatidylglycerol, phosphatidylcholine, monogalactosyldiacylglycerol, and digalactosyldiacylglycerol, whereas cardiolipin, phosphatidylethanolamine, and phosphatidic acid are present in the yeast bc(1) complex. The lipidic chlorophyll a and β-carotene (β-car) in cyanobacterial b(6)f, as well as eicosane in C. reinhardtii, are unique to the b(6)f complex. Inferences of lipid binding sites and functions were supported by sequence, interatomic distance, and B-factor information on interacting lipid groups and coordinating amino acid residues. The lipid functions inferred in the b(6)f complex are as follows: (i) substitution of a transmembrane helix by a lipid and chlorin ring, (ii) lipid and β-car connection of peripheral and core domains, (iii) stabilization of the iron-sulfur protein transmembrane helix, (iv) n-side charge and polarity compensation, and (v) β-car-mediated super-complex with the photosystem I complex.
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Affiliation(s)
- S Saif Hasan
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
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Zhang X, Tamot B, Hiser C, Reid GE, Benning C, Ferguson-Miller S. Cardiolipin deficiency in Rhodobacter sphaeroides alters the lipid profile of membranes and of crystallized cytochrome oxidase, but structure and function are maintained. Biochemistry 2011; 50:3879-90. [PMID: 21476578 DOI: 10.1021/bi101702c] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Many recent studies highlight the importance of lipids in membrane proteins, including in the formation of well-ordered crystals. To examine the effect of changes in one lipid, cardiolipin, on the lipid profile and the production, function, and crystallization of an intrinsic membrane protein, cytochrome c oxidase, we mutated the cardiolipin synthase (cls) gene of Rhodobacter sphaeroides, causing a >90% reduction in cardiolipin content in vivo and selective changes in the abundances of other lipids. Under these conditions, a fully native cytochrome c oxidase (CcO) was produced, as indicated by its activity, spectral properties, and crystal characteristics. Analysis by MALDI tandem mass spectrometry (MS/MS) revealed that the cardiolipin level in CcO crystals, as in the membranes, was greatly decreased. Lipid species present in the crystals were directly analyzed for the first time using MS/MS, documenting their identities and fatty acid chain composition. The fatty acid content of cardiolipin in R. sphaeroides CcO (predominantly 18:1) differs from that in mammalian CcO (18:2). In contrast to the cardiolipin dependence of mammalian CcO activity, major depletion of cardiolipin in R. sphaeroides did not impact any aspect of CcO structure or behavior, suggesting a greater tolerance of interchange of cardiolipin with other lipids in this bacterial system.
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Affiliation(s)
- Xi Zhang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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Cramer WA, Hasan SS, Yamashita E. The Q cycle of cytochrome bc complexes: a structure perspective. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:788-802. [PMID: 21352799 DOI: 10.1016/j.bbabio.2011.02.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 02/08/2011] [Accepted: 02/13/2011] [Indexed: 12/01/2022]
Abstract
Aspects of the crystal structures of the hetero-oligomeric cytochrome bc(1) and b(6)f ("bc") complexes relevant to their electron/proton transfer function and the associated redox reactions of the lipophilic quinones are discussed. Differences between the b(6)f and bc(1) complexes are emphasized. The cytochrome bc(1) and b(6)f dimeric complexes diverge in structure from a core of subunits that coordinate redox groups consisting of two bis-histidine coordinated hemes, a heme b(n) and b(p) on the electrochemically negative (n) and positive (p) sides of the complex, the high potential [2Fe-2S] cluster and c-type heme at the p-side aqueous interface and aqueous phase, respectively, and quinone/quinol binding sites on the n- and p-sides of the complex. The bc(1) and b(6)f complexes diverge in subunit composition and structure away from this core. b(6)f Also contains additional prosthetic groups including a c-type heme c(n) on the n-side, and a chlorophyll a and β-carotene. Common structure aspects; functions of the symmetric dimer. (I) Quinone exchange with the bilayer. An inter-monomer protein-free cavity of approximately 30Å along the membrane normal×25Å (central inter-monomer distance)×15Å (depth in the center), is common to both bc(1) and b(6)f complexes, providing a niche in which the lipophilic quinone/quinol (Q/QH(2)) can be exchanged with the membrane bilayer. (II) Electron transfer. The dimeric structure and the proximity of the two hemes b(p) on the electrochemically positive side of the complex in the two monomer units allow the possibility of two alternate routes of electron transfer across the complex from heme b(p) to b(n): intra-monomer and inter-monomer involving electron cross-over between the two hemes b(p). A structure-based summary of inter-heme distances in seven bc complexes, representing mitochondrial, chromatophore, cyanobacterial, and algal sources, indicates that, based on the distance parameter, the intra-monomer pathway would be favored kinetically. (III) Separation of quinone binding sites. A consequence of the dimer structure and the position of the Q/QH(2) binding sites is that the p-side QH(2) oxidation and n-side Q reduction sites are each well separated. Therefore, in the event of an overlap in residence time by QH(2) or Q molecules at the two oxidation or reduction sites, their spatial separation would result in minimal steric interference between extended Q or QH(2) isoprenoid chains. (IV) Trans-membrane QH(2)/Q transfer. (i) n/p-side QH(2)/Q transfer may be hindered by lipid acyl chains; (ii) the shorter less hindered inter-monomer pathway across the complex would not pass through the center of the cavity, as inferred from the n-side antimycin site on one monomer and the p-side stigmatellin site on the other residing on the same surface of the complex. (V) Narrow p-side portal for QH(2)/Q passage. The [2Fe-2S] cluster that serves as oxidant, and whose histidine ligand serves as a H(+) acceptor in the oxidation of QH(2), is connected to the inter-monomer cavity by a narrow extended portal, which is also occupied in the b(6)f complex by the 20 carbon phytyl chain of the bound chlorophyll.
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Affiliation(s)
- William A Cramer
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
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Hovers J, Potschies M, Polidori A, Pucci B, Raynal S, Bonneté F, Serrano-Vega MJ, Tate CG, Picot D, Pierre Y, Popot JL, Nehmé R, Bidet M, Mus-Veteau I, Busskamp H, Jung KH, Marx A, Timmins PA, Welte W. A class of mild surfactants that keep integral membrane proteins water-soluble for functional studies and crystallization. Mol Membr Biol 2011; 28:171-81. [PMID: 21314479 DOI: 10.3109/09687688.2011.552440] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mixed protein-surfactant micelles are used for in vitro studies and 3D crystallization when solutions of pure, monodisperse integral membrane proteins are required. However, many membrane proteins undergo inactivation when transferred from the biomembrane into micelles of conventional surfactants with alkyl chains as hydrophobic moieties. Here we describe the development of surfactants with rigid, saturated or aromatic hydrocarbon groups as hydrophobic parts. Their stabilizing properties are demonstrated with three different integral membrane proteins. The temperature at which 50% of the binding sites for specific ligands are lost is used as a measure of stability and dodecyl-β-D-maltoside ('C12-b-M') as a reference for conventional surfactants. One surfactant increased the stability of two different G protein-coupled receptors and the human Patched protein receptor by approximately 10°C compared to C12-b-M. Another surfactant yielded the highest stabilization of the human Patched protein receptor compared to C12-b-M (13°C) but was inferior for the G protein-coupled receptors. In addition, one of the surfactants was successfully used to stabilize and crystallize the cytochrome b(6 )f complex from Chlamydomonas reinhardtii. The structure was solved to the same resolution as previously reported in C12-b-M.
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Affiliation(s)
- Jens Hovers
- Fachbereich Biologie, Universität Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
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Romanowska E. Isolation of cytochrome b6f complex from grana and stroma membranes from spinach chloroplasts. Methods Mol Biol 2011; 684:53-64. [PMID: 20960121 DOI: 10.1007/978-1-60761-925-3_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The cytochrome b6f complex is located in the appressed granal membranes and nonappressed stroma thylakoids. The procedure presents isolation of the complex from both types of thylakoids by washing with NaBr, detergent treatment, ammonium sulfate fractionation, and sucrose gradient centrifugation. Optimal concentration of the detergent is lower for grana than for stroma vesicles. The cytochrome b6f complex from stroma lamellae locates at a higher density in the sucrose gradient than the granal complex. Electrophoretic analyses indicate that both complexes are dimeric and contain four large subunits and at least three small subunits with masses below 4 kDa. Plastocyanin and 15 kDa protein are also identified in the complexes but in variable amounts.
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Cross TA, Sharma M, Yi M, Zhou HX. Influence of solubilizing environments on membrane protein structures. Trends Biochem Sci 2010; 36:117-25. [PMID: 20724162 DOI: 10.1016/j.tibs.2010.07.005] [Citation(s) in RCA: 159] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Revised: 07/02/2010] [Accepted: 07/13/2010] [Indexed: 12/21/2022]
Abstract
Membrane protein structures are stabilized by weak interactions and are influenced by additional interactions with the solubilizing environment. Structures of influenza virus A M2 protein, a proven drug target, have been determined in three different environments, thus providing a unique opportunity to assess environmental influences. Structures determined in detergents and detergent micelles can have notable differences from those determined in lipid bilayers. These differences make it imperative to validate membrane protein structures.
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Affiliation(s)
- Timothy A Cross
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA.
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36
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Purification of transmembrane proteins from Saccharomyces cerevisiae for X-ray crystallography. Protein Expr Purif 2010; 71:207-23. [PMID: 20045057 DOI: 10.1016/j.pep.2009.12.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Revised: 12/23/2009] [Accepted: 12/26/2009] [Indexed: 01/15/2023]
Abstract
To enhance the quantity and quality of eukaryotic transmembrane proteins (TMPs) available for structure determination by X-ray crystallography, we have optimized protocols for purification of TMPs expressed in the yeast Saccharomyces cerevisiae. We focused on a set of the highest-expressing endogenous yeast TMPs for which there are established biochemical assays. Genes encoding the target TMPs are transferred via ligation-independent cloning to a series of vectors that allow expression of reading frames fused to C-terminal His10 and ZZ (IgG-binding) domains that are separated from the reading frame by a cleavage site for rhinovirus 3C protease. Several TMP targets expressed from these vectors have been purified via affinity chromatography and gel filtration chromatography at levels and purities sufficient for ongoing crystallization trials. Initial purifications were based on expression of the genes under control of a galactose-inducible promoter, but higher cell densities and improved expression have been obtained through use of the yeast ADH2 promoter. Wide variations have been observed in the behavior of different TMP targets during purification; some can be readily purified, while others do not bind efficiently to affinity matrices, are not efficiently cleaved from the matrices, or remain tightly associated with the matrices even after cleavage of the affinity tags. The size, oligomeric state, and composition of purified protein-detergent complexes purified under different conditions were analyzed using a colorimetric assay of detergent concentrations and by analytical size-exclusion chromatography using static light scattering, refractive index, and UV absorption detection to monitor the elution profiles. Effective procedures were developed for obtaining high concentrations of purified TMPs without excessively concentrating detergents.
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37
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Li M, Chang WR. Protein crystallization. PHOTOSYNTHESIS RESEARCH 2009; 102:223-229. [PMID: 19449124 DOI: 10.1007/s11120-009-9427-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2008] [Accepted: 04/23/2009] [Indexed: 05/27/2023]
Affiliation(s)
- Mei Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, 100101 Beijing, People’s Republic of China.
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38
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Kors CA, Wallace E, Davies DR, Li L, Laible PD, Nollert P. Effects of impurities on membrane-protein crystallization in different systems. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:1062-73. [PMID: 19770503 PMCID: PMC2748966 DOI: 10.1107/s0907444909029163] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Accepted: 07/22/2009] [Indexed: 11/18/2022]
Abstract
When starting a protein-crystallization project, scientists are faced with several unknowns. Amongst them are these questions: (i) is the purity of the starting material sufficient? and (ii) which type of crystallization experiment is the most promising to conduct? The difficulty in purifying active membrane-protein samples for crystallization trials and the high costs associated with producing such samples require an extremely pragmatic approach. Additionally, practical guidelines are needed to increase the efficiency of membrane-protein crystallization. In order to address these conundrums, the effects of commonly encountered impurities on various membrane-protein crystallization regimes have been investigated and it was found that the lipidic cubic phase (LCP) based crystallization methodology is more robust than crystallization in detergent environments using vapor diffusion or microbatch approaches in its ability to tolerate contamination in the forms of protein, lipid or other general membrane components. LCP-based crystallizations produced crystals of the photosynthetic reaction center (RC) of Rhodobacter sphaeroides from samples with substantial levels of residual impurities. Crystals were obtained with protein contamination levels of up to 50% and the addition of lipid material and membrane fragments to pure samples of RC had little effect on the number or on the quality of crystals obtained in LCP-based crystallization screens. If generally applicable, this tolerance for impurities may avoid the need for samples of ultrahigh purity when undertaking initial crystallization screening trials to determine preliminary crystallization conditions that can be optimized for a given target protein.
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Affiliation(s)
- Christopher A. Kors
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Ellen Wallace
- deCODE biostructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Douglas R. Davies
- deCODE biostructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Liang Li
- Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Philip D. Laible
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Peter Nollert
- deCODE biostructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
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39
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Kodan A, Shibata H, Matsumoto T, Terakado K, Sakiyama K, Matsuo M, Ueda K, Kato H. Improved expression and purification of human multidrug resistance protein MDR1 from baculovirus-infected insect cells. Protein Expr Purif 2009; 66:7-14. [DOI: 10.1016/j.pep.2009.02.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Revised: 02/10/2009] [Accepted: 02/10/2009] [Indexed: 11/25/2022]
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40
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Improved yield of a ligand-binding GPCR expressed in E. coli for structural studies. Protein Expr Purif 2009; 64:32-8. [DOI: 10.1016/j.pep.2008.10.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Revised: 10/03/2008] [Accepted: 10/03/2008] [Indexed: 11/24/2022]
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41
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Baniulis D, Yamashita E, Zhang H, Hasan SS, Cramer WA. Structure-function of the cytochrome b6f complex. Photochem Photobiol 2009; 84:1349-58. [PMID: 19067956 DOI: 10.1111/j.1751-1097.2008.00444.x] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The structure and function of the cytochrome b6f complex is considered in the context of recent crystal structures of the complex as an eight subunit, 220 kDa symmetric dimeric complex obtained from the thermophilic cyanobacterium, Mastigocladus laminosus, and the green alga, Chlamydomonas reinhardtii. A major problem confronted in crystallization of the cyanobacterial complex, proteolysis of three of the subunits, is discussed along with initial efforts to identify the protease. The evolution of these cytochrome complexes is illustrated by conservation of the hydrophobic heme-binding transmembrane domain of the cyt b polypeptide between b6f and bc1 complexes, and the rubredoxin-like membrane proximal domain of the Rieske [2Fe-2S] protein. Pathways of coupled electron and proton transfer are discussed in the framework of a modified Q cycle, in which the heme c(n), not found in the bc1 complex, but electronically tightly coupled to the heme b(n) of the b6f complex, is included. Crystal structures of the cyanobacterial complex with the quinone analogue inhibitors, NQNO or tridecyl-stigmatellin, show the latter to be ligands of heme c(n), implicating heme c(n) as an n-side plastoquinone reductase. Existing questions include (a) the details of the shuttle of: (i) the [2Fe-2S] protein between the membrane-bound PQH2 electron/H+ donor and the cytochrome f acceptor to complete the p-side electron transfer circuit; (ii) PQ/PQH2 between n- and p-sides of the complex across the intermonomer quinone exchange cavity, through the narrow portal connecting the cavity with the p-side [2Fe-2S] niche; (b) the role of the n-side of the b6f complex and heme c(n) in regulation of the relative rates of noncyclic and cyclic electron transfer. The likely presence of cyclic electron transport in the b6f complex, and of heme c(n) in the firmicute bc complex suggests the concept that hemes b(n)-c(n) define a branch point in bc complexes that can support electron transport pathways that differ in detail from the Q cycle supported by the bc1 complex.
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Affiliation(s)
- D Baniulis
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
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42
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Kern J, Zouni A, Guskov A, Krauß N. Lipids in the Structure of Photosystem I, Photosystem II and the Cytochrome b 6 f Complex. LIPIDS IN PHOTOSYNTHESIS 2009. [DOI: 10.1007/978-90-481-2863-1_10] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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43
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Fromme P, Grotjohann I. Chapter 9 Crystallization of Photosynthetic Membrane Proteins. CURRENT TOPICS IN MEMBRANES 2009. [DOI: 10.1016/s1063-5823(09)63009-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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44
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Chapter 6 Membrane Protein Crystallization: Approaching the Problem and Understanding the Solutions. CURRENT TOPICS IN MEMBRANES 2009. [DOI: 10.1016/s1063-5823(09)63006-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Yan J, Dashdorj N, Baniulis D, Yamashita E, Savikhin S, Cramer WA. On the Structural Role of the Aromatic Residue Environment of the Chlorophyll a in the Cytochrome b6f Complex. Biochemistry 2008; 47:3654-61. [PMID: 18302324 DOI: 10.1021/bi702299b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jiusheng Yan
- Departments of Biological Sciences and Physics, Purdue University, West Lafayette, Indiana 47907
| | - Naranbaatar Dashdorj
- Departments of Biological Sciences and Physics, Purdue University, West Lafayette, Indiana 47907
| | - Danas Baniulis
- Departments of Biological Sciences and Physics, Purdue University, West Lafayette, Indiana 47907
| | - Eiki Yamashita
- Departments of Biological Sciences and Physics, Purdue University, West Lafayette, Indiana 47907
| | - Sergei Savikhin
- Departments of Biological Sciences and Physics, Purdue University, West Lafayette, Indiana 47907
| | - William A. Cramer
- Departments of Biological Sciences and Physics, Purdue University, West Lafayette, Indiana 47907
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46
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47
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Midgett CR, Madden DR. Breaking the bottleneck: Eukaryotic membrane protein expression for high-resolution structural studies. J Struct Biol 2007; 160:265-74. [PMID: 17702603 DOI: 10.1016/j.jsb.2007.07.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Revised: 06/26/2007] [Accepted: 07/06/2007] [Indexed: 10/23/2022]
Abstract
The recombinant expression of eukaryotic membrane proteins has been a major stumbling block in efforts to determine their structures. In the last two years, however, five such proteins have yielded high-resolution X-ray or electron diffraction data, opening the prospect of increased throughput for eukaryotic membrane protein structure determination. Here, we summarize the major expression systems available, and highlight technical advances that should facilitate more systematic screening of expression conditions for this physiologically important class of targets.
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Affiliation(s)
- Charles R Midgett
- Department of Biochemistry, Dartmouth Medical School, 7200 Vail Building, Hanover, NH 03755, USA
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48
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Affiliation(s)
- Kevin R Mackenzie
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, USA
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49
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Poget SF, Girvin ME. Solution NMR of membrane proteins in bilayer mimics: small is beautiful, but sometimes bigger is better. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3098-106. [PMID: 17961504 DOI: 10.1016/j.bbamem.2007.09.006] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2007] [Revised: 09/07/2007] [Accepted: 09/10/2007] [Indexed: 10/22/2022]
Abstract
Considerable progress has been made recently on solution NMR studies of multi-transmembrane helix membrane protein systems of increasing size. Careful correlation of structure with function has validated the physiological relevance of these studies in detergent micelles. However, larger micelle and bicelle systems are sometimes required to stabilize the active forms of dynamic membrane proteins, such as the bacterial small multidrug resistance transporters. Even in these systems with aggregate molecular weights well over 100 kDa, solution NMR structural studies are feasible-but challenging.
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Affiliation(s)
- Sébastien F Poget
- Biochemistry Department, Albert Einstein College of Medicine, 1300 Morris Park Ave. Bronx, NY 10461, USA
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50
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Guan L, Mirza O, Verner G, Iwata S, Kaback HR. Structural determination of wild-type lactose permease. Proc Natl Acad Sci U S A 2007; 104:15294-8. [PMID: 17881559 PMCID: PMC2000551 DOI: 10.1073/pnas.0707688104] [Citation(s) in RCA: 196] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Here we describe an x-ray structure of wild-type lactose permease (LacY) from Escherichia coli determined by manipulating phospholipid content during crystallization. The structure exhibits the same global fold as the previous x-ray structures of a mutant that binds sugar but cannot catalyze translocation across the membrane. LacY is organized into two six-helix bundles with twofold pseudosymmetry separated by a large interior hydrophilic cavity open only to the cytoplasmic side and containing the side chains important for sugar and H(+) binding. To initiate transport, binding of sugar and/or an H(+) electrochemical gradient increases the probability of opening on the periplasmic side. Because the inward-facing conformation represents the lowest free-energy state, the rate-limiting step for transport may be the conformational change leading to the outward-facing conformation.
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Affiliation(s)
- Lan Guan
- *Department of Physiology and Department of Microbiology, Immunology, and Molecular Genetics, Molecular Biology Institute, University of California, Los Angeles, CA 90095-1662
| | - Osman Mirza
- Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Gillian Verner
- *Department of Physiology and Department of Microbiology, Immunology, and Molecular Genetics, Molecular Biology Institute, University of California, Los Angeles, CA 90095-1662
| | - So Iwata
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom
- Exploratory Research for Advanced Technology Human Receptor Crystallography Project, Kawasaki, 210-0855 Kanagawa, Japan; and
- RIKEN Genomics Sciences Center, 1-7-22 Suchiro-cho, Tsumi, Yokohama 230-0045, Japan
| | - H. Ronald Kaback
- *Department of Physiology and Department of Microbiology, Immunology, and Molecular Genetics, Molecular Biology Institute, University of California, Los Angeles, CA 90095-1662
- To whom correspondence should be addressed. E-mail:
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