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Sowlati-Hashjin S, Gandhi A, Garton M. Dawn of a New Era for Membrane Protein Design. BIODESIGN RESEARCH 2022; 2022:9791435. [PMID: 37850134 PMCID: PMC10521746 DOI: 10.34133/2022/9791435] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/20/2022] [Indexed: 10/19/2023] Open
Abstract
A major advancement has recently occurred in the ability to predict protein secondary structure from sequence using artificial neural networks. This new accessibility to high-quality predicted structures provides a big opportunity for the protein design community. It is particularly welcome for membrane protein design, where the scarcity of solved structures has been a major limitation of the field for decades. Here, we review the work done to date on the membrane protein design and set out established and emerging tools that can be used to most effectively exploit this new access to structures.
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Affiliation(s)
- Shahin Sowlati-Hashjin
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, Canada, M5S 3E2
| | - Aanshi Gandhi
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, Canada, M5S 3E2
| | - Michael Garton
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, Canada, M5S 3E2
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Ardalan A, Sowlati-Hashjin S, Uwumarenogie SO, Fish M, Mitchell J, Karttunen M, Smith MD, Jelokhani-Niaraki M. Functional Oligomeric Forms of Uncoupling Protein 2: Strong Evidence for Asymmetry in Protein and Lipid Bilayer Systems. J Phys Chem B 2020; 125:169-183. [PMID: 33373220 DOI: 10.1021/acs.jpcb.0c09422] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Stoichiometry of uncoupling proteins (UCPs) and their coexistence as functional monomeric and associated forms in lipid membranes remain intriguing open questions. In this study, tertiary and quaternary structures of UCP2 were analyzed experimentally and through molecular dynamics (MD) simulations. UCP2 was overexpressed in the inner membrane of Escherichia coli, then purified and reconstituted in lipid vesicles. Structure and proton transport function of UCP2 were characterized by circular dichroism (CD) spectroscopy and fluorescence methods. Findings suggest a tetrameric functional form for UCP2. MD simulations conclude that tetrameric UCP2 is a dimer of dimers, is more stable than its monomeric and dimeric forms, is asymmetrical and induces asymmetry in the membrane's lipid structure, and a biphasic on-off switch between the dimeric units is its possible mode of transport. MD simulations also show that the water density inside the UCP2 monomer is asymmetric, with the cytoplasmic side having a higher water density and a wider radius. In contrast, the structurally comparable adenosine 5'-diphosphate (ADP)/adenosine 5'-triphosphate (ATP) carrier (AAC1) did not form tetramers, implying that tetramerization cannot be generalized to all mitochondrial carriers.
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Affiliation(s)
- Afshan Ardalan
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario, Canada N2L 3C5
| | - Shahin Sowlati-Hashjin
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 3K7.,Center for Advanced Materials and Biomaterials Research, The University of Western Ontario, London, Ontario, Canada N6K 3K7
| | - Stephanie O Uwumarenogie
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario, Canada N2L 3C5
| | - Michael Fish
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario, Canada N2L 3C5.,Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada N2L 3C5
| | - Joel Mitchell
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario, Canada N2L 3C5
| | - Mikko Karttunen
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 3K7.,Center for Advanced Materials and Biomaterials Research, The University of Western Ontario, London, Ontario, Canada N6K 3K7.,Department of Applied Mathematics, The University of Western Ontario, London, Ontario, Canada N6A 5B7
| | - Matthew D Smith
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada N2L 3C5
| | - Masoud Jelokhani-Niaraki
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario, Canada N2L 3C5
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Bai L, Wang T, Zhao G, Kovach A, Li H. The atomic structure of a eukaryotic oligosaccharyltransferase complex. Nature 2018; 555:328-333. [PMID: 29466327 PMCID: PMC6112861 DOI: 10.1038/nature25755] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 01/16/2018] [Indexed: 11/29/2022]
Abstract
N-glycosylation is a ubiquitous modification of eukaryotic secretory and membrane-bound proteins; about 90% of glycoproteins are N-glycosylated. The reaction is catalyzed by an eight-protein oligosaccharyltransferase complex, OST, embedded in the ER membrane. Our understanding of eukaryotic protein N-glycosylation has been limited due to the lack of high-resolution structures. Here we report a 3.5-Å resolution cryo-EM structure of the Saccharomyces cerevisiae OST, revealing the structures of Ost1–5, Stt3, Wbp1, and Swp1. We found that seven phospholipids mediate many of the inter-subunit interactions, and an Stt3 N-glycan mediates interaction with Wbp1 and Swp1 in the lumen. Ost3 was found to mediate the OST-Sec61 translocon interface, funneling the acceptor peptide towards the OST catalytic site as the nascent peptide emerges from the translocon. The structure provides novel insights into co-translational protein N-glycosylation and may facilitate the development of small-molecule inhibitors targeting this process.
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Affiliation(s)
- Lin Bai
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, USA
| | - Tong Wang
- Advanced Science Research Center at the Graduate Center of the City University of New York, New York, New York, USA
| | - Gongpu Zhao
- David Van Andel Advanced Cryo-Electron Microscopy Suite, Van Andel Research Institute, Grand Rapids, Michigan, USA
| | - Amanda Kovach
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, USA
| | - Huilin Li
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, USA
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