1
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Gao Y, Zhang Y, Hakke S, Mohren R, Sijbers LJPM, Peters PJ, Ravelli RBG. Cryo-EM structure of cytochrome bo 3 quinol oxidase assembled in peptidiscs reveals an "open" conformation for potential ubiquinone-8 release. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149045. [PMID: 38614453 DOI: 10.1016/j.bbabio.2024.149045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 04/03/2024] [Accepted: 04/07/2024] [Indexed: 04/15/2024]
Abstract
Cytochrome bo3 quinol oxidase belongs to the heme‑copper-oxidoreductase (HCO) superfamily, which is part of the respiratory chain and essential for cell survival. While the reaction mechanism of cyt bo3 has been studied extensively over the last decades, specific details about its substrate binding and product release have remained unelucidated due to the lack of structural information. Here, we report a 2.8 Å cryo-electron microscopy structure of cyt bo3 from Escherichia coli assembled in peptidiscs. Our structural model shows a conformation for amino acids 1-41 of subunit I different from all previously published structures while the remaining parts of this enzyme are similar. Our new conformation shows a "U-shape" assembly in contrast to the transmembrane helix, named "TM0", in other reported structural models. However, TM0 blocks ubiquinone-8 (reaction product) release, suggesting that other cyt bo3 conformations should exist. Our structural model presents experimental evidence for an "open" conformation to facilitate substrate/product exchange. This work helps further understand the reaction cycle of this oxidase, which could be a benefit for potential drug/antibiotic design for health science.
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Affiliation(s)
- Ye Gao
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands; Division of Imaging Mass Spectrometry, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands.
| | - Yue Zhang
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands; Division of Imaging Mass Spectrometry, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Sneha Hakke
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands; Division of Imaging Mass Spectrometry, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Ronny Mohren
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands; Division of Imaging Mass Spectrometry, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Lyanne J P M Sijbers
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands; Division of Imaging Mass Spectrometry, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Peter J Peters
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands; Division of Imaging Mass Spectrometry, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands.
| | - Raimond B G Ravelli
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands; Division of Imaging Mass Spectrometry, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
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2
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Chang L, Cui H, Li F, Job Zhang YHP, Zhang L. ATP regeneration by ATPases for in vitro biotransformation. Biotechnol Adv 2024; 73:108377. [PMID: 38763231 DOI: 10.1016/j.biotechadv.2024.108377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/10/2024] [Accepted: 05/12/2024] [Indexed: 05/21/2024]
Abstract
Adenosine triphosphate (ATP) regeneration is a significant step in both living cells and in vitro biotransformation (ivBT). Rotary motor ATP synthases (ATPases), which regenerate ATP in living cells, have been widely assembled in biomimetic structures for in vitro ATP synthesis. In this review, we present a comprehensive overview of ATPases, including the working principle, orientation and distribution density properties of ATPases, as well as the assembly strategies and applications of ATPase-based ATP regeneration modules. The original sources of ATPases for in vitro ATP regeneration include chromatophores, chloroplasts, mitochondria, and inverted Escherichia coli (E. coli) vesicles, which are readily accessible but unstable. Although significant advances have been made in the assembly methods for ATPase-artificial membranes in recent decades, it remains challenging to replicate the high density and orientation of ATPases observed in vivo using in vitro assembly methods. The use of bioproton pumps or chemicals for constructing proton motive forces (PMF) enables the versatility and potential of ATPase-based ATP regeneration modules. Additionally, overall robustness can be achieved via membrane component selection, such as polymers offering great mechanical stability, or by constructing a solid supporting matrix through layer-by-layer assembly techniques. Finally, the prospects of ATPase-based ATP regeneration modules can be expected with the technological development of ATPases and artificial membranes.
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Affiliation(s)
- Lijing Chang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; In vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Huijuan Cui
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; In vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Fei Li
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; In vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Yi-Heng P Job Zhang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; In vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Lingling Zhang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; In vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
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3
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Gyawali R, Dhakal A, Wang L, Cheng J. Accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and specialized U-Net. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.02.560572. [PMID: 37873264 PMCID: PMC10592924 DOI: 10.1101/2023.10.02.560572] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Picking protein particles in cryo-electron microscopy (cryo-EM) micrographs is a crucial step in the cryo-EM-based structure determination. However, existing methods trained on a limited amount of cryo-EM data still cannot accurately pick protein particles from noisy cryo-EM images. The general foundational artificial intelligence (AI)-based image segmentation model such as Meta's Segment Anything Model (SAM) cannot segment protein particles well because their training data do not include cryo-EM images. Here, we present a novel approach (CryoSegNet) of integrating an attention-gated U-shape network (U-Net) specially designed and trained for cryo-EM particle picking and the SAM. The U-Net is first trained on a large cryo-EM image dataset and then used to generate input from original cryo-EM images for SAM to make particle pickings. CryoSegNet shows both high precision and recall in segmenting protein particles from cryo-EM micrographs, irrespective of protein type, shape, and size. On several independent datasets of various protein types, CryoSegNet outperforms two top machine learning particle pickers crYOLO and Topaz as well as SAM itself. The average resolution of density maps reconstructed from the particles picked by CryoSegNet is 3.32 Å, 7% better than 3.57 Å of Topaz and 14% better than 3.85 Å of crYOLO.
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Affiliation(s)
- Rajan Gyawali
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, 65211, USA
- NextGen Precision Health, University of Missouri, Columbia, MO, 65211, USA
| | - Ashwin Dhakal
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, 65211, USA
- NextGen Precision Health, University of Missouri, Columbia, MO, 65211, USA
| | - Liguo Wang
- Laboratory for BioMolecular Structure (LBMS), Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, 65211, USA
- NextGen Precision Health, University of Missouri, Columbia, MO, 65211, USA
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4
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Brown C, Ghosh S, McAllister R, Kumar M, Walker G, Sun E, Aman T, Panda A, Kumar S, Li W, Coleman J, Liu Y, Rothman JE, Bhattacharyya M, Gupta K. A proteome-wide quantitative platform for nanoscale spatially resolved extraction of membrane proteins into native nanodiscs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.10.579775. [PMID: 38405833 PMCID: PMC10888908 DOI: 10.1101/2024.02.10.579775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The intricate molecular environment of the native membrane profoundly influences every aspect of membrane protein (MP) biology. Despite this, the most prevalent method of studying MPs uses detergent-like molecules that disrupt and remove this vital local membrane context. This severely impedes our ability to quantitatively decipher the local molecular context and comprehend its regulatory role in the structure, function, and biogenesis of MPs. Using a library of membrane-active polymers we have developed a platform for the high-throughput analysis of the membrane proteome. The platform enables near-complete spatially resolved extraction of target MPs directly from their endogenous membranes into native nanodiscs that maintain the local membrane context. We accompany this advancement with an open-access quantitative database that provides the most efficient extraction conditions of 2065 unique mammalian MPs. Our method enables rapid and near-complete extraction and purification of target MPs directly from their endogenous organellar membranes at physiological expression levels while maintaining the nanoscale local membrane environment. Going beyond the plasma membrane proteome, our platform enables extraction from any target organellar membrane including the endoplasmic reticulum, mitochondria, lysosome, Golgi, and even transient organelles such as the autophagosome. To further validate this platform we took several independent MPs and demonstrated how our resource can enable rapid extraction and purification of target MPs from different organellar membranes with high efficiency and purity. Further, taking two synaptic vesicle MPs, we show how the database can be extended to capture multiprotein complexes between overexpressed MPs. We expect these publicly available resources to empower researchers across disciplines to capture membrane 'nano-scoops' containing a target MP efficiently and interface with structural, functional, and other bioanalytical approaches. We demonstrate an example of this by combining our extraction platform with single-molecule TIRF imaging to demonstrate how it can enable rapid determination of homo-oligomeric states of target MPs in native cell membranes.
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Affiliation(s)
- Caroline Brown
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Snehasish Ghosh
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Rachel McAllister
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Mukesh Kumar
- F.M. Kirby Neurobiology Center, Department of Neurobiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Gerard Walker
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Eric Sun
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Talat Aman
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Aniruddha Panda
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Shailesh Kumar
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Wenxue Li
- Department of Pharmacology, Yale University, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Jeff Coleman
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Yansheng Liu
- Department of Pharmacology, Yale University, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - James E Rothman
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Kallol Gupta
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
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5
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Nastasi MR, Borisov VB, Forte E. Membrane-Bound Redox Enzyme Cytochrome bd-I Promotes Carbon Monoxide-Resistant Escherichia coli Growth and Respiration. Int J Mol Sci 2024; 25:1277. [PMID: 38279276 PMCID: PMC10815991 DOI: 10.3390/ijms25021277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/23/2023] [Accepted: 01/18/2024] [Indexed: 01/28/2024] Open
Abstract
The terminal oxidases of bacterial aerobic respiratory chains are redox-active electrogenic enzymes that catalyze the four-electron reduction of O2 to 2H2O taking out electrons from quinol or cytochrome c. Living bacteria often deal with carbon monoxide (CO) which can act as both a signaling molecule and a poison. Bacterial terminal oxidases contain hemes; therefore, they are potential targets for CO. However, our knowledge of this issue is limited and contradictory. Here, we investigated the effect of CO on the cell growth and aerobic respiration of three different Escherichia coli mutants, each expressing only one terminal quinol oxidase: cytochrome bd-I, cytochrome bd-II, or cytochrome bo3. We found that following the addition of CO to bd-I-only cells, a minimal effect on growth was observed, whereas the growth of both bd-II-only and bo3-only strains was severely impaired. Consistently, the degree of resistance of aerobic respiration of bd-I-only cells to CO is high, as opposed to high CO sensitivity displayed by bd-II-only and bo3-only cells consuming O2. Such a difference between the oxidases in sensitivity to CO was also observed with isolated membranes of the mutants. Accordingly, O2 consumption of wild-type cells showed relatively low CO sensitivity under conditions favoring the expression of a bd-type oxidase.
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Affiliation(s)
- Martina R. Nastasi
- Department of Biochemical Sciences, Sapienza University of Rome, 00185 Rome, Italy;
| | - Vitaliy B. Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Elena Forte
- Department of Biochemical Sciences, Sapienza University of Rome, 00185 Rome, Italy;
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6
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Dhakal A, Gyawali R, Wang L, Cheng J. CryoTransformer: A Transformer Model for Picking Protein Particles from Cryo-EM Micrographs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563155. [PMID: 37961171 PMCID: PMC10634673 DOI: 10.1101/2023.10.19.563155] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of large protein complexes. Picking single protein particles from cryo-EM micrographs (images) is a crucial step in reconstructing protein structures from them. However, the widely used template-based particle picking process requires some manual particle picking and is labor-intensive and time-consuming. Though machine learning and artificial intelligence (AI) can potentially automate particle picking, the current AI methods pick particles with low precision or low recall. The erroneously picked particles can severely reduce the quality of reconstructed protein structures, especially for the micrographs with low signal-to-noise (SNR) ratios. To address these shortcomings, we devised CryoTransformer based on transformers, residual networks, and image processing techniques to accurately pick protein particles from cryo-EM micrographs. CryoTransformer was trained and tested on the largest labelled cryo-EM protein particle dataset - CryoPPP. It outperforms the current state-of-the-art machine learning methods of particle picking in terms of the resolution of 3D density maps reconstructed from the picked particles as well as F1-score and is poised to facilitate the automation of the cryo-EM protein particle picking.
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Affiliation(s)
- Ashwin Dhakal
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA
- NextGen Precision Health, University of Missouri, Columbia, Columbia, MO 65211, USA
| | - Rajan Gyawali
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA
- NextGen Precision Health, University of Missouri, Columbia, Columbia, MO 65211, USA
| | - Liguo Wang
- Laboratory for BioMolecular Structure (LBMS), Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA
- NextGen Precision Health, University of Missouri, Columbia, Columbia, MO 65211, USA
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7
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Kägi J, Sloan W, Schimpf J, Nasiri HR, Lashley D, Friedrich T. Exploring ND-011992, a quinazoline-type inhibitor targeting quinone reductases and quinol oxidases. Sci Rep 2023; 13:12226. [PMID: 37507428 PMCID: PMC10382516 DOI: 10.1038/s41598-023-39430-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023] Open
Abstract
Bacterial energy metabolism has become a promising target for next-generation tuberculosis chemotherapy. One strategy to hamper ATP production is to inhibit the respiratory oxidases. The respiratory chain of Mycobacterium tuberculosis comprises a cytochrome bcc:aa3 and a cytochrome bd ubiquinol oxidase that require a combined approach to block their activity. A quinazoline-type compound called ND-011992 has previously been reported to ineffectively inhibit bd oxidases, but to act bactericidal in combination with inhibitors of cytochrome bcc:aa3 oxidase. Due to the structural similarity of ND-011992 to quinazoline-type inhibitors of respiratory complex I, we suspected that this compound is also capable of blocking other respiratory chain complexes. Here, we synthesized ND-011992 and a bromine derivative to study their effect on the respiratory chain complexes of Escherichia coli. And indeed, ND-011992 was found to inhibit respiratory complex I and bo3 oxidase in addition to bd-I and bd-II oxidases. The IC50 values are all in the low micromolar range, with inhibition of complex I providing the lowest value with an IC50 of 0.12 µM. Thus, ND-011992 acts on both, quinone reductases and quinol oxidases and could be very well suited to regulate the activity of the entire respiratory chain.
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Affiliation(s)
- Jan Kägi
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Willough Sloan
- Department of Chemistry, William & Mary, Williamsburg, VA, USA
| | - Johannes Schimpf
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Hamid R Nasiri
- Department of Cellular Microbiology, University Hohenheim, Stuttgart, Germany
| | - Dana Lashley
- Department of Chemistry, William & Mary, Williamsburg, VA, USA.
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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8
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Dhakal A, Gyawali R, Wang L, Cheng J. A large expert-curated cryo-EM image dataset for machine learning protein particle picking. Sci Data 2023; 10:392. [PMID: 37349345 PMCID: PMC10287764 DOI: 10.1038/s41597-023-02280-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023] Open
Abstract
Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of biological macromolecular complexes. Picking single-protein particles from cryo-EM micrographs is a crucial step in reconstructing protein structures. However, the widely used template-based particle picking process is labor-intensive and time-consuming. Though machine learning and artificial intelligence (AI) based particle picking can potentially automate the process, its development is hindered by lack of large, high-quality labelled training data. To address this bottleneck, we present CryoPPP, a large, diverse, expert-curated cryo-EM image dataset for protein particle picking and analysis. It consists of labelled cryo-EM micrographs (images) of 34 representative protein datasets selected from the Electron Microscopy Public Image Archive (EMPIAR). The dataset is 2.6 terabytes and includes 9,893 high-resolution micrographs with labelled protein particle coordinates. The labelling process was rigorously validated through 2D particle class validation and 3D density map validation with the gold standard. The dataset is expected to greatly facilitate the development of both AI and classical methods for automated cryo-EM protein particle picking.
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Affiliation(s)
- Ashwin Dhakal
- Department of Electrical Engineering and Computer Science, NextGen Precision Health, University of Missouri, Columbia, MO, 65211, USA
| | - Rajan Gyawali
- Department of Electrical Engineering and Computer Science, NextGen Precision Health, University of Missouri, Columbia, MO, 65211, USA
| | - Liguo Wang
- Laboratory for BioMolecular Structure (LBMS), Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, NextGen Precision Health, University of Missouri, Columbia, MO, 65211, USA.
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9
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Flynn AJ, Antonyuk SV, Eady RR, Muench SP, Hasnain SS. A 2.2 Å cryoEM structure of a quinol-dependent NO Reductase shows close similarity to respiratory oxidases. Nat Commun 2023; 14:3416. [PMID: 37296134 PMCID: PMC10256718 DOI: 10.1038/s41467-023-39140-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
Quinol-dependent nitric oxide reductases (qNORs) are considered members of the respiratory heme-copper oxidase superfamily, are unique to bacteria, and are commonly found in pathogenic bacteria where they play a role in combating the host immune response. qNORs are also essential enzymes in the denitrification pathway, catalysing the reduction of nitric oxide to nitrous oxide. Here, we determine a 2.2 Å cryoEM structure of qNOR from Alcaligenes xylosoxidans, an opportunistic pathogen and a denitrifying bacterium of importance in the nitrogen cycle. This high-resolution structure provides insight into electron, substrate, and proton pathways, and provides evidence that the quinol binding site not only contains the conserved His and Asp residues but also possesses a critical Arg (Arg720) observed in cytochrome bo3, a respiratory quinol oxidase.
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Affiliation(s)
- Alex J Flynn
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Svetlana V Antonyuk
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, England
| | - Robert R Eady
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, England
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - S Samar Hasnain
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, England.
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10
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Heerde T, Bansal A, Schmidt M, Fändrich M. Cryo-EM structure of a catalytic amyloid fibril. Sci Rep 2023; 13:4070. [PMID: 36906667 PMCID: PMC10008563 DOI: 10.1038/s41598-023-30711-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/28/2023] [Indexed: 03/13/2023] Open
Abstract
Catalytic amyloid fibrils are novel types of bioinspired, functional materials that combine the chemical and mechanical robustness of amyloids with the ability to catalyze a certain chemical reaction. In this study we used cryo-electron microcopy to analyze the amyloid fibril structure and the catalytic center of amyloid fibrils that hydrolyze ester bonds. Our findings show that catalytic amyloid fibrils are polymorphic and consist of similarly structured, zipper-like building blocks that consist of mated cross-β sheets. These building blocks define the fibril core, which is decorated by a peripheral leaflet of peptide molecules. The observed structural arrangement differs from previously described catalytic amyloid fibrils and yielded a new model of the catalytic center.
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Affiliation(s)
- Thomas Heerde
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany.
| | - Akanksha Bansal
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
| | - Matthias Schmidt
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
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11
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Guo Y, Karimullina E, Emde T, Otwinowski Z, Borek D, Savchenko A. Monomer and dimer structures of cytochrome bo 3 ubiquinol oxidase from Escherichia coli. Protein Sci 2023; 32:e4616. [PMID: 36880269 PMCID: PMC10037687 DOI: 10.1002/pro.4616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023]
Abstract
The E. coli cytochrome bo3 ubiquinol oxidase is a four-subunit heme-copper oxidase that serves as a proton pump in the E. coli aerobic respiratory chain. Despite many mechanistic studies, it is unclear whether this ubiquinol oxidase functions as a monomer, or as a dimer in a manner similar to its eukaryotic counterparts - the mitochondrial electron transport complexes. In this study, we determined the monomeric and dimeric structures of the E. coli cytochrome bo3 ubiquinol oxidase reconstituted in amphipol by cryogenic electron microscopy single particle reconstruction (cryo-EM SPR) to a resolution of 3.15 Å and 3.46 Å, respectively. We have discovered that the protein can form a dimer with C2 symmetry, with the dimerization interface maintained by interactions between the subunit II of one monomer and the subunit IV of the other monomer. Moreover, the dimerization does not induce significant structural changes in the monomers, except the movement of a loop in subunit IV (residues 67-74). This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yirui Guo
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, US
- Ligo Analytics, 2207 Chunk Ct, Dallas, Texas, United States
| | - Elina Karimullina
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, Illinois, USA
- Centers for Research on Structural Biology of Infectious Diseases (CSBID), Chicago, Illinois, USA
| | - Tabitha Emde
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, US
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, Illinois, USA
- Centers for Research on Structural Biology of Infectious Diseases (CSBID), Chicago, Illinois, USA
| | - Zbyszek Otwinowski
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, US
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, Illinois, USA
- Centers for Research on Structural Biology of Infectious Diseases (CSBID), Chicago, Illinois, USA
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, US
| | - Dominika Borek
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, US
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, Illinois, USA
- Centers for Research on Structural Biology of Infectious Diseases (CSBID), Chicago, Illinois, USA
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, US
| | - Alexei Savchenko
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, Illinois, USA
- Centers for Research on Structural Biology of Infectious Diseases (CSBID), Chicago, Illinois, USA
- BioZone, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
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12
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Muenks A, Zepeda S, Zhou G, Veesler D, DiMaio F. Automatic and accurate ligand structure determination guided by cryo-electron microscopy maps. Nat Commun 2023; 14:1164. [PMID: 36859493 PMCID: PMC9976687 DOI: 10.1038/s41467-023-36732-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/15/2023] [Indexed: 03/03/2023] Open
Abstract
Advances in cryo-electron microscopy (cryoEM) and deep-learning guided protein structure prediction have expedited structural studies of protein complexes. However, methods for accurately determining ligand conformations are lacking. In this manuscript, we develop EMERALD, a tool for automatically determining ligand structures guided by medium-resolution cryoEM density. We show this method is robust at predicting ligands along with surrounding side chains in maps as low as 4.5 Å local resolution. Combining this with a measure of placement confidence and running on all protein/ligand structures in the EMDB, we show that 57% of ligands replicate the deposited model, 16% confidently find alternate conformations, 22% have ambiguous density where multiple conformations might be present, and 5% are incorrectly placed. For five cases where our approach finds an alternate conformation with high confidence, high-resolution crystal structures validate our placement. EMERALD and the resulting analysis should prove critical in using cryoEM to solve protein-ligand complexes.
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Affiliation(s)
- Andrew Muenks
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Samantha Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Guangfeng Zhou
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA.
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13
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Dhakal A, Gyawali R, Wang L, Cheng J. CryoPPP: A Large Expert-Labelled Cryo-EM Image Dataset for Machine Learning Protein Particle Picking. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.21.529443. [PMID: 36865277 PMCID: PMC9980126 DOI: 10.1101/2023.02.21.529443] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Cryo-electron microscopy (cryo-EM) is currently the most powerful technique for determining the structures of large protein complexes and assemblies. Picking single-protein particles from cryo-EM micrographs (images) is a key step in reconstructing protein structures. However, the widely used template-based particle picking process is labor-intensive and time-consuming. Though the emerging machine learning-based particle picking can potentially automate the process, its development is severely hindered by lack of large, high-quality, manually labelled training data. Here, we present CryoPPP, a large, diverse, expert-curated cryo-EM image dataset for single protein particle picking and analysis to address this bottleneck. It consists of manually labelled cryo-EM micrographs of 32 non-redundant, representative protein datasets selected from the Electron Microscopy Public Image Archive (EMPIAR). It includes 9,089 diverse, high-resolution micrographs (∼300 cryo-EM images per EMPIAR dataset) in which the coordinates of protein particles were labelled by human experts. The protein particle labelling process was rigorously validated by both 2D particle class validation and 3D density map validation with the gold standard. The dataset is expected to greatly facilitate the development of machine learning and artificial intelligence methods for automated cryo-EM protein particle picking. The dataset and data processing scripts are available at https://github.com/BioinfoMachineLearning/cryoppp.
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Affiliation(s)
- Ashwin Dhakal
- Department of Electrical Engineering and Computer Science, NextGen Precision Health, University of Missouri, Columbia, MO 65211, USA. Fax: 573-882-8318
| | - Rajan Gyawali
- Department of Electrical Engineering and Computer Science, NextGen Precision Health, University of Missouri, Columbia, MO 65211, USA. Fax: 573-882-8318
| | - Liguo Wang
- Laboratory for BioMolecular Structure (LBMS), Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, NextGen Precision Health, University of Missouri, Columbia, MO 65211, USA. Fax: 573-882-8318
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14
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Nishida Y, Yanagisawa S, Morita R, Shigematsu H, Shinzawa-Itoh K, Yuki H, Ogasawara S, Shimuta K, Iwamoto T, Nakabayashi C, Matsumura W, Kato H, Gopalasingam C, Nagao T, Qaqorh T, Takahashi Y, Yamazaki S, Kamiya K, Harada R, Mizuno N, Takahashi H, Akeda Y, Ohnishi M, Ishii Y, Kumasaka T, Murata T, Muramoto K, Tosha T, Shiro Y, Honma T, Shigeta Y, Kubo M, Takashima S, Shintani Y. Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases. Nat Commun 2022; 13:7591. [PMID: 36481732 PMCID: PMC9731990 DOI: 10.1038/s41467-022-34771-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 11/07/2022] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global health problem. Despite the enormous efforts made in the last decade, threats from some species, including drug-resistant Neisseria gonorrhoeae, continue to rise and would become untreatable. The development of antibiotics with a different mechanism of action is seriously required. Here, we identified an allosteric inhibitory site buried inside eukaryotic mitochondrial heme-copper oxidases (HCOs), the essential respiratory enzymes for life. The steric conformation around the binding pocket of HCOs is highly conserved among bacteria and eukaryotes, yet the latter has an extra helix. This structural difference in the conserved allostery enabled us to rationally identify bacterial HCO-specific inhibitors: an antibiotic compound against ceftriaxone-resistant Neisseria gonorrhoeae. Molecular dynamics combined with resonance Raman spectroscopy and stopped-flow spectroscopy revealed an allosteric obstruction in the substrate accessing channel as a mechanism of inhibition. Our approach opens fresh avenues in modulating protein functions and broadens our options to overcome AMR.
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Affiliation(s)
- Yuya Nishida
- grid.410796.d0000 0004 0378 8307Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka Japan ,grid.136593.b0000 0004 0373 3971Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka Japan
| | - Sachiko Yanagisawa
- grid.266453.00000 0001 0724 9317Graduate School of Science, University of Hyogo, Hyogo, Japan
| | - Rikuri Morita
- grid.20515.330000 0001 2369 4728Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki Japan
| | - Hideki Shigematsu
- grid.472717.0RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo Japan ,grid.410592.b0000 0001 2170 091XPresent Address: Structural Biology Division, Japan Synchrotron Radiation Research Institute, SPring-8; Sayo, Hyogo, Japan
| | - Kyoko Shinzawa-Itoh
- grid.266453.00000 0001 0724 9317Graduate School of Science, University of Hyogo, Hyogo, Japan
| | - Hitomi Yuki
- grid.508743.dRIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa Japan
| | - Satoshi Ogasawara
- grid.136304.30000 0004 0370 1101Department of Chemistry, Graduate School of Science, Chiba University, Inage, Chiba Japan
| | - Ken Shimuta
- grid.410795.e0000 0001 2220 1880Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan ,grid.410795.e0000 0001 2220 1880Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takashi Iwamoto
- grid.136593.b0000 0004 0373 3971Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka Japan
| | - Chisa Nakabayashi
- grid.410796.d0000 0004 0378 8307Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka Japan ,grid.136593.b0000 0004 0373 3971Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka Japan
| | - Waka Matsumura
- grid.266453.00000 0001 0724 9317Graduate School of Science, University of Hyogo, Hyogo, Japan
| | - Hisakazu Kato
- grid.136593.b0000 0004 0373 3971Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka Japan
| | | | - Takemasa Nagao
- grid.410796.d0000 0004 0378 8307Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka Japan
| | - Tasneem Qaqorh
- grid.410796.d0000 0004 0378 8307Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka Japan ,grid.136593.b0000 0004 0373 3971Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka Japan
| | - Yusuke Takahashi
- grid.410796.d0000 0004 0378 8307Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka Japan
| | - Satoru Yamazaki
- grid.410796.d0000 0004 0378 8307Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka Japan
| | - Katsumasa Kamiya
- grid.419709.20000 0004 0371 3508Center for Basic Education Integrated Learning, Kanagawa Institute of Technology, Atsugi, Kanagawa Japan
| | - Ryuhei Harada
- grid.20515.330000 0001 2369 4728Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki Japan
| | - Nobuhiro Mizuno
- grid.410592.b0000 0001 2170 091XProtein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, SPring-8, Sayo, Hyogo Japan
| | - Hideyuki Takahashi
- grid.410795.e0000 0001 2220 1880Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yukihiro Akeda
- grid.410795.e0000 0001 2220 1880Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- grid.410795.e0000 0001 2220 1880Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshikazu Ishii
- grid.265050.40000 0000 9290 9879Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Takashi Kumasaka
- grid.410592.b0000 0001 2170 091XProtein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, SPring-8, Sayo, Hyogo Japan
| | - Takeshi Murata
- grid.136304.30000 0004 0370 1101Department of Chemistry, Graduate School of Science, Chiba University, Inage, Chiba Japan
| | - Kazumasa Muramoto
- grid.266453.00000 0001 0724 9317Graduate School of Science, University of Hyogo, Hyogo, Japan
| | - Takehiko Tosha
- grid.472717.0RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo Japan
| | - Yoshitsugu Shiro
- grid.266453.00000 0001 0724 9317Graduate School of Science, University of Hyogo, Hyogo, Japan
| | - Teruki Honma
- grid.508743.dRIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa Japan
| | - Yasuteru Shigeta
- grid.20515.330000 0001 2369 4728Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki Japan
| | - Minoru Kubo
- grid.266453.00000 0001 0724 9317Graduate School of Science, University of Hyogo, Hyogo, Japan
| | - Seiji Takashima
- grid.136593.b0000 0004 0373 3971Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka Japan
| | - Yasunori Shintani
- grid.410796.d0000 0004 0378 8307Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka Japan ,grid.136593.b0000 0004 0373 3971Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka Japan
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15
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Gómez-Fernández JC, Goñi FM. The Myth of The Annular Lipids. Biomedicines 2022; 10:2672. [PMID: 36359192 PMCID: PMC9687668 DOI: 10.3390/biomedicines10112672] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 12/08/2023] Open
Abstract
In the early 1970s, the existence of a "lipid annulus" stably surrounding the individual intrinsic protein molecules was proposed by several authors. They referred to a number of lipid molecules in slow exchange with the bulk lipid in the bilayer, i.e., more or less protein-bound, and more ordered than the bulk lipid. The annular lipids would control enzyme activity. This idea was uncritically accepted by most scientists working with intrinsic membrane proteins at the time, so that the idea operated like a myth in the field. However, in the following decade, hard spectroscopic and biochemical evidence showed that the proposed annular lipids were not immobilized for a sufficiently long time to influence enzyme or transporter activity, nor were they ordered by the protein. Surprisingly, forty years later, the myth survives, and the term 'annular lipid' is still in use, in a different, but even more illogical sense.
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Affiliation(s)
- Juan C. Gómez-Fernández
- Department of Biochemistry and Molecular Biology (A), Faculty of Veterinary Science, Universidad de Murcia, 30100 Murcia, Spain;
| | - Félix M. Goñi
- Instituto Biofisika (CSIC, UPV/EHU), Department of Biochemistry, University of the Basque Country, 48940 Leioa, Spain
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16
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Krishnarjuna B, Ramamoorthy A. Detergent-Free Isolation of Membrane Proteins and Strategies to Study Them in a Near-Native Membrane Environment. Biomolecules 2022; 12:1076. [PMID: 36008970 PMCID: PMC9406181 DOI: 10.3390/biom12081076] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 07/31/2022] [Accepted: 08/02/2022] [Indexed: 02/06/2023] Open
Abstract
Atomic-resolution structural studies of membrane-associated proteins and peptides in a membrane environment are important to fully understand their biological function and the roles played by them in the pathology of many diseases. However, the complexity of the cell membrane has severely limited the application of commonly used biophysical and biochemical techniques. Recent advancements in NMR spectroscopy and cryoEM approaches and the development of novel membrane mimetics have overcome some of the major challenges in this area. For example, the development of a variety of lipid-nanodiscs has enabled stable reconstitution and structural and functional studies of membrane proteins. In particular, the ability of synthetic amphipathic polymers to isolate membrane proteins directly from the cell membrane, along with the associated membrane components such as lipids, without the use of a detergent, has opened new avenues to study the structure and function of membrane proteins using a variety of biophysical and biological approaches. This review article is focused on covering the various polymers and approaches developed and their applications for the functional reconstitution and structural investigation of membrane proteins. The unique advantages and limitations of the use of synthetic polymers are also discussed.
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Affiliation(s)
- Bankala Krishnarjuna
- Department of Chemistry and Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry and Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
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17
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Catania R, Machin J, Rappolt M, Muench SP, Beales PA, Jeuken LJC. Detergent-Free Functionalization of Hybrid Vesicles with Membrane Proteins Using SMALPs. Macromolecules 2022; 55:3415-3422. [PMID: 35571225 PMCID: PMC9097535 DOI: 10.1021/acs.macromol.2c00326] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/08/2022] [Indexed: 11/28/2022]
Abstract
![]()
Hybrid
vesicles (HVs) that consist of mixtures of block copolymers
and lipids are robust biomimetics of liposomes, providing a valuable
building block in bionanotechnology, catalysis, and synthetic biology.
However, functionalization of HVs with membrane proteins remains laborious
and expensive, creating a significant current challenge in the field.
Here, using a new approach of extraction with styrene-maleic acid
(SMA), we show that a membrane protein (cytochrome bo3) directly transfers into HVs with an efficiency of 73.9
± 13.5% without the requirement of detergent, long incubation
times, or mechanical disruption. Direct transfer of membrane proteins
using this approach was not possible into liposomes, suggesting that
HVs are more amenable than liposomes to membrane protein incorporation
from a SMA lipid particle system. Finally, we show that this transfer
method is not limited to cytochrome bo3 and can also be performed with complex membrane protein mixtures.
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Affiliation(s)
- Rosa Catania
- Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Jonathan Machin
- Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Michael Rappolt
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, U.K
| | - Stephen P. Muench
- Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Paul A. Beales
- Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
- School of Chemistry, University of Leeds, Leeds LS2 9JT, U.K
| | - Lars J. C. Jeuken
- Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, U.K
- Leiden Institute of Chemistry, University Leiden, Leiden 2300RA, The Netherlands
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18
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Dimitrova VS, Song S, Karagiaridi A, Marand A, Pinkett HW. Detergent Alternatives: Membrane Protein Purification Using Synthetic Nanodisc Polymers. Methods Mol Biol 2022; 2507:375-387. [PMID: 35773593 PMCID: PMC9361707 DOI: 10.1007/978-1-0716-2368-8_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The development of styrene maleic acid (SMA) and diisobutylene maleic acid (DIBMA) copolymers provides an alternative to traditional detergent extraction of integral membrane proteins. By inserting into the membrane, these polymers can extract membrane proteins along with lipids in the form of native nanodiscs made by poly(styrene co-maleic anhydride) derivatives. Unlike detergent solubilization, where membrane proteins may lose annular lipids necessary for proper folding and stability, native nanodiscs allow for proteins to reside in the natural lipid environment. In addition, polymer-based nanodiscs can be purified using common chromatography methods similar to protocols established with detergent solubilization purification. Here we describe the solubilization screening and purification of an integral membrane protein using several commercial copolymers.
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Affiliation(s)
| | - Saemee Song
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Department of Infectious Diseases Research, Korea Research Institute of Chemical Technology, Daejeon, South Korea
| | | | - Anika Marand
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Heather W Pinkett
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
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19
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Short-chain aurachin D derivatives are selective inhibitors of E. coli cytochrome bd-I and bd-II oxidases. Sci Rep 2021; 11:23852. [PMID: 34903826 PMCID: PMC8668966 DOI: 10.1038/s41598-021-03288-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/01/2021] [Indexed: 11/12/2022] Open
Abstract
Cytochrome bd-type oxidases play a crucial role for survival of pathogenic bacteria during infection and proliferation. This role and the fact that there are no homologues in the mitochondrial respiratory chain qualify cytochrome bd as a potential antimicrobial target. However, few bd oxidase selective inhibitors have been described so far. In this report, inhibitory effects of Aurachin C (AurC-type) and new Aurachin D (AurD-type) derivatives on oxygen reductase activity of isolated terminal bd-I, bd-II and bo3 oxidases from Escherichia coli were potentiometrically measured using a Clark-type electrode. We synthesized long- (C10, decyl or longer) and short-chain (C4, butyl to C8, octyl) AurD-type compounds and tested this set of molecules towards their selectivity and potency. We confirmed strong inhibition of all three terminal oxidases for AurC-type compounds, whereas the 4(1H)-quinolone scaffold of AurD-type compounds mainly inhibits bd-type oxidases. We assessed a direct effect of chain length on inhibition activity with highest potency and selectivity observed for heptyl AurD-type derivatives. While Aurachin C and Aurachin D are widely considered as selective inhibitors for terminal oxidases, their structure–activity relationship is incompletely understood. This work fills this gap and illustrates how structural differences of Aurachin derivatives determine inhibitory potency and selectivity for bd-type oxidases of E. coli.
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20
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Borisov VB, Forte E. Impact of Hydrogen Sulfide on Mitochondrial and Bacterial Bioenergetics. Int J Mol Sci 2021; 22:12688. [PMID: 34884491 PMCID: PMC8657789 DOI: 10.3390/ijms222312688] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/20/2021] [Accepted: 11/22/2021] [Indexed: 02/06/2023] Open
Abstract
This review focuses on the effects of hydrogen sulfide (H2S) on the unique bioenergetic molecular machines in mitochondria and bacteria-the protein complexes of electron transport chains and associated enzymes. H2S, along with nitric oxide and carbon monoxide, belongs to the class of endogenous gaseous signaling molecules. This compound plays critical roles in physiology and pathophysiology. Enzymes implicated in H2S metabolism and physiological actions are promising targets for novel pharmaceutical agents. The biological effects of H2S are biphasic, changing from cytoprotection to cytotoxicity through increasing the compound concentration. In mammals, H2S enhances the activity of FoF1-ATP (adenosine triphosphate) synthase and lactate dehydrogenase via their S-sulfhydration, thereby stimulating mitochondrial electron transport. H2S serves as an electron donor for the mitochondrial respiratory chain via sulfide quinone oxidoreductase and cytochrome c oxidase at low H2S levels. The latter enzyme is inhibited by high H2S concentrations, resulting in the reversible inhibition of electron transport and ATP production in mitochondria. In the branched respiratory chain of Escherichia coli, H2S inhibits the bo3 terminal oxidase but does not affect the alternative bd-type oxidases. Thus, in E. coli and presumably other bacteria, cytochrome bd permits respiration and cell growth in H2S-rich environments. A complete picture of the impact of H2S on bioenergetics is lacking, but this field is fast-moving, and active ongoing research on this topic will likely shed light on additional, yet unknown biological effects.
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Affiliation(s)
- Vitaliy B. Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia
| | - Elena Forte
- Department of Biochemical Sciences, Sapienza University of Rome, 00185 Rome, Italy;
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21
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Deutschmann S, Rimle L, von Ballmoos C. Rapid Estimation of Membrane Protein Orientation in Liposomes. Chembiochem 2021; 23:e202100543. [PMID: 34763366 PMCID: PMC9299231 DOI: 10.1002/cbic.202100543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/11/2021] [Indexed: 11/25/2022]
Abstract
The topological organization of proteins embedded in biological membranes is crucial for the tight interplay between these enzymes and their accessibility to substrates in order to fulfil enzymatic activity. The orientation of a membrane protein reconstituted in artificial membranes depends on many parameters and is hardly predictable. Here, we present a convenient approach to assess this important property independent of the enzymatic activity of the reconstituted protein. Based on cysteine‐specific chemical modification of a target membrane protein with a cyanine fluorophore and a corresponding membrane‐impermeable fluorescence quencher, the novel strategy allows rapid evaluation of the distribution of the two orientations after reconstitution. The assay has been tested for the respiratory complexes bo3 oxidase and ATP synthase of Escherichia coli and the results agree well with other orientation determination approaches. Given the simple procedure, the proposed method is a powerful tool for optimization of reconstitution conditions or quantitative orientation information prior to functional measurements.
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Affiliation(s)
- Sabina Deutschmann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012, Bern, Switzerland
| | - Lukas Rimle
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012, Bern, Switzerland
| | - Christoph von Ballmoos
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
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22
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Siletsky SA, Borisov VB. Proton Pumping and Non-Pumping Terminal Respiratory Oxidases: Active Sites Intermediates of These Molecular Machines and Their Derivatives. Int J Mol Sci 2021; 22:10852. [PMID: 34639193 PMCID: PMC8509429 DOI: 10.3390/ijms221910852] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 11/16/2022] Open
Abstract
Terminal respiratory oxidases are highly efficient molecular machines. These most important bioenergetic membrane enzymes transform the energy of chemical bonds released during the transfer of electrons along the respiratory chains of eukaryotes and prokaryotes from cytochromes or quinols to molecular oxygen into a transmembrane proton gradient. They participate in regulatory cascades and physiological anti-stress reactions in multicellular organisms. They also allow microorganisms to adapt to low-oxygen conditions, survive in chemically aggressive environments and acquire antibiotic resistance. To date, three-dimensional structures with atomic resolution of members of all major groups of terminal respiratory oxidases, heme-copper oxidases, and bd-type cytochromes, have been obtained. These groups of enzymes have different origins and a wide range of functional significance in cells. At the same time, all of them are united by a catalytic reaction of four-electron reduction in oxygen into water which proceeds without the formation and release of potentially dangerous ROS from active sites. The review analyzes recent structural and functional studies of oxygen reduction intermediates in the active sites of terminal respiratory oxidases, the features of catalytic cycles, and the properties of the active sites of these enzymes.
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Affiliation(s)
- Sergey A. Siletsky
- Department of Bioenergetics, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - Vitaliy B. Borisov
- Department of Molecular Energetics of Microorganisms, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia;
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