1
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Samani EK, Hasan SMN, Waas M, Keszei AFA, Xu X, Heydari M, Hill ME, McLaurin J, Kislinger T, Mazhab-Jafari MT. Unveiling the structural proteome of an Alzheimer's disease rat brain model. Structure 2025; 33:51-61.e3. [PMID: 39615488 DOI: 10.1016/j.str.2024.11.004] [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: 08/16/2024] [Revised: 10/01/2024] [Accepted: 11/06/2024] [Indexed: 12/08/2024]
Abstract
Studying native protein structures at near-atomic resolution in a crowded environment presents challenges. Consequently, understanding the structural intricacies of proteins within pathologically affected tissues often relies on mass spectrometry and proteomic analysis. Here, we utilized cryoelectron microscopy (cryo-EM) and the Build and Retrieve (BaR) method to investigate protein complexes' structural characteristics such as post-translational modification, active site occupancy, and arrested conformational state in Alzheimer's disease (AD) using brain lysate from a rat model (TgF344-AD). Our findings reveal novel insights into the architecture of these complexes, corroborated through mass spectrometry analysis. Interestingly, it has been shown that the dysfunction of these protein complexes extends beyond AD, implicating them in cancer, as well as other neurodegenerative disorders such as Parkinson's disease, Huntington's disease, and schizophrenia. By elucidating these structural details, our work not only enhances our understanding of disease pathology but also suggests new avenues for future approaches in therapeutic intervention.
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Affiliation(s)
- Elnaz Khalili Samani
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - S M Naimul Hasan
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Matthew Waas
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Alexander F A Keszei
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Xiaoxiao Xu
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Mahtab Heydari
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Mary Elizabeth Hill
- Biological Sciences, Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - JoAnne McLaurin
- Biological Sciences, Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, Toronto, Ontario, Canada; Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Thomas Kislinger
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Mohammad T Mazhab-Jafari
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.
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2
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Coulibaly F. Cryo-EM vs. Disease X. Cell 2024; 187:5497-5499. [PMID: 39366340 DOI: 10.1016/j.cell.2024.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 09/03/2024] [Accepted: 09/03/2024] [Indexed: 10/06/2024]
Abstract
In this issue of Cell, Penzes et al. describe the use of cryo-EM to identify the cause of a mysterious disease affecting farmed superworms across the US. The study illustrates the power of ex vivo cryo-EM, which uses amplification-free samples to advance at once diagnostic, DNA packaging mechanism, and preventative measures.
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Affiliation(s)
- Fasséli Coulibaly
- Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia; Department of Biochemistry and Molecular BIology, Monash University, Clayton, VIC, Australia.
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3
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Wu Y, Li G, Tang H. Antibiotics Trigger Host Innate Immune Response via Microbiota-Brain Communication in C. elegans. Int J Mol Sci 2024; 25:8866. [PMID: 39201552 PMCID: PMC11354627 DOI: 10.3390/ijms25168866] [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: 07/08/2024] [Revised: 08/12/2024] [Accepted: 08/13/2024] [Indexed: 09/02/2024] Open
Abstract
Besides their direct bactericidal effect, antibiotics have also been suggested to stimulate the host immune response to defend against pathogens. However, it remains unclear whether any antibiotics may stimulate the host immune response by affecting bacterial activity. In this study, reasoning that genetic mutations inhibit bacterial activities and, thereby, may mimic the effects of antibiotics, we performed genome-wide screening and identified 77 E. coli genes whose inactivation induces C. elegans cyp-14A4, representing an innate immune and detoxification response. Further analyses reveal that this host immune response can clearly be induced through either inactivating the E. coli respiratory chain via the bacterial cyoB mutation or using the antibiotic Q203, which is able to enhance host survival when encountering the pathogen Pseudomonas aeruginosa. Mechanistically, the innate immune response triggered by both the cyoB mutation and Q203 is found to depend on the host brain response, as evidenced by their reliance on the host neural gene unc-13, which is required for neurotransmitter release in head neurons. Therefore, our findings elucidate the critical involvement of the microbiota-brain axis in modulating the host immune response, providing mechanistic insights into the role of antibiotics in triggering the host immune response and, thus, facilitating host defense against pathogens.
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Affiliation(s)
- Yangyang Wu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China;
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Guanqun Li
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Hongyun Tang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, China
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4
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Kyrilis FL, Low JKK, Mackay JP, Kastritis PL. Structural biology in cellulo: Minding the gap between conceptualization and realization. Curr Opin Struct Biol 2024; 87:102843. [PMID: 38788606 DOI: 10.1016/j.sbi.2024.102843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/26/2024]
Abstract
Recent technological advances have deepened our perception of cellular structure. However, most structural data doesn't originate from intact cells, limiting our understanding of cellular processes. Here, we discuss current and future developments that will bring us towards a structural picture of the cell. Electron cryotomography is the standard bearer, with its ability to provide in cellulo snapshots. Single-particle electron microscopy (of purified biomolecules and of complex mixtures) and covalent crosslinking combined with mass spectrometry also have significant roles to play, as do artificial intelligence algorithms in their many guises. To integrate these multiple approaches, data curation and standardisation will be critical - as is the need to expand efforts beyond our current protein-centric view to the other (macro)molecules that sustain life.
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Affiliation(s)
- Fotis L Kyrilis
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece. https://twitter.com/Fotansky_16
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| | - Panagiotis L Kastritis
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece; Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany; Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany; Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, Halle/Saale, Germany.
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5
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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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6
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Su CC, Zhang Z, Lyu M, Cui M, Yu EW. Cryo-EM structures of the human band 3 transporter indicate a transport mechanism involving the coupled movement of chloride and bicarbonate ions. PLoS Biol 2024; 22:e3002719. [PMID: 39167625 PMCID: PMC11338459 DOI: 10.1371/journal.pbio.3002719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 06/20/2024] [Indexed: 08/23/2024] Open
Abstract
The band 3 transporter is a critical integral membrane protein of the red blood cell (RBC), as it is responsible for catalyzing the exchange of bicarbonate and chloride anions across the plasma membrane. To elucidate the structural mechanism of the band 3 transporter, detergent solubilized human ghost membrane reconstituted in nanodiscs was applied to a cryo-EM holey carbon grid to define its composition. With this approach, we identified and determined structural information of the human band 3 transporter. Here, we present 5 different cryo-EM structures of the transmembrane domain of dimeric band 3, either alone or bound with chloride or bicarbonate. Interestingly, we observed that human band 3 can form both symmetric and asymmetric dimers with a different combination of outward-facing (OF) and inward-facing (IF) states. These structures also allow us to obtain the first model of a human band 3 molecule at the IF conformation. Based on the structural data of these dimers, we propose a model of ion transport that is in favor of the elevator-type mechanism.
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Affiliation(s)
- Chih-Chia Su
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Zhemin Zhang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Meinan Lyu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Meng Cui
- Department of Pharmaceutical Sciences, Northeastern University School of Pharmacy, Boston, Massachusetts, United States of America
| | - Edward W. Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
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7
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Nogales E, Mahamid J. Bridging structural and cell biology with cryo-electron microscopy. Nature 2024; 628:47-56. [PMID: 38570716 PMCID: PMC11211576 DOI: 10.1038/s41586-024-07198-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/13/2024] [Indexed: 04/05/2024]
Abstract
Most life scientists would agree that understanding how cellular processes work requires structural knowledge about the macromolecules involved. For example, deciphering the double-helical nature of DNA revealed essential aspects of how genetic information is stored, copied and repaired. Yet, being reductionist in nature, structural biology requires the purification of large amounts of macromolecules, often trimmed off larger functional units. The advent of cryogenic electron microscopy (cryo-EM) greatly facilitated the study of large, functional complexes and generally of samples that are hard to express, purify and/or crystallize. Nevertheless, cryo-EM still requires purification and thus visualization outside of the natural context in which macromolecules operate and coexist. Conversely, cell biologists have been imaging cells using a number of fast-evolving techniques that keep expanding their spatial and temporal reach, but always far from the resolution at which chemistry can be understood. Thus, structural and cell biology provide complementary, yet unconnected visions of the inner workings of cells. Here we discuss how the interplay between cryo-EM and cryo-electron tomography, as a connecting bridge to visualize macromolecules in situ, holds great promise to create comprehensive structural depictions of macromolecules as they interact in complex mixtures or, ultimately, inside the cell itself.
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Affiliation(s)
- Eva Nogales
- Molecular and Cell Biology Department, Institute for Quantitative Biomedicine, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Howard Hughes Medical Institute, Berkeley, CA, USA.
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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8
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Zhang Z, Yan Y, Pang J, Dai L, Zhang Q, Yu EW. Structural basis of DNA recognition of the Campylobacter jejuni CosR regulator. mBio 2024; 15:e0343023. [PMID: 38323832 PMCID: PMC10936212 DOI: 10.1128/mbio.03430-23] [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: 12/21/2023] [Accepted: 01/09/2024] [Indexed: 02/08/2024] Open
Abstract
Campylobacter jejuni is a foodborne pathogen commonly found in the intestinal tracts of animals. This pathogen is a leading cause of gastroenteritis in humans. Besides its highly infectious nature, C. jejuni is increasingly resistant to a number of clinically administrated antibiotics. As a consequence, the Centers for Disease Control and Prevention has designated antibiotic-resistant Campylobacter as a serious antibiotic resistance threat in the United States. The C. jejuni CosR regulator is essential to the viability of this bacterium and is responsible for regulating the expression of a number of oxidative stress defense enzymes. Importantly, it also modulates the expression of the CmeABC multidrug efflux system, the most predominant and clinically important system in C. jejuni that mediates resistance to multiple antimicrobials. Here, we report structures of apo-CosR and CosR bound with a 21 bp DNA sequence located at the cmeABC promotor region using both single-particle cryo-electron microscopy and X-ray crystallography. These structures allow us to propose a novel mechanism for CosR regulation that involves a long-distance conformational coupling and rearrangement of the secondary structural elements of the regulator to bind target DNA. IMPORTANCE Campylobacter jejuni has emerged as an antibiotic-resistant threat worldwide. CosR is an essential regulator for this bacterium and is important for Campylobacter adaptation to various stresses. Here, we describe the structural basis of CosR binding to target DNA as determined by cryo-electron microscopy and X-ray crystallography. Since CosR is a potential target for intervention, our studies may facilitate the development of novel therapeutics to combat C. jejuni infection.
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Affiliation(s)
- Zhemin Zhang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Yuqi Yan
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Jinji Pang
- Department of Veterinary Microbiology, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Lei Dai
- Department of Veterinary Microbiology, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Qijing Zhang
- Department of Veterinary Microbiology, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Edward W. Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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9
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Cisse A, Desfosses A, Stainer S, Kandiah E, Traore DAK, Bezault A, Schachner-Nedherer AL, Leitinger G, Hoerl G, Hinterdorfer P, Gutsche I, Prassl R, Peters J, Kornmueller K. Targeting structural flexibility in low density lipoprotein by integrating cryo-electron microscopy and high-speed atomic force microscopy. Int J Biol Macromol 2023; 252:126345. [PMID: 37619685 DOI: 10.1016/j.ijbiomac.2023.126345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/08/2023] [Accepted: 08/13/2023] [Indexed: 08/26/2023]
Abstract
Low-density lipoprotein (LDL) plays a crucial role in cholesterol metabolism. Responsible for cholesterol transport from the liver to the organs, LDL accumulation in the arteries is a primary cause of cardiovascular diseases, such as atherosclerosis. This work focuses on the fundamental question of the LDL molecular structure, as well as the topology and molecular motions of apolipoprotein B-100 (apo B-100), which is addressed by single-particle cryo-electron microscopy (cryo-EM) and high-speed atomic force microscopy (HS-AFM). Our results suggest a revised model of the LDL core organization with respect to the cholesterol ester (CE) arrangement. In addition, a high-density region close to the flattened poles could be identified, likely enriched in free cholesterol. The most remarkable new details are two protrusions on the LDL surface, attributed to the protein apo B-100. HS-AFM adds the dimension of time and reveals for the first time a highly dynamic direct description of LDL, where we could follow large domain fluctuations of the protrusions in real time. To tackle the inherent flexibility and heterogeneity of LDL, the cryo-EM maps are further assessed by 3D variability analysis. Our study gives a detailed explanation how to approach the intrinsic flexibility of a complex system comprising lipids and protein.
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Affiliation(s)
- Aline Cisse
- Université Grenoble Alpes, CNRS, LiPhy, Grenoble, France; Institut Laue-Langevin, Grenoble, France
| | - Ambroise Desfosses
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Sarah Stainer
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria
| | | | - Daouda A K Traore
- Institut Laue-Langevin, Grenoble, France; Faculté de Pharmacie, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali; Faculty of Natural Sciences, School of Life Sciences, Keele University, Staffordshire, UK
| | - Armel Bezault
- Institut Européen de Chimie et Biologie, UAR3033/US001, Université de Bordeaux, CNRS, INSERM 2, Pessac, France; Structural Image Analysis Unit, Department of Structural Biology and Chemistry, Institut Pasteur, Université Paris Cité, CNRS UMR3528, Paris, France
| | - Anna-Laurence Schachner-Nedherer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical Physics and Biophysics Division, Medical University of Graz, Graz, Austria
| | - Gerd Leitinger
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
| | - Gerd Hoerl
- Otto Loewi Research Center, Physiological Chemistry, Medical University of Graz, Graz, Austria
| | - Peter Hinterdorfer
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Irina Gutsche
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Ruth Prassl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical Physics and Biophysics Division, Medical University of Graz, Graz, Austria
| | - Judith Peters
- Université Grenoble Alpes, CNRS, LiPhy, Grenoble, France; Institut Laue-Langevin, Grenoble, France; Institut Universitaire de France, France.
| | - Karin Kornmueller
- Institut Laue-Langevin, Grenoble, France; Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical Physics and Biophysics Division, Medical University of Graz, Graz, Austria.
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10
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Semchonok DA, Kyrilis FL, Hamdi F, Kastritis PL. Cryo-EM of a heterogeneous biochemical fraction elucidates multiple protein complexes from a multicellular thermophilic eukaryote. J Struct Biol X 2023; 8:100094. [PMID: 37638207 PMCID: PMC10451023 DOI: 10.1016/j.yjsbx.2023.100094] [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: 09/05/2022] [Revised: 07/27/2023] [Accepted: 08/07/2023] [Indexed: 08/29/2023] Open
Abstract
Biomolecular complexes and their interactions govern cellular structure and function. Understanding their architecture is a prerequisite for dissecting the cell's inner workings, but their higher-order assembly is often transient and challenging for structural analysis. Here, we performed cryo-EM on a single, highly heterogeneous biochemical fraction derived from Chaetomium thermophilum cell extracts to visualize the biomolecular content of the multicellular eukaryote. After cryo-EM single-particle image processing, results showed that a simultaneous three-dimensional structural characterization of multiple chemically diverse biomacromolecules is feasible. Namely, the thermophilic, eukaryotic complexes of (a) ATP citrate-lyase, (b) Hsp90, (c) 20S proteasome, (d) Hsp60 and (e) UDP-glucose pyrophosphorylase were characterized. In total, all five complexes have been structurally dissected in a thermophilic eukaryote in a total imaged sample area of 190.64 μm2, and two, in particular, 20S proteasome and Hsp60, exhibit side-chain resolution features. The C. thermophilum Hsp60 near-atomic model was resolved at 3.46 Å (FSC = 0.143) and shows a hinge-like conformational change of its equatorial domain, highly similar to the one previously shown for its bacterial orthologue, GroEL. This work demonstrates that cryo-EM of cell extracts will greatly accelerate the structural analysis of cellular complexes and provide unprecedented opportunities to annotate architectures of biomolecules in a holistic approach.
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Affiliation(s)
- Dmitry A. Semchonok
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
| | - Fotis L. Kyrilis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Farzad Hamdi
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
| | - Panagiotis L. Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
- Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, Halle/Saale, Germany
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11
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Zhang Z, Tringides ML, Morgan CE, Miyagi M, Mears JA, Hoppel CL, Yu EW. High-Resolution Structural Proteomics of Mitochondria Using the 'Build and Retrieve' Methodology. Mol Cell Proteomics 2023; 22:100666. [PMID: 37839702 PMCID: PMC10709515 DOI: 10.1016/j.mcpro.2023.100666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 10/17/2023] Open
Abstract
The application of integrated systems biology to the field of structural biology is a promising new direction, although it is still in the infant stages of development. Here we report the use of single particle cryo-EM to identify multiple proteins from three enriched heterogeneous fractions prepared from human liver mitochondrial lysate. We simultaneously identify and solve high-resolution structures of nine essential mitochondrial enzymes with key metabolic functions, including fatty acid catabolism, reactive oxidative species clearance, and amino acid metabolism. Our methodology also identified multiple distinct members of the acyl-CoA dehydrogenase family. This work highlights the potential of cryo-EM to explore tissue proteomics at the atomic level.
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Affiliation(s)
- Zhemin Zhang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Marios L Tringides
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Christopher E Morgan
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Masaru Miyagi
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Jason A Mears
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Charles L Hoppel
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Edward W Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.
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12
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Qin Y, Yu D, Wu D, Dong J, Li WT, Ye C, Cheung KC, Zhang Y, Xu Y, Wang Y, Shi YS, Dang S. Cryo-EM structure of TMEM63C suggests it functions as a monomer. Nat Commun 2023; 14:7265. [PMID: 37945568 PMCID: PMC10636204 DOI: 10.1038/s41467-023-42956-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023] Open
Abstract
The TMEM63 family proteins (A, B, and C), calcium-permeable channels in animals that are preferentially activated by hypo-osmolality, have been implicated in various physiological functions. Deficiency of these channels would cause many diseases including hearing loss. However, their structures and physiological roles are not yet well understood. In this study, we determine the cryo-electron microscopy (cryo-EM) structure of the mouse TMEM63C at 3.56 Å, and revealed structural differences compared to TMEM63A, TMEM63B, and the plant orthologues OSCAs. Further structural guided mutagenesis and calcium imaging demonstrated the important roles of the coupling of TM0 and TM6 in channel activity. Additionally, we confirm that TMEM63C exists primarily as a monomer under physiological conditions, in contrast, TMEM63B is a mix of monomer and dimer in cells, suggesting that oligomerization is a regulatory mechanism for TMEM63 proteins.
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Affiliation(s)
- Yuqi Qin
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Daqi Yu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Dan Wu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital Affiliated to Medical School, Nanjing University, Nanjing, 210032, China
| | - Jiangqing Dong
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - William Thomas Li
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Chang Ye
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital Affiliated to Medical School, Nanjing University, Nanjing, 210032, China
| | - Kai Chit Cheung
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Yingyi Zhang
- Biological Cryo-EM Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Yun Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital Affiliated to Medical School, Nanjing University, Nanjing, 210032, China
| | - YongQiang Wang
- Howard Hughes Medical Institute, University of California, San Francisco, CA, 94158, USA.
| | - Yun Stone Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital Affiliated to Medical School, Nanjing University, Nanjing, 210032, China.
- Guangdong Institute of Intelligence Science and Technology, Hengqin, Zhuhai, 519031, China.
| | - Shangyu Dang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.
- HKUST-Shenzhen Research Institute, Nanshan, Shenzhen, 518057, China.
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13
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Ochner H, Bharat TAM. Charting the molecular landscape of the cell. Structure 2023; 31:1297-1305. [PMID: 37699393 PMCID: PMC7615466 DOI: 10.1016/j.str.2023.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 09/14/2023]
Abstract
Biological function of macromolecules is closely tied to their cellular location, as well as to interactions with other molecules within the native environment of the cell. Therefore, to obtain detailed mechanistic insights into macromolecular functionality, one of the outstanding targets for structural biology is to produce an atomic-level understanding of the cell. One structural biology technique that has already been used to directly derive atomic models of macromolecules from cells, without any additional external information, is electron cryotomography (cryoET). In this perspective article, we discuss possible routes to chart the molecular landscape of the cell by advancing cryoET imaging as well as by embedding cryoET into correlative imaging workflows.
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Affiliation(s)
- Hannah Ochner
- Structural Studies Division, MRC Laboratory of Molecular Biology, CB2 0QH Cambridge, UK
| | - Tanmay A M Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, CB2 0QH Cambridge, UK.
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14
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KIM S, KAMARULZAMAN L, TANIGUCHI Y. Recent methodological advances towards single-cell proteomics. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2023; 99:306-327. [PMID: 37673661 PMCID: PMC10749393 DOI: 10.2183/pjab.99.021] [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: 02/14/2023] [Accepted: 07/20/2023] [Indexed: 09/08/2023]
Abstract
Studying the central dogma at the single-cell level has gained increasing attention to reveal hidden cell lineages and functions that cannot be studied using traditional bulk analyses. Nonetheless, most single-cell studies exploiting genomic and transcriptomic levels fail to address information on proteins that are central to many important biological processes. Single-cell proteomics enables understanding of the functional status of individual cells and is particularly crucial when the specimen is composed of heterogeneous entities of cells. With the growing importance of this field, significant methodological advancements have emerged recently. These include miniaturized and automated sample preparation, multi-omics analyses, and combined analyses of multiple techniques such as mass spectrometry and microscopy. Moreover, artificial intelligence and single-molecule detection technologies have advanced throughput and improved sensitivity limitations, respectively, over conventional methods. In this review, we summarize cutting-edge methodologies for single-cell proteomics and relevant emerging technologies that have been reported in the last 5 years, and provide an outlook on this research field.
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Affiliation(s)
- Sooyeon KIM
- Laboratory for Cell Systems Control, Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Latiefa KAMARULZAMAN
- Laboratory for Cell Systems Control, Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Yuichi TANIGUCHI
- Laboratory for Cell Systems Control, Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo-ku, Kyoto, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
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15
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Yin YM, Sun ZY, Wang DW, Xi Z. Discovery of Benzothiazolylpyrazole-4-Carboxamides as Potent Succinate Dehydrogenase Inhibitors through Active Fragment Exchange and Link Approach. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:14471-14482. [PMID: 37775473 DOI: 10.1021/acs.jafc.3c03646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
Succinate dehydrogenase (SDH) is an attractive target for developing green fungicides to manage agricultural pathogens in modern agriculture research. Herein, in this work, we report the discovery of benzothiazolylpyrazole-4-carboxamides I-III as potent SDH inhibitors using active fragment exchange and link approach. The results of the fungicidal activity assays showed that some of the synthesized compounds exhibited excellent inhibition against the tested fungi. Systematic structure-activity relationship studies led to the discovery of compound Ip, N-(1-((4,6-difluorobenzo[d]thiazol-2-yl)thio)propan-2-yl)-3-(difluoromethyl)-N-methoxy-1-methyl-1H-pyrazole-4-carboxamide, which showed higher fungicidal activity against Fusarium graminearum Schw (EC50 = 0.93 μg/mL) than the commercial fungicides thifluzamide (EC50 > 50 μg/mL) and boscalid (EC50 > 50 μg/mL). The molecular simulation studies suggested that hydrophobic interactions were the primary driving forces between ligands and SDH. Promisingly, we found that Ip could stimulate the growth of wheat seedlings and Arabidopsis thaliana and increase the biomass of the treated plants. Preliminary studies on the plant growth promoter mechanism of Ip indicated that it could increase nitrate reductase activity in planta, that, in turn, stimulates the growth of plants.
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Affiliation(s)
- Yan-Ming Yin
- State Key Laboratory of Elemento-Organic Chemistry, National Pesticide Engineering Research Center, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, PR China
| | - Zong-Yue Sun
- State Key Laboratory of Elemento-Organic Chemistry, National Pesticide Engineering Research Center, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, PR China
| | - Da-Wei Wang
- State Key Laboratory of Elemento-Organic Chemistry, National Pesticide Engineering Research Center, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, PR China
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry, National Pesticide Engineering Research Center, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, PR China
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16
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Vénien-Bryan C, Fernandes CAH. Overview of Membrane Protein Sample Preparation for Single-Particle Cryo-Electron Microscopy Analysis. Int J Mol Sci 2023; 24:14785. [PMID: 37834233 PMCID: PMC10573263 DOI: 10.3390/ijms241914785] [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: 08/12/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Single-particle cryo-electron microscopy (cryo-EM SPA) has recently emerged as an exceptionally well-suited technique for determining the structure of membrane proteins (MPs). Indeed, in recent years, huge increase in the number of MPs solved via cryo-EM SPA at a resolution better than 3.0 Å in the Protein Data Bank (PDB) has been observed. However, sample preparation remains a significant challenge in the field. Here, we evaluated the MPs solved using cryo-EM SPA deposited in the PDB in the last two years at a resolution below 3.0 Å. The most critical parameters for sample preparation are as follows: (i) the surfactant used for protein extraction from the membrane, (ii) the surfactant, amphiphiles, nanodiscs or other molecules present in the vitrification step, (iii) the vitrification method employed, and (iv) the type of grids used. The aim is not to provide a definitive answer on the optimal sample conditions for cryo-EM SPA of MPs but rather assess the current trends in the MP structural biology community towards obtaining high-resolution cryo-EM structures.
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Affiliation(s)
| | - Carlos A. H. Fernandes
- Unité Mixte de Recherche (UMR) 7590, Centre National de la Recherche Scientifique (CNRS), Muséum National d’Histoire Naturelle, Institut de Recherche pour le Développement (IRD), Institut de Minéralogie, Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Université, 75005 Paris, France;
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17
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Chojnowski G. DoubleHelix: nucleic acid sequence identification, assignment and validation tool for cryo-EM and crystal structure models. Nucleic Acids Res 2023; 51:8255-8269. [PMID: 37395405 PMCID: PMC10450167 DOI: 10.1093/nar/gkad553] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/29/2023] [Accepted: 06/16/2023] [Indexed: 07/04/2023] Open
Abstract
Sequence assignment is a key step of the model building process in both cryogenic electron microscopy (cryo-EM) and macromolecular crystallography (MX). If the assignment fails, it can result in difficult to identify errors affecting the interpretation of a model. There are many model validation strategies that help experimentalists in this step of protein model building, but they are virtually non-existent for nucleic acids. Here, I present doubleHelix-a comprehensive method for assignment, identification, and validation of nucleic acid sequences in structures determined using cryo-EM and MX. The method combines a neural network classifier of nucleobase identities and a sequence-independent secondary structure assignment approach. I show that the presented method can successfully assist sequence-assignment step in nucleic-acid model building at lower resolutions, where visual map interpretation is very difficult. Moreover, I present examples of sequence assignment errors detected using doubleHelix in cryo-EM and MX structures of ribosomes deposited in the Protein Data Bank, which escaped the scrutiny of available model-validation approaches. The doubleHelix program source code is available under BSD-3 license at https://gitlab.com/gchojnowski/doublehelix.
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Affiliation(s)
- Grzegorz Chojnowski
- European Molecular Biology Laboratory, Hamburg Unit, Notkestraße 85, 22607 Hamburg, Germany
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18
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Azinas S, Carroni M. Cryo-EM uniqueness in structure determination of macromolecular complexes: A selected structural anthology. Curr Opin Struct Biol 2023; 81:102621. [PMID: 37315343 DOI: 10.1016/j.sbi.2023.102621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 06/16/2023]
Abstract
Cryogenic electron microscopy (cryo-EM) has become in the past 10 years one of the major tools for the structure determination of proteins. Nowadays, the structure prediction field is experiencing the same revolution and, using AlphaFold2, it is possible to have high-confidence atomic models for virtually any polypeptide chain, smaller than 4000 amino acids, in a simple click. Even in a scenario where all polypeptide chain folding were to be known, cryo-EM retains specific characteristics that make it a unique tool for the structure determination of macromolecular complexes. Using cryo-EM, it is possible to obtain near-atomic structures of large and flexible mega-complexes, describe conformational panoramas, and potentially develop a structural proteomic approach from fully ex vivo specimens.
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Affiliation(s)
- Stavros Azinas
- SciLifeLab, Department of Biochemistry and Biophysics, Stockholm University, Tomtebodavägen 23A, Solna, 17165, Sweden. https://twitter.com/@stav____
| | - Marta Carroni
- SciLifeLab, Department of Biochemistry and Biophysics, Stockholm University, Tomtebodavägen 23A, Solna, 17165, Sweden.
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19
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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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20
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Zheng F, Georgescu RE, Yao NY, O'Donnell ME, Li H. Structures of 9-1-1 DNA checkpoint clamp loading at gaps from start to finish and ramification on biology. Cell Rep 2023; 42:112694. [PMID: 37392384 PMCID: PMC10529453 DOI: 10.1016/j.celrep.2023.112694] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/01/2023] [Accepted: 06/09/2023] [Indexed: 07/03/2023] Open
Abstract
Rad24-RFC (replication factor C) loads the 9-1-1 checkpoint clamp onto the recessed 5' ends by binding a 5' DNA at an external surface site and threading the 3' single-stranded DNA (ssDNA) into 9-1-1. We find here that Rad24-RFC loads 9-1-1 onto DNA gaps in preference to a recessed 5' end, thus presumably leaving 9-1-1 on duplex 3' ss/double-stranded DNA (dsDNA) after Rad24-RFC ejects from DNA. We captured five Rad24-RFC-9-1-1 loading intermediates using a 10-nt gap DNA. We also determined the structure of Rad24-RFC-9-1-1 using a 5-nt gap DNA. The structures reveal that Rad24-RFC is unable to melt DNA ends and that a Rad24 loop limits the dsDNA length in the chamber. These observations explain Rad24-RFC's preference for a preexisting gap of over 5-nt ssDNA and suggest a direct role of the 9-1-1 in gap repair with various TLS (trans-lesion synthesis) polymerases in addition to signaling the ATR kinase.
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Affiliation(s)
- Fengwei Zheng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Roxana E Georgescu
- DNA Replication Laboratory, The Rockefeller University, New York, NY, USA
| | - Nina Y Yao
- DNA Replication Laboratory, The Rockefeller University, New York, NY, USA
| | - Michael E O'Donnell
- DNA Replication Laboratory, The Rockefeller University, New York, NY, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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21
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Moseng MA, Su CC, Klenotic PA, Delpire E, Yu EW. Response to Comment on "Inhibition mechanism of NKCC1 involves the carboxyl terminus and long-range conformational coupling". SCIENCE ADVANCES 2023; 9:eadi5716. [PMID: 37436983 DOI: 10.1126/sciadv.adi5716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/07/2023] [Indexed: 07/14/2023]
Abstract
Moseng et al. recently reported four cryo-electron microscopy structures of the human Na-K-2Cl cotransporter-1 (hNKCC1), both in the absence and presence of bound loop diuretic (furosemide or bumetanide). This research article included high-resolution structural information for a previously undefined structure of apo-hNKCC1 containing both the transmembrane and cytosolic carboxyl-terminal domains. The manuscript also demonstrated various conformational states of this cotransporter induced by diuretic drugs. On the basis of the structural information, the authors proposed a scissor-like inhibition mechanism that involves a coupled movement between the cytosolic and transmembrane domains of hNKCC1. This work has provided important insights into the mechanism of inhibition and substantiated the concept of a long-distance coupling involving movements of both the transmembrane and carboxyl-terminal cytoplasmic domains for inhibition.
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Affiliation(s)
- Mitchell A Moseng
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Chih-Chia Su
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Philip A Klenotic
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Eric Delpire
- Department of Anesthesiology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Edward W Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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22
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Su CC, Lyu M, Zhang Z, Miyagi M, Huang W, Taylor DJ, Yu EW. High-resolution structural-omics of human liver enzymes. Cell Rep 2023; 42:112609. [PMID: 37289586 PMCID: PMC10592444 DOI: 10.1016/j.celrep.2023.112609] [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: 12/26/2022] [Revised: 03/28/2023] [Accepted: 05/20/2023] [Indexed: 06/10/2023] Open
Abstract
We applied raw human liver microsome lysate to a holey carbon grid and used cryo-electron microscopy (cryo-EM) to define its composition. From this sample we identified and simultaneously determined high-resolution structural information for ten unique human liver enzymes involved in diverse cellular processes. Notably, we determined the structure of the endoplasmic bifunctional protein H6PD, where the N- and C-terminal domains independently possess glucose-6-phosphate dehydrogenase and 6-phosphogluconolactonase enzymatic activity, respectively. We also obtained the structure of heterodimeric human GANAB, an ER glycoprotein quality-control machinery that contains a catalytic α subunit and a noncatalytic β subunit. In addition, we observed a decameric peroxidase, PRDX4, which directly contacts a disulfide isomerase-related protein, ERp46. Structural data suggest that several glycosylations, bound endogenous compounds, and ions associate with these human liver enzymes. These results highlight the importance of cryo-EM in facilitating the elucidation of human organ proteomics at the atomic level.
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Affiliation(s)
- Chih-Chia Su
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Meinan Lyu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Zhemin Zhang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Masaru Miyagi
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Wei Huang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Derek J Taylor
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Edward W Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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23
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Taylor DW. Structural biology of an organ. Cell Rep 2023; 42:112622. [PMID: 37289587 PMCID: PMC11104778 DOI: 10.1016/j.celrep.2023.112622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/10/2023] Open
Abstract
Su et al.1 use a build-and-retrieve approach to both identify and determine structures of ten macromolecular machines in the human liver. The authors' method will launch researchers forward in understanding the structural biology of the cell (or organ).
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Affiliation(s)
- David W Taylor
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA; Interdisciplinary Life Sciences Graduate Program, University of Texas at Austin, Austin, TX, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA; LIVESTRONG Cancer Institute, Dell Medical School, University of Texas at Austin, Austin, TX, USA.
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24
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Iverson TM, Singh PK, Cecchini G. An evolving view of complex II-noncanonical complexes, megacomplexes, respiration, signaling, and beyond. J Biol Chem 2023; 299:104761. [PMID: 37119852 PMCID: PMC10238741 DOI: 10.1016/j.jbc.2023.104761] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/20/2023] [Accepted: 04/22/2023] [Indexed: 05/01/2023] Open
Abstract
Mitochondrial complex II is traditionally studied for its participation in two key respiratory processes: the electron transport chain and the Krebs cycle. There is now a rich body of literature explaining how complex II contributes to respiration. However, more recent research shows that not all of the pathologies associated with altered complex II activity clearly correlate with this respiratory role. Complex II activity has now been shown to be necessary for a range of biological processes peripherally related to respiration, including metabolic control, inflammation, and cell fate. Integration of findings from multiple types of studies suggests that complex II both participates in respiration and controls multiple succinate-dependent signal transduction pathways. Thus, the emerging view is that the true biological function of complex II is well beyond respiration. This review uses a semichronological approach to highlight major paradigm shifts that occurred over time. Special emphasis is given to the more recently identified functions of complex II and its subunits because these findings have infused new directions into an established field.
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Affiliation(s)
- T M Iverson
- Departments of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA; Departments of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee, USA.
| | - Prashant K Singh
- Departments of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Gary Cecchini
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, California, USA; Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA.
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25
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Zheng F, Georgescu RE, Yao NY, O’Donnell ME, Li H. Structures of 9-1-1 DNA checkpoint clamp loading at gaps from start to finish and ramification to biology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539266. [PMID: 37205533 PMCID: PMC10187155 DOI: 10.1101/2023.05.03.539266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Recent structural studies show the Rad24-RFC loads the 9-1-1 checkpoint clamp onto a recessed 5' end by binding the 5' DNA on Rad24 at an external surface site and threading the 3' ssDNA into the well-established internal chamber and into 9-1-1. We find here that Rad24-RFC loads 9-1-1 onto DNA gaps in preference to a recessed 5' DNA end, thus presumably leaving 9-1-1 on a 3' ss/ds DNA after Rad24-RFC ejects from the 5' gap end and may explain reports of 9-1-1 directly functioning in DNA repair with various TLS polymerases, in addition to signaling the ATR kinase. To gain a deeper understanding of 9-1-1 loading at gaps we report high-resolution structures of Rad24-RFC during loading of 9-1-1 onto 10-nt and 5-nt gapped DNAs. At a 10-nt gap we captured five Rad24-RFC-9-1-1 loading intermediates in which the 9-1-1 DNA entry gate varies from fully open to fully closed around DNA using ATPγS, supporting the emerging view that ATP hydrolysis is not needed for clamp opening/closing, but instead for dissociation of the loader from the clamp encircling DNA. The structure of Rad24-RFC-9-1-1 at a 5-nt gap shows a 180° axially rotated 3'-dsDNA which orients the template strand to bridge the 3'- and 5'- junctions with a minimum 5-nt ssDNA. The structures reveal a unique loop on Rad24 that limits the length of dsDNA in the inner chamber, and inability to melt DNA ends unlike RFC, thereby explaining Rad24-RFC's preference for a preexisting ssDNA gap and suggesting a direct role in gap repair in addition to its checkpoint role.
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Affiliation(s)
- Fengwei Zheng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Roxana E. Georgescu
- DNA Replication Laboratory, The Rockefeller University, New York, New York, USA
| | - Nina Y. Yao
- DNA Replication Laboratory, The Rockefeller University, New York, New York, USA
| | - Michael E. O’Donnell
- DNA Replication Laboratory, The Rockefeller University, New York, New York, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA
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26
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Morgan CE, Kang YS, Green AB, Smith KP, Dowgiallo MG, Miller BC, Chiaraviglio L, Truelson KA, Zulauf KE, Rodriguez S, Kang AD, Manetsch R, Yu EW, Kirby JE. Streptothricin F is a bactericidal antibiotic effective against highly drug-resistant gram-negative bacteria that interacts with the 30S subunit of the 70S ribosome. PLoS Biol 2023; 21:e3002091. [PMID: 37192172 DOI: 10.1371/journal.pbio.3002091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 03/22/2023] [Indexed: 05/18/2023] Open
Abstract
The streptothricin natural product mixture (also known as nourseothricin) was discovered in the early 1940s, generating intense initial interest because of excellent gram-negative activity. Here, we establish the activity spectrum of nourseothricin and its main components, streptothricin F (S-F, 1 lysine) and streptothricin D (S-D, 3 lysines), purified to homogeneity, against highly drug-resistant, carbapenem-resistant Enterobacterales (CRE) and Acinetobacter baumannii. For CRE, the MIC50 and MIC90 for S-F and S-D were 2 and 4 μM, and 0.25 and 0.5 μM, respectively. S-F and nourseothricin showed rapid, bactericidal activity. S-F and S-D both showed approximately 40-fold greater selectivity for prokaryotic than eukaryotic ribosomes in in vitro translation assays. In vivo, delayed renal toxicity occurred at >10-fold higher doses of S-F compared with S-D. Substantial treatment effect of S-F in the murine thigh model was observed against the otherwise pandrug-resistant, NDM-1-expressing Klebsiella pneumoniae Nevada strain with minimal or no toxicity. Cryo-EM characterization of S-F bound to the A. baumannii 70S ribosome defines extensive hydrogen bonding of the S-F steptolidine moiety, as a guanine mimetic, to the 16S rRNA C1054 nucleobase (Escherichia coli numbering) in helix 34, and the carbamoylated gulosamine moiety of S-F with A1196, explaining the high-level resistance conferred by corresponding mutations at the residues identified in single rrn operon E. coli. Structural analysis suggests that S-F probes the A-decoding site, which potentially may account for its miscoding activity. Based on unique and promising activity, we suggest that the streptothricin scaffold deserves further preclinical exploration as a potential therapeutic for drug-resistant, gram-negative pathogens.
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Affiliation(s)
- Christopher E Morgan
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Yoon-Suk Kang
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alex B Green
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Kenneth P Smith
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Matthew G Dowgiallo
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Brandon C Miller
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Lucius Chiaraviglio
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Katherine A Truelson
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Katelyn E Zulauf
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Shade Rodriguez
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Anthony D Kang
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Roman Manetsch
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States of America
- Center for Drug Discovery, Northeastern University, Boston, Massachusetts, United States of America
| | - Edward W Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - James E Kirby
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
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27
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Zhou J, Lan Q, Li W, Ji LN, Wang K, Xia XH. Single Molecule Protein Segments Sequencing by a Plasmonic Nanopore. NANO LETTERS 2023; 23:2800-2807. [PMID: 36927001 DOI: 10.1021/acs.nanolett.3c00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Obtaining sequential and conformational information on proteins is vital to understand their functions. Although the nanopore-based electrical detection can sense single molecule (SM) protein and distinguish among different amino acids, this approach still faces difficulties in slowing down protein translocation and improving ionic current signal-to-noise ratio. Here, we observe the unfolding and multistep sequential translocation of SM cytochrome c (cyt c) through a surface enhanced Raman scattering (SERS) active conical gold nanopore. High bias voltage unfolds SM protein causing more exposure of amino acid residues to the nanopore, which slows down the protein translocation. Specific SERS traces of different SM cyt c segments are then recorded sequentially when they pass through the hotspot inside the gold nanopore. This study shows that the combination of SM SERS with a nanopore can provide a direct insight into protein segments and expedite the development of nanopore toward SM protein sequencing.
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Affiliation(s)
- Juan Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Qing Lan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wang Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Li-Na Ji
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Kang Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xing-Hua Xia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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28
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Reid DJ, Thibert S, Zhou M. Dissecting the structural heterogeneity of proteins by native mass spectrometry. Protein Sci 2023; 32:e4612. [PMID: 36851867 PMCID: PMC10031758 DOI: 10.1002/pro.4612] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/01/2023]
Abstract
A single gene yields many forms of proteins via combinations of posttranscriptional/posttranslational modifications. Proteins also fold into higher-order structures and interact with other molecules. The combined molecular diversity leads to the heterogeneity of proteins that manifests as distinct phenotypes. Structural biology has generated vast amounts of data, effectively enabling accurate structural prediction by computational methods. However, structures are often obtained heterologously under homogeneous states in vitro. The lack of native heterogeneity under cellular context creates challenges in precisely connecting the structural data to phenotypes. Mass spectrometry (MS) based proteomics methods can profile proteome composition of complex biological samples. Most MS methods follow the "bottom-up" approach, which denatures and digests proteins into short peptide fragments for ease of detection. Coupled with chemical biology approaches, higher-order structures can be probed via incorporation of covalent labels on native proteins that are maintained at the peptide level. Alternatively, native MS follows the "top-down" approach and directly analyzes intact proteins under nondenaturing conditions. Various tandem MS activation methods can dissect the intact proteins for in-depth structural elucidation. Herein, we review recent native MS applications for characterizing heterogeneous samples, including proteins binding to mixtures of ligands, homo/hetero-complexes with varying stoichiometry, intrinsically disordered proteins with dynamic conformations, glycoprotein complexes with mixed modification states, and active membrane protein complexes in near-native membrane environments. We summarize the benefits, challenges, and ongoing developments in native MS, with the hope to demonstrate an emerging technology that complements other tools by filling the knowledge gaps in understanding the molecular heterogeneity of proteins.
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Affiliation(s)
- Deseree J. Reid
- Chemical and Biological Signature SciencesPacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Stephanie Thibert
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Mowei Zhou
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWashingtonUSA
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29
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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] [MESH Headings] [Grants] [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 Escherichia 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 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).
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Affiliation(s)
- Yirui Guo
- Department of BiophysicsThe University of Texas Southwestern Medical CenterDallasTexasUSA
- Ligo AnalyticsDallasTexasUSA
| | - Elina Karimullina
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryAlbertaCanada
- Center for Structural Genomics of Infectious Diseases (CSGID)ChicagoIllinoisUSA
- Centers for Research on Structural Biology of Infectious Diseases (CSBID)ChicagoIllinoisUSA
| | - Tabitha Emde
- Department of BiophysicsThe University of Texas Southwestern Medical CenterDallasTexasUSA
- Center for Structural Genomics of Infectious Diseases (CSGID)ChicagoIllinoisUSA
- Centers for Research on Structural Biology of Infectious Diseases (CSBID)ChicagoIllinoisUSA
| | - Zbyszek Otwinowski
- Department of BiophysicsThe University of Texas Southwestern Medical CenterDallasTexasUSA
- Center for Structural Genomics of Infectious Diseases (CSGID)ChicagoIllinoisUSA
- Centers for Research on Structural Biology of Infectious Diseases (CSBID)ChicagoIllinoisUSA
- Department of BiochemistryThe University of Texas Southwestern Medical CenterDallasTexasUSA
| | - Dominika Borek
- Department of BiophysicsThe University of Texas Southwestern Medical CenterDallasTexasUSA
- Center for Structural Genomics of Infectious Diseases (CSGID)ChicagoIllinoisUSA
- Centers for Research on Structural Biology of Infectious Diseases (CSBID)ChicagoIllinoisUSA
- Department of BiochemistryThe University of Texas Southwestern Medical CenterDallasTexasUSA
| | - Alexei Savchenko
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryAlbertaCanada
- Center for Structural Genomics of Infectious Diseases (CSGID)ChicagoIllinoisUSA
- Centers for Research on Structural Biology of Infectious Diseases (CSBID)ChicagoIllinoisUSA
- BioZone, Department of Chemical Engineering and Applied ChemistryUniversity of TorontoTorontoOntarioCanada
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30
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Park H, Wang W, Min SH, Ren Y, Shin K, Han X. Artificial organelles for sustainable chemical energy conversion and production in artificial cells: Artificial mitochondrion and chloroplasts. BIOPHYSICS REVIEWS 2023; 4:011311. [PMID: 38510162 PMCID: PMC10903398 DOI: 10.1063/5.0131071] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 02/17/2023] [Indexed: 03/22/2024]
Abstract
Sustainable energy conversion modules are the main challenges for building complex reaction cascades in artificial cells. Recent advances in biotechnology have enabled this sustainable energy supply, especially the adenosine triphosphate (ATP), by mimicking the organelles, which are the core structures for energy conversion in living cells. Three components are mainly shared by the artificial organelles: the membrane compartment separating the inner and outer parts, membrane proteins for proton translocation, and the molecular rotary machine for ATP synthesis. Depending on the initiation factors, they are further categorized into artificial mitochondrion and artificial chloroplasts, which use chemical nutrients for oxidative phosphorylation and light for photosynthesis, respectively. In this review, we summarize the essential components needed for artificial organelles and then review the recent progress on two different artificial organelles. Recent strategies, purified and identified proteins, and working principles are discussed. With more study on the artificial mitochondrion and artificial chloroplasts, they are expected to be very powerful tools, allowing us to achieve complex cascading reactions in artificial cells, like the ones that happen in real cells.
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Affiliation(s)
- Hyun Park
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, South Korea
| | - Weichen Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Seo Hyeon Min
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, South Korea
| | - Yongshuo Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Kwanwoo Shin
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, South Korea
| | - Xiaojun Han
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
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31
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Tringides ML, Zhang Z, Morgan CE, Su CC, Yu EW. A cryo-electron microscopic approach to elucidate protein structures from human brain microsomes. Life Sci Alliance 2023; 6:6/2/e202201724. [PMID: 36450447 PMCID: PMC9713474 DOI: 10.26508/lsa.202201724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 12/05/2022] Open
Abstract
We recently developed a "Build and Retrieve" cryo-electron microscopy (cryo-EM) methodology, which is capable of simultaneously producing near-atomic resolution cryo-EM maps for several individual proteins from a heterogeneous, multiprotein sample. Here we report the use of "Build and Retrieve" to define the composition of a raw human brain microsomal lysate. From this sample, we simultaneously identify and solve cryo-EM structures of five different brain enzymes whose functions affect neurotransmitter recycling, iron metabolism, glycolysis, axonal development, energy homeostasis, and retinoic acid biosynthesis. Interestingly, malfunction of these important proteins has been directly linked to several neurodegenerative disorders, such as Alzheimer's, Huntington's, and Parkinson's diseases. Our work underscores the importance of cryo-EM in facilitating tissue and organ proteomics at the atomic level.
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Affiliation(s)
- Marios L Tringides
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Zhemin Zhang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Christopher E Morgan
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Chih-Chia Su
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Edward W Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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32
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Lyu M, Su CC, Miyagi M, Yu EW. Simultaneous solving high-resolution structures of various enzymes from human kidney microsomes. Life Sci Alliance 2023; 6:6/2/e202201580. [PMID: 36450445 PMCID: PMC9713302 DOI: 10.26508/lsa.202201580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 12/02/2022] Open
Abstract
The ability to investigate tissues and organs through an integrated systems biology approach has been thought to be unobtainable in the field of structural biology, where the techniques mainly focus on a particular biomacromolecule of interest. Here we report the use of cryo-electron microscopy (cryo-EM) to define the composition of a raw human kidney microsomal lysate. We simultaneously identify and solve cryo-EM structures of four distinct kidney enzymes whose functions have been linked to protein biosynthesis and quality control, biosynthesis of retinoic acid, gluconeogenesis and glycolysis, and the regulation and metabolism of amino acids. Interestingly, all four of these enzymes are directly linked to cellular processes that, when disrupted, can contribute to the onset and progression of diabetes. This work underscores the potential of cryo-EM to facilitate tissue and organ proteomics at the atomic level.
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Affiliation(s)
- Meinan Lyu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Chih-Chia Su
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Masaru Miyagi
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Edward W Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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33
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Johansen NT, Tidemand FG, Pedersen MC, Arleth L. Travel light: Essential packing for membrane proteins with an active lifestyle. Biochimie 2023; 205:3-26. [PMID: 35963461 DOI: 10.1016/j.biochi.2022.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/29/2022] [Accepted: 07/23/2022] [Indexed: 11/02/2022]
Abstract
We review the considerable progress during the recent decade in the endeavours of designing, optimising, and utilising carrier particle systems for structural and functional studies of membrane proteins in near-native environments. New and improved systems are constantly emerging, novel studies push the perceived limits of a given carrier system, and specific carrier systems consolidate and entrench themselves as the system of choice for particular classes of target membrane protein systems. This review covers the most frequently used carrier systems for such studies and emphasises similarities and differences between these systems as well as current trends and future directions for the field. Particular interest is devoted to the biophysical properties and membrane mimicking ability of each system and the manner in which this may impact an embedded membrane protein and an eventual structural or functional study.
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Affiliation(s)
- Nicolai Tidemand Johansen
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark.
| | - Frederik Grønbæk Tidemand
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Martin Cramer Pedersen
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
| | - Lise Arleth
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
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34
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Golmohammadzadeh M, Sexton DL, Parmar S, Tocheva EI. Advanced imaging techniques: Microscopy. ADVANCES IN APPLIED MICROBIOLOGY 2023; 122:1-25. [PMID: 37085191 DOI: 10.1016/bs.aambs.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
For decades, bacteria were thought of as "bags" of enzymes, lacking organelles and significant subcellular structures. This stood in sharp contrast with eukaryotes, where intracellular compartmentalization and the role of large-scale order had been known for a long time. However, the emerging field of Bacterial Cell Biology has established that bacteria are in fact highly organized, with most macromolecular components having specific subcellular locations that can change depending on the cell's physiological state (Barry & Gitai, 2011; Lenz & Søgaard-Andersen, 2011; Thanbichler & Shapiro, 2008). For example, we now know that many processes in bacteria are orchestrated by cytoskeletal proteins, which polymerize into surprisingly diverse superstructures, such as rings, sheets, and tread-milling rods (Pilhofer & Jensen, 2013). These superstructures connect individual proteins, macromolecular assemblies, and even two neighboring cells, to affect essential higher-order processes including cell division, DNA segregation, and motility. Understanding these processes requires resolving the in vivo dynamics and ultrastructure at different functional stages of the cell, at macromolecular resolution and in 3-dimensions (3D). Fluorescence light microscopy (fLM) of tagged proteins is highly valuable for investigating protein localization and dynamics, and the resolution power of transmission electron microscopy (TEM) is required to elucidate the structure of macromolecular complexes in vivo and in vitro. This chapter summarizes the most recent advances in LM and TEM approaches that have revolutionized our knowledge and understanding of the microbial world.
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Affiliation(s)
- Mona Golmohammadzadeh
- Department of Microbiology and Immunology, Life Sciences Institute, Health Sciences Mall, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Danielle L Sexton
- Department of Microbiology and Immunology, Life Sciences Institute, Health Sciences Mall, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Shweta Parmar
- Department of Microbiology and Immunology, Life Sciences Institute, Health Sciences Mall, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Elitza I Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, Health Sciences Mall, The University of British Columbia, Vancouver, British Columbia, Canada.
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35
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Morgan CE, Zhang Z, Miyagi M, Golczak M, Yu EW. Toward structural-omics of the bovine retinal pigment epithelium. Cell Rep 2022; 41:111876. [PMID: 36577381 PMCID: PMC9875382 DOI: 10.1016/j.celrep.2022.111876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 10/12/2022] [Accepted: 12/02/2022] [Indexed: 12/28/2022] Open
Abstract
The use of an integrated systems biology approach to investigate tissues and organs has been thought to be impracticable in the field of structural biology, where the techniques mainly focus on determining the structure of a particular biomacromolecule of interest. Here, we report the use of cryoelectron microscopy (cryo-EM) to define the composition of a raw bovine retinal pigment epithelium (RPE) lysate. From this sample, we simultaneously identify and solve cryo-EM structures of seven different RPE enzymes whose functions affect neurotransmitter recycling, iron metabolism, gluconeogenesis, glycolysis, axonal development, and energy homeostasis. Interestingly, dysfunction of these important proteins has been directly linked to several neurodegenerative disorders, including Huntington's disease, amyotrophic lateral sclerosis (ALS), Parkinson's disease, Alzheimer's disease, and schizophrenia. Our work underscores the importance of cryo-EM in facilitating tissue and organ proteomics at the atomic level.
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Affiliation(s)
- Christopher E. Morgan
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA,Department of Chemistry, Thiel College, Greenville, PA 16125, USA,These authors contributed equally
| | - Zhemin Zhang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA,These authors contributed equally
| | - Masaru Miyagi
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Marcin Golczak
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA,Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Edward W. Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA,Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA,Lead contact,Correspondence:
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36
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Janson K, Kyrilis FL, Tüting C, Alfes M, Das M, Träger TK, Schmidt C, Hamdi F, Vargas C, Keller S, Meister A, Kastritis PL. Cryo-Electron Microscopy Snapshots of Eukaryotic Membrane Proteins in Native Lipid-Bilayer Nanodiscs. Biomacromolecules 2022; 23:5084-5094. [PMID: 36399657 DOI: 10.1021/acs.biomac.2c00935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
New technologies for purifying membrane-bound protein complexes in combination with cryo-electron microscopy (EM) have recently allowed the exploration of such complexes under near-native conditions. In particular, polymer-encapsulated nanodiscs enable the study of membrane proteins at high resolution while retaining protein-protein and protein-lipid interactions within a lipid bilayer. However, this powerful technology has not been exploited to address the important question of how endogenous─as opposed to overexpressed─membrane proteins are organized within a lipid environment. In this work, we demonstrate that biochemical enrichment protocols for native membrane-protein complexes from Chaetomium thermophilum in combination with polymer-based lipid-bilayer nanodiscs provide a substantial improvement in the quality of recovered endogenous membrane-protein complexes. Mass spectrometry results revealed ∼1123 proteins, while multiple 2D class averages and two 3D reconstructions from cryo-EM data furnished prominent structural signatures. This integrated methodological approach to enriching endogenous membrane-protein complexes provides unprecedented opportunities for a deeper understanding of eukaryotic membrane proteomes.
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Affiliation(s)
- Kevin Janson
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale 06120, Germany
| | - Fotis L Kyrilis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale 06120, Germany
| | - Christian Tüting
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale 06120, Germany
| | - Marie Alfes
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale 06120, Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale 06120, Germany
| | - Manabendra Das
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Straße 13, Kaiserslautern 67663, Germany
| | - Toni K Träger
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale 06120, Germany.,Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale 06120, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale 06120, Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale 06120, Germany
| | - Farzad Hamdi
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale 06120, Germany
| | - Carolyn Vargas
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Straße 13, Kaiserslautern 67663, Germany.,Biophysics, Institute of Molecular Bioscience (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, Graz 8010, Austria.,Field of Excellence BioHealth, University of Graz, Graz 8010, Austria.,BioTechMed-Graz, Graz 8010, Austria
| | - Sandro Keller
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Straße 13, Kaiserslautern 67663, Germany.,Biophysics, Institute of Molecular Bioscience (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, Graz 8010, Austria.,Field of Excellence BioHealth, University of Graz, Graz 8010, Austria.,BioTechMed-Graz, Graz 8010, Austria
| | - Annette Meister
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale 06120, Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale 06120, Germany
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale 06120, Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale 06120, Germany
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37
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El Mazouni D, Gros P. Cryo-EM structures of peripherin-2 and ROM1 suggest multiple roles in photoreceptor membrane morphogenesis. SCIENCE ADVANCES 2022; 8:eadd3677. [PMID: 36351012 PMCID: PMC9645710 DOI: 10.1126/sciadv.add3677] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
Mammalian peripherin-2 (PRPH2) and rod outer segment membrane protein 1 (ROM1) are retina-specific tetraspanins that partake in the constant renewal of stacked membrane discs of photoreceptor cells that enable vision. Here, we present single-particle cryo-electron microscopy structures of solubilized PRPH2-ROM1 heterodimers and higher-order oligomers. High-risk PRPH2 and ROM1 mutations causing blindness map to the protein-dimer interface. Cysteine bridges connect dimers forming positive-curved oligomers, whereas negative-curved oligomers were observed occasionally. Hexamers and octamers exhibit a secondary micelle that envelopes four carboxyl-terminal helices, supporting a potential role in membrane remodeling. Together, the data indicate multiple structures for PRPH2-ROM1 in creating and maintaining compartmentalization of photoreceptor cells.
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Affiliation(s)
- Dounia El Mazouni
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Netherlands
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38
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Moseng MA, Su CC, Rios K, Cui M, Lyu M, Glaza P, Klenotic PA, Delpire E, Yu EW. Inhibition mechanism of NKCC1 involves the carboxyl terminus and long-range conformational coupling. SCIENCE ADVANCES 2022; 8:eabq0952. [PMID: 36306358 PMCID: PMC9616490 DOI: 10.1126/sciadv.abq0952] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
The Na-K-2Cl cotransporter-1 (NKCC1) is an electroneutral Na+-dependent transporter responsible for simultaneously translocating Na+, K+, and Cl- ions into cells. In human tissue, NKCC1 plays a critical role in regulating cytoplasmic volume, fluid intake, chloride homeostasis, and cell polarity. Here, we report four structures of human NKCC1 (hNKCC1), both in the absence and presence of loop diuretic (bumetanide or furosemide), using single-particle cryo-electron microscopy. These structures allow us to directly observe various novel conformations of the hNKCC1 dimer. They also reveal two drug-binding sites located at the transmembrane and cytosolic carboxyl-terminal domains, respectively. Together, our findings enable us to delineate an inhibition mechanism that involves a coupled movement between the cytosolic and transmembrane domains of hNKCC1.
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Affiliation(s)
- Mitchell A. Moseng
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Chih-Chia Su
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Kerri Rios
- Department of Anesthesiology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Meng Cui
- Department of Pharmaceutical Sciences, Northeastern University School of Pharmacy, Boston, MA 02115, USA
| | - Meinan Lyu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Przemyslaw Glaza
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Philip A. Klenotic
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Eric Delpire
- Department of Anesthesiology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Edward W. Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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39
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Zhao G, Wang W, Zheng L, Chen L, Duan G, Chang R, Chen Z, Zhang S, Dai M, Yang G. Catalase-peroxidase StKatG is a bacterial manganese oxidase from endophytic Salinicola tamaricis. Int J Biol Macromol 2022; 224:281-291. [DOI: 10.1016/j.ijbiomac.2022.10.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/09/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022]
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40
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Piper SJ, Johnson RM, Wootten D, Sexton PM. Membranes under the Magnetic Lens: A Dive into the Diverse World of Membrane Protein Structures Using Cryo-EM. Chem Rev 2022; 122:13989-14017. [PMID: 35849490 PMCID: PMC9480104 DOI: 10.1021/acs.chemrev.1c00837] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Indexed: 11/29/2022]
Abstract
Membrane proteins are highly diverse in both structure and function and can, therefore, present different challenges for structure determination. They are biologically important for cells and organisms as gatekeepers for information and molecule transfer across membranes, but each class of membrane proteins can present unique obstacles to structure determination. Historically, many membrane protein structures have been investigated using highly engineered constructs or using larger fusion proteins to improve solubility and/or increase particle size. Other strategies included the deconstruction of the full-length protein to target smaller soluble domains. These manipulations were often required for crystal formation to support X-ray crystallography or to circumvent lower resolution due to high noise and dynamic motions of protein subdomains. However, recent revolutions in membrane protein biochemistry and cryo-electron microscopy now provide an opportunity to solve high resolution structures of both large, >1 megadalton (MDa), and small, <100 kDa (kDa), drug targets in near-native conditions, routinely reaching resolutions around or below 3 Å. This review provides insights into how the recent advances in membrane biology and biochemistry, as well as technical advances in cryo-electron microscopy, help us to solve structures of a large variety of membrane protein groups, from small receptors to large transporters and more complex machineries.
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Affiliation(s)
- Sarah J. Piper
- Drug
Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
- ARC
Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute
of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Rachel M. Johnson
- Drug
Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
- ARC
Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute
of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Denise Wootten
- Drug
Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
- ARC
Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute
of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Patrick M. Sexton
- Drug
Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
- ARC
Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute
of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
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41
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Chung JM, Durie CL, Lee J. Artificial Intelligence in Cryo-Electron Microscopy. Life (Basel) 2022; 12:1267. [PMID: 36013446 PMCID: PMC9410485 DOI: 10.3390/life12081267] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/15/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
Cryo-electron microscopy (cryo-EM) has become an unrivaled tool for determining the structure of macromolecular complexes. The biological function of macromolecular complexes is inextricably tied to the flexibility of these complexes. Single particle cryo-EM can reveal the conformational heterogeneity of a biochemically pure sample, leading to well-founded mechanistic hypotheses about the roles these complexes play in biology. However, the processing of increasingly large, complex datasets using traditional data processing strategies is exceedingly expensive in both user time and computational resources. Current innovations in data processing capitalize on artificial intelligence (AI) to improve the efficiency of data analysis and validation. Here, we review new tools that use AI to automate the data analysis steps of particle picking, 3D map reconstruction, and local resolution determination. We discuss how the application of AI moves the field forward, and what obstacles remain. We also introduce potential future applications of AI to use cryo-EM in understanding protein communities in cells.
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Affiliation(s)
- Jeong Min Chung
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si 14662, Gyeonggi, Korea
| | - Clarissa L. Durie
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Jinseok Lee
- Department of Biomedical Engineering, Kyung Hee University, Yongin-si 17104, Gyeonggi, Korea
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42
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Dragan P, Atzei A, Sanmukh SG, Latek D. Computational and experimental approaches to probe GPCR activation and signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 193:1-36. [PMID: 36357073 DOI: 10.1016/bs.pmbts.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
G protein-coupled receptors (GPCRs) regulate different physiological functions, e.g., sensation, growth, digestion, reproductivity, nervous and immune systems response, and many others. In eukaryotes, they are also responsible for intercellular communication in response to pathogens. The major primary messengers binding to these cell-surface receptors constitute small-molecule or peptide hormones and neurotransmitters, nucleotides, lipids as well as small proteins. The simplicity of the way how GPCR signaling can be regulated by their endogenous agonists prompted the usage of GPCRs as major drug targets in modern pharmacology. Drugs targeting GPCRs inhibit pathological processes at the very beginning. This enables to significantly reduce the occurrence of morphological changes caused by diseases. Until recently, X-ray crystallography was the method of the first choice to obtain high-resolution structural information about GPCRs. Following X-ray crystallography, cryo-EM gained attention in GPCR studies as a quick and low-cost alternative. FRET microscopy is also widely used for GPCRs in the analysis of protein-protein interactions (PPIs) in intact cells as well as for screening purposes. Regarding computational methods, molecular dynamics (MD) for many years has proven its usefulness in studying the GPCR activation. MODELLER and Rosetta were widely used to generate preliminary homology models of GPCRs for MD simulation systems. Apart from the conventional all-atom approach with explicitly defined solvent, also other techniques have been applied to GPCRs, e.g., MARTINI or hybrid methods involving the coarse-grained representation, less demanding regarding computational resources, and thus offering much larger simulation timescales.
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Affiliation(s)
- Paulina Dragan
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | | | | | - Dorota Latek
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland.
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43
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Sae-Lee W, McCafferty CL, Verbeke EJ, Havugimana PC, Papoulas O, McWhite CD, Houser JR, Vanuytsel K, Murphy GJ, Drew K, Emili A, Taylor DW, Marcotte EM. The protein organization of a red blood cell. Cell Rep 2022; 40:111103. [PMID: 35858567 PMCID: PMC9764456 DOI: 10.1016/j.celrep.2022.111103] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/18/2022] [Accepted: 06/24/2022] [Indexed: 11/28/2022] Open
Abstract
Red blood cells (RBCs) (erythrocytes) are the simplest primary human cells, lacking nuclei and major organelles and instead employing about a thousand proteins to dynamically control cellular function and morphology in response to physiological cues. In this study, we define a canonical RBC proteome and interactome using quantitative mass spectrometry and machine learning. Our data reveal an RBC interactome dominated by protein homeostasis, redox biology, cytoskeletal dynamics, and carbon metabolism. We validate protein complexes through electron microscopy and chemical crosslinking and, with these data, build 3D structural models of the ankyrin/Band 3/Band 4.2 complex that bridges the spectrin cytoskeleton to the RBC membrane. The model suggests spring-like compression of ankyrin may contribute to the characteristic RBC cell shape and flexibility. Taken together, our study provides an in-depth view of the global protein organization of human RBCs and serves as a comprehensive resource for future research.
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Affiliation(s)
- Wisath Sae-Lee
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Caitlyn L McCafferty
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Eric J Verbeke
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Pierre C Havugimana
- Center for Network Systems Biology, Boston University, Boston, MA 02118, USA
| | - Ophelia Papoulas
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Claire D McWhite
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - John R Houser
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Kim Vanuytsel
- Center for Regenerative Medicine, Boston University School of Medicine, 670 Albany Street, Boston, MA 02118, USA
| | - George J Murphy
- Center for Regenerative Medicine, Boston University School of Medicine, 670 Albany Street, Boston, MA 02118, USA
| | - Kevin Drew
- Department of Biological Sciences, University of Illinois at Chicago, 900 S. Ashland Avenue, Chicago, IL 60607, USA
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA 02118, USA
| | - David W Taylor
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA.
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44
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Zheng F, Georgescu RE, Yao NY, Li H, O'Donnell ME. Cryo-EM structures reveal that RFC recognizes both the 3'- and 5'-DNA ends to load PCNA onto gaps for DNA repair. eLife 2022; 11:77469. [PMID: 35829698 PMCID: PMC9293004 DOI: 10.7554/elife.77469] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/06/2022] [Indexed: 12/27/2022] Open
Abstract
RFC uses ATP to assemble PCNA onto primed sites for replicative DNA polymerases d and e. The RFC pentamer forms a central chamber that binds 3' ss/ds DNA junctions to load PCNA onto DNA during replication. We show here five structures that identify a 2nd DNA binding site in RFC that binds a 5' duplex. This 5' DNA site is located between the N-terminal BRCT domain and AAA+ module of the large Rfc1 subunit. Our structures reveal ideal binding to a 7-nt gap, which includes 2 bp unwound by the clamp loader. Biochemical studies show enhanced binding to 5 and 10 nt gaps, consistent with the structural results. Because both 3' and 5' ends are present at a ssDNA gap, we propose that the 5' site facilitates RFC's PCNA loading activity at a DNA damage-induced gap to recruit gap-filling polymerases. These findings are consistent with genetic studies showing that base excision repair of gaps greater than 1 base requires PCNA and involves the 5' DNA binding domain of Rfc1. We further observe that a 5' end facilitates PCNA loading at an RPA coated 30-nt gap, suggesting a potential role of the RFC 5'-DNA site in lagging strand DNA synthesis.
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Affiliation(s)
- Fengwei Zheng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, United States
| | - Roxana E Georgescu
- DNA Replication Laboratory, Rockefeller University, New York, United States
| | - Nina Y Yao
- DNA Replication Laboratory, Rockefeller University, New York, United States
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, United States
| | - Michael E O'Donnell
- Howard Hughes Medical Institute, Rockefeller University, New York, United States
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45
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Oken AC, Krishnamurthy I, Savage JC, Lisi NE, Godsey MH, Mansoor SE. Molecular Pharmacology of P2X Receptors: Exploring Druggable Domains Revealed by Structural Biology. Front Pharmacol 2022; 13:925880. [PMID: 35784697 PMCID: PMC9248971 DOI: 10.3389/fphar.2022.925880] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/10/2022] [Indexed: 11/18/2022] Open
Abstract
Extracellular ATP is a critical signaling molecule that is found in a wide range of concentrations across cellular environments. The family of nonselective cation channels that sense extracellular ATP, termed P2X receptors (P2XRs), is composed of seven subtypes (P2X1-P2X7) that assemble as functional homotrimeric and heterotrimeric ion channels. Each P2XR is activated by a distinct concentration of extracellular ATP, spanning from high nanomolar to low millimolar. P2XRs are implicated in a variety of physiological and pathophysiological processes in the cardiovascular, immune, and central nervous systems, corresponding to the spatiotemporal expression, regulation, and activation of each subtype. The therapeutic potential of P2XRs is an emerging area of research in which structural biology has seemingly exceeded medicinal chemistry, as there are several published P2XR structures but currently no FDA-approved drugs targeting these ion channels. Cryogenic electron microscopy is ideally suited to facilitate structure-based drug design for P2XRs by revealing and characterizing novel ligand-binding sites. This review covers structural elements in P2XRs including the extracellular orthosteric ATP-binding site, extracellular allosteric modulator sites, channel pore, and cytoplasmic substructures, with an emphasis on potential therapeutic ligand development.
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Affiliation(s)
- Adam C. Oken
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, United States
| | - Ipsita Krishnamurthy
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, United States
| | - Jonathan C. Savage
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, United States
| | - Nicolas E. Lisi
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, United States
| | - Michael H. Godsey
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, United States
| | - Steven E. Mansoor
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, United States
- Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, United States
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46
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Abstract
Native mass spectrometry (MS) is aimed at preserving and determining the native structure, composition, and stoichiometry of biomolecules and their complexes from solution after they are transferred into the gas phase. Major improvements in native MS instrumentation and experimental methods over the past few decades have led to a concomitant increase in the complexity and heterogeneity of samples that can be analyzed, including protein-ligand complexes, protein complexes with multiple coexisting stoichiometries, and membrane protein-lipid assemblies. Heterogeneous features of these biomolecular samples can be important for understanding structure and function. However, sample heterogeneity can make assignment of ion mass, charge, composition, and structure very challenging due to the overlap of tens or even hundreds of peaks in the mass spectrum. In this review, we cover data analysis, experimental, and instrumental advances and strategies aimed at solving this problem, with an in-depth discussion of theoretical and practical aspects of the use of available deconvolution algorithms and tools. We also reflect upon current challenges and provide a view of the future of this exciting field.
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Affiliation(s)
- Amber D. Rolland
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA 97403-1253
| | - James S. Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA 97403-1253
- Materials Science Institute, 1252 University of Oregon, Eugene, OR, USA 97403-1252
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47
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Rogawski R, Sharon M. Characterizing Endogenous Protein Complexes with Biological Mass Spectrometry. Chem Rev 2022; 122:7386-7414. [PMID: 34406752 PMCID: PMC9052418 DOI: 10.1021/acs.chemrev.1c00217] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Indexed: 01/11/2023]
Abstract
Biological mass spectrometry (MS) encompasses a range of methods for characterizing proteins and other biomolecules. MS is uniquely powerful for the structural analysis of endogenous protein complexes, which are often heterogeneous, poorly abundant, and refractive to characterization by other methods. Here, we focus on how biological MS can contribute to the study of endogenous protein complexes, which we define as complexes expressed in the physiological host and purified intact, as opposed to reconstituted complexes assembled from heterologously expressed components. Biological MS can yield information on complex stoichiometry, heterogeneity, topology, stability, activity, modes of regulation, and even structural dynamics. We begin with a review of methods for isolating endogenous complexes. We then describe the various biological MS approaches, focusing on the type of information that each method yields. We end with future directions and challenges for these MS-based methods.
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Affiliation(s)
- Rivkah Rogawski
- Department of Biomolecular
Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Michal Sharon
- Department of Biomolecular
Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
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48
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An AI-assisted cryo-EM pipeline for structural studies of cellular extracts. Structure 2022; 30:532-534. [PMID: 35395193 DOI: 10.1016/j.str.2022.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Proteins, the building blocks of life, often form large assemblies to perform their function but are traditionally studied separately in structural biology. In this issue of Structure, Skalidis et al. (2022) present a workflow to identify members of intact protein communities and solve their structures de novo to near-atomic resolution.
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49
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Xu C, Wang B, Heng H, Huang J, Wan C. Comparative Network Biology Discovers Protein Complexes That Underline Cellular Differentiation in Anabaena sp. Mol Cell Proteomics 2022; 21:100224. [PMID: 35288331 PMCID: PMC9035410 DOI: 10.1016/j.mcpro.2022.100224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 02/20/2022] [Accepted: 03/10/2022] [Indexed: 01/11/2023] Open
Abstract
The filamentous cyanobacterium Anabaena sp. PCC 7120 can differentiate into heterocysts to fix atmospheric nitrogen. During cell differentiation, cellular morphology and gene expression undergo a series of significant changes. To uncover the mechanisms responsible for these alterations, we built protein–protein interaction (PPI) networks for these two cell types by cofractionation coupled with mass spectrometry. We predicted 280 and 215 protein complexes, with 6322 and 2791 high-confidence PPIs in vegetative cells and heterocysts, respectively. Most of the proteins in both types of cells presented similar elution profiles, whereas the elution peaks of 438 proteins showed significant changes. We observed that some well-known complexes recruited new members in heterocysts, such as ribosomes, diflavin flavoprotein, and cytochrome c oxidase. Photosynthetic complexes, including photosystem I, photosystem II, and phycobilisome, remained in both vegetative cells and heterocysts for electron transfer and energy generation. Besides that, PPI data also reveal new functions of proteins. For example, the hypothetical protein Alr4359 was found to interact with FraH and Alr4119 in heterocysts and was located on heterocyst poles, thereby influencing the diazotrophic growth of filaments. The overexpression of Alr4359 suspended heterocyst formation and altered the pigment composition and filament length. This work demonstrates the differences in protein assemblies and provides insight into physiological regulation during cell differentiation. PPIs in two types of cells of Anabaena sp. 7120 were systematically identified. 10,302 and 8557 high-confidence PPIs were obtained and over 80% were novel. About 438 proteins showed significant changes in vegetative cells and heterocysts. Protein Alr4359 was found to influence the diazotrophic growth of filaments.
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Affiliation(s)
- Chen Xu
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, China
| | - Bing Wang
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, China
| | - Hailu Heng
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, China
| | - Jiangmei Huang
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, China
| | - Cuihong Wan
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, China.
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Zheng F, Georgescu RE, Yao NY, O'Donnell ME, Li H. DNA is loaded through the 9-1-1 DNA checkpoint clamp in the opposite direction of the PCNA clamp. Nat Struct Mol Biol 2022; 29:376-385. [PMID: 35314830 PMCID: PMC9010301 DOI: 10.1038/s41594-022-00742-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 02/11/2022] [Indexed: 12/11/2022]
Abstract
The 9-1-1 DNA checkpoint clamp is loaded onto 5'-recessed DNA to activate the DNA damage checkpoint that arrests the cell cycle. The 9-1-1 clamp is a heterotrimeric ring that is loaded in Saccharomyces cerevisiae by Rad24-RFC (hRAD17-RFC), an alternate clamp loader in which Rad24 replaces Rfc1 in the RFC1-5 clamp loader of proliferating cell nuclear antigen (PCNA). The 9-1-1 clamp loading mechanism has been a mystery, because, unlike RFC, which loads PCNA onto a 3'-recessed junction, Rad24-RFC loads the 9-1-1 ring onto a 5'-recessed DNA junction. Here we report two cryo-EM structures of Rad24-RFC-DNA with a closed or 27-Å open 9-1-1 clamp. The structures reveal a completely unexpected mechanism by which a clamp can be loaded onto DNA. Unlike RFC, which encircles DNA, Rad24 binds 5'-DNA on its surface, not inside the loader, and threads the 3' ssDNA overhang into the 9-1-1 clamp from above the ring.
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Affiliation(s)
- Fengwei Zheng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Roxana E Georgescu
- DNA Replication Laboratory, The Rockefeller University, New York, NY, USA
| | - Nina Y Yao
- DNA Replication Laboratory, The Rockefeller University, New York, NY, USA
| | - Michael E O'Donnell
- DNA Replication Laboratory, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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