1
|
Träger TK, Kyrilis FL, Hamdi F, Tüting C, Alfes M, Hofmann T, Schmidt C, Kastritis PL. Disorder-to-order active site capping regulates the rate-limiting step of the inositol pathway. Proc Natl Acad Sci U S A 2024; 121:e2400912121. [PMID: 39145930 DOI: 10.1073/pnas.2400912121] [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: 01/23/2024] [Accepted: 07/16/2024] [Indexed: 08/16/2024] Open
Abstract
Myo-inositol-1-phosphate synthase (MIPS) catalyzes the NAD+-dependent isomerization of glucose-6-phosphate (G6P) into inositol-1-phosphate (IMP), controlling the rate-limiting step of the inositol pathway. Previous structural studies focused on the detailed molecular mechanism, neglecting large-scale conformational changes that drive the function of this 240 kDa homotetrameric complex. In this study, we identified the active, endogenous MIPS in cell extracts from the thermophilic fungus Thermochaetoides thermophila. By resolving the native structure at 2.48 Å (FSC = 0.143), we revealed a fully populated active site. Utilizing 3D variability analysis, we uncovered conformational states of MIPS, enabling us to directly visualize an order-to-disorder transition at its catalytic center. An acyclic intermediate of G6P occupied the active site in two out of the three conformational states, indicating a catalytic mechanism where electrostatic stabilization of high-energy intermediates plays a crucial role. Examination of all isomerases with known structures revealed similar fluctuations in secondary structure within their active sites. Based on these findings, we established a conformational selection model that governs substrate binding and eventually inositol availability. In particular, the ground state of MIPS demonstrates structural configurations regardless of substrate binding, a pattern observed across various isomerases. These findings contribute to the understanding of MIPS structure-based function, serving as a template for future studies targeting regulation and potential therapeutic applications.
Collapse
Affiliation(s)
- Toni K Träger
- Faculty of Natural Sciences I, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale 06120, Germany
- Biozentrum, Martin Luther University Halle-Wittenberg, Halle/Saale 06120, Germany
| | - Fotis L Kyrilis
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
| | - Farzad Hamdi
- Faculty of Natural Sciences I, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale 06120, Germany
- Biozentrum, Martin Luther University Halle-Wittenberg, Halle/Saale 06120, Germany
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle/Saale 06120, Germany
| | - Christian Tüting
- Faculty of Natural Sciences I, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale 06120, Germany
- Biozentrum, Martin Luther University Halle-Wittenberg, Halle/Saale 06120, Germany
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle/Saale 06120, Germany
| | - Marie Alfes
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle/Saale 06120, Germany
- Biologics Analytical R&D, AbbVie Deutschland GmbH & Co. KG, Ludwigshafen 67061, Germany
| | - Tommy Hofmann
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle/Saale 06120, Germany
- Impfstoffwerk Dessau-Tornau Biologika, Dessau-Roßlau 06861, Germany
| | - Carla Schmidt
- Faculty of Natural Sciences I, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale 06120, Germany
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle/Saale 06120, Germany
- Department of Chemistry-Biochemistry, Johannes Gutenberg University Mainz, Mainz 55128, Germany
| | - Panagiotis L Kastritis
- Faculty of Natural Sciences I, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale 06120, Germany
- Biozentrum, Martin Luther University Halle-Wittenberg, Halle/Saale 06120, Germany
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle/Saale 06120, Germany
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Schmidt L, Tüting C, Kyrilis FL, Hamdi F, Semchonok DA, Hause G, Meister A, Ihling C, Stubbs MT, Sinz A, Kastritis PL. Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts. Commun Biol 2024; 7:557. [PMID: 38730276 PMCID: PMC11087493 DOI: 10.1038/s42003-024-06204-7] [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: 08/18/2022] [Accepted: 04/17/2024] [Indexed: 05/12/2024] Open
Abstract
The high abundance of most viruses in infected host cells benefits their structural characterization. However, endogenous viruses are present in low copy numbers and are therefore challenging to investigate. Here, we retrieve cell extracts enriched with an endogenous virus, the yeast L-A virus. The determined cryo-EM structure discloses capsid-stabilizing cation-π stacking, widespread across viruses and within the Totiviridae, and an interplay of non-covalent interactions from ten distinct capsomere interfaces. The capsid-embedded mRNA decapping active site trench is supported by a constricting movement of two flexible opposite-facing loops. tRNA-loaded polysomes and other biomacromolecules, presumably mRNA, are found in virus proximity within the cell extract. Mature viruses participate in larger viral communities resembling their rare in-cell equivalents in terms of size, composition, and inter-virus distances. Our results collectively describe a 3D-architecture of a viral milieu, opening the door to cell-extract-based high-resolution structural virology.
Collapse
Affiliation(s)
- Lisa Schmidt
- 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
- Technical Biogeochemistry, Helmholtz Centre for Environmental Research, Permoserstraße 15, Leipzig, Germany
| | - Christian Tüting
- 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.
| | - 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
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
| | - Dmitry A Semchonok
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
| | - Gerd Hause
- Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, Halle/Saale, Germany
| | - Annette Meister
- 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
| | - Christian Ihling
- Institute of Pharmacy, Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle (Saale), Germany
| | - Milton T Stubbs
- 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
| | - Andrea Sinz
- Institute of Pharmacy, Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 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.
| |
Collapse
|
4
|
Palukuri MV, Marcotte EM. DeepSLICEM: Clustering CryoEM particles using deep image and similarity graph representations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.04.578778. [PMID: 38370702 PMCID: PMC10871265 DOI: 10.1101/2024.02.04.578778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Finding the 3D structure of proteins and their complexes has several applications, such as developing vaccines that target viral proteins effectively. Methods such as cryogenic electron microscopy (cryo-EM) have improved in their ability to capture high-resolution images, and when applied to a purified sample containing copies of a macromolecule, they can be used to produce a high-quality snapshot of different 2D orientations of the macromolecule, which can be combined to reconstruct its 3D structure. Instead of purifying a sample so that it contains only one macromolecule, a process that can be difficult, time-consuming, and expensive, a cell sample containing multiple particles can be photographed directly and separated into its constituent particles using computational methods. Previous work, SLICEM, has separated 2D projection images of different particles into their respective groups using 2 methods, clustering a graph with edges weighted by pairwise similarities of common lines of the 2D projections. In this work, we develop DeepSLICEM, a pipeline that clusters rich representations of 2D projections, obtained by combining graphical features from a similarity graph based on common lines, with additional image features extracted from a convolutional neural network. DeepSLICEM explores 6 pretrained convolutional neural networks and one supervised Siamese CNN for image representation, 10 pretrained deep graph neural networks for similarity graph node representations, and 4 methods for clustering, along with 8 methods for directly clustering the similarity graph. On 6 synthetic and experimental datasets, the DeepSLICEM pipeline finds 92 method combinations achieving better clustering accuracy than previous methods from SLICEM. Thus, in this paper, we demonstrate that deep neural networks have great potential for accurately separating mixtures of 2D projections of different macromolecules computationally.
Collapse
Affiliation(s)
- Meghana V Palukuri
- Oden Institute for Computational Engineering and Sciences, University of Texas, Austin, TX 78712, USA
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Edward M Marcotte
- Oden Institute for Computational Engineering and Sciences, University of Texas, Austin, TX 78712, USA
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Mostafabadi BK, Kachoie MA, Rahimi E. Antimicrobial effects of Cynara scolymus essential oil: In vitro analysis. MAIN GROUP CHEMISTRY 2022. [DOI: 10.3233/mgc-220006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
By benefits of using silicon and vermicompost based biofertilizers and also induction of drought stress for growing more efficient medicinal plants, we investigated such issues on growing Cynara scolymus (C. scolymus), as one of the most significant edible medicinal plants. In this regard, the antimicrobial effects of grown C. scolymus essential oil was investigated against some foodborne pathogens. Different concentrations of silicon and vermicompost with and without drought stress were considered for growing the plant and the extracted essential oils were extracted to examine their antimicrobial effects against different bacterial agents. Using vermicompost and silicon and 50% moisture discharge yielded significant increase in the mean diameter of growth inhibition zone and significant decrease in the minimum inhibitory concentration of tested bacteria (P < 0.05). The highest diameters of the inhibition zones of S. aureus, S. saprophyticus, P. aeruginosa, S. dysenteriae, and S. typhi were found for C. scolymus essential oil treated with 8 mmol silicon and conventional irrigation (14.92 mm), 4 mmol silicon and 50% moisture discharge (15.28 mm), 50% vermicompost and 50% moisture discharge (15.71 mm), 8 mmol silicon and conventional irrigation (17.34 mm) and 25% vermicompost, and 50% moisture discharge (15.48 mm), respectively. Antimicrobial effects of some treatments of C. scolymus were higher than some kinds of referenced antibiotics such as erythromycin. These findings could be used for the production of antibiotic drugs for specific purposes against certain bacteria.
Collapse
Affiliation(s)
| | - Mehrdad Ataie Kachoie
- Department of Agro-ecology, Faculty of Agriculture, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Ebrahim Rahimi
- Department of Food Hygiene and Public Health, Faculty of Veterinary Medicine, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| |
Collapse
|
7
|
Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
Collapse
Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| |
Collapse
|
8
|
Skalidis I, Kyrilis FL, Tüting C, Hamdi F, Chojnowski G, Kastritis PL. Cryo-EM and artificial intelligence visualize endogenous protein community members. Structure 2022; 30:575-589.e6. [DOI: 10.1016/j.str.2022.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/05/2021] [Accepted: 01/03/2022] [Indexed: 12/29/2022]
|
9
|
Arimura Y, Shih RM, Froom R, Funabiki H. Structural features of nucleosomes in interphase and metaphase chromosomes. Mol Cell 2021; 81:4377-4397.e12. [PMID: 34478647 PMCID: PMC8571072 DOI: 10.1016/j.molcel.2021.08.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/17/2022]
Abstract
Structural heterogeneity of nucleosomes in functional chromosomes is unknown. Here, we devise the template-, reference- and selection-free (TRSF) cryo-EM pipeline to simultaneously reconstruct cryo-EM structures of protein complexes from interphase or metaphase chromosomes. The reconstructed interphase and metaphase nucleosome structures are on average indistinguishable from canonical nucleosome structures, despite DNA sequence heterogeneity, cell-cycle-specific posttranslational modifications, and interacting proteins. Nucleosome structures determined by a decoy-classifying method and structure variability analyses reveal the nucleosome structural variations in linker DNA, histone tails, and nucleosome core particle configurations, suggesting that the opening of linker DNA, which is correlated with H2A C-terminal tail positioning, is suppressed in chromosomes. High-resolution (3.4-3.5 Å) nucleosome structures indicate DNA-sequence-independent stabilization of superhelical locations ±0-1 and ±3.5-4.5. The linker histone H1.8 preferentially binds to metaphase chromatin, from which chromatosome cryo-EM structures with H1.8 at the on-dyad position are reconstituted. This study presents the structural characteristics of nucleosomes in chromosomes.
Collapse
Affiliation(s)
- Yasuhiro Arimura
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA.
| | - Rochelle M Shih
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Ruby Froom
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA.
| |
Collapse
|
10
|
Kyrilis FL, Belapure J, Kastritis PL. Detecting Protein Communities in Native Cell Extracts by Machine Learning: A Structural Biologist's Perspective. Front Mol Biosci 2021; 8:660542. [PMID: 33937337 PMCID: PMC8082361 DOI: 10.3389/fmolb.2021.660542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/18/2021] [Indexed: 11/13/2022] Open
Abstract
Native cell extracts hold great promise for understanding the molecular structure of ordered biological systems at high resolution. This is because higher-order biomolecular interactions, dubbed as protein communities, may be retained in their (near-)native state, in contrast to extensively purifying or artificially overexpressing the proteins of interest. The distinct machine-learning approaches are applied to discover protein-protein interactions within cell extracts, reconstruct dedicated biological networks, and report on protein community members from various organisms. Their validation is also important, e.g., by the cross-linking mass spectrometry or cell biology methods. In addition, the cell extracts are amenable to structural analysis by cryo-electron microscopy (cryo-EM), but due to their inherent complexity, sorting structural signatures of protein communities derived by cryo-EM comprises a formidable task. The application of image-processing workflows inspired by machine-learning techniques would provide improvements in distinguishing structural signatures, correlating proteomic and network data to structural signatures and subsequently reconstructed cryo-EM maps, and, ultimately, characterizing unidentified protein communities at high resolution. In this review article, we summarize recent literature in detecting protein communities from native cell extracts and identify the remaining challenges and opportunities. We argue that the progress in, and the integration of, machine learning, cryo-EM, and complementary structural proteomics approaches would provide the basis for a multi-scale molecular description of protein communities within native cell extracts.
Collapse
Affiliation(s)
- Fotis L. Kyrilis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Jaydeep Belapure
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Panagiotis L. Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- Biozentrum, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| |
Collapse
|
11
|
Terwilliger TC, Sobolev OV, Afonine PV, Adams PD, Ho CM, Li X, Zhou ZH. Protein identification from electron cryomicroscopy maps by automated model building and side-chain matching. Acta Crystallogr D Struct Biol 2021; 77:457-462. [PMID: 33825706 PMCID: PMC8025881 DOI: 10.1107/s2059798321001765] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 02/12/2021] [Indexed: 11/10/2022] Open
Abstract
Using single-particle electron cryo-microscopy (cryo-EM), it is possible to obtain multiple reconstructions showing the 3D structures of proteins imaged as a mixture. Here, it is shown that automatic map interpretation based on such reconstructions can be used to create atomic models of proteins as well as to match the proteins to the correct sequences and thereby to identify them. This procedure was tested using two proteins previously identified from a mixture at resolutions of 3.2 Å, as well as using 91 deposited maps with resolutions between 2 and 4.5 Å. The approach is found to be highly effective for maps obtained at resolutions of 3.5 Å and better, and to have some utility at resolutions as low as 4 Å.
Collapse
Affiliation(s)
- Thomas C. Terwilliger
- New Mexico Consortium, Los Alamos, NM 87544, USA
- Bioscience Division, Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87545, USA
| | - Oleg V. Sobolev
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Pavel V. Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Paul D. Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, California, USA
| | - Chi-Min Ho
- The Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, USA
| | - Xiaorun Li
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| | - Z. Hong Zhou
- The Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
| |
Collapse
|
12
|
Kyrilis FL, Semchonok DA, Skalidis I, Tüting C, Hamdi F, O'Reilly FJ, Rappsilber J, Kastritis PL. Integrative structure of a 10-megadalton eukaryotic pyruvate dehydrogenase complex from native cell extracts. Cell Rep 2021; 34:108727. [PMID: 33567276 DOI: 10.1016/j.celrep.2021.108727] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 12/02/2020] [Accepted: 01/14/2021] [Indexed: 12/29/2022] Open
Abstract
The pyruvate dehydrogenase complex (PDHc) is a giant enzymatic assembly involved in pyruvate oxidation. PDHc components have been characterized in isolation, but the complex's quaternary structure has remained elusive due to sheer size, heterogeneity, and plasticity. Here, we identify fully assembled Chaetomium thermophilum α-keto acid dehydrogenase complexes in native cell extracts and characterize their domain arrangements utilizing mass spectrometry, activity assays, crosslinking, electron microscopy (EM), and computational modeling. We report the cryo-EM structure of the PDHc core and observe unique features of the previously unknown native state. The asymmetric reconstruction of the 10-MDa PDHc resolves spatial proximity of its components, agrees with stoichiometric data (60 E2p:12 E3BP:∼20 E1p: ≤ 12 E3), and proposes a minimum reaction path among component enzymes. The PDHc shows the presence of a dynamic pyruvate oxidation compartment, organized by core and peripheral protein species. Our data provide a framework for further understanding PDHc and α-keto acid dehydrogenase complex structure and function.
Collapse
Affiliation(s)
- 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
| | - Dmitry A Semchonok
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
| | - Ioannis Skalidis
- 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
| | - Christian Tüting
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
| | - Farzad Hamdi
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
| | - Francis J O'Reilly
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, United Kingdom
| | - 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; Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, Halle/Saale, Germany.
| |
Collapse
|
13
|
Lin SN, Wuite GJ, Dame RT. Effect of Different Crowding Agents on the Architectural Properties of the Bacterial Nucleoid-Associated Protein HU. Int J Mol Sci 2020; 21:ijms21249553. [PMID: 33334011 PMCID: PMC7765392 DOI: 10.3390/ijms21249553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 12/31/2022] Open
Abstract
HU is a nucleoid-associated protein expressed in most eubacteria at a high amount of copies (tens of thousands). The protein is believed to bind across the genome to organize and compact the DNA. Most of the studies on HU have been carried out in a simple in vitro system, and to what extent these observations can be extrapolated to a living cell is unclear. In this study, we investigate the DNA binding properties of HU under conditions approximating physiological ones. We report that these properties are influenced by both macromolecular crowding and salt conditions. We use three different crowding agents (blotting grade blocker (BGB), bovine serum albumin (BSA), and polyethylene glycol 8000 (PEG8000)) as well as two different MgCl2 conditions to mimic the intracellular environment. Using tethered particle motion (TPM), we show that the transition between two binding regimes, compaction and extension of the HU protein, is strongly affected by crowding agents. Our observations suggest that magnesium ions enhance the compaction of HU–DNA and suppress filamentation, while BGB and BSA increase the local concentration of the HU protein by more than 4-fold. Moreover, BGB and BSA seem to suppress filament formation. On the other hand, PEG8000 is not a good crowding agent for concentrations above 9% (w/v), because it might interact with DNA, the protein, and/or surfaces. Together, these results reveal a complex interplay between the HU protein and the various crowding agents that should be taken into consideration when using crowding agents to mimic an in vivo system.
Collapse
Affiliation(s)
- Szu-Ning Lin
- Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands;
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Gijs J.L. Wuite
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- LaserLaB Amsterdam, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- Correspondence: (G.J.L.W.); (R.T.D.)
| | - Remus T. Dame
- Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands;
- Centre for Microbial Cell Biology, Leiden University, 2333 CC Leiden, The Netherlands
- Correspondence: (G.J.L.W.); (R.T.D.)
| |
Collapse
|
14
|
Kirykowicz AM, Woodward JD. Shotgun EM of mycobacterial protein complexes during stationary phase stress. Curr Res Struct Biol 2020; 2:204-212. [PMID: 34235480 PMCID: PMC8244302 DOI: 10.1016/j.crstbi.2020.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 10/27/2022] Open
Abstract
There is little structural information about the protein complexes conferring resistance in Mycobacterium tuberculosis (Mtb) to anti-microbial oxygen and nitrogen radicals in the phagolysosome. Here, we expose the model Mycobacterium, Mycobacterium smegmatis, to simulated oxidative-stress conditions and apply a shotgun EM method for the structural detection of the resulting protein assemblies. We identified: glutamine synthetase I, essential for Mtb virulence; bacterioferritin A, critical for Mtb iron regulation; aspartyl aminopeptidase M18, a protease; and encapsulin, which produces a cage-like structure to enclose cargo proteins. After further investigation, we found that encapsulin carries dye-decolourising peroxidase, a protein antioxidant, as its primary cargo under the conditions tested.
Collapse
Affiliation(s)
- Angela M. Kirykowicz
- Department of Biochemistry, University of Cambridge, Sanger Building, Tennis Court Road, Cambridge, CB2 1GA, UK
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Anzio Road, Observatory, 7925, Cape Town, South Africa
| | - Jeremy D. Woodward
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Anzio Road, Observatory, 7925, Cape Town, South Africa
- Structural Biology Research Unit, University of Cape Town, South Africa
| |
Collapse
|
15
|
Skalidis I, Tüting C, Kastritis PL. Unstructured regions of large enzymatic complexes control the availability of metabolites with signaling functions. Cell Commun Signal 2020; 18:136. [PMID: 32843078 PMCID: PMC7448341 DOI: 10.1186/s12964-020-00631-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/17/2020] [Indexed: 12/23/2022] Open
Abstract
Metabolites produced via traditional biochemical processes affect intracellular communication, inflammation, and malignancy. Unexpectedly, acetyl-CoA, α-ketoglutarate and palmitic acid, which are chemical species of reactions catalyzed by highly abundant, gigantic enzymatic complexes, dubbed as "metabolons", have broad "nonmetabolic" signaling functions. Conserved unstructured regions within metabolons determine the yield of these metabolites. Unstructured regions tether functional protein domains, act as spatial constraints to confine constituent enzyme communication, and, in the case of acetyl-CoA production, tend to be regulated by intricate phosphorylation patterns. This review presents the multifaceted roles of these three significant metabolites and describes how their perturbation leads to altered or transformed cellular function. Their dedicated enzymatic systems are then introduced, namely, the pyruvate dehydrogenase (PDH) and oxoglutarate dehydrogenase (OGDH) complexes, and the fatty acid synthase (FAS), with a particular focus on their structural characterization and the localization of unstructured regions. Finally, upstream metabolite regulation, in which spatial occupancy of unstructured regions within dedicated metabolons may affect metabolite availability and subsequently alter cell functions, is discussed. Video abstract.
Collapse
Affiliation(s)
- Ioannis Skalidis
- 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
| | - Christian Tüting
- 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
| | - 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. .,ZIK HALOmem, Martin Luther University Halle-Wittenberg, Biozentrum, Room A.2.14, Weinbergweg 22, 06120, Halle/Saale, Germany.
| |
Collapse
|
16
|
Koukos P, Bonvin A. Integrative Modelling of Biomolecular Complexes. J Mol Biol 2020; 432:2861-2881. [DOI: 10.1016/j.jmb.2019.11.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 12/31/2022]
|
17
|
Verbeke EJ, Zhou Y, Horton AP, Mallam AL, Taylor DW, Marcotte EM. Separating distinct structures of multiple macromolecular assemblies from cryo-EM projections. J Struct Biol 2020; 209:107416. [PMID: 31726096 PMCID: PMC6952565 DOI: 10.1016/j.jsb.2019.107416] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 11/06/2019] [Accepted: 11/09/2019] [Indexed: 02/08/2023]
Abstract
Single particle analysis for structure determination in cryo-electron microscopy is traditionally applied to samples purified to near homogeneity as current reconstruction algorithms are not designed to handle heterogeneous mixtures of structures from many distinct macromolecular complexes. We extend on long established methods and demonstrate that relating two-dimensional projection images by their common lines in a graphical framework is sufficient for partitioning distinct protein and multiprotein complexes within the same data set. The feasibility of this approach is first demonstrated on a large set of synthetic reprojections from 35 unique macromolecular structures spanning a mass range of hundreds to thousands of kilodaltons. We then apply our algorithm on cryo-EM data collected from a mixture of five protein complexes and use existing methods to solve multiple three-dimensional structures ab initio. Incorporating methods to sort single particle cryo-EM data from extremely heterogeneous mixtures will alleviate the need for stringent purification and pave the way toward investigation of samples containing many unique structures.
Collapse
Affiliation(s)
- Eric J Verbeke
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Yi Zhou
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Andrew P Horton
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Anna L Mallam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - David W Taylor
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; LIVESTRONG Cancer Institutes, Dell Medical School, Austin, TX 78712, USA.
| | - Edward M Marcotte
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
| |
Collapse
|
18
|
Affiliation(s)
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | - Matthias J Feige
- Center for Integrated Protein Science Munich at the Department of Chemistry and Institute for Advanced Study, Technical University of Munich, D-85748 Garching, Germany
| |
Collapse
|