1
|
Cook BD, Narehood SM, McGuire KL, Li Y, Akif Tezcan F, Herzik MA. Preparation of oxygen-sensitive proteins for high-resolution cryoEM structure determination using blot-free vitrification. Nat Commun 2025; 16:3528. [PMID: 40229244 PMCID: PMC11997128 DOI: 10.1038/s41467-025-58243-1] [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: 08/20/2024] [Accepted: 03/11/2025] [Indexed: 04/16/2025] Open
Abstract
High-quality grid preparation for single-particle cryogenic electron microscopy (cryoEM) remains a bottleneck for routinely obtaining high-resolution structures. The issues that arise from traditional grid preparation workflows are particularly exacerbated for oxygen-sensitive proteins, including metalloproteins, whereby oxygen-induced damage and alteration of oxidation states can result in protein inactivation, denaturation, and/or aggregation. Indeed, 99% of the current structures in the EMBD were prepared aerobically and limited successes for anaerobic cryoEM grid preparation exist. Current practices for anaerobic grid preparation involve a vitrification device located in an anoxic chamber, which presents significant challenges including temperature and humidity control, optimization of freezing conditions, costs for purchase and operation, as well as accessibility. Here, we present a streamlined approach that allows for the vitrification of oxygen-sensitive proteins in reduced states using an automated blot-free grid vitrification device - the SPT Labtech chameleon. This robust workflow allows for high-resolution structure determination of dynamic, oxygen-sensitive proteins, of varying complexity and molecular weight.
Collapse
Affiliation(s)
- Brian D Cook
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, USA
| | - Sarah M Narehood
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, USA
| | - Kelly L McGuire
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, USA
| | - Yizhou Li
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, USA
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, USA
| | - Mark A Herzik
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, USA.
| |
Collapse
|
2
|
Kim S, Kim JW, Park JG, Lee SS, Choi SH, Lee JO, Jin MS. Disulfide-stabilized diabodies enable near-atomic cryo-EM imaging of small proteins: A case study of the bacterial Na +/citrate symporter CitS. Structure 2025:S0969-2126(25)00103-0. [PMID: 40169000 DOI: 10.1016/j.str.2025.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Revised: 02/05/2025] [Accepted: 03/05/2025] [Indexed: 04/03/2025]
Abstract
Diabodies are engineered antibody fragments with two antigen-binding Fv domains. Previously, we demonstrated that they are often highly flexible but can be rigidified by introducing a disulfide bond at the Fv interface. In this study, we explored the potential of disulfide-bridged, bispecific diabodies for near-atomic cryoelectron microscopy (cryo-EM) imaging of small proteins because they can predictably link target proteins to "structural marker" proteins. As a case study, we used the bacterial citrate transporter CitS as the target protein, and the horseshoe-shaped ectodomain of human Toll-like receptor 3 (TLR3) as the marker. We show that diabodies containing one or two disulfide bonds enabled the 3D reconstruction of CitS at resolutions of 3.3 Å and 3.1 Å, respectively. This resolution surpassed previous crystallographic results and allowed us to visualize the high-resolution structural features of the transporter. Our work expands the application of diabodies in structural biology to address a key limitation in the field.
Collapse
Affiliation(s)
- Subin Kim
- Department of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Ji Won Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea; Institute of Membrane Proteins, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Jun Gyou Park
- Department of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Sang Soo Lee
- Department of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Seung Hun Choi
- Department of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Jie-Oh Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea; Institute of Membrane Proteins, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
| | - Mi Sun Jin
- Department of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea; Integrated Institute of Biomedical Research, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea.
| |
Collapse
|
3
|
Rubach P, Majorek KA, Gucwa M, Murzyn K, Wlodawer A, Minor W. Advances in cryo-electron microscopy (cryoEM) for structure-based drug discovery. Expert Opin Drug Discov 2025; 20:163-176. [PMID: 39789967 DOI: 10.1080/17460441.2025.2450636] [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: 10/13/2024] [Revised: 11/20/2024] [Accepted: 01/04/2025] [Indexed: 01/12/2025]
Abstract
INTRODUCTION Macromolecular X-ray crystallography (XRC), nuclear magnetic resonance (NMR), and cryo-electron microscopy (cryoEM) are the primary techniques for determining atomic-level, three-dimensional structures of macromolecules essential for drug discovery. With advancements in artificial intelligence (AI) and cryoEM, the Protein Data Bank (PDB) is solidifying its role as a key resource for 3D macromolecular structures. These developments underscore the growing need for enhanced quality metrics and robust validation standards for experimental structures. AREAS COVERED This review examines recent advancements in cryoEM for drug discovery, analyzing structure quality metrics, resolution improvements, metal-ligand and water molecule identification, and refinement software. It compares cryoEM with other techniques like XRC and NMR, emphasizing the global expansion of cryoEM facilities and its increasing significance in drug discovery. EXPERT OPINION CryoEM is revolutionizing structural biology and drug discovery, particularly for large, complex structures in induced proximity and antibody-antigen interactions. It supports vaccine design, CAR T-cell optimization, gene editing, and gene therapy. Combined with AI, cryoEM enhances particle identification and 3D structure determination. With recent breakthroughs, cryoEM is emerging as a crucial tool in drug discovery, driving the development of new, effective therapies.
Collapse
Affiliation(s)
- Pawel Rubach
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
- Institute of Information Systems and Digital Economy, Warsaw School of Economics, Warsaw, Poland
| | - Karolina A Majorek
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Michal Gucwa
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University, Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Krzysztof Murzyn
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University, Krakow, Poland
| | - Alexander Wlodawer
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| |
Collapse
|
4
|
Mahoney BJ, Lyman LR, Ford J, Soule J, Cheung NA, Goring AK, Ellis-Guardiola K, Collazo MJ, Cascio D, Ton-That H, Schmitt MP, Clubb RT. Molecular basis of hemoglobin binding and heme removal in Corynebacterium diphtheriae. Proc Natl Acad Sci U S A 2025; 122:e2411833122. [PMID: 39739808 PMCID: PMC11725911 DOI: 10.1073/pnas.2411833122] [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: 06/12/2024] [Accepted: 12/06/2024] [Indexed: 01/02/2025] Open
Abstract
To successfully mount infections, nearly all bacterial pathogens must acquire iron, a key metal cofactor that primarily resides within human hemoglobin. Corynebacterium diphtheriae causes the life-threatening respiratory disease diphtheria and captures hemoglobin for iron scavenging using the surface-displayed receptor HbpA. Here, we show using X-ray crystallography, NMR, and in situ binding measurements that C. diphtheriae selectively captures iron-loaded hemoglobin by partially ensconcing the heme molecules of its α subunits. Quantitative growth and heme release measurements are compatible with C. diphtheriae acquiring heme passively released from hemoglobin's β subunits. We propose a model in which HbpA and heme-binding receptors collectively function on the C. diphtheriae surface to capture hemoglobin and its spontaneously released heme. Acquisition mechanisms that exploit the propensity of hemoglobin's β subunit to release heme likely represent a common strategy used by bacterial pathogens to obtain iron during infections.
Collapse
Affiliation(s)
- Brendan J. Mahoney
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
- University of California, Los Angeles-United States Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA90095
| | - Lindsey R. Lyman
- Laboratory of Respiratory and Special Pathogens, Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD20903
| | - Jordan Ford
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Jess Soule
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Nicole A. Cheung
- University of California, Los Angeles-United States Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA90095
- Molecular Biology Institute, University of California, Los Angeles, CA90095
| | - Andrew K. Goring
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Kat Ellis-Guardiola
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
- University of California, Los Angeles-United States Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA90095
| | - Michael J. Collazo
- University of California, Los Angeles-United States Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA90095
| | - Duilio Cascio
- University of California, Los Angeles-United States Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA90095
| | - Hung Ton-That
- Molecular Biology Institute, University of California, Los Angeles, CA90095
- Division of Oral and Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, CA90095
| | - Michael P. Schmitt
- Laboratory of Respiratory and Special Pathogens, Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD20903
| | - Robert T. Clubb
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
- University of California, Los Angeles-United States Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA90095
- Molecular Biology Institute, University of California, Los Angeles, CA90095
| |
Collapse
|
5
|
Xie P, Li Y, Lamon G, Kuang H, Wang DN, Traaseth NJ. A fiducial-assisted strategy compatible with resolving small MFS transporter structures in multiple conformations using cryo-EM. Nat Commun 2025; 16:7. [PMID: 39746942 PMCID: PMC11695964 DOI: 10.1038/s41467-024-54986-5] [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: 04/26/2024] [Accepted: 11/24/2024] [Indexed: 01/04/2025] Open
Abstract
Advancements in cryo-EM have stimulated a revolution in structural biology. Yet, for membrane proteins near the cryo-EM size threshold of approximately 40 kDa, including transporters and G-protein coupled receptors, the absence of distinguishable structural features makes image alignment and structure determination a significant challenge. Furthermore, resolving more than one protein conformation within a sample, a major advantage of cryo-EM, represents an even greater degree of difficulty. Here, we describe a strategy for introducing a rigid fiducial marker (BRIL domain) at the C-terminus of membrane transporters from the Major Facilitator Superfamily (MFS) with AlphaFold2. This approach involves fusion of the last transmembrane domain helix of the target protein with the first helix of BRIL through a short poly-alanine linker to promote helicity. Combining this strategy with a BRIL-specific Fab, we elucidated four cryo-EM structures of the 42 kDa Staphylococcus aureus transporter NorA, three of which were derived from a single sample corresponding to inward-open, inward-occluded, and occluded conformations. Hence, this fusion construct facilitated experiments to characterize the conformational landscape of NorA and validated our design to position the BRIL/antibody pair in an orientation that avoids steric clash with the transporter. The latter was enabled through AlphaFold2 predictions, which minimized guesswork and reduced the need for screening several constructs. We further validated the suitability of the method to three additional MFS transporters (GlpT, Bmr, and Blt), results that supported a rigid linker between the transporter and BRIL. The successful application to four MFS proteins, the largest family of secondary transporters in nature, and analysis of predicted structures for the family indicates this strategy will be a valuable tool for studying other MFS members using cryo-EM.
Collapse
Affiliation(s)
- Pujun Xie
- Department of Chemistry, New York University, New York, NY, USA
| | - Yan Li
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Gaëlle Lamon
- Department of Chemistry, New York University, New York, NY, USA
| | - Huihui Kuang
- Cryo-EM Core Laboratory, New York University School of Medicine, New York, NY, USA
| | - Da-Neng Wang
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA.
| | | |
Collapse
|
6
|
Luo D, Alsuwaykit Z, Khan D, Strnad O, Isenberg T, Viola I. DiffFit: Visually-Guided Differentiable Fitting of Molecule Structures to a Cryo-EM Map. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2025; 31:558-568. [PMID: 39255135 DOI: 10.1109/tvcg.2024.3456404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
We introduce DiffFit, a differentiable algorithm for fitting protein atomistic structures into an experimental reconstructed Cryo-Electron Microscopy (cryo-EM) volume map. In structural biology, this process is necessary to semi-automatically composite large mesoscale models of complex protein assemblies and complete cellular structures that are based on measured cryo-EM data. The current approaches require manual fitting in three dimensions to start, resulting in approximately aligned structures followed by an automated fine-tuning of the alignment. The DiffFit approach enables domain scientists to fit new structures automatically and visualize the results for inspection and interactive revision. The fitting begins with differentiable three-dimensional (3D) rigid transformations of the protein atom coordinates followed by sampling the density values at the atom coordinates from the target cryo-EM volume. To ensure a meaningful correlation between the sampled densities and the protein structure, we proposed a novel loss function based on a multi-resolution volume-array approach and the exploitation of the negative space. This loss function serves as a critical metric for assessing the fitting quality, ensuring the fitting accuracy and an improved visualization of the results. We assessed the placement quality of DiffFit with several large, realistic datasets and found it to be superior to that of previous methods. We further evaluated our method in two use cases: automating the integration of known composite structures into larger protein complexes and facilitating the fitting of predicted protein domains into volume densities to aid researchers in identifying unknown proteins. We implemented our algorithm as an open-source plugin (github.com/nanovis/DiffFit) in ChimeraX, a leading visualization software in the field. All supplemental materials are available at osf. io/5tx4q.
Collapse
|
7
|
Feathers JR, Vignogna RC, Fromme JC. Structural basis for Rab6 activation by the Ric1-Rgp1 complex. Nat Commun 2024; 15:10561. [PMID: 39632878 PMCID: PMC11618376 DOI: 10.1038/s41467-024-54869-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 11/22/2024] [Indexed: 12/07/2024] Open
Abstract
Rab GTPases act as molecular switches to regulate organelle homeostasis and membrane trafficking. Rab6 plays a central role in regulating cargo flux through the Golgi and is activated via nucleotide exchange by the Ric1-Rgp1 protein complex. Ric1-Rgp1 is conserved throughout eukaryotes but the structural and mechanistic basis for its function has not been established. Here we report the cryoEM structure of a Ric1-Rgp1-Rab6 complex representing a key intermediate of the nucleotide exchange reaction. Ric1-Rgp1 interacts with the nucleotide-binding domain of Rab6 using an uncharacterized helical domain, which we establish as a RabGEF domain by identifying residues required for Rab6 activation. Unexpectedly, the complex uses an arrestin fold to interact with the Rab6 hypervariable domain, indicating that interactions with the unstructured C-terminal regions of Rab GTPases may be a common binding mechanism used by their activators. Collectively, our findings provide a detailed mechanistic understanding of regulated Rab6 activation at the Golgi.
Collapse
Affiliation(s)
- J Ryan Feathers
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14850, USA
- 201 Schultz Laboratory, Princeton University, Princeton, NJ, 08544, USA
| | - Ryan C Vignogna
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14850, USA
| | - J Christopher Fromme
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14850, USA.
| |
Collapse
|
8
|
Bonilla SL, Jang K. Challenges, advances, and opportunities in RNA structural biology by Cryo-EM. Curr Opin Struct Biol 2024; 88:102894. [PMID: 39121532 DOI: 10.1016/j.sbi.2024.102894] [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: 03/26/2024] [Revised: 07/03/2024] [Accepted: 07/15/2024] [Indexed: 08/12/2024]
Abstract
RNAs are remarkably versatile molecules that can fold into intricate three-dimensional (3D) structures to perform diverse cellular and viral functions. Despite their biological importance, relatively few RNA 3D structures have been solved, and our understanding of RNA structure-function relationships remains in its infancy. This limitation partly arises from challenges posed by RNA's complex conformational landscape, characterized by structural flexibility, formation of multiple states, and a propensity to misfold. Recently, cryo-electron microscopy (cryo-EM) has emerged as a powerful tool for the visualization of conformationally dynamic RNA-only 3D structures. However, RNA's characteristics continue to pose challenges. We discuss experimental methods developed to overcome these hurdles, including the engineering of modular modifications that facilitate the visualization of small RNAs, improve particle alignment, and validate structural models.
Collapse
Affiliation(s)
- Steve L Bonilla
- Laboratory of RNA Structural Biology and Biophysics, The Rockefeller University, New York, NY, 10065, USA.
| | - Karen Jang
- Laboratory of RNA Structural Biology and Biophysics, The Rockefeller University, New York, NY, 10065, USA
| |
Collapse
|
9
|
Baranova I, Angelova A, Stransky J, Andreasson J, Angelov B. Hemoglobin-PEG Interactions Probed by Small-Angle X-ray Scattering: Insights for Crystallization and Diagnostics Applications. J Phys Chem B 2024; 128:9262-9273. [PMID: 39252421 PMCID: PMC11440596 DOI: 10.1021/acs.jpcb.4c03003] [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: 05/07/2024] [Revised: 09/02/2024] [Accepted: 09/03/2024] [Indexed: 09/11/2024]
Abstract
Protein-protein interactions, controlling protein aggregation in the solution phase, are crucial for the formulation of protein therapeutics and the use of proteins in diagnostic applications. Additives in the solution phase are factors that may enhance the protein's conformational stability or induce crystallization. Protein-PEG interactions do not always stabilize the native protein structure. Structural information is needed to validate excipients for protein stabilization in the development of protein therapeutics or use proteins in diagnostic assays. The present study investigates the impact of polyethylene glycol (PEG) molecular weight and concentration on the spatial structure of human hemoglobin (Hb) at neutral pH. Small-angle X-ray scattering (SAXS) in combination with size-exclusion chromatography is employed to characterize the Hb structure in solution without and with the addition of PEG. Our results evidence that human hemoglobin maintains a tetrameric conformation at neutral pH. The dummy atom model, reconstructed from the SAXS data, aligns closely with the known crystallographic structure of methemoglobin (metHb) from the Protein Data Bank. We established that the addition of short-chain PEG600, at concentrations of up to 10% (w/v), acts as a stabilizer for hemoglobin, preserving its spatial structure without significant alterations. By contrast, 5% (w/v) PEG with higher molecular weights of 2000 and 4000 leads to a slight reduction in the maximum particle dimension (Dmax), while the radius of gyration (Rg) remains essentially unchanged. This implies a reduced hydration shell around the protein due to the dehydrating effect of longer PEG chains. At a concentration of 10% (w/v), PEG2000 interacts with Hb to form a complex that does not distort the protein's spatial configuration. The obtained results provide a deeper understanding of PEG's influence on the Hb structure in solution and broader knowledge regarding protein-PEG interactions.
Collapse
Affiliation(s)
- Iuliia Baranova
- Extreme
Light Infrastructure ERIC, Za Radnicí 835, Dolní Břežany 252 41, Czech Republic
- Faculty
of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague 121 16, Czech Republic
| | - Angelina Angelova
- Université
Paris-Saclay, CNRS, Institut Galien Paris-Saclay, F-91400 Orsay, France
| | - Jan Stransky
- Institute
of Biotechnology of the Czech Academy of Sciences, v.v.i., Prumyslová 595, Vestec 252 50, Czech Republic
| | - Jakob Andreasson
- Extreme
Light Infrastructure ERIC, Za Radnicí 835, Dolní Břežany 252 41, Czech Republic
| | - Borislav Angelov
- Extreme
Light Infrastructure ERIC, Za Radnicí 835, Dolní Břežany 252 41, Czech Republic
| |
Collapse
|
10
|
Catalano C, Lucier KW, To D, Senko S, Tran NL, Farwell AC, Silva SM, Dip PV, Poweleit N, Scapin G. The CryoEM structure of human serum albumin in complex with ligands. J Struct Biol 2024; 216:108105. [PMID: 38852682 DOI: 10.1016/j.jsb.2024.108105] [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: 03/29/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/11/2024]
Abstract
Human serum albumin (HSA) is the most prevalent plasma protein in the human body, accounting for 60 % of the total plasma protein. HSA plays a major pharmacokinetic function, serving as a facilitator in the distribution of endobiotics and xenobiotics within the organism. In this paper we report the cryoEM structures of HSA in the apo form and in complex with two ligands (salicylic acid and teniposide) at a resolution of 3.5, 3.7 and 3.4 Å, respectively. We expand upon previously published work and further demonstrate that sub-4 Å maps of ∼60 kDa proteins can be routinely obtained using a 200 kV microscope, employing standard workflows. Most importantly, these maps allowed for the identification of small molecule ligands, emphasizing the practical applicability of this methodology and providing a starting point for subsequent computational modeling and in silico optimization.
Collapse
Affiliation(s)
- Claudio Catalano
- NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA.
| | - Kyle W Lucier
- NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA
| | - Dennis To
- NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA
| | - Skerdi Senko
- NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA
| | - Nhi L Tran
- NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA
| | - Ashlyn C Farwell
- NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA
| | - Sabrina M Silva
- NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA
| | - Phat V Dip
- NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA
| | - Nicole Poweleit
- NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA
| | - Giovanna Scapin
- NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA
| |
Collapse
|
11
|
Wang CR, McFarlane LO, Pukala TL. Exploring snake venoms beyond the primary sequence: From proteoforms to protein-protein interactions. Toxicon 2024; 247:107841. [PMID: 38950738 DOI: 10.1016/j.toxicon.2024.107841] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/03/2024]
Abstract
Snakebite envenomation has been a long-standing global issue that is difficult to treat, largely owing to the flawed nature of current immunoglobulin-based antivenom therapy and the complexity of snake venoms as sophisticated mixtures of bioactive proteins and peptides. Comprehensive characterisation of venom compositions is essential to better understanding snake venom toxicity and inform effective and rationally designed antivenoms. Additionally, a greater understanding of snake venom composition will likely unearth novel biologically active proteins and peptides that have promising therapeutic or biotechnological applications. While a bottom-up proteomic workflow has been the main approach for cataloguing snake venom compositions at the toxin family level, it is unable to capture snake venom heterogeneity in the form of protein isoforms and higher-order protein interactions that are important in driving venom toxicity but remain underexplored. This review aims to highlight the importance of understanding snake venom heterogeneity beyond the primary sequence, in the form of post-translational modifications that give rise to different proteoforms and the myriad of higher-order protein complexes in snake venoms. We focus on current top-down proteomic workflows to identify snake venom proteoforms and further discuss alternative or novel separation, instrumentation, and data processing strategies that may improve proteoform identification. The current higher-order structural characterisation techniques implemented for snake venom proteins are also discussed; we emphasise the need for complementary and higher resolution structural bioanalytical techniques such as mass spectrometry-based approaches, X-ray crystallography and cryogenic electron microscopy, to elucidate poorly characterised tertiary and quaternary protein structures. We envisage that the expansion of the snake venom characterisation "toolbox" with top-down proteomics and high-resolution protein structure determination techniques will be pivotal in advancing structural understanding of snake venoms towards the development of improved therapeutic and biotechnology applications.
Collapse
Affiliation(s)
- C Ruth Wang
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, 5005, Australia
| | - Lewis O McFarlane
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, 5005, Australia
| | - Tara L Pukala
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, 5005, Australia.
| |
Collapse
|
12
|
Knejski PP, Erramilli SK, Kossiakoff AA. Chaperone-assisted cryo-EM structure of P. aeruginosa PhuR reveals molecular basis for heme binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.01.551527. [PMID: 37577460 PMCID: PMC10418163 DOI: 10.1101/2023.08.01.551527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Pathogenic bacteria, such as Pseudomonas aeruginosa, depend on scavenging heme for the acquisition of iron, an essential nutrient. The TonB-dependent transporter (TBDT) PhuR is the major heme uptake protein in P. aeruginosa clinical isolates. However, a comprehensive understanding of heme recognition and TBDT transport mechanisms, especially PhuR, remains limited. In this study, we employed single-particle cryogenic electron microscopy (cryo-EM) and a phage display-generated synthetic antibody (sAB) as a fiducial marker to enable the determination of a high-resolution (2.5 Å) structure of PhuR with a bound heme. Notably, the structure reveals iron coordination by Y529 on a conserved extracellular loop, shedding light on the role of tyrosine in heme binding. Biochemical assays and negative-stain EM demonstrated that the sAB specifically targets the heme-bound state of PhuR. These findings provide insights into PhuR's heme binding and offer a template for developing conformation-specific sABs against outer membrane proteins (OMPs) for structure-function investigations.
Collapse
Affiliation(s)
- Paweł P. Knejski
- Deparment of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
- Laboratory of Medical Biology, Faculty of Biotechnology, University of Wrocław, Wrocław 50-383, Poland
- Present address: Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich 8093, Switzerland
| | - Satchal K. Erramilli
- Deparment of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
- Present address: Meso Scale Diagnostics, LLC, Rockville, Maryland 20850, USA
| | - Anthony A. Kossiakoff
- Deparment of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
13
|
Takahashi K, Lee Y, Fago A, Bautista NM, Storz JF, Kawamoto A, Kurisu G, Nishizawa T, Tame JRH. The unique allosteric property of crocodilian haemoglobin elucidated by cryo-EM. Nat Commun 2024; 15:6505. [PMID: 39090102 PMCID: PMC11294572 DOI: 10.1038/s41467-024-49947-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 06/25/2024] [Indexed: 08/04/2024] Open
Abstract
The principal effect controlling the oxygen affinity of vertebrate haemoglobins (Hbs) is the allosteric switch between R and T forms with relatively high and low oxygen affinity respectively. Uniquely among jawed vertebrates, crocodilians possess Hb that shows a profound drop in oxygen affinity in the presence of bicarbonate ions. This allows them to stay underwater for extended periods by consuming almost all the oxygen present in the blood-stream, as metabolism releases carbon dioxide, whose conversion to bicarbonate and hydrogen ions is catalysed by carbonic anhydrase. Despite the apparent universal utility of bicarbonate as an allosteric regulator of Hb, this property evolved only in crocodilians. We report here the molecular structures of both human and a crocodilian Hb in the deoxy and liganded states, solved by cryo-electron microscopy. We reveal the precise interactions between two bicarbonate ions and the crocodilian protein at symmetry-related sites found only in the T state. No other known effector of vertebrate Hbs binds anywhere near these sites.
Collapse
Affiliation(s)
- Katsuya Takahashi
- Graduate School of Medical Life Science, Yokohama City University, Suehiro 1-7-29, Yokohama, 230-0045, Japan
| | - Yongchan Lee
- Graduate School of Medical Life Science, Yokohama City University, Suehiro 1-7-29, Yokohama, 230-0045, Japan
| | - Angela Fago
- Department of Biology, Aarhus University, C. F. Møllers Alle 3, Aarhus, DK-8000, Aarhus C, Denmark
| | - Naim M Bautista
- School of Biological Sciences, University of Nebraska, 1104 T St., Lincoln, NE 68588-0118, NE, USA
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, 1104 T St., Lincoln, NE 68588-0118, NE, USA
| | - Akihiro Kawamoto
- Institute for Protein Research, Osaka University, 3-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, 3-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tomohiro Nishizawa
- Graduate School of Medical Life Science, Yokohama City University, Suehiro 1-7-29, Yokohama, 230-0045, Japan.
| | - Jeremy R H Tame
- Graduate School of Medical Life Science, Yokohama City University, Suehiro 1-7-29, Yokohama, 230-0045, Japan.
| |
Collapse
|
14
|
Oktawiec J, Ebrahim OM, Chen Y, Su K, Sharpe C, Rosenmann ND, Barbut C, Weigand SJ, Thompson MP, Byrnes J, Qiao B, Gianneschi NC. Conformational modulation and polymerization-induced folding of proteomimetic peptide brush polymers. Chem Sci 2024:d4sc03420a. [PMID: 39129772 PMCID: PMC11308386 DOI: 10.1039/d4sc03420a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 07/16/2024] [Indexed: 08/13/2024] Open
Abstract
Peptide-brush polymers generated by graft-through living polymerization of peptide-modified monomers exhibit high proteolytic stability, therapeutic efficacy, and potential as functional tandem repeat protein mimetics. Prior work has focused on polymers generated from structurally disordered peptides that lack defined conformations. To obtain insight into how the structure of these polymers is influenced by the folding of their peptide sidechains, a set of polymers with varying degrees of polymerization was prepared from peptide monomers that adopt α-helical secondary structure for comparison to those having random coil structures. Circular dichroism and nuclear magnetic resonance spectroscopy confirm the maintenance of the secondary structure of the constituent peptide when polymerized. Small-angle X-ray scattering (SAXS) studies reveal the solution-phase conformation of PLPs in different solvent environments. In particular, X-ray scattering shows that modulation of solvent hydrophobicity, as well as hydrogen bonding patterns of the peptide sidechain, plays an important role in the degree of globularity and conformation of the overall polymer, with polymers of helical peptide brushes showing less spherical compaction in conditions where greater helicity is observed. These structural insights into peptide brush folding and polymer conformation inform the design of these proteomimetic materials with promise for controlling and predicting their artificial fold and morphology.
Collapse
Affiliation(s)
- Julia Oktawiec
- Department of Chemistry, Northwestern University Evanston IL 60208 USA
| | - Omar M Ebrahim
- Department of Chemistry, Northwestern University Evanston IL 60208 USA
| | - Yu Chen
- Department of Materials Science and Engineering, Northwestern University Evanston IL 60208 USA
| | - Kaylen Su
- Department of Natural Sciences, Baruch College, City University of New York New York NY 10010 USA
| | - Christopher Sharpe
- Department of Materials Science and Engineering, Northwestern University Evanston IL 60208 USA
| | - Nathan D Rosenmann
- Department of Materials Science and Engineering, Northwestern University Evanston IL 60208 USA
| | - Clara Barbut
- Department of Chemistry, Northwestern University Evanston IL 60208 USA
| | - Steven J Weigand
- DuPont-Northwestern-Dow Collaborative Access Team (DND-CAT) Synchrotron Research Center, Northwestern University Argonne IL 60208 USA
| | | | - James Byrnes
- Beamline 16ID, NSLS-II, Brookhaven National Laboratory Upton NY 11973 USA
| | - Baofu Qiao
- Department of Natural Sciences, Baruch College, City University of New York New York NY 10010 USA
| | - Nathan C Gianneschi
- Department of Chemistry, Northwestern University Evanston IL 60208 USA
- Department of Materials Science and Engineering, Northwestern University Evanston IL 60208 USA
- International Institute for Nanotechnology, Chemistry of Life Processes Institute, Simpson Querrey Institute, Lurie Cancer Center, Department of Biomedical Engineering, and Department of Pharmacology, Northwestern University Evanston IL 60208 USA
| |
Collapse
|
15
|
Cook BD, Narehood SM, McGuire KL, Li Y, Tezcan FA, Herzik MA. Preparation of oxygen-sensitive proteins for high-resolution cryoEM structure determination using (an)aerobic blot-free vitrification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.19.604374. [PMID: 39091810 PMCID: PMC11291078 DOI: 10.1101/2024.07.19.604374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
High-quality grid preparation for single-particle cryogenic electron microscopy (cryoEM) remains a bottleneck for routinely obtaining high-resolution structures. The issues that arise from traditional grid preparation workflows are particularly exacerbated for oxygen-sensitive proteins, including metalloproteins, whereby oxygen-induced damage and alteration of oxidation states can result in protein inactivation, denaturation, and/or aggregation. Indeed, 99% of the current structures in the EMBD were prepared aerobically and limited successes for anaerobic cryoEM grid preparation exist. Current practices for anaerobic grid preparation involve a vitrification device located in an anoxic chamber, which presents significant challenges including temperature and humidity control, optimization of freezing conditions, costs for purchase and operation, as well as accessibility. Here, we present a streamlined approach that allows for the (an)aerobic vitrification of oxygen-sensitive proteins using an automated aerobic blot-free grid vitrification device - the SPT Labtech chameleon. This robust workflow allows for high-resolution structure determination of dynamic, oxygen-sensitive proteins, of varying complexity and molecular weight.
Collapse
Affiliation(s)
- Brian D. Cook
- Department of Chemistry and Biochemistry, University of California, San Diego, California, USA
| | - Sarah M. Narehood
- Department of Chemistry and Biochemistry, University of California, San Diego, California, USA
| | - Kelly L. McGuire
- Department of Chemistry and Biochemistry, University of California, San Diego, California, USA
| | - Yizhou Li
- Department of Chemistry and Biochemistry, University of California, San Diego, California, USA
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, California, USA
| | - Mark A. Herzik
- Department of Chemistry and Biochemistry, University of California, San Diego, California, USA
| |
Collapse
|
16
|
Ukleja M, Kricks L, Torrens G, Peschiera I, Rodrigues-Lopes I, Krupka M, García-Fernández J, Melero R, Del Campo R, Eulalio A, Mateus A, López-Bravo M, Rico AI, Cava F, Lopez D. Flotillin-mediated stabilization of unfolded proteins in bacterial membrane microdomains. Nat Commun 2024; 15:5583. [PMID: 38961085 PMCID: PMC11222466 DOI: 10.1038/s41467-024-49951-1] [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: 02/21/2024] [Accepted: 06/26/2024] [Indexed: 07/05/2024] Open
Abstract
The function of many bacterial processes depends on the formation of functional membrane microdomains (FMMs), which resemble the lipid rafts of eukaryotic cells. However, the mechanism and the biological function of these membrane microdomains remain unclear. Here, we show that FMMs in the pathogen methicillin-resistant Staphylococcus aureus (MRSA) are dedicated to confining and stabilizing proteins unfolded due to cellular stress. The FMM scaffold protein flotillin forms a clamp-shaped oligomer that holds unfolded proteins, stabilizing them and favoring their correct folding. This process does not impose a direct energy cost on the cell and is crucial to survival of ATP-depleted bacteria, and thus to pathogenesis. Consequently, FMM disassembling causes the accumulation of unfolded proteins, which compromise MRSA viability during infection and cause penicillin re-sensitization due to PBP2a unfolding. Thus, our results indicate that FMMs mediate ATP-independent stabilization of unfolded proteins, which is essential for bacterial viability during infection.
Collapse
Affiliation(s)
- Marta Ukleja
- Department of Microbiology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain
| | - Lara Kricks
- Department of Microbiology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain
| | - Gabriel Torrens
- Department of Molecular Biology, Umeå University, Umeå, SE-901 87, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS). Umeå Center for Microbial Research (UCMR). Science for Life Laboratory (SciLifeLab), Umeå, SE-901 87, Sweden
| | - Ilaria Peschiera
- Department of Microbiology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain
| | - Ines Rodrigues-Lopes
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504, Coimbra, Portugal
| | - Marcin Krupka
- Department of Microbiology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain
| | - Julia García-Fernández
- Department of Microbiology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain
| | - Roberto Melero
- Department of Structural Biology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain
| | - Rosa Del Campo
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ramón y Cajal Hospital, 28034, Madrid, Spain
| | - Ana Eulalio
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504, Coimbra, Portugal
- Department of Life Sciences, Center for Bacterial Resistance Biology, Imperial College London, London, SW7 2AZ, United Kingdom
| | - André Mateus
- The Laboratory for Molecular Infection Medicine Sweden (MIMS). Umeå Center for Microbial Research (UCMR). Science for Life Laboratory (SciLifeLab), Umeå, SE-901 87, Sweden
- Department of Chemistry, Umeå University, Umeå, SE-901 87, Sweden
| | - María López-Bravo
- Department of Microbiology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain
| | - Ana I Rico
- Department of Microbiology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain
| | - Felipe Cava
- Department of Molecular Biology, Umeå University, Umeå, SE-901 87, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS). Umeå Center for Microbial Research (UCMR). Science for Life Laboratory (SciLifeLab), Umeå, SE-901 87, Sweden
| | - Daniel Lopez
- Department of Microbiology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain.
| |
Collapse
|
17
|
Hirst IJ, Thomas WJ, Davies RA, Muench SP. CryoEM grid preparation: a closer look at advancements and impact of preparation mode and new approaches. Biochem Soc Trans 2024; 52:1529-1537. [PMID: 38864435 PMCID: PMC11346429 DOI: 10.1042/bst20231553] [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: 04/25/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/13/2024]
Abstract
Sample preparation can present a significant hurdle within single particle cryo-electron microscopy (cryoEM), resulting in issues with reproducibility, data quality or an inability to visualise the sample. There are several factors which can influence this, including sample or buffer composition, grid type, route of sample preparation and interactions with the air-water interface (AWI). Here, we review some of the current routes for sample preparation and the associated challenges. We discuss a range of approaches for overcoming these challenges, such as minimising the grid preparation time, surfactants, grid type and biochemical approaches such as nanomagnetic beads. Finally, we discuss how a set of commercially available protein samples may serve as a benchmark suite for future technologies. This provides a route to compare techniques' abilities not just to generate high-resolution structures but also to overcome the challenges traditionally associated with cryoEM. As the field continues to produce new approaches to sample preparation and we start to better understand the underlying principles behind the behaviour of proteins within a thin film and in response to different environments, especially grid composition, it is hoped that more universal solutions can be provided that make the intractable systems tractable, improve resolution and, importantly, speed up data collection and reduce the currently required dataset sizes.
Collapse
Affiliation(s)
- Isobel J. Hirst
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - William J.R. Thomas
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Rhiannon A. Davies
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Stephen P. Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| |
Collapse
|
18
|
Lin HH, Wang CH, Huang SH, Lin SY, Kato T, Namba K, Hosogi N, Song C, Murata K, Yen CH, Hsu TL, Wong CH, Wu YM, Tu IP, Chang WH. Use of phase plate cryo-EM reveals conformation diversity of therapeutic IgG with 50 kDa Fab fragment resolved below 6 Å. Sci Rep 2024; 14:14079. [PMID: 38890341 PMCID: PMC11189423 DOI: 10.1038/s41598-024-62045-8] [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: 06/28/2023] [Accepted: 05/13/2024] [Indexed: 06/20/2024] Open
Abstract
While cryogenic electron microscopy (cryo-EM) is fruitfully used for harvesting high-resolution structures of sizable macromolecules, its application to small or flexible proteins composed of small domains like immunoglobulin (IgG) remain challenging. Here, we applied single particle cryo-EM to Rituximab, a therapeutic IgG mediating anti-tumor toxicity, to explore its solution conformations. We found Rituximab molecules exhibited aggregates in cryo-EM specimens contrary to its solution behavior, and utilized a non-ionic detergent to successfully disperse them as isolated particles amenable to single particle analysis. As the detergent adversely reduced the protein-to-solvent contrast, we employed phase plate contrast to mitigate the impaired protein visibility. Assisted by phase plate imaging, we obtained a canonical three-arm IgG structure with other structures displaying variable arm densities co-existing in solution, affirming high flexibility of arm-connecting linkers. Furthermore, we showed phase plate imaging enables reliable structure determination of Fab to sub-nanometer resolution from ab initio, yielding a characteristic two-lobe structure that could be unambiguously docked with crystal structure. Our findings revealed conformation diversity of IgG and demonstrated phase plate was viable for cryo-EM analysis of small proteins without symmetry. This work helps extend cryo-EM boundaries, providing a valuable imaging and structural analysis framework for macromolecules with similar challenging features.
Collapse
Affiliation(s)
- Hsin-Hung Lin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Chun-Hsiung Wang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Academia Sinica Cryo-EM Facility, Academia Sinica, Taipei, Taiwan
| | - Shih-Hsin Huang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei City, Taiwan
| | - Sung-Yao Lin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Takayuki Kato
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, Japan
- Institute of Protein Research, Osaka University, Suita, Osaka, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, Japan
| | - Naoki Hosogi
- JEOL Ltd., 1-2 Musashino 3-chome, Akishima, Tokyo, Japan
| | - Chihong Song
- Exploratory Research Center on Life and Living Systems (ExCELLS) and National Institute for Physiological Sciences (NIPS), National Institutes of Natural Sciences, 38 Nishigonaka Myodaiji, Okazaki, Aichi, Japan
| | - Kazuyoshi Murata
- Exploratory Research Center on Life and Living Systems (ExCELLS) and National Institute for Physiological Sciences (NIPS), National Institutes of Natural Sciences, 38 Nishigonaka Myodaiji, Okazaki, Aichi, Japan
| | | | - Tsui-Ling Hsu
- Genomic Research Center, Academia Sinica, Taipei, Taiwan
| | - Chi-Huey Wong
- Genomic Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-Min Wu
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Cryo-EM Facility, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - I-Ping Tu
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Wei-Hau Chang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan.
- Genomic Research Center, Academia Sinica, Taipei, Taiwan.
- Institute of Physics, Academia Sinica, Taipei, Taiwan.
| |
Collapse
|
19
|
Xu D, Ando N. Miffi: Improving the accuracy of CNN-based cryo-EM micrograph filtering with fine-tuning and Fourier space information. J Struct Biol 2024; 216:108072. [PMID: 38431179 PMCID: PMC11162944 DOI: 10.1016/j.jsb.2024.108072] [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: 12/11/2023] [Revised: 02/11/2024] [Accepted: 02/25/2024] [Indexed: 03/05/2024]
Abstract
Efficient and high-accuracy filtering of cryo-electron microscopy (cryo-EM) micrographs is an emerging challenge with the growing speed of data collection and sizes of datasets. Convolutional neural networks (CNNs) are machine learning models that have been proven successful in many computer vision tasks, and have been previously applied to cryo-EM micrograph filtering. In this work, we demonstrate that two strategies, fine-tuning models from pretrained weights and including the power spectrum of micrographs as input, can greatly improve the attainable prediction accuracy of CNN models. The resulting software package, Miffi, is open-source and freely available for public use (https://github.com/ando-lab/miffi).
Collapse
Affiliation(s)
- Da Xu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Nozomi Ando
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
20
|
Feathers JR, Vignogna RC, Fromme JC. Structural basis for Rab6 activation by the Ric1-Rgp1 complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.592747. [PMID: 38766083 PMCID: PMC11100747 DOI: 10.1101/2024.05.06.592747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Rab GTPases act as molecular switches to regulate organelle homeostasis and membrane trafficking. Rab6 plays a central role in regulating cargo flux through the Golgi and is activated via nucleotide exchange by the Ric1-Rgp1 protein complex. Ric1-Rgp1 is conserved throughout eukaryotes but the structural and mechanistic basis for its function has not been established. Here we report the cryoEM structure of a Ric1-Rgp1-Rab6 complex representing a key intermediate of the nucleotide exchange reaction. This structure reveals the overall architecture of the complex and enabled us to identify interactions critical for proper recognition and activation of Rab6 on the Golgi membrane surface. Ric1-Rgp1 interacts with the nucleotide-binding domain of Rab6 using an uncharacterized helical domain, which we establish as a novel RabGEF domain by identifying residues required for Rab6 nucleotide exchange. Unexpectedly, the complex uses an arrestin fold to interact with the Rab6 hypervariable domain, indicating that interactions with the unstructured C-terminal regions of Rab GTPases may be a common specificity mechanism used by their activators. Collectively, our findings provide a detailed mechanistic understanding of regulated Rab6 activation at the Golgi.
Collapse
Affiliation(s)
- J. Ryan Feathers
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
- Current address: 201 Schultz Laboratory, Princeton University, Princeton, NJ 08544 USA
| | - Ryan C. Vignogna
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
| | - J. Christopher Fromme
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
| |
Collapse
|
21
|
Ravichandran A, Araque JC, Lawson JW. Predicting the functional state of protein kinases using interpretable graph neural networks from sequence and structural data. Proteins 2024; 92:623-636. [PMID: 38083830 DOI: 10.1002/prot.26641] [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: 02/26/2023] [Revised: 10/13/2023] [Accepted: 11/09/2023] [Indexed: 04/13/2024]
Abstract
Protein kinases are central to cellular activities and are actively pursued as drug targets for several conditions including cancer and autoimmune diseases. Despite the availability of a large structural database for kinases, methodologies to elucidate the structure-function relationship of these proteins (without manual intervention) are lacking. Such techniques are essential in structural biology and to accelerate drug discovery efforts. Here, we implement an interpretable graph neural network (GNN) framework for classifying the functionally active and inactive states of a large set of protein kinases by only using their tertiary structure and amino acid sequence. We show that the GNN models can classify kinase structures with high accuracy (>97%). We implement the Gradient-weighted Class Activation Mapping for graphs (Graph Grad-CAM) to automatically identify structurally important residues and residue-residue contacts of the kinases without any a priori input. We show that the motifs identified through the Graph Grad-CAM methodology are functionally critical, consistent with the existing kinase literature. Notably, the highly conserved DFG and HRD motifs of the well-known hydrophobic spine are identified by the interpretable framework in addition to some of the lesser known motifs. Further, using Grad-CAM maps as the vector embedding of the protein structures, we identify the subtle differences in the crystal structures among different sub-classes of kinases in the Protein Data Bank (PDB). Frameworks such as the one implemented here, for high-throughput identification of protein structure-function relationships are essential in designing targeted small molecules therapies as well as in engineering new proteins for novel applications.
Collapse
Affiliation(s)
- Ashwin Ravichandran
- KBR Inc., Intelligent Systems Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Juan C Araque
- KBR Inc., Intelligent Systems Division, NASA Ames Research Center, Moffett Field, California, USA
| | - John W Lawson
- Intelligent Systems Division, NASA Ames Research Center, Moffett Field, California, USA
| |
Collapse
|
22
|
Berkeley RF, Cook BD, Herzik MA. Machine learning approaches to cryoEM density modification differentially affect biomacromolecule and ligand density quality. Front Mol Biosci 2024; 11:1404885. [PMID: 38698773 PMCID: PMC11063317 DOI: 10.3389/fmolb.2024.1404885] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 04/03/2024] [Indexed: 05/05/2024] Open
Abstract
The application of machine learning to cryogenic electron microscopy (cryoEM) data analysis has added a valuable set of tools to the cryoEM data processing pipeline. As these tools become more accessible and widely available, the implications of their use should be assessed. We noticed that machine learning map modification tools can have differential effects on cryoEM densities. In this perspective, we evaluate these effects to show that machine learning tools generally improve densities for biomacromolecules while generating unpredictable results for ligands. This unpredictable behavior manifests both in quantitative metrics of map quality and in qualitative investigations of modified maps. The results presented here highlight the power and potential of machine learning tools in cryoEM, while also illustrating some of the risks of their unexamined use.
Collapse
|
23
|
Khoshouei A, Kempf G, Mykhailiuk V, Griessing JM, Honemann MN, Kater L, Cavadini S, Dietz H. Designing Rigid DNA Origami Templates for Molecular Visualization Using Cryo-EM. NANO LETTERS 2024; 24. [PMID: 38602296 PMCID: PMC11057029 DOI: 10.1021/acs.nanolett.4c00915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 04/12/2024]
Abstract
DNA origami, a method for constructing nanostructures from DNA, offers potential for diverse scientific and technological applications due to its ability to integrate various molecular functionalities in a programmable manner. In this study, we examined the impact of internal crossover distribution and the compositional uniformity of staple strands on the structure of multilayer DNA origami using cryogenic electron microscopy (cryo-EM) single-particle analysis. A refined DNA object was utilized as an alignment framework in a host-guest model, where we successfully resolved an 8 kDa thrombin binding aptamer (TBA) linked to the host object. Our results broaden the spectrum of DNA in structural applications.
Collapse
Affiliation(s)
- Ali Khoshouei
- Laboratory
for Biomolecular Nanotechnology, Department of Biosciences, School
of Natural Sciences, Technical University
of Munich, Am Coulombwall 4a, 85748 Garching, Germany
- Munich
Institute of Biomedical Engineering, Technical
University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Georg Kempf
- Friedrich
Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Volodymyr Mykhailiuk
- Laboratory
for Biomolecular Nanotechnology, Department of Biosciences, School
of Natural Sciences, Technical University
of Munich, Am Coulombwall 4a, 85748 Garching, Germany
- Munich
Institute of Biomedical Engineering, Technical
University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Johanna Mariko Griessing
- Laboratory
for Biomolecular Nanotechnology, Department of Biosciences, School
of Natural Sciences, Technical University
of Munich, Am Coulombwall 4a, 85748 Garching, Germany
- Munich
Institute of Biomedical Engineering, Technical
University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Maximilian Nicolas Honemann
- Laboratory
for Biomolecular Nanotechnology, Department of Biosciences, School
of Natural Sciences, Technical University
of Munich, Am Coulombwall 4a, 85748 Garching, Germany
- Munich
Institute of Biomedical Engineering, Technical
University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Lukas Kater
- Friedrich
Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Simone Cavadini
- Friedrich
Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Hendrik Dietz
- Laboratory
for Biomolecular Nanotechnology, Department of Biosciences, School
of Natural Sciences, Technical University
of Munich, Am Coulombwall 4a, 85748 Garching, Germany
- Munich
Institute of Biomedical Engineering, Technical
University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| |
Collapse
|
24
|
Knejski PP, Erramilli SK, Kossiakoff AA. Chaperone-assisted cryo-EM structure of P. aeruginosa PhuR reveals molecular basis for heme binding. Structure 2024; 32:411-423.e6. [PMID: 38325368 PMCID: PMC10997469 DOI: 10.1016/j.str.2024.01.007] [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: 08/02/2023] [Revised: 12/14/2023] [Accepted: 01/11/2024] [Indexed: 02/09/2024]
Abstract
Pathogenic bacteria, such as Pseudomonas aeruginosa, depend on scavenging heme for the acquisition of iron, an essential nutrient. The TonB-dependent transporter (TBDT) PhuR is the major heme uptake protein in P. aeruginosa clinical isolates. However, a comprehensive understanding of heme recognition and TBDT transport mechanisms, especially PhuR, remains limited. In this study, we employed single-particle cryogenic electron microscopy (cryo-EM) and a phage display-generated synthetic antibody (sAB) as a fiducial marker to enable the determination of a high-resolution (2.5 Å) structure of PhuR with a bound heme. Notably, the structure reveals iron coordination by Y529 on a conserved extracellular loop, shedding light on the role of tyrosine in heme binding. Biochemical assays and negative-stain EM demonstrated that the sAB specifically targets the heme-bound state of PhuR. These findings provide insights into PhuR's heme binding and offer a template for developing conformation-specific sABs against outer membrane proteins (OMPs) for structure-function investigations.
Collapse
Affiliation(s)
- Paweł P Knejski
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA; Laboratory of Medical Biology, Faculty of Biotechnology, University of Wrocław, 50-383 Wrocław, Poland
| | - Satchal K Erramilli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA; Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA.
| |
Collapse
|
25
|
Greber BJ. High-resolution cryo-EM of a small protein complex: The structure of the human CDK-activating kinase. Structure 2024:S0969-2126(24)00085-6. [PMID: 38565138 DOI: 10.1016/j.str.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/27/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024]
Abstract
The human CDK-activating kinase (CAK) is a multifunctional protein complex and key regulator of cell growth and division. Because of its critical functions in regulating the cell cycle and transcription initiation, it is a key target for multiple cancer drug discovery programs. However, the structure of the active human CAK, insights into its regulation, and its interactions with cellular substrates and inhibitors remained elusive until recently due to the lack of high-resolution structures of the intact complex. This review covers the progress in structure determination of the human CAK by cryogenic electron microscopy (cryo-EM), from early efforts to recent near-atomic resolution maps routinely resolved at 2Å or better. These results were enabled by the latest cryo-EM technologies introduced after the initial phase of the "resolution revolution" and allowed the application of high-resolution methods to new classes of molecular targets, including small protein complexes that were intractable using earlier technology.
Collapse
Affiliation(s)
- Basil J Greber
- Division of Structural Biology, The Institute of Cancer Research, London SW3 6JB, UK.
| |
Collapse
|
26
|
Gee M, Atai K, Coller HA, Yeates TO, Castells-Graells R. Designed fluorescent protein cages as fiducial markers for targeted cell imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582585. [PMID: 38464160 PMCID: PMC10925312 DOI: 10.1101/2024.02.28.582585] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Understanding how proteins function within their cellular environments is essential for cellular biology and biomedical research. However, current imaging techniques exhibit limitations, particularly in the study of small complexes and individual proteins within cells. Previously, protein cages have been employed as imaging scaffolds to study purified small proteins using cryo-electron microscopy (cryo-EM). Here we demonstrate an approach to deliver designed protein cages - endowed with fluorescence and targeted binding properties - into cells, thereby serving as fiducial markers for cellular imaging. We used protein cages with anti-GFP DARPin domains to target a mitochondrial protein (MFN1) expressed in mammalian cells, which was genetically fused to GFP. We demonstrate that the protein cages can penetrate cells, are directed to specific subcellular locations, and are detectable with confocal microscopy. This innovation represents a milestone in developing tools for in-depth cellular exploration, especially in conjunction with methods such as cryo-correlative light and electron microscopy (cryo-CLEM).
Collapse
Affiliation(s)
- Morgan Gee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA 90095
| | - Kaiser Atai
- Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, Los Angeles, CA, USA 90095
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA 90095
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA 90095
| | - Hilary A Coller
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA 90095
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA 90095
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA 90095
| | - Todd O Yeates
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA 90095
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA 90095
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA 90095
| | | |
Collapse
|
27
|
Xu D, Ando N. Miffi: Improving the accuracy of CNN-based cryo-EM micrograph filtering with fine-tuning and Fourier space information. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.08.570849. [PMID: 38405773 PMCID: PMC10888874 DOI: 10.1101/2023.12.08.570849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Efficient and high-accuracy filtering of cryo-electron microscopy (cryo-EM) micrographs is an emerging challenge with the growing speed of data collection and sizes of datasets. Convolutional neural networks (CNNs) are machine learning models that have been proven successful in many computer vision tasks, and have been previously applied to cryo-EM micrograph filtering. In this work, we demonstrate that two strategies, fine-tuning models from pretrained weights and including the power spectrum of micrographs as input, can greatly improve the attainable prediction accuracy of CNN models. The resulting software package, Miffi, is open-source and freely available for public use (https://github.com/ando-lab/miffi).
Collapse
Affiliation(s)
- Da Xu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850, USA
| | - Nozomi Ando
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850, USA
| |
Collapse
|
28
|
Aiyer S, Baldwin PR, Tan SM, Shan Z, Oh J, Mehrani A, Bowman ME, Louie G, Passos DO, Đorđević-Marquardt S, Mietzsch M, Hull JA, Hoshika S, Barad BA, Grotjahn DA, McKenna R, Agbandje-McKenna M, Benner SA, Noel JAP, Wang D, Tan YZ, Lyumkis D. Overcoming resolution attenuation during tilted cryo-EM data collection. Nat Commun 2024; 15:389. [PMID: 38195598 PMCID: PMC10776679 DOI: 10.1038/s41467-023-44555-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024] Open
Abstract
Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting "preferred orientations" on grids, leading to anisotropic map resolution and impeding structure determination. Tilting the specimen stage during data collection is a generalizable solution but has historically led to substantial resolution attenuation. Here, we develop updated data collection and image processing workflows and demonstrate, using multiple specimens, that resolution attenuation is negligible or significantly reduced across tilt angles. Reconstructions with and without the stage tilted as high as 60° are virtually indistinguishable. These strategies allowed the reconstruction to 3 Å resolution of a bacterial RNA polymerase with preferred orientation, containing an unnatural nucleotide for studying novel base pair recognition. Furthermore, we present a quantitative framework that allows cryo-EM practitioners to define an optimal tilt angle during data acquisition. These results reinforce the utility of employing stage tilt for data collection and provide quantitative metrics to obtain isotropic maps.
Collapse
Affiliation(s)
- Sriram Aiyer
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Philip R Baldwin
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shi Min Tan
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
| | - Zelin Shan
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- College of Pharmacy, Kyung Hee University, Seoul, 02247, Republic of Korea
| | - Atousa Mehrani
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Marianne E Bowman
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Gordon Louie
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Dario Oliveira Passos
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | | | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Joshua A Hull
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd Box 7, Alachua, FL, 32615, USA
| | - Benjamin A Barad
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Danielle A Grotjahn
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd Box 7, Alachua, FL, 32615, USA
| | - Joseph A P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yong Zi Tan
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore.
- Disease Intervention Technology Laboratory (DITL), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Singapore, 138648, Singapore.
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore.
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Graduate School of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA, 92093, USA.
| |
Collapse
|
29
|
Ignatiou A, Macé K, Redzej A, Costa TRD, Waksman G, Orlova EV. Structural Analysis of Protein Complexes by Cryo-Electron Microscopy. Methods Mol Biol 2024; 2715:431-470. [PMID: 37930544 DOI: 10.1007/978-1-0716-3445-5_27] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Structural studies of bio-complexes using single particle cryo-Electron Microscopy (cryo-EM) is nowadays a well-established technique in structural biology and has become competitive with X-ray crystallography. Development of digital registration systems for electron microscopy images and algorithms for the fast and efficient processing of the recorded images and their following analysis has facilitated the determination of structures at near-atomic resolution. The latest advances in EM have enabled the determination of protein complex structures at 1.4-3 Å resolution for an extremely broad range of sizes (from ~100 kDa up to hundreds of MDa (Bartesaghi et al., Science 348(6239):1147-1151, 2015; Herzik et al., Nat Commun 10:1032, 2019; Wu et al., J Struct Biol X 4:100020, 2020; Zhang et al., Nat Commun 10:5511, 2019; Zhang et al., Cell Res 30(12):1136-1139, 2020; Yip et al., Nature 587(7832):157-161, 2020; https://www.ebi.ac.uk/emdb/statistics/emdb_resolution_year )). In 2022, nearly 1200 structures deposited to the EMDB database were at a resolution of better than 3 Å ( https://www.ebi.ac.uk/emdb/statistics/emdb_resolution_year ).To date, the highest resolutions have been achieved for apoferritin, which comprises a homo-oligomer of high point group symmetry (O432) and has rigid organization together with high stability (Zhang et al., Cell Res 30(12):1136-1139, 2020; Yip et al., Nature 587(7832):157-161, 2020). It has been used as a test object for the assessments of modern cryo-microscopes and processing methods during the last 5 years. In contrast to apoferritin bacterial secretion systems are typical examples of multi protein complexes exhibiting high flexibility owing to their functions relating to the transportation of small molecules, proteins, and DNA into the extracellular space or target cells. This makes their structural characterization extremely challenging (Barlow, Methods Mol Biol 532:397-411, 2009; Costa et al., Nat Rev Microbiol 13:343-359, 2015). The most feasible approach to reveal their spatial organization and functional modification is cryo-electron microscopy (EM). During the last decade, structural cryo-EM has become broadly used for the analysis of the bio-complexes that comprise multiple components and are not amenable to crystallization (Lyumkis, J Biol Chem 294:5181-5197, 2019; Orlova and Saibil, Methods Enzymol 482:321-341, 2010; Orlova and Saibil, Chem Rev 111(12):7710-7748, 2011).In this review, we will describe the basics of sample preparation for cryo-EM, the principles of digital data collection, and the logistics of image analysis focusing on the common steps required for reconstructions of both small and large biological complexes together with refinement of their structures to nearly atomic resolution. The workflow of processing will be illustrated by examples of EM analysis of Type IV Secretion System.
Collapse
Affiliation(s)
- Athanasios Ignatiou
- Institute for Structural and Molecular Biology, School of Biological Sciences, Birkbeck College, London, UK
| | - Kévin Macé
- Institute for Structural and Molecular Biology, School of Biological Sciences, Birkbeck College, London, UK
| | - Adam Redzej
- Institute for Structural and Molecular Biology, School of Biological Sciences, Birkbeck College, London, UK
| | - Tiago R D Costa
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College, London, UK
| | - Gabriel Waksman
- Institute for Structural and Molecular Biology, School of Biological Sciences, Birkbeck College, London, UK
| | - Elena V Orlova
- Institute for Structural and Molecular Biology, School of Biological Sciences, Birkbeck College, London, UK.
| |
Collapse
|
30
|
Langeberg CJ, Kieft JS. A generalizable scaffold-based approach for structure determination of RNAs by cryo-EM. Nucleic Acids Res 2023; 51:e100. [PMID: 37791881 PMCID: PMC10639074 DOI: 10.1093/nar/gkad784] [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: 03/20/2023] [Revised: 08/31/2023] [Accepted: 09/24/2023] [Indexed: 10/05/2023] Open
Abstract
Single-particle cryo-electron microscopy (cryo-EM) can reveal the structures of large and often dynamic molecules, but smaller biomolecules (≤50 kDa) remain challenging targets due to their intrinsic low signal to noise ratio. Methods to help resolve small proteins have been applied but development of similar approaches to aid in structural determination of small, structured RNA elements have lagged. Here, we present a scaffold-based approach that we used to recover maps of sub-25 kDa RNA domains to 4.5-5.0 Å. While lacking the detail of true high-resolution maps, these maps are suitable for model building and preliminary structure determination. We demonstrate this method helped faithfully recover the structure of several RNA elements of known structure, and that it promises to be generalized to other RNAs without disturbing their native fold. This approach may streamline the sample preparation process and reduce the optimization required for data collection. This first-generation scaffold approach provides a robust system to aid in RNA structure determination by cryo-EM and lays the groundwork for further scaffold optimization to achieve higher resolution.
Collapse
Affiliation(s)
- Conner J Langeberg
- Department of Biochemistry and Molecular Genetics, Aurora, CO 80045, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, Aurora, CO 80045, USA
- RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
- New York Structural Biology Center, New York, NY 10027, USA
| |
Collapse
|
31
|
Santiago-Frangos A, Henriques WS, Wiegand T, Gauvin CC, Buyukyoruk M, Graham AB, Wilkinson RA, Triem L, Neselu K, Eng ET, Lander GC, Wiedenheft B. Structure reveals why genome folding is necessary for site-specific integration of foreign DNA into CRISPR arrays. Nat Struct Mol Biol 2023; 30:1675-1685. [PMID: 37710013 PMCID: PMC10872659 DOI: 10.1038/s41594-023-01097-2] [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: 03/22/2023] [Accepted: 08/15/2023] [Indexed: 09/16/2023]
Abstract
Bacteria and archaea acquire resistance to viruses and plasmids by integrating fragments of foreign DNA into the first repeat of a CRISPR array. However, the mechanism of site-specific integration remains poorly understood. Here, we determine a 560-kDa integration complex structure that explains how Pseudomonas aeruginosa Cas (Cas1-Cas2/3) and non-Cas proteins (for example, integration host factor) fold 150 base pairs of host DNA into a U-shaped bend and a loop that protrude from Cas1-2/3 at right angles. The U-shaped bend traps foreign DNA on one face of the Cas1-2/3 integrase, while the loop places the first CRISPR repeat in the Cas1 active site. Both Cas3 proteins rotate 100 degrees to expose DNA-binding sites on either side of the Cas2 homodimer, which each bind an inverted repeat motif in the leader. Leader sequence motifs direct Cas1-2/3-mediated integration to diverse repeat sequences that have a 5'-GT. Collectively, this work reveals new DNA-binding surfaces on Cas2 that are critical for DNA folding and site-specific delivery of foreign DNA.
Collapse
Affiliation(s)
| | - William S Henriques
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Tanner Wiegand
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Colin C Gauvin
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
- Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Murat Buyukyoruk
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Ava B Graham
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Royce A Wilkinson
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Lenny Triem
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Kasahun Neselu
- Simons Electron Microscopy Center, National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY, USA
| | - Edward T Eng
- Simons Electron Microscopy Center, National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY, USA
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Blake Wiedenheft
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
| |
Collapse
|
32
|
Castells-Graells R, Meador K, Arbing MA, Sawaya MR, Gee M, Cascio D, Gleave E, Debreczeni JÉ, Breed J, Leopold K, Patel A, Jahagirdar D, Lyons B, Subramaniam S, Phillips C, Yeates TO. Cryo-EM structure determination of small therapeutic protein targets at 3 Å-resolution using a rigid imaging scaffold. Proc Natl Acad Sci U S A 2023; 120:e2305494120. [PMID: 37669364 PMCID: PMC10500258 DOI: 10.1073/pnas.2305494120] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/14/2023] [Indexed: 09/07/2023] Open
Abstract
Cryoelectron microscopy (Cryo-EM) has enabled structural determination of proteins larger than about 50 kDa, including many intractable by any other method, but it has largely failed for smaller proteins. Here, we obtain structures of small proteins by binding them to a rigid molecular scaffold based on a designed protein cage, revealing atomic details at resolutions reaching 2.9 Å. We apply this system to the key cancer signaling protein KRAS (19 kDa in size), obtaining four structures of oncogenic mutational variants by cryo-EM. Importantly, a structure for the key G12C mutant bound to an inhibitor drug (AMG510) reveals significant conformational differences compared to prior data in the crystalline state. The findings highlight the promise of cryo-EM scaffolds for advancing the design of drug molecules against small therapeutic protein targets in cancer and other human diseases.
Collapse
Affiliation(s)
- Roger Castells-Graells
- Department of Energy, Institute for Genomics and Proteomics, University of California, Los Angeles, CA90095
| | - Kyle Meador
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Mark A. Arbing
- Department of Energy, Institute for Genomics and Proteomics, University of California, Los Angeles, CA90095
| | - Michael R. Sawaya
- Department of Energy, Institute for Genomics and Proteomics, University of California, Los Angeles, CA90095
| | - Morgan Gee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Duilio Cascio
- Department of Energy, Institute for Genomics and Proteomics, University of California, Los Angeles, CA90095
| | - Emma Gleave
- Discovery Sciences, R&D, AstraZeneca, CambridgeCB2 0AA, United Kingdom
| | | | - Jason Breed
- Discovery Sciences, R&D, AstraZeneca, CambridgeCB2 0AA, United Kingdom
| | - Karoline Leopold
- Gandeeva Therapeutics, Inc., Burnaby, British ColumbiaV5C 6N5, Canada
| | - Ankoor Patel
- Gandeeva Therapeutics, Inc., Burnaby, British ColumbiaV5C 6N5, Canada
| | | | - Bronwyn Lyons
- Gandeeva Therapeutics, Inc., Burnaby, British ColumbiaV5C 6N5, Canada
| | - Sriram Subramaniam
- Gandeeva Therapeutics, Inc., Burnaby, British ColumbiaV5C 6N5, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Chris Phillips
- Discovery Sciences, R&D, AstraZeneca, CambridgeCB2 0AA, United Kingdom
| | - Todd O. Yeates
- Department of Energy, Institute for Genomics and Proteomics, University of California, Los Angeles, CA90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| |
Collapse
|
33
|
Reinhardt R, Leonard TA. A critical evaluation of protein kinase regulation by activation loop autophosphorylation. eLife 2023; 12:e88210. [PMID: 37470698 PMCID: PMC10359097 DOI: 10.7554/elife.88210] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/07/2023] [Indexed: 07/21/2023] Open
Abstract
Phosphorylation of proteins is a ubiquitous mechanism of regulating their function, localization, or activity. Protein kinases, enzymes that use ATP to phosphorylate protein substrates are, therefore, powerful signal transducers in eukaryotic cells. The mechanism of phosphoryl-transfer is universally conserved among protein kinases, which necessitates the tight regulation of kinase activity for the orchestration of cellular processes with high spatial and temporal fidelity. In response to a stimulus, many kinases enhance their own activity by autophosphorylating a conserved amino acid in their activation loop, but precisely how this reaction is performed is controversial. Classically, kinases that autophosphorylate their activation loop are thought to perform the reaction in trans, mediated by transient dimerization of their kinase domains. However, motivated by the recently discovered regulation mechanism of activation loop cis-autophosphorylation by a kinase that is autoinhibited in trans, we here review the various mechanisms of autoregulation that have been proposed. We provide a framework for critically evaluating biochemical, kinetic, and structural evidence for protein kinase dimerization and autophosphorylation, and share some thoughts on the implications of these mechanisms within physiological signaling networks.
Collapse
Affiliation(s)
- Ronja Reinhardt
- Max Perutz Labs, Vienna Biocenter Campus (VBC)ViennaAustria
- Medical University of Vienna, Center for Medical BiochemistryViennaAustria
| | - Thomas A Leonard
- Max Perutz Labs, Vienna Biocenter Campus (VBC)ViennaAustria
- Medical University of Vienna, Center for Medical BiochemistryViennaAustria
| |
Collapse
|
34
|
Aiyer S, Baldwin PR, Tan SM, Shan Z, Oh J, Mehrani A, Bowman ME, Louie G, Passos DO, Đorđević-Marquardt S, Mietzsch M, Hull JA, Hoshika S, Barad BA, Grotjahn DA, McKenna R, Agbandje-McKenna M, Benner SA, Noel JAP, Wang D, Tan YZ, Lyumkis D. Overcoming Resolution Attenuation During Tilted Cryo-EM Data Collection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.14.548955. [PMID: 37503021 PMCID: PMC10369999 DOI: 10.1101/2023.07.14.548955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting "preferred orientations" on grids, leading to anisotropic map resolution and impeding structure determination. Tilting the specimen stage during data collection is a generalizable solution but has historically led to substantial resolution attenuation. Here, we develop updated data collection and image processing workflows and demonstrate, using multiple specimens, that resolution attenuation is negligible or significantly reduced across tilt angles. Reconstructions with and without the stage tilted as high as 60° are virtually indistinguishable. These strategies allowed the reconstruction to 3 Å resolution of a bacterial RNA polymerase with preferred orientation. Furthermore, we present a quantitative framework that allows cryo-EM practitioners to define an optimal tilt angle for dataset acquisition. These data reinforce the utility of employing stage tilt for data collection and provide quantitative metrics to obtain isotropic maps.
Collapse
|
35
|
Langeberg CJ, Kieft JS. A Generalizable Scaffold-Based Approach for Structure Determination of RNAs by Cryo-EM. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.547879. [PMID: 37461535 PMCID: PMC10350027 DOI: 10.1101/2023.07.06.547879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Single-particle cryo-electron microscopy (cryo-EM) can reveal the structures of large and often dynamic molecules, but smaller biomolecules remain challenging targets due to their intrinsic low signal to noise ratio. Methods to resolve small proteins have been applied but development of similar approaches for small structured RNA elements have lagged. Here, we present a scaffold-based approach that we used to recover maps of sub-25 kDa RNA domains to 4.5 - 5.0 Å. While lacking the detail of true high-resolution maps, these are suitable for model building and preliminary structure determination. We demonstrate this method faithfully recovers the structure of several RNA elements of known structure, and it promises to be generalized to other RNAs without disturbing their native fold. This approach may streamline the sample preparation process and reduce the optimization required for data collection. This first-generation scaffold approach provides a system for RNA structure determination by cryo-EM and lays the groundwork for further scaffold optimization to achieve higher resolution.
Collapse
|
36
|
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: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [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.
Collapse
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.
| |
Collapse
|
37
|
Monsen RC. Higher-order G-quadruplexes in promoters are untapped drug targets. Front Chem 2023; 11:1211512. [PMID: 37351517 PMCID: PMC10282141 DOI: 10.3389/fchem.2023.1211512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023] Open
Abstract
G-quadruplexes (G4s) are four-stranded nucleic acid secondary structures that form within guanine-rich regions of chromatin. G4 motifs are abundant in the genome, with a sizable proportion (∼40%) existing within gene promoter regions. G4s are proven epigenetic features that decorate the promoter landscape as binding centers for transcription factors. Stabilizing or disrupting promoter G4s can directly influence adjacent gene transcription, making G4s attractive as indirect drug targets for hard-to-target proteins, particularly in cancer. However, no G4 ligands have progressed through clinical trials, mostly owing to off targeting effects. A major hurdle in G4 drug discovery is the lack of distinctiveness of the small monomeric G4 structures currently used as receptors. This mini review describes and contrasts monomeric and higher-order G-quadruplex structure and function and provides a rationale for switching focus to the higher-order forms as selective molecular targets. The human telomerase reverse transcriptase (hTERT) core promoter G-quadruplex is then used as a case study that highlights the potential for higher-order G4s as selective indirect inhibitors of hard-to-target proteins in cancer.
Collapse
|
38
|
Mészáros B, Park E, Malinverni D, Sejdiu BI, Immadisetty K, Sandhu M, Lang B, Babu MM. Recent breakthroughs in computational structural biology harnessing the power of sequences and structures. Curr Opin Struct Biol 2023; 80:102608. [PMID: 37182396 DOI: 10.1016/j.sbi.2023.102608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 05/16/2023]
Abstract
Recent advances in computational approaches and their integration into structural biology enable tackling increasingly complex questions. Here, we discuss several key areas, highlighting breakthroughs and remaining challenges. Theoretical modeling has provided tools to accurately predict and design protein structures on a scale currently difficult to achieve using experimental approaches. Molecular Dynamics simulations have become faster and more precise, delivering actionable information inaccessible by current experimental methods. Virtual screening workflows allow a high-throughput approach to discover ligands that bind and modulate protein function, while Machine Learning methods enable the design of proteins with new functionalities. Integrative structural biology combines several of these approaches, pushing the frontiers of structural and functional characterization to ever larger systems, advancing towards a complete understanding of the living cell. These breakthroughs will accelerate and significantly impact diverse areas of science.
Collapse
Affiliation(s)
- Bálint Mészáros
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Electa Park
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Duccio Malinverni
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/DucMalinverni
| | - Besian I Sejdiu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/bisejdiu
| | - Kalyan Immadisetty
- Department of Bone Marrow Transplantation & Cellular Therapy, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/k_immadisetty
| | - Manbir Sandhu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/M5andhu
| | - Benjamin Lang
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/langbnj
| | - M Madan Babu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| |
Collapse
|
39
|
Bendory T, Khoo Y, Kileel J, Mickelin O, Singer A. Autocorrelation analysis for cryo-EM with sparsity constraints: Improved sample complexity and projection-based algorithms. Proc Natl Acad Sci U S A 2023; 120:e2216507120. [PMID: 37094135 PMCID: PMC10161091 DOI: 10.1073/pnas.2216507120] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/24/2023] [Indexed: 04/26/2023] Open
Abstract
The number of noisy images required for molecular reconstruction in single-particle cryoelectron microscopy (cryo-EM) is governed by the autocorrelations of the observed, randomly oriented, noisy projection images. In this work, we consider the effect of imposing sparsity priors on the molecule. We use techniques from signal processing, optimization, and applied algebraic geometry to obtain theoretical and computational contributions for this challenging nonlinear inverse problem with sparsity constraints. We prove that molecular structures modeled as sums of Gaussians are uniquely determined by the second-order autocorrelation of their projection images, implying that the sample complexity is proportional to the square of the variance of the noise. This theory improves upon the nonsparse case, where the third-order autocorrelation is required for uniformly oriented particle images and the sample complexity scales with the cube of the noise variance. Furthermore, we build a computational framework to reconstruct molecular structures which are sparse in the wavelet basis. This method combines the sparse representation for the molecule with projection-based techniques used for phase retrieval in X-ray crystallography.
Collapse
Affiliation(s)
- Tamir Bendory
- School of Electrical Engineering, Tel Aviv University, Tel Aviv69978, Israel
| | - Yuehaw Khoo
- Department of Statistics, University of Chicago, Chicago, IL60637
| | - Joe Kileel
- Department of Mathematics, Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, TX78712
| | - Oscar Mickelin
- Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ08540
| | - Amit Singer
- Department of Mathematics, Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ08540
| |
Collapse
|
40
|
Narwal M, Armache JP, Edwards TJ, Murakami KS. SARS-CoV-2 polyprotein substrate regulates the stepwise M pro cleavage reaction. J Biol Chem 2023; 299:104697. [PMID: 37044215 PMCID: PMC10084705 DOI: 10.1016/j.jbc.2023.104697] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/22/2023] [Accepted: 04/04/2023] [Indexed: 04/14/2023] Open
Abstract
The processing of the Coronavirus polyproteins pp1a and pp1ab by the main protease Mpro to produce mature proteins is a crucial event in virus replication and a promising target for antiviral drug development. Mpro cleaves polyproteins in a defined order, but how Mpro and/or the polyproteins determine the order of cleavage remains enigmatic due to a lack of structural information about polyprotein-bound Mpro. Here, we present the cryo-EM structures of SARS-CoV-2 Mpro in an apo form and in complex with the nsp7-10 region of the pp1a polyprotein. The complex structure shows that Mpro interacts with only the recognition site residues between nsp9 and nsp10, without any association with the rest of the polyprotein. Comparison between the apo form and polyprotein-bound structures of Mpro highlights the flexible nature of the active site region of Mpro, which allows it to accommodate 10 recognition sites found in the polyprotein. These observations suggest that the role of Mpro in selecting a preferred cleavage site is limited and underscore the roles of the structure, conformation and/or dynamics of the polyproteins in determining the sequence of polyprotein cleavage by Mpro.
Collapse
Affiliation(s)
- Manju Narwal
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Jean-Paul Armache
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Center for Structural Biology, Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.
| | - Thomas J Edwards
- National Cryo-EM Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Katsuhiko S Murakami
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Center for Structural Biology, Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA; Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
| |
Collapse
|
41
|
Wagstaff JM, Planelles-Herrero VJ, Sharov G, Alnami A, Kozielski F, Derivery E, Löwe J. Diverse cytomotive actins and tubulins share a polymerization switch mechanism conferring robust dynamics. SCIENCE ADVANCES 2023; 9:eadf3021. [PMID: 36989372 PMCID: PMC10058229 DOI: 10.1126/sciadv.adf3021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
Protein filaments are used in myriads of ways to organize other molecules within cells. Some filament-forming proteins couple the hydrolysis of nucleotides to their polymerization cycle, thus powering the movement of other molecules. These filaments are termed cytomotive. Only members of the actin and tubulin protein superfamilies are known to form cytomotive filaments. We examined the basis of cytomotivity via structural studies of the polymerization cycles of actin and tubulin homologs from across the tree of life. We analyzed published data and performed structural experiments designed to disentangle functional components of these complex filament systems. Our analysis demonstrates the existence of shared subunit polymerization switches among both cytomotive actins and tubulins, i.e., the conformation of subunits switches upon assembly into filaments. These cytomotive switches can explain filament robustness, by enabling the coupling of kinetic and structural polarities required for cytomotive behaviors and by ensuring that single cytomotive filaments do not fall apart.
Collapse
Affiliation(s)
- James Mark Wagstaff
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | | | - Grigory Sharov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Aisha Alnami
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Frank Kozielski
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Emmanuel Derivery
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| |
Collapse
|
42
|
Kumar R. Cryo-EM technique and its application: Structure of steroid hormone receptors. VITAMINS AND HORMONES 2023; 123:385-397. [PMID: 37717991 DOI: 10.1016/bs.vh.2023.02.002] [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: 03/12/2023]
Abstract
In recent years, cryo-electron microscopy (cryo-EM) has become one of the most powerful tools to solve the 3-D structure of macromolecules. Unlike X-ray crystallography, the cryo-EM method has advantage of providing an in-depth insight into the dynamic behavior of macromolecules, which is particularly useful to determine 3-D structural analyses of large protein complexes. Due to recent technical advancements, cryo-EM has become the method of choice for the determination of protein structures. Among other proteins, solving 3-D structure of steroid hormone receptors (SHRs) complexed with DNA and coactivators has been a challenge for decades. The limitations with X-ray crystallography and NMR to solve SHR protein structures prompted investigators to move towards cryo-EM technique. The cryo-EM structural analyses have been successful in revealing structural dynamics of several SHRs in recent years. Though, limited by low-resolution, the structural analyses of these SHRs may be useful in understanding many receptor functions as well as provide a platform to refine high-resolution structural analyses in future. This review article discusses the cryo-EM technique in general as well as structural information gained for SHRs using cryo-EM.
Collapse
Affiliation(s)
- Raj Kumar
- Department of Pharmaceutical and Biomedical Sciences, Touro College of Pharmacy, New York, NY, United States.
| |
Collapse
|
43
|
Bendory T, Boumal N, Leeb W, Levin E, Singer A. Toward Single Particle Reconstruction without Particle Picking: Breaking the Detection Limit. SIAM JOURNAL ON IMAGING SCIENCES 2023; 16:886-910. [PMID: 39144526 PMCID: PMC11324246 DOI: 10.1137/22m1503828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
Single-particle cryo-electron microscopy (cryo-EM) has recently joined X-ray crystallography and NMR spectroscopy as a high-resolution structural method to resolve biological macromolecules. In a cryo-EM experiment, the microscope produces images called micrographs. Projections of the molecule of interest are embedded in the micrographs at unknown locations, and under unknown viewing directions. Standard imaging techniques first locate these projections (detection) and then reconstruct the 3-D structure from them. Unfortunately, high noise levels hinder detection. When reliable detection is rendered impossible, the standard techniques fail. This is a problem, especially for small molecules. In this paper, we pursue a radically different approach: we contend that the structure could, in principle, be reconstructed directly from the micrographs, without intermediate detection. The aim is to bring small molecules within reach for cryo-EM. To this end, we design an autocorrelation analysis technique that allows one to go directly from the micrographs to the sought structures. This involves only one pass over the micrographs, allowing online, streaming processing for large experiments. We show numerical results and discuss challenges that lay ahead to turn this proof-of-concept into a complementary approach to state-of-the-art algorithms.
Collapse
Affiliation(s)
- Tamir Bendory
- The School of Electrical Engineering, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nicolas Boumal
- Institute of Mathematics, Ecole Polytechnique Fédérale DE Lausanne EPFL, 1015 Lausanne, Switzerland
| | - William Leeb
- School of Mathematics, University of Minnesota, Minneapolis, MN 55455 USA
| | - Eitan Levin
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125 USA
| | - Amit Singer
- The Program in Applied and Computational Mathematics and Department of Mathematics, Princeton University, Princeton, NJ 08544 USA
| |
Collapse
|
44
|
Zheng L, Liu N, Gao X, Zhu W, Liu K, Wu C, Yan R, Zhang J, Gao X, Yao Y, Deng B, Xu J, Lu Y, Liu Z, Li M, Wei X, Wang HW, Peng H. Uniform thin ice on ultraflat graphene for high-resolution cryo-EM. Nat Methods 2023; 20:123-130. [PMID: 36522503 PMCID: PMC9834055 DOI: 10.1038/s41592-022-01693-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 10/20/2022] [Indexed: 12/23/2022]
Abstract
Cryo-electron microscopy (cryo-EM) visualizes the atomic structure of macromolecules that are embedded in vitrified thin ice at their close-to-native state. However, the homogeneity of ice thickness, a key factor to ensure high image quality, is poorly controlled during specimen preparation and has become one of the main challenges for high-resolution cryo-EM. Here we found that the uniformity of thin ice relies on the surface flatness of the supporting film, and developed a method to use ultraflat graphene (UFG) as the support for cryo-EM specimen preparation to achieve better control of vitreous ice thickness. We show that the uniform thin ice on UFG improves the image quality of vitrified specimens. Using such a method we successfully determined the three-dimensional structures of hemoglobin (64 kDa), α-fetoprotein (67 kDa) with no symmetry, and streptavidin (52 kDa) at a resolution of 3.5 Å, 2.6 Å and 2.2 Å, respectively. Furthermore, our results demonstrate the potential of UFG for the fields of cryo-electron tomography and structure-based drug discovery.
Collapse
Affiliation(s)
- Liming Zheng
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Beijing Graphene Institute (BGI), Beijing, China
| | - Nan Liu
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Xiaoyin Gao
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Wenqing Zhu
- State Key Laboratory for Turbulence and Complex System, Department of Mechanics and Engineering Science, College of Engineering, Peking University, Beijing, China
| | - Kun Liu
- Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical College, Haikou, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Cang Wu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Rui Yan
- Beijing Graphene Institute (BGI), Beijing, China
| | - Jincan Zhang
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xin Gao
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yating Yao
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Bing Deng
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Jie Xu
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Ye Lu
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Zhongmin Liu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Mengsen Li
- Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical College, Haikou, China
| | - Xiaoding Wei
- State Key Laboratory for Turbulence and Complex System, Department of Mechanics and Engineering Science, College of Engineering, Peking University, Beijing, China.
- Beijing Innovation Center for Engineering Science and Advanced Technology, Peking University, Beijing, China.
- Peking University Nanchang Innovation Institute, Nanchang, China.
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China.
| | - Hailin Peng
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Beijing Graphene Institute (BGI), Beijing, China.
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
| |
Collapse
|
45
|
Feathers JR, Richael EK, Simanek KA, Fromme JC, Paczkowski JE. Structure of the RhlR-PqsE complex from Pseudomonas aeruginosa reveals mechanistic insights into quorum-sensing gene regulation. Structure 2022; 30:1626-1636.e4. [PMID: 36379213 PMCID: PMC9722607 DOI: 10.1016/j.str.2022.10.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/26/2022] [Accepted: 10/20/2022] [Indexed: 11/16/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that is responsible for thousands of deaths every year in the United States. P. aeruginosa virulence factor production is mediated by quorum sensing, a mechanism of bacterial cell-cell communication that relies on the production and detection of signal molecules called autoinducers. In P. aeruginosa, the transcription factor receptor RhlR is activated by a RhlI-synthesized autoinducer. We recently showed that RhlR-dependent transcription is enhanced by a physical interaction with the enzyme PqsE via increased affinity of RhlR for promoter DNA. However, the molecular basis for complex formation and how complex formation enhanced RhlR transcriptional activity remained unclear. Here, we report the structure of ligand-bound RhlR in complex with PqsE. Additionally, we determined the structure of the complex bound with DNA, revealing the mechanism by which RhlR-mediated transcription is enhanced by PqsE, thereby establishing the molecular basis for RhlR-dependent virulence factor production in P. aeruginosa.
Collapse
Affiliation(s)
- J Ryan Feathers
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Erica K Richael
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Kayla A Simanek
- Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, NY 12201, USA
| | - J Christopher Fromme
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jon E Paczkowski
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA; Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, NY 12201, USA.
| |
Collapse
|
46
|
Mukherjee S, Cassini TA, Hu N, Yang T, Li B, Shen W, Moth CW, Rinker DC, Sheehan JH, Cogan JD, Undiagnosed Diseases Network, Newman JH, Hamid R, Macdonald RL, Roden DM, Meiler J, Kuenze G, Phillips JA, Capra JA. Personalized structural biology reveals the molecular mechanisms underlying heterogeneous epileptic phenotypes caused by de novo KCNC2 variants. HGG ADVANCES 2022; 3:100131. [PMID: 36035247 PMCID: PMC9399384 DOI: 10.1016/j.xhgg.2022.100131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/11/2022] [Indexed: 11/28/2022] Open
Abstract
Whole-exome sequencing (WES) in the clinic has identified several rare monogenic developmental and epileptic encephalopathies (DEE) caused by ion channel variants. However, WES often fails to provide actionable insight for rare diseases, such as DEEs, due to the challenges of interpreting variants of unknown significance (VUS). Here, we describe a "personalized structural biology" (PSB) approach that leverages recent innovations in the analysis of protein 3D structures to address this challenge. We illustrate this approach in an Undiagnosed Diseases Network (UDN) individual with DEE symptoms and a de novo VUS in KCNC2 (p.V469L), the Kv3.2 voltage-gated potassium channel. A nearby KCNC2 variant (p.V471L) was recently suggested to cause DEE-like phenotypes. Computational structural modeling suggests that both affect protein function. However, despite their proximity, the p.V469L variant is likely to sterically block the channel pore, while the p.V471L variant is likely to stabilize the open state. Biochemical and electrophysiological analyses demonstrate heterogeneous loss-of-function and gain-of-function effects, as well as differential response to 4-aminopyridine treatment. Molecular dynamics simulations illustrate that the pore of the p.V469L variant is more constricted, increasing the energetic barrier for K+ permeation, whereas the p.V471L variant stabilizes the open conformation. Our results implicate variants in KCNC2 as causative for DEE and guide the interpretation of a UDN individual. They further delineate the molecular basis for the heterogeneous clinical phenotypes resulting from two proximal pathogenic variants. This demonstrates how the PSB approach can provide an analytical framework for individualized hypothesis-driven interpretation of protein-coding VUS.
Collapse
Affiliation(s)
- Souhrid Mukherjee
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Thomas A. Cassini
- Department of Internal Medicine, National Institutes of Health Clinical Center, Bethesda, MD 20814, USA
| | - Ningning Hu
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Tao Yang
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Bian Li
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Wangzhen Shen
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Christopher W. Moth
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - David C. Rinker
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Jonathan H. Sheehan
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
- John T. Milliken Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joy D. Cogan
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Undiagnosed Diseases Network
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Pulmonary Hypertension Center, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- John T. Milliken Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Internal Medicine, National Institutes of Health Clinical Center, Bethesda, MD 20814, USA
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, SAC 04103, Germany
- Department of Chemistry, Leipzig University, Leipzig, SAC 04109, Germany
- Department of Computer Science, Leipzig University, Leipzig, SAC 04109, Germany
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Bakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John H. Newman
- Pulmonary Hypertension Center, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Rizwan Hamid
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Robert L. Macdonald
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Dan M. Roden
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, SAC 04103, Germany
- Department of Chemistry, Leipzig University, Leipzig, SAC 04109, Germany
- Department of Computer Science, Leipzig University, Leipzig, SAC 04109, Germany
| | - Georg Kuenze
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, SAC 04103, Germany
| | - John A. Phillips
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - John A. Capra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Bakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA
| |
Collapse
|
47
|
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: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [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.
Collapse
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
| |
Collapse
|
48
|
Thangaratnarajah C, Rheinberger J, Paulino C. Cryo-EM studies of membrane proteins at 200 keV. Curr Opin Struct Biol 2022; 76:102440. [PMID: 36029606 DOI: 10.1016/j.sbi.2022.102440] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 11/03/2022]
Abstract
Single-particle cryogenic electron-microscopy (cryo-EM) has emerged as a powerful technique for the structural characterisation of membrane proteins, especially for targets previously thought to be intractable. Taking advantage of the latest hard- and software developments, high-resolution three-dimensional (3D) reconstructions of membrane proteins by cryo-EM has become routine, with 300-kV transmission electron microscopes (TEMs) being the current standard. The use of 200-kV cryo-TEMs is gaining increasingly prominence, showing the capabilities of reaching better than 2 Å resolution for soluble proteins and better than 3 Å resolution for membrane proteins. Here, we highlight the challenges working with membrane proteins and the impact of cryo-EM, and review the technical and practical benefits, achievements and limitations of imaging at lower electron acceleration voltages.
Collapse
Affiliation(s)
- Chancievan Thangaratnarajah
- University of Groningen, Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy and Membrane Enzymology Group, Nijenborgh 4, 9747 AG, Groningen, Netherlands.
| | - Jan Rheinberger
- University of Groningen, Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy and Membrane Enzymology Group, Nijenborgh 4, 9747 AG, Groningen, Netherlands. https://twitter.com/rheinbergerj
| | - Cristina Paulino
- University of Groningen, Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy and Membrane Enzymology Group, Nijenborgh 4, 9747 AG, Groningen, Netherlands.
| |
Collapse
|
49
|
Abdulaziz EN, Bell TA, Rashid B, Heacock ML, Begic T, Skinner OS, Yaseen MA, Chao LH, Mootha VK, Pierik AJ, Cracan V. A natural fusion of flavodiiron, rubredoxin, and rubredoxin oxidoreductase domains is a self-sufficient water-forming oxidase of Trichomonas vaginalis. J Biol Chem 2022; 298:102210. [PMID: 35780837 PMCID: PMC9364112 DOI: 10.1016/j.jbc.2022.102210] [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: 01/26/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 11/29/2022] Open
Abstract
Microaerophilic pathogens such as Giardia lamblia, Entamoeba histolytica, and Trichomonas vaginalis have robust oxygen consumption systems to detoxify oxygen and maintain intracellular redox balance. This oxygen consumption results from H2O-forming NADH oxidase (NOX) activity of two distinct flavin-containing systems: H2O-forming NOXes and multicomponent flavodiiron proteins (FDPs). Neither system is membrane bound, and both recycle NADH into oxidized NAD+ while simultaneously removing O2 from the local environment. However, little is known about the specific contributions of these systems in T. vaginalis. In this study, we use bioinformatics and biochemical analyses to show that T. vaginalis lacks a NOX-like enzyme and instead harbors three paralogous genes (FDPF1-3), each encoding a natural fusion product between the N-terminal FDP, central rubredoxin (Rb), and C-terminal NADH:Rb oxidoreductase domains. Unlike a "stand-alone" FDP that lacks Rb and oxidoreductase domains, this natural fusion protein with fully populated flavin redox centers directly accepts reducing equivalents of NADH to catalyze the four-electron reduction of oxygen to water within a single polypeptide with an extremely high turnover. Furthermore, using single-particle cryo-EM, we present structural insights into the spatial organization of the FDP core within this multidomain fusion protein. Together, these results contribute to our understanding of systems that allow protozoan parasites to maintain optimal redox balance and survive transient exposure to oxic conditions.
Collapse
Affiliation(s)
- Evana N Abdulaziz
- Redox Biology and Metabolism Laboratory, Scintillon Institute, San Diego, California, USA
| | - Tristan A Bell
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Bazlur Rashid
- Faculty of Chemistry, University of Kaiserslautern, Kaiserslautern, Germany
| | - Mina L Heacock
- Redox Biology and Metabolism Laboratory, Scintillon Institute, San Diego, California, USA
| | - Tarik Begic
- Faculty of Chemistry, University of Kaiserslautern, Kaiserslautern, Germany
| | - Owen S Skinner
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Mohammad A Yaseen
- Department of Bioengineering, Northeastern University, Boston, Massachusetts, USA
| | - Luke H Chao
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Vamsi K Mootha
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Antonio J Pierik
- Faculty of Chemistry, University of Kaiserslautern, Kaiserslautern, Germany
| | - Valentin Cracan
- Redox Biology and Metabolism Laboratory, Scintillon Institute, San Diego, California, USA; Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.
| |
Collapse
|
50
|
Saville JW, Berezuk AM, Srivastava SS, Subramaniam S. Three-Dimensional Visualization of Viral Structure, Entry, and Replication Underlying the Spread of SARS-CoV-2. Chem Rev 2022; 122:14066-14084. [PMID: 35863749 PMCID: PMC9344915 DOI: 10.1021/acs.chemrev.1c01062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
![]()
The global spread
of SARS-CoV-2 has proceeded at an unprecedented
rate. Remarkably, characterization of the virus using modern tools
in structural biology has also progressed at exceptional speed. Advances
in electron-based imaging techniques, combined with decades of foundational
studies on related viruses, have enabled the research community to
rapidly investigate structural aspects of the novel coronavirus from
the level of individual viral proteins to imaging the whole virus
in a native context. Here, we provide a detailed review of the structural
biology and pathobiology of SARS-CoV-2 as it relates to all facets
of the viral life cycle, including cell entry, replication, and three-dimensional
(3D) packaging based on insights obtained from X-ray crystallography,
cryo-electron tomography, and single-particle cryo-electron microscopy.
The structural comparison between SARS-CoV-2 and the related earlier
viruses SARS-CoV and MERS-CoV is a common thread throughout this review.
We conclude by highlighting some of the outstanding unanswered structural
questions and underscore areas that are under rapid current development
such as the design of effective therapeutics that block viral infection.
Collapse
Affiliation(s)
- James W Saville
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3
| | - Alison M Berezuk
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3
| | - Shanti S Srivastava
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3
| | - Sriram Subramaniam
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3.,Gandeeva Therapeutics Inc., Vancouver, British Columbia, Canada, V5C 6N5
| |
Collapse
|