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Chavas LMG, Coulibaly F, Garriga D. Bridging the microscopic divide: a comprehensive overview of micro-crystallization and in vivo crystallography. IUCRJ 2024; 11:476-485. [PMID: 38958014 DOI: 10.1107/s205225252400513x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/30/2024] [Indexed: 07/04/2024]
Abstract
A series of events underscoring the significant advancements in micro-crystallization and in vivo crystallography were held during the 26th IUCr Congress in Melbourne, positioning microcrystallography as a pivotal field within structural biology. Through collaborative discussions and the sharing of innovative methodologies, these sessions outlined frontier approaches in macromolecular crystallography. This review provides an overview of this rapidly moving field in light of the rich dialogues and forward-thinking proposals explored during the congress workshop and microsymposium. These advances in microcrystallography shed light on the potential to reshape current research paradigms and enhance our comprehension of biological mechanisms at the molecular scale.
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Affiliation(s)
| | - Fasséli Coulibaly
- Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
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Danelius E, Porter NJ, Unge J, Arnold FH, Gonen T. MicroED Structure of a Protoglobin Reactive Carbene Intermediate. J Am Chem Soc 2023; 145:7159-7165. [PMID: 36948184 PMCID: PMC10080679 DOI: 10.1021/jacs.2c12004] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Microcrystal electron diffraction (MicroED) is an emerging technique that has shown great potential for describing new chemical and biological molecular structures. Several important structures of small molecules, natural products, and peptides have been determined using ab initio methods. However, only a couple of novel protein structures have thus far been derived by MicroED. Taking advantage of recent technological advances, including higher acceleration voltage and using a low-noise detector in counting mode, we have determined the first structure of an Aeropyrum pernix protoglobin (ApePgb) variant by MicroED using an AlphaFold2 model for phasing. The structure revealed that mutations introduced during directed evolution enhance carbene transfer activity by reorienting an α helix of ApePgb into a dynamic loop, making the catalytic active site more readily accessible. After exposing the tiny crystals to the substrate, we also trapped the reactive iron-carbenoid intermediate involved in this engineered ApePgb's new-to-nature activity, a challenging carbene transfer from a diazirine via a putative metallo-carbene. The bound structure discloses how an enlarged active site pocket stabilizes the carbene bound to the heme iron and, presumably, the transition state for the formation of this key intermediate. This work demonstrates that improved MicroED technology and the advancement in protein structure prediction now enable investigation of structures that was previously beyond reach.
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Affiliation(s)
- Emma Danelius
- Department of Biological Chemistry, University of California, Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California 90095, United States
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Nicholas J Porter
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
| | - Johan Unge
- Department of Biological Chemistry, University of California, Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California 90095, United States
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
| | - Tamir Gonen
- Department of Biological Chemistry, University of California, Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California 90095, United States
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Physiology, University of California, Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California 90095, United States
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Panigrahi R, Glover JNM, Nallusamy S. A look into DGAT1 through the EM lenses. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184069. [PMID: 36216097 DOI: 10.1016/j.bbamem.2022.184069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/03/2022] [Indexed: 11/05/2022]
Abstract
With the advent of modern detectors and robust structure solution pipeline, cryogenic electron microscopy has recently proved to be game changer in structural biology. Membrane proteins are challenging targets for structural biologists. This minireview focuses a membrane embedded triglyceride synthesizing machine, DGAT1. Decades of research had built the foundational knowledge on this enzyme's activity. However, recently solved cryo-EM structures of this enzyme, in apo and bound form, has provided critical mechanistic insights. The flipping of the catalytic histidine is critical of enzyme catalysis. The structures explain why the enzyme has preference to long fatty acyl chains over the short forms.
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Affiliation(s)
- Rashmi Panigrahi
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Saranya Nallusamy
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India.
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Vilas JL, Carazo JM, Sorzano COS. Emerging Themes in CryoEM─Single Particle Analysis Image Processing. Chem Rev 2022; 122:13915-13951. [PMID: 35785962 PMCID: PMC9479088 DOI: 10.1021/acs.chemrev.1c00850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cryo-electron microscopy (CryoEM) has become a vital technique in structural biology. It is an interdisciplinary field that takes advantage of advances in biochemistry, physics, and image processing, among other disciplines. Innovations in these three basic pillars have contributed to the boosting of CryoEM in the past decade. This work reviews the main contributions in image processing to the current reconstruction workflow of single particle analysis (SPA) by CryoEM. Our review emphasizes the time evolution of the algorithms across the different steps of the workflow differentiating between two groups of approaches: analytical methods and deep learning algorithms. We present an analysis of the current state of the art. Finally, we discuss the emerging problems and challenges still to be addressed in the evolution of CryoEM image processing methods in SPA.
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Affiliation(s)
- Jose Luis Vilas
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - Jose Maria Carazo
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - Carlos Oscar S Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
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Gorelik TE, Tehrani KHME, Gruene T, Monecke T, Niessing D, Kaiser U, Blankenfeldt W, Müller R. Crystal structure of natural product argyrin-D determined by 3D electron diffraction. CrystEngComm 2022. [DOI: 10.1039/d2ce00707j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Crystal structure of natural product argyrin D was determined from electron diffraction data.
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Affiliation(s)
- Tatiana E. Gorelik
- Electron Microscopy Group of Materials Science, Albert-Einstein-Allee 11, 89081 Ulm, Germany
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, Germany
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrucken, 66123, Germany
| | - Kamaleddin H. M. E. Tehrani
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrucken, 66123, Germany
| | - Tim Gruene
- Faculty of Chemistry, Department of Inorganic Chemistry, University of Vienna, AT-1090 Vienna, Austria
| | - Thomas Monecke
- Institute of Pharmaceutical Biotechnology, Ulm University, James-Franck-Ring N27, 89081 Ulm, Germany
| | - Dierk Niessing
- Institute of Pharmaceutical Biotechnology, Ulm University, James-Franck-Ring N27, 89081 Ulm, Germany
| | - Ute Kaiser
- Electron Microscopy Group of Materials Science, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Wulf Blankenfeldt
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, Germany
| | - Rolf Müller
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrucken, 66123, Germany
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