51
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Martynowycz MW, Clabbers MTB, Hattne J, Gonen T. Ab initio phasing macromolecular structures using electron-counted MicroED data. Nat Methods 2022; 19:724-729. [PMID: 35637302 PMCID: PMC9184278 DOI: 10.1038/s41592-022-01485-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 04/07/2022] [Indexed: 12/31/2022]
Abstract
Structures of two globular proteins were determined ab initio using microcrystal electron diffraction (MicroED) data that were collected on a direct electron detector in counting mode. Microcrystals were identified using a scanning electron microscope (SEM) and thinned with a focused ion beam (FIB) to produce crystalline lamellae of ideal thickness. Continuous-rotation data were collected using an ultra-low exposure rate to enable electron counting in diffraction. For the first sample, triclinic lysozyme extending to a resolution of 0.87 Å, an ideal helical fragment of only three alanine residues provided initial phases. These phases were improved using density modification, allowing the entire atomic structure to be built automatically. A similar approach was successful on a second macromolecular sample, proteinase K, which is much larger and diffracted to a resolution of 1.5 Å. These results demonstrate that macromolecules can be determined to sub-ångström resolution by MicroED and that ab initio phasing can be successfully applied to counting data.
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Affiliation(s)
- Michael W. Martynowycz
- grid.19006.3e0000 0000 9632 6718Howard Hughes Medical Institute, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA USA
| | - Max T. B. Clabbers
- grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA USA
| | - Johan Hattne
- grid.19006.3e0000 0000 9632 6718Howard Hughes Medical Institute, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, USA. .,Department of Biological Chemistry, University of California, Los Angeles, CA, USA. .,Department of Physiology, University of California, Los Angeles, CA, USA.
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52
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Fan J, Liu Y, Kong R, Ni D, Yu Z, Lu S, Zhang J. Harnessing Reversed Allosteric Communication: A Novel Strategy for Allosteric Drug Discovery. J Med Chem 2021; 64:17728-17743. [PMID: 34878270 DOI: 10.1021/acs.jmedchem.1c01695] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Allostery is a fundamental and extensive mechanism of intramolecular signal transmission. Allosteric drugs possess several unique pharmacological advantages over traditional orthosteric drugs, including greater selectivity, better physicochemical properties, and lower off-target toxicity. However, owing to the complexity of allosteric regulation, experimental approaches for the development of allosteric modulators are traditionally serendipitous. Recently, the reversed allosteric communication theory has been proposed, providing a feasible tool for the unbiased detection of allosteric sites. Herein, we review the latest research on the reversed allosteric communication effect using the examples of sirtuin 6, epidermal growth factor receptor, 3-phosphoinositide-dependent protein kinase 1, and Related to A and C kinases (RAC) serine/threonine protein kinase B and recapitulate the methodologies of reversed allosteric communication strategy. The novel reversed allosteric communication strategy greatly expands the horizon of allosteric site identification and allosteric mechanism exploration and is expected to accelerate an end-to-end framework for drug discovery.
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Affiliation(s)
- Jigang Fan
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, China.,State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.,Zhiyuan Innovative Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yaqin Liu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Ren Kong
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Duan Ni
- The Charles Perkins Centre, University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - Shaoyong Lu
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, China.,State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.,Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Jian Zhang
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, China.,State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.,Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.,School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
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53
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Microcrystal electron diffraction in macromolecular and pharmaceutical structure determination. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 37:93-105. [PMID: 34895659 DOI: 10.1016/j.ddtec.2020.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/08/2020] [Accepted: 12/11/2020] [Indexed: 02/05/2023]
Abstract
Microcrystal electron diffraction (MicroED) has recently shown to be a promising technique for structure determination in structural biology and pharmaceutical chemistry. Here, we discuss the unique properties of electrons and motivate its use for diffraction experiments. We review the latest developments in MicroED, and illustrate its applications in macromolecular crystallography, fragment screening and structure guided drug discovery. We discuss the perspectives of MicroED in synthetic chemistry and pharmaceutical development. We anticipate that the rapid advances MicroED showcased here will promote further development of electron crystallography and open up new opportunities for drug discovery.
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54
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Wigge C, Stefanovic A, Radjainia M. The rapidly evolving role of cryo-EM in drug design. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 38:91-102. [PMID: 34895645 DOI: 10.1016/j.ddtec.2020.12.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/09/2020] [Accepted: 12/22/2020] [Indexed: 01/18/2023]
Abstract
Since the early 2010s, cryo-electron microscopy (cryo-EM) has evolved to a mainstream structural biology method in what has been dubbed the "resolution revolution". Pharma companies also began to use cryo-EM in drug discovery, evidenced by a growing number of industry publications. Hitherto limited in resolution, throughput and attainable molecular weight, cryo-EM is rapidly overcoming its main limitations for more widespread use through a new wave of technological advances. This review discusses how cryo-EM has already impacted drug discovery, and how the state-of-the-art is poised to further revolutionize its application to previously intractable proteins as well as new use cases.
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Affiliation(s)
- Christoph Wigge
- Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | | | - Mazdak Radjainia
- Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands.
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55
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Place BJ, Ulrich EM, Challis JK, Chao A, Du B, Favela K, Feng YL, Fisher CM, Gardinali P, Hood A, Knolhoff AM, McEachran AD, Nason SL, Newton SR, Ng B, Nuñez J, Peter KT, Phillips AL, Quinete N, Renslow R, Sobus JR, Sussman EM, Warth B, Wickramasekara S, Williams AJ. An Introduction to the Benchmarking and Publications for Non-Targeted Analysis Working Group. Anal Chem 2021; 93:16289-16296. [PMID: 34842413 PMCID: PMC8848292 DOI: 10.1021/acs.analchem.1c02660] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Non-targeted analysis (NTA) encompasses a rapidly evolving set of mass spectrometry techniques aimed at characterizing the chemical composition of complex samples, identifying unknown compounds, and/or classifying samples, without prior knowledge regarding the chemical content of the samples. Recent advances in NTA are the result of improved and more accessible instrumentation for data generation and analysis tools for data evaluation and interpretation. As researchers continue to develop NTA approaches in various scientific fields, there is a growing need to identify, disseminate, and adopt community-wide method reporting guidelines. In 2018, NTA researchers formed the Benchmarking and Publications for Non-Targeted Analysis Working Group (BP4NTA) to address this need. Consisting of participants from around the world and representing fields ranging from environmental science and food chemistry to 'omics and toxicology, BP4NTA provides resources addressing a variety of challenges associated with NTA. Thus far, BP4NTA group members have aimed to establish a consensus on NTA-related terms and concepts and to create consistency in reporting practices by providing resources on a public Web site, including consensus definitions, reference content, and lists of available tools. Moving forward, BP4NTA will provide a setting for NTA researchers to continue discussing emerging challenges and contribute to additional harmonization efforts.
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Affiliation(s)
- Benjamin J. Place
- National Institute of Standards and Technology, Gaithersburg, MD, USA 20899,Corresponding author,
| | - Elin M. Ulrich
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Research Triangle Park, NC, USA 27711
| | | | - Alex Chao
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Research Triangle Park, NC, USA 27711
| | - Bowen Du
- Southern California Coastal Water Research Project Authority, Costa Mesa, CA, USA 92626
| | - Kristin Favela
- Southwest Research Institute, San Antonio, TX, USA 78238
| | - Yong-Lai Feng
- Exposure and Biomonitoring Division, Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada, K1A 0K9
| | - Christine M. Fisher
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD, USA 20740
| | - Piero Gardinali
- Institute of Environment & Department of Chemistry and Biochemistry, Florida International University, North Miami, FL 33181
| | - Alan Hood
- U.S. Food and Drug Administration, Center for Devices and Radiological Health, Silver Spring, MD, USA 20993
| | - Ann M. Knolhoff
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD, USA 20740
| | | | - Sara L. Nason
- Connecticut Agricultural Experiment Station, New Haven, CT, USA 06511
| | - Seth R. Newton
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Research Triangle Park, NC, USA 27711
| | - Brian Ng
- Institute of Environment & Department of Chemistry and Biochemistry, Florida International University, North Miami, FL 33181
| | - Jamie Nuñez
- Pacific Northwest National Laboratory, Richland, WA, USA 99352
| | - Katherine T. Peter
- National Institute of Standards and Technology, Charleston, SC, USA 29412
| | - Allison L. Phillips
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Public Health and Environmental Assessment, Research Triangle Park, NC, USA 27711
| | - Natalia Quinete
- Institute of Environment & Department of Chemistry and Biochemistry, Florida International University, North Miami, FL 33181
| | - Ryan Renslow
- Pacific Northwest National Laboratory, Richland, WA, USA 99352
| | - Jon R. Sobus
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Research Triangle Park, NC, USA 27711
| | - Eric M. Sussman
- U.S. Food and Drug Administration, Center for Devices and Radiological Health, Silver Spring, MD, USA 20993
| | - Benedikt Warth
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Samanthi Wickramasekara
- U.S. Food and Drug Administration, Center for Devices and Radiological Health, Silver Spring, MD, USA 20993
| | - Antony J. Williams
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Research Triangle Park, NC, USA 27711
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56
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Hovestreydt E. Electron diffraction: Accelerating drug development. Drug Discov Today 2021; 27:371-373. [PMID: 34906690 DOI: 10.1016/j.drudis.2021.12.006] [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: 09/16/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 11/03/2022]
Abstract
Electron Diffraction (ED) is gaining momentum in science and industry. The application of ED for performing nanocrystallography is a disruptive innovation that is opening up fascinating new perspectives particularly for organic compounds required in the fields of chemical, pharmaceutical and advanced materials research.
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57
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Martynowycz MW, Clabbers MTB, Unge J, Hattne J, Gonen T. Benchmarking the ideal sample thickness in cryo-EM. Proc Natl Acad Sci U S A 2021; 118:e2108884118. [PMID: 34873060 PMCID: PMC8670461 DOI: 10.1073/pnas.2108884118] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 12/14/2022] Open
Abstract
The relationship between sample thickness and quality of data obtained is investigated by microcrystal electron diffraction (MicroED). Several electron microscopy (EM) grids containing proteinase K microcrystals of similar sizes from the same crystallization batch were prepared. Each grid was transferred into a focused ion beam and a scanning electron microscope in which the crystals were then systematically thinned into lamellae between 95- and 1,650-nm thick. MicroED data were collected at either 120-, 200-, or 300-kV accelerating voltages. Lamellae thicknesses were expressed in multiples of the corresponding inelastic mean free path to allow the results from different acceleration voltages to be compared. The quality of the data and subsequently determined structures were assessed using standard crystallographic measures. Structures were reliably determined with similar quality from crystalline lamellae up to twice the inelastic mean free path. Lower resolution diffraction was observed at three times the mean free path for all three accelerating voltages, but the data quality was insufficient to yield structures. Finally, no coherent diffraction was observed from lamellae thicker than four times the calculated inelastic mean free path. This study benchmarks the ideal specimen thickness with implications for all cryo-EM methods.
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Affiliation(s)
- Michael W Martynowycz
- HHMI, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Max T B Clabbers
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Johan Unge
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Johan Hattne
- HHMI, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Tamir Gonen
- HHMI, University of California, Los Angeles, CA 90095;
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
- Department of Physiology, University of California, Los Angeles, CA 90095
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58
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Evans AM, Strauss MJ, Corcos AR, Hirani Z, Ji W, Hamachi LS, Aguilar-Enriquez X, Chavez AD, Smith BJ, Dichtel WR. Two-Dimensional Polymers and Polymerizations. Chem Rev 2021; 122:442-564. [PMID: 34852192 DOI: 10.1021/acs.chemrev.0c01184] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Synthetic chemists have developed robust methods to synthesize discrete molecules, linear and branched polymers, and disordered cross-linked networks. However, two-dimensional polymers (2DPs) prepared from designed monomers have been long missing from these capabilities, both as objects of chemical synthesis and in nature. Recently, new polymerization strategies and characterization methods have enabled the unambiguous realization of covalently linked macromolecular sheets. Here we review 2DPs and 2D polymerization methods. Three predominant 2D polymerization strategies have emerged to date, which produce 2DPs either as monolayers or multilayer assemblies. We discuss the fundamental understanding and scope of each of these approaches, including: the bond-forming reactions used, the synthetic diversity of 2DPs prepared, their multilayer stacking behaviors, nanoscale and mesoscale structures, and macroscale morphologies. Additionally, we describe the analytical tools currently available to characterize 2DPs in their various isolated forms. Finally, we review emergent 2DP properties and the potential applications of planar macromolecules. Throughout, we highlight achievements in 2D polymerization and identify opportunities for continued study.
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Affiliation(s)
- Austin M Evans
- Department of Chemistry, Northwestern University, 1425 Sheridan Road, Evanston, Illinois 60208, United States
| | - Michael J Strauss
- Department of Chemistry, Northwestern University, 1425 Sheridan Road, Evanston, Illinois 60208, United States
| | - Amanda R Corcos
- Department of Chemistry, Northwestern University, 1425 Sheridan Road, Evanston, Illinois 60208, United States
| | - Zoheb Hirani
- Department of Chemistry, Northwestern University, 1425 Sheridan Road, Evanston, Illinois 60208, United States
| | - Woojung Ji
- Department of Chemistry, Northwestern University, 1425 Sheridan Road, Evanston, Illinois 60208, United States
| | - Leslie S Hamachi
- Department of Chemistry, Northwestern University, 1425 Sheridan Road, Evanston, Illinois 60208, United States.,Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Xavier Aguilar-Enriquez
- Department of Chemistry, Northwestern University, 1425 Sheridan Road, Evanston, Illinois 60208, United States
| | - Anton D Chavez
- Department of Chemistry, Northwestern University, 1425 Sheridan Road, Evanston, Illinois 60208, United States
| | - Brian J Smith
- Department of Chemistry, Bucknell University,1 Dent Drive, Lewisburg, Pennsylvania 17837, United States
| | - William R Dichtel
- Department of Chemistry, Northwestern University, 1425 Sheridan Road, Evanston, Illinois 60208, United States
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59
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Meng Z, Jones CG, Farid S, Khan IU, Nelson HM, Mirica KA. Unraveling the Electrical and Magnetic Properties of Layered Conductive Metal-Organic Framework With Atomic Precision. Angew Chem Int Ed Engl 2021; 61:e202113569. [PMID: 34784436 DOI: 10.1002/anie.202113569] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Indexed: 12/16/2022]
Abstract
This paper describes structural elucidation of a layered conductive metal-organic framework (MOF) material Cu3 (C6 O6 )2 by microcrystal electron diffraction with sub-angstrom precision. This insight enables the first identification of an unusual π-stacking interaction in a layered MOF material characterized by an extremely short (2.73 Å) close packing of the ligand arising from pancake bonding and ordered water clusters within pores. Band structure analysis suggests semiconductive properties of the MOF, which are likely related to the localized nature of pancake bonds and the formation of a singlet dimer of the ligand. The spin of CuII within the Kagomé arrangement dominates the paramagnetism of the MOF, leading to strong geometrical magnetic frustration.
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Affiliation(s)
- Zheng Meng
- Department of Chemistry, Dartmouth College, Burke Laboratory, Hanover, NH, 03755, USA
| | - Christopher G Jones
- The Arnold and Mabel Beckman Laboratory of Chemical Synthesis, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Sidra Farid
- Material Chemistry Laboratory, Department of Chemistry, GC University, Lahore, 54000, Pakistan
| | - Islam Ullah Khan
- Material Chemistry Laboratory, Department of Chemistry, GC University, Lahore, 54000, Pakistan.,Department of Chemistry, University of Mianwali, Mianwali, 42200, Pakistan
| | - Hosea M Nelson
- The Arnold and Mabel Beckman Laboratory of Chemical Synthesis, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Katherine A Mirica
- Department of Chemistry, Dartmouth College, Burke Laboratory, Hanover, NH, 03755, USA
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60
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Clark LJ, Bu G, Nannenga BL, Gonen T. MicroED for the study of protein–ligand interactions and the potential for drug discovery. Nat Rev Chem 2021; 5:853-858. [PMID: 37117388 DOI: 10.1038/s41570-021-00332-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2021] [Indexed: 12/18/2022]
Abstract
Microcrystal electron diffraction (MicroED) is an electron cryo-microscopy (cryo-EM) technique used to determine molecular structures with crystals that are a millionth the size needed for traditional single-crystal X-ray crystallography. An exciting use of MicroED is in drug discovery and development, where it can be applied to the study of proteins and small molecule interactions, and for structure determination of natural products. The structures are then used for rational drug design and optimization. In this Perspective, we discuss the current applications of MicroED for structure determination of protein-ligand complexes and potential future applications in drug discovery.
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61
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Reprint of: Inversion of dynamical Bragg intensities to complex structure factors by iterated projections. For Ultramic. 2020. ("Pico" Festschrift, May 2021). Ultramicroscopy 2021; 231:113409. [PMID: 34756481 DOI: 10.1016/j.ultramic.2021.113409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/16/2021] [Accepted: 01/19/2021] [Indexed: 11/22/2022]
Abstract
A method for recovering complex structure factors from many simultaneously excited Bragg beam in- tensities is described. The method is applied to simulated transmission electron diffraction data over a wide range of crystal thickness and beam energies. The method is based on iterated projections between structure and scattering matrices, which are related by a matrix unit ary transformation, exponential, which we invert. The algorithm removes multiple-scattering perturbations from diffraction data and might be extended to other fields, including X-ray and neutron diffraction and cryo-electron microscopy. Because coherent multiple scattering involves interference between Bragg beams, the method also solves the phase problem. Unlike dynamical inversion from electron microscope images or ptychography data, the method, which starts with Bragg beam intensities, provides complex structure factors unaffected by focusing errors or resolution limitations imposed by lenses. We provide inversions from simulated data with 441 simultaneously excited Bragg beams over a range of thickness and beam energy. We discuss the retrieval of chirality information from enantiomorphs, the efficient incorporation of symmetry information using the irreducible representation of the group of structure matrices, and the effect of HOLZ lines to provide three-dimensional information.
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62
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Kamyshinsky RA, Kralin VA, Chesnokov MY, Samygina VR, Orekhov AS. Electron Diffraction of Microcrystals on the Example of Lysozyme. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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63
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Latychevskaia T, Cassidy C, Shintake T. Bragg holography of nano-crystals. Ultramicroscopy 2021; 230:113376. [PMID: 34537574 DOI: 10.1016/j.ultramic.2021.113376] [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: 05/12/2021] [Revised: 08/02/2021] [Accepted: 08/09/2021] [Indexed: 10/20/2022]
Abstract
Crystal diffraction is a well-established technique for high-resolution structural analysis of material science and biological samples. However, the recovered structure is a result of averaging over all the unit cells in the crystal, which smears out the imperfections, atomic defects, or asymmetries and chiral properties of the individual molecules. We propose Bragg holography, where a nano-crystal is imaged at a defocus distance allowing separation of the diffracted beams, without turning them into peaks. The presence of a reference wave gives rise to a Bragg hologram, which can be reconstructed by conventional holographic reconstruction algorithms. The recovered complex-valued wavefront contains the complete information about the atomic distribution in the crystal, including defects. Bragg holography is demonstrated for gold nano-crystals, and its feasibility for biological nano-crystals is shown.
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Affiliation(s)
| | - Cathal Cassidy
- Quantum wave microscopy unit, Okinawa Institute of Science and Technology, 1919-1, Tancha, Onna, Kunigami District, Okinawa 904-0495, Japan
| | - Tsumoru Shintake
- Quantum wave microscopy unit, Okinawa Institute of Science and Technology, 1919-1, Tancha, Onna, Kunigami District, Okinawa 904-0495, Japan
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64
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Testing the Scalability of the HS-AUTOFIT Tool in a High-Performance Computing Environment. ELECTRONICS 2021. [DOI: 10.3390/electronics10182251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In the last years, the development of broadband chirped-pulse Fourier transform microwave spectrometers has revolutionized the field of rotational spectroscopy. Currently, it is possible to experimentally obtain a large quantity of spectra that would be difficult to analyze manually due to two main reasons. First, recent instruments allow obtaining a considerable amount of data in very short times, and second, it is possible to analyze complex mixtures of molecules that all contribute to the density of the spectra. AUTOFIT is a spectral assignment software application that was developed in 2013 to support and facilitate the analysis. Notwithstanding the benefits AUTOFIT brings in terms of automation of the analysis of the accumulated data, it still does not guarantee a good performance in terms of execution time because it leverages the computing power of a single computing machine. To cater to this requirement, we developed a parallel version of AUTOFIT, called HS-AUTOFIT, capable of running on high-performance computing (HPC) clusters to shorten the time to explore and analyze spectral big data. In this paper, we report some tests conducted on a real HPC cluster aimed at providing a quantitative assessment of HS-AUTOFIT’s scaling capabilities in a multi-node computing context. The collected results demonstrate the benefits of the proposed approach in terms of a significant reduction in computing time.
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65
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Britt HM, Cragnolini T, Thalassinos K. Integration of Mass Spectrometry Data for Structural Biology. Chem Rev 2021; 122:7952-7986. [PMID: 34506113 DOI: 10.1021/acs.chemrev.1c00356] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Mass spectrometry (MS) is increasingly being used to probe the structure and dynamics of proteins and the complexes they form with other macromolecules. There are now several specialized MS methods, each with unique sample preparation, data acquisition, and data processing protocols. Collectively, these methods are referred to as structural MS and include cross-linking, hydrogen-deuterium exchange, hydroxyl radical footprinting, native, ion mobility, and top-down MS. Each of these provides a unique type of structural information, ranging from composition and stoichiometry through to residue level proximity and solvent accessibility. Structural MS has proved particularly beneficial in studying protein classes for which analysis by classic structural biology techniques proves challenging such as glycosylated or intrinsically disordered proteins. To capture the structural details for a particular system, especially larger multiprotein complexes, more than one structural MS method with other structural and biophysical techniques is often required. Key to integrating these diverse data are computational strategies and software solutions to facilitate this process. We provide a background to the structural MS methods and briefly summarize other structural methods and how these are combined with MS. We then describe current state of the art approaches for the integration of structural MS data for structural biology. We quantify how often these methods are used together and provide examples where such combinations have been fruitful. To illustrate the power of integrative approaches, we discuss progress in solving the structures of the proteasome and the nuclear pore complex. We also discuss how information from structural MS, particularly pertaining to protein dynamics, is not currently utilized in integrative workflows and how such information can provide a more accurate picture of the systems studied. We conclude by discussing new developments in the MS and computational fields that will further enable in-cell structural studies.
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Affiliation(s)
- Hannah M Britt
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Tristan Cragnolini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
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66
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Ghosh R, Bu G, Nannenga BL, Sumner LW. Recent Developments Toward Integrated Metabolomics Technologies (UHPLC-MS-SPE-NMR and MicroED) for Higher-Throughput Confident Metabolite Identifications. Front Mol Biosci 2021; 8:720955. [PMID: 34540897 PMCID: PMC8445028 DOI: 10.3389/fmolb.2021.720955] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 08/17/2021] [Indexed: 02/03/2023] Open
Abstract
Metabolomics has emerged as a powerful discipline to study complex biological systems from a small molecule perspective. The success of metabolomics hinges upon reliable annotations of spectral features obtained from MS and/or NMR. In spite of tremendous progress with regards to analytical instrumentation and computational tools, < 20% of spectral features are confidently identified in most untargeted metabolomics experiments. This article explores the integration of multiple analytical instruments such as UHPLC-MS/MS-SPE-NMR and the cryo-EM method MicroED to achieve large-scale and confident metabolite identifications in a higher-throughput manner. UHPLC-MS/MS-SPE allows for the simultaneous automated purification of metabolites followed by offline structure elucidation and structure validation by NMR and MicroED. Large-scale study of complex metabolomes such as that of the model plant legume Medicago truncatula can be achieved using an integrated UHPLC-MS/MS-SPE-NMR metabolomics platform. Additionally, recent developments in MicroED to study structures of small organic molecules have enabled faster, easier and precise structure determinations of metabolites. A MicroED small molecule structure elucidation workflow (e.g., crystal screening, sample preparation, data collection and data processing/structure determination) has been described. Ongoing MicroED methods development and its future scope related to structure elucidation of specialized metabolites and metabolomics are highlighted. The incorporation of MicroED with a UHPLC-MS/MS-SPE-NMR instrumental ensemble offers the potential to accelerate and achieve higher rates of metabolite identification.
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Affiliation(s)
- Rajarshi Ghosh
- Division of Biochemistry, University of Missouri, Columbia, MO, United States
- MU Metabolomics Center, University of Missouri, Columbia, MO, United States
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, SC, United States
- Interdisciplinary Plant Group, University of Missouri, Columbia, SC, United States
| | - Guanhong Bu
- Chemical Engineering, School for Engineering of Matter, Transport & Energy, Arizona State University, Tempe, AZ, United States
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Brent L. Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport & Energy, Arizona State University, Tempe, AZ, United States
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Lloyd W. Sumner
- Division of Biochemistry, University of Missouri, Columbia, MO, United States
- MU Metabolomics Center, University of Missouri, Columbia, MO, United States
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, SC, United States
- Interdisciplinary Plant Group, University of Missouri, Columbia, SC, United States
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67
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Zhao J, Xu H, Lebrette H, Carroni M, Taberman H, Högbom M, Zou X. A simple pressure-assisted method for MicroED specimen preparation. Nat Commun 2021; 12:5036. [PMID: 34413316 PMCID: PMC8377027 DOI: 10.1038/s41467-021-25335-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/19/2021] [Indexed: 11/16/2022] Open
Abstract
Micro-crystal electron diffraction (MicroED) has shown great potential for structure determination of macromolecular crystals too small for X-ray diffraction. However, specimen preparation remains a major bottleneck. Here, we report a simple method for preparing MicroED specimens, named Preassis, in which excess liquid is removed through an EM grid with the assistance of pressure. We show the ice thicknesses can be controlled by tuning the pressure in combination with EM grids with appropriate carbon hole sizes. Importantly, Preassis can handle a wide range of protein crystals grown in various buffer conditions including those with high viscosity, as well as samples with low crystal concentrations. Preassis is a simple and universal method for MicroED specimen preparation, and will significantly broaden the applications of MicroED.
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Affiliation(s)
- Jingjing Zhao
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Marta Carroni
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
- Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Helena Taberman
- Max Delbrück Centrum for Molecular Medicine, Berlin, Germany
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Berlin, Germany
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
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Rizvi A, Mulvey JT, Carpenter BP, Talosig R, Patterson JP. A Close Look at Molecular Self-Assembly with the Transmission Electron Microscope. Chem Rev 2021; 121:14232-14280. [PMID: 34329552 DOI: 10.1021/acs.chemrev.1c00189] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Molecular self-assembly is pervasive in the formation of living and synthetic materials. Knowledge gained from research into the principles of molecular self-assembly drives innovation in the biological, chemical, and materials sciences. Self-assembly processes span a wide range of temporal and spatial domains and are often unintuitive and complex. Studying such complex processes requires an arsenal of analytical and computational tools. Within this arsenal, the transmission electron microscope stands out for its unique ability to visualize and quantify self-assembly structures and processes. This review describes the contribution that the transmission electron microscope has made to the field of molecular self-assembly. An emphasis is placed on which TEM methods are applicable to different structures and processes and how TEM can be used in combination with other experimental or computational methods. Finally, we provide an outlook on the current challenges to, and opportunities for, increasing the impact that the transmission electron microscope can have on molecular self-assembly.
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Affiliation(s)
- Aoon Rizvi
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Justin T Mulvey
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Brooke P Carpenter
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Rain Talosig
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Joseph P Patterson
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
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69
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Gruene T, Holstein JJ, Clever GH, Keppler B. Establishing electron diffraction in chemical crystallography. Nat Rev Chem 2021; 5:660-668. [PMID: 37118416 DOI: 10.1038/s41570-021-00302-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
The emerging field of 3D electron diffraction (3D ED) opens new opportunities for structure determination from sub-micrometre-sized crystals. Although the foundations of this technology emerged earlier, the past decade has seen developments in cryo-electron microscopy and (X-ray) crystallography that particularly enable the widespread use of 3D ED. This Perspective describes to chemists and chemical crystallographers just how similar electron and X-ray diffraction are and discusses their complementary aspects. We wish to establish 3D ED in the broader chemistry community, such that electron crystallography becomes a common part of the analytical chemistry toolkit. With a suitable instrument at their disposal, every skilled crystallographer can quickly learn to perform structure determinations using 3D ED.
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70
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Jha KK, Gruza B, Chodkiewicz ML, Jelsch C, Dominiak PM. Refinements on electron diffraction data of β-glycine in MoPro: a quest for an improved structure model. J Appl Crystallogr 2021. [DOI: 10.1107/s160057672100580x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The advancement in 3D electron diffraction (3D ED) techniques that lead to a revolution in molecular structure determination using nano-sized crystals is now achieving atomic resolution. The structures can be obtained from 3D ED data with tools similar to those used for X-ray structure determination. In this context, the MoPro software, originally designed for structure and charge density refinements using X-ray diffraction data, has been adapted. Structure refinement on 3D ED data was achieved via implementation of electron scattering factors available in the literature and by application of the Mott–Bethe equation to X-ray scattering factors computed from the multipolar atom model. The multipolar model was parametrized using the transferable pseudoatom databanks ELMAM2 and UBDB. Applying the independent atom model (IAM), i.e. spherical neutral atom refinement, to 3D ED data on β-glycine in MoPro resulted in structure and refinement statistics comparable to those obtained from other well known software. Use of the transferred aspherical atom model (TAAM) led to improvement of the refinement statistics and a better fit of the model to the 3D ED data as compared with the spherical atom refinement. The anisotropic displacement parameters of non-H atoms appear underestimated by typically 0.003 Å2 for the non-H atoms in IAM refinement compared with TAAM. Thus, MoPro is shown to be an effective tool for crystal structure refinement on 3D ED data and allows use of a spherical or a multipolar atom model. Electron density databases can be readily transferred with no further modification needed when the Mott–Bethe equation is applied.
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71
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Levine AM, He G, Bu G, Ramos P, Wu F, Soliman A, Serrano J, Pietraru D, Chan C, Batteas JD, Kowalczyk M, Jang SJ, Nannenga BL, Sfeir MY, Tsai EHR, Braunschweig AB. Efficient Free Triplet Generation Follows Singlet Fission in Diketo-pyrrolopyrrole Polymorphs with Goldilocks Coupling. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2021; 125:12207-12213. [PMID: 34868444 PMCID: PMC8641251 DOI: 10.1021/acs.jpcc.1c02737] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Microcrystal electron diffraction, grazing incidence wide-angle scattering, and UV-Vis spectroscopy were used to determine the unit cell structure and the relative composition of dimethylated diketopyrrolopyrrole (MeDPP) H- and J-polymorphs within thin films subjected to vapor solvent annealing (VSA) for different times. Electronic structure and excited state deactivation pathways of the different polymorphs were examined by transient absorption spectroscopy, conductive probe atomic force microscopy, and molecular modeling. We find VSA initially converts amorphous films into mixtures of H- and J-polymorphs and promotes further conversion from H to J with longer VSA times. Though both polymorphs exhibit efficient SF to form coupled triplets, free triplet yields are higher in J-polymorph films compared to mixed films because coupling in J-aggregates is lower, and, in turn, more favorable for triplet decoupling.
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Affiliation(s)
- Andrew M. Levine
- Nanoscience Initiative, Advanced Science Research Center, Graduate Center, City University of New York, 85 St. Nicholas Terrace, New York, NY 10031, USA
- Department of Chemistry, Hunter College, 695 Park Avenue, New York, NY 10065, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Guiying He
- Photonics Initiative, Advanced Science Research Center, Graduate Center, City University of New York, 85 St. Nicholas Terrace, New York, NY 10031, USA
- Department of Physics, Graduate Center, City University of New York, New York, NY 10016, USA
| | - Guanhong Bu
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ 85287, USA
| | - Pablo Ramos
- Department of Chemistry and Biochemistry, Queens College, City University of New York, 65-30 Kissena Boulevard, Queens, New York 11367, United States
| | - Fanglue Wu
- Department of Materials Science and Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - Aisha Soliman
- Nanoscience Initiative, Advanced Science Research Center, Graduate Center, City University of New York, 85 St. Nicholas Terrace, New York, NY 10031, USA
- Department of Chemistry, Hunter College, 695 Park Avenue, New York, NY 10065, USA
| | - Jacqueline Serrano
- Nanoscience Initiative, Advanced Science Research Center, Graduate Center, City University of New York, 85 St. Nicholas Terrace, New York, NY 10031, USA
- Department of Chemistry, Hunter College, 695 Park Avenue, New York, NY 10065, USA
| | - Dorian Pietraru
- Nanoscience Initiative, Advanced Science Research Center, Graduate Center, City University of New York, 85 St. Nicholas Terrace, New York, NY 10031, USA
- Department of Chemistry, Hunter College, 695 Park Avenue, New York, NY 10065, USA
| | - Christopher Chan
- Nanoscience Initiative, Advanced Science Research Center, Graduate Center, City University of New York, 85 St. Nicholas Terrace, New York, NY 10031, USA
| | - James D. Batteas
- Department of Materials Science and Engineering, Texas A&M University, College Station, Texas 77843, USA
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
| | - Marta Kowalczyk
- Department of Chemistry and Biochemistry, Queens College, City University of New York, 65-30 Kissena Boulevard, Queens, New York 11367, United States
- Department of Natural Sciences, LaGuardia Community College, City University of New York, New York, NY 11101, USA
| | - Seogjoo J. Jang
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
- Department of Physics, Graduate Center, City University of New York, New York, NY 10016, USA
- Department of Chemistry and Biochemistry, Queens College, City University of New York, 65-30 Kissena Boulevard, Queens, New York 11367, United States
| | - Brent L. Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ 85287, USA
| | - Matthew Y. Sfeir
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
- Photonics Initiative, Advanced Science Research Center, Graduate Center, City University of New York, 85 St. Nicholas Terrace, New York, NY 10031, USA
- Department of Physics, Graduate Center, City University of New York, New York, NY 10016, USA
| | - Esther H. R. Tsai
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Adam B. Braunschweig
- Nanoscience Initiative, Advanced Science Research Center, Graduate Center, City University of New York, 85 St. Nicholas Terrace, New York, NY 10031, USA
- Department of Chemistry, Hunter College, 695 Park Avenue, New York, NY 10065, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
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Plant transporters involved in combating boron toxicity: beyond 3D structures. Biochem Soc Trans 2021; 48:1683-1696. [PMID: 32779723 PMCID: PMC7458394 DOI: 10.1042/bst20200164] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 12/12/2022]
Abstract
Membrane transporters control the movement and distribution of solutes, including the disposal or compartmentation of toxic substances that accumulate in plants under adverse environmental conditions. In this minireview, in the light of the approaching 100th anniversary of unveiling the significance of boron to plants (K. Warington, 1923; Ann. Bot.37, 629) we discuss the current state of the knowledge on boron transport systems that plants utilise to combat boron toxicity. These transport proteins include: (i) nodulin-26-like intrinsic protein-types of aquaporins, and (ii) anionic efflux (borate) solute carriers. We describe the recent progress made on the structure–function relationships of these transport proteins and point out that this progress is integral to quantitative considerations of the transporter's roles in tissue boron homeostasis. Newly acquired knowledge at the molecular level has informed on the transport mechanics and conformational states of boron transport systems that can explain their impact on cell biology and whole plant physiology. We expect that this information will form the basis for engineering transporters with optimised features to alleviate boron toxicity tolerance in plants exposed to suboptimal soil conditions for sustained food production.
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73
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Bücker R, Hogan-Lamarre P, Miller RJD. Serial Electron Diffraction Data Processing With diffractem and CrystFEL. Front Mol Biosci 2021; 8:624264. [PMID: 34095217 PMCID: PMC8171297 DOI: 10.3389/fmolb.2021.624264] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 04/28/2021] [Indexed: 12/03/2022] Open
Abstract
Serial electron diffraction (SerialED) is an emerging technique, which applies the snapshot data-collection mode of serial X-ray crystallography to three-dimensional electron diffraction (3D Electron Diffraction), forgoing the conventional rotation method. Similarly to serial X-ray crystallography, this approach leads to almost complete absence of radiation damage effects even for the most sensitive samples, and allows for a high level of automation. However, SerialED also necessitates new techniques of data processing, which combine existing pipelines for rotation electron diffraction and serial X-ray crystallography with some more particular solutions for challenges arising in SerialED specifically. Here, we introduce our analysis pipeline for SerialED data, and its implementation using the CrystFEL and diffractem program packages. Detailed examples are provided in extensive supplementary code.
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Affiliation(s)
- Robert Bücker
- Max Planck Institute for the Structure and Dynamics of Matter, Center for Free-Electron Laser Science, Hamburg, Germany.,Centre for Structural Systems Biology, Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Pascal Hogan-Lamarre
- Max Planck Institute for the Structure and Dynamics of Matter, Center for Free-Electron Laser Science, Hamburg, Germany.,Department of Physics, University of Toronto, Toronto, ON, Canada.,Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - R J Dwayne Miller
- Department of Physics, University of Toronto, Toronto, ON, Canada.,Department of Chemistry, University of Toronto, Toronto, ON, Canada
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74
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An overview of the recent advances in cryo-electron microscopy for life sciences. Emerg Top Life Sci 2021; 5:151-168. [PMID: 33760078 DOI: 10.1042/etls20200295] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/26/2021] [Accepted: 03/09/2021] [Indexed: 01/18/2023]
Abstract
Cryo-electron microscopy (CryoEM) has superseded X-ray crystallography and NMR to emerge as a popular and effective tool for structure determination in recent times. It has become indispensable for the characterization of large macromolecular assemblies, membrane proteins, or samples that are limited, conformationally heterogeneous, and recalcitrant to crystallization. Besides, it is the only tool capable of elucidating high-resolution structures of macromolecules and biological assemblies in situ. A state-of-the-art electron microscope operable at cryo-temperature helps preserve high-resolution details of the biological sample. The structures can be determined, either in isolation via single-particle analysis (SPA) or helical reconstruction, electron diffraction (ED) or within the cellular environment via cryo-electron tomography (cryoET). All the three streams of SPA, ED, and cryoET (along with subtomogram averaging) have undergone significant advancements in recent times. This has resulted in breaking the boundaries with respect to both the size of the macromolecules/assemblies whose structures could be determined along with the visualization of atomic details at resolutions unprecedented for cryoEM. In addition, the collection of larger datasets combined with the ability to sort and process multiple conformational states from the same sample are providing the much-needed link between the protein structures and their functions. In overview, these developments are helping scientists decipher the molecular mechanism of critical cellular processes, solve structures of macromolecules that were challenging targets for structure determination until now, propelling forward the fields of biology and biomedicine. Here, we summarize recent advances and key contributions of the three cryo-electron microscopy streams of SPA, ED, and cryoET.
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75
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Burley SK, Berman HM. Open-access data: A cornerstone for artificial intelligence approaches to protein structure prediction. Structure 2021; 29:515-520. [PMID: 33984281 DOI: 10.1016/j.str.2021.04.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/08/2021] [Accepted: 04/23/2021] [Indexed: 12/28/2022]
Abstract
The Protein Data Bank (PDB) was established in 1971 to archive three-dimensional (3D) structures of biological macromolecules as a public good. Fifty years later, the PDB is providing millions of data consumers around the world with open access to more than 175,000 experimentally determined structures of proteins and nucleic acids (DNA, RNA) and their complexes with one another and small-molecule ligands. PDB data users are working, teaching, and learning in fundamental biology, biomedicine, bioengineering, biotechnology, and energy sciences. They also represent the fields of agriculture, chemistry, physics and materials science, mathematics, statistics, computer science, and zoology, and even the social sciences. The enormous wealth of 3D structure data stored in the PDB has underpinned significant advances in our understanding of protein architecture, culminating in recent breakthroughs in protein structure prediction accelerated by artificial intelligence approaches and deep or machine learning methods.
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Affiliation(s)
- Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA; Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Helen M Berman
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; The Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA.
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76
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Abstract
MicroED has recently emerged as a convenient and powerful tool for the unequivocal structure determination of small molecules and it could likely be used in cannabinoid research as well.
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Affiliation(s)
- Crist N Filer
- PerkinElmer Health Sciences Inc., 940 Winter Street, Waltham, MA, 02451, USA. .,PerkinElmer, 549 Albany St, Boston, MA, 02118, USA.
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77
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Clabbers MTB, Holmes S, Muusse TW, Vajjhala PR, Thygesen SJ, Malde AK, Hunter DJB, Croll TI, Flueckiger L, Nanson JD, Rahaman MH, Aquila A, Hunter MS, Liang M, Yoon CH, Zhao J, Zatsepin NA, Abbey B, Sierecki E, Gambin Y, Stacey KJ, Darmanin C, Kobe B, Xu H, Ve T. MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography. Nat Commun 2021; 12:2578. [PMID: 33972532 PMCID: PMC8110528 DOI: 10.1038/s41467-021-22590-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/18/2021] [Indexed: 02/03/2023] Open
Abstract
MyD88 and MAL are Toll-like receptor (TLR) adaptors that signal to induce pro-inflammatory cytokine production. We previously observed that the TIR domain of MAL (MALTIR) forms filaments in vitro and induces formation of crystalline higher-order assemblies of the MyD88 TIR domain (MyD88TIR). These crystals are too small for conventional X-ray crystallography, but are ideally suited to structure determination by microcrystal electron diffraction (MicroED) and serial femtosecond crystallography (SFX). Here, we present MicroED and SFX structures of the MyD88TIR assembly, which reveal a two-stranded higher-order assembly arrangement of TIR domains analogous to that seen previously for MALTIR. We demonstrate via mutagenesis that the MyD88TIR assembly interfaces are critical for TLR4 signaling in vivo, and we show that MAL promotes unidirectional assembly of MyD88TIR. Collectively, our studies provide structural and mechanistic insight into TLR signal transduction and allow a direct comparison of the MicroED and SFX techniques.
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Affiliation(s)
- Max T B Clabbers
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, California, USA
| | - Susannah Holmes
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Timothy W Muusse
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Parimala R Vajjhala
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Sara J Thygesen
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Alpeshkumar K Malde
- Institute for Glycomics, Griffith University, Southport, Queensland, Australia
| | - Dominic J B Hunter
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, New South Wales, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Tristan I Croll
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Leonie Flueckiger
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Jeffrey D Nanson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Md Habibur Rahaman
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Jingjing Zhao
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
| | - Nadia A Zatsepin
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Brian Abbey
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Emma Sierecki
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, New South Wales, Australia
| | - Yann Gambin
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, New South Wales, Australia
| | - Katryn J Stacey
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Connie Darmanin
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, Queensland, Australia.
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Sekharan S, Liu X, Yang Z, Liu X, Deng L, Ruan S, Abramov Y, Sun G, Li S, Zhou T, Shi B, Zeng Q, Zeng Q, Chang C, Jin Y, Shi X. Selecting a stable solid form of remdesivir using microcrystal electron diffraction and crystal structure prediction. RSC Adv 2021; 11:17408-17412. [PMID: 35479679 PMCID: PMC9033196 DOI: 10.1039/d1ra03100g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 04/27/2021] [Indexed: 12/20/2022] Open
Abstract
Therapeutic options in response to the coronavirus disease 2019 (COVID-19) outbreak are urgently needed. In this communication, we demonstrate how to support selection of a stable solid form of an antiviral drug remdesivir in quick time using the microcrystal electron diffraction (MicroED) technique and a cloud-based and artificial intelligence implemented crystal structure prediction platform. We present the MicroED structures of remdesivir forms II and IV and conclude that form II is more stable than form IV at ambient temperature in agreement with experimental observations. The combined experimental and theoretical study can serve as a template for formulation scientists in the pharmaceutical industry.
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Affiliation(s)
| | - Xuetao Liu
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Zhuocen Yang
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Xiang Liu
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Li Deng
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Shigang Ruan
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Yuriy Abramov
- XtalPi Inc. 245 Main St, Floor 11 Cambridge MA 02142 USA
| | - GuangXu Sun
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Sizhu Li
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Tian Zhou
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Baime Shi
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Qun Zeng
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Qiao Zeng
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Chao Chang
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Yingdi Jin
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Xuekun Shi
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
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79
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Kubota R, Tanaka W, Hamachi I. Microscopic Imaging Techniques for Molecular Assemblies: Electron, Atomic Force, and Confocal Microscopies. Chem Rev 2021; 121:14281-14347. [DOI: 10.1021/acs.chemrev.0c01334] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Wataru Tanaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8530, Japan
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80
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Peck A, Yao Q, Brewster AS, Zwart PH, Heumann JM, Sauter NK, Jensen GJ. Challenges in solving structures from radiation-damaged tomograms of protein nanocrystals assessed by simulation. Acta Crystallogr D Struct Biol 2021; 77:572-586. [PMID: 33950014 PMCID: PMC8098477 DOI: 10.1107/s2059798321002369] [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: 09/19/2020] [Accepted: 03/02/2021] [Indexed: 11/11/2022] Open
Abstract
Structure-determination methods are needed to resolve the atomic details that underlie protein function. X-ray crystallography has provided most of our knowledge of protein structure, but is constrained by the need for large, well ordered crystals and the loss of phase information. The rapidly developing methods of serial femtosecond crystallography, micro-electron diffraction and single-particle reconstruction circumvent the first of these limitations by enabling data collection from nanocrystals or purified proteins. However, the first two methods also suffer from the phase problem, while many proteins fall below the molecular-weight threshold required for single-particle reconstruction. Cryo-electron tomography of protein nanocrystals has the potential to overcome these obstacles of mainstream structure-determination methods. Here, a data-processing scheme is presented that combines routines from X-ray crystallography and new algorithms that have been developed to solve structures from tomograms of nanocrystals. This pipeline handles image-processing challenges specific to tomographic sampling of periodic specimens and is validated using simulated crystals. The tolerance of this workflow to the effects of radiation damage is also assessed. The simulations indicate a trade-off between a wider tilt range to facilitate merging data from multiple tomograms and a smaller tilt increment to improve phase accuracy. Since phase errors, but not merging errors, can be overcome with additional data sets, these results recommend distributing the dose over a wide angular range rather than using a finer sampling interval to solve the protein structure.
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Affiliation(s)
- Ariana Peck
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Qing Yao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Petrus H. Zwart
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Center for Advanced Mathematics in Energy Research Applications, Lawrence Berkeley National Laboratory, Berkeley CA 94720, USA
| | - John M. Heumann
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Grant J. Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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81
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Below 3 Å structure of apoferritin using a multipurpose TEM with a side entry cryoholder. Sci Rep 2021; 11:8395. [PMID: 33863933 PMCID: PMC8052451 DOI: 10.1038/s41598-021-87183-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/22/2021] [Indexed: 12/22/2022] Open
Abstract
Recently, the structural analysis of protein complexes by cryo-electron microscopy (cryo-EM) single particle analysis (SPA) has had great impact as a biophysical method. Many results of cryo-EM SPA are based on data acquired on state-of-the-art cryo-electron microscopes customized for SPA. These are currently only available in limited locations around the world, where securing machine time is highly competitive. One potential solution for this time-competitive situation is to reuse existing multi-purpose equipment, although this comes with performance limitations. Here, a multi-purpose TEM with a side entry cryo-holder was used to evaluate the potential of high-resolution SPA, resulting in a 3 Å resolution map of apoferritin with local resolution extending to 2.6 Å. This map clearly showed two positions of an aromatic side chain. Further, examination of optimal imaging conditions depending on two different multi-purpose electron microscope and camera combinations was carried out, demonstrating that higher magnifications are not always necessary or desirable. Since automation is effectively a requirement for large-scale data collection, and augmenting the multi-purpose equipment is possible, we expanded testing by acquiring data with SerialEM using a β-galactosidase test sample. This study demonstrates the possibilities of more widely available and established electron microscopes, and their applications for cryo-EM SPA.
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82
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Jasim A, He X, Xing Y, White TA, Young MJ. Cryo-ePDF: Overcoming Electron Beam Damage to Study the Local Atomic Structure of Amorphous ALD Aluminum Oxide Thin Films within a TEM. ACS OMEGA 2021; 6:8986-9000. [PMID: 33842769 PMCID: PMC8028128 DOI: 10.1021/acsomega.0c06124] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
Atomic layer deposition (ALD) provides uniform and conformal thin films that are of interest for a range of applications. To better understand the properties of amorphous ALD films, we need an improved understanding of their local atomic structure. Previous work demonstrated measurement of how the local atomic structure of ALD-grown aluminum oxide (AlO x ) evolves in operando during growth by employing synchrotron high-energy X-ray diffraction (HE-XRD). In this work, we report on efforts to employ electron diffraction pair distribution function (ePDF) measurements using more broadly available transmission electron microscope (TEM) instrumentation to study the atomic structure of amorphous ALD-AlO x . We observe electron beam damage in the ALD-coated samples during ePDF at ambient temperature and successfully mitigate this beam damage using ePDF at cryogenic temperatures (cryo-ePDF). We employ cryo-ePDF and reverse Monte Carlo (RMC) modeling to obtain structural models of ALD-AlO x coatings formed at a range of deposition temperatures from 150 to 332 °C. From these model structures, we derive structural metrics including stoichiometry, pair distances, and coordination environments in the ALD-AlO x films as a function of deposition temperature. The structural variations we observe with growth temperature are consistent with temperature-dependent changes in the surface hydroxyl density on the growth surface. The sample preparation and cryo-ePDF procedures we report here can be used for the routine measurement of ALD-grown amorphous thin films to improve our understanding of the atomic structure of these materials, establish structure-property relationships, and help accelerate the timescale for the application of ALD to address technological needs.
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Affiliation(s)
- Ahmed
M. Jasim
- Department
of Biomedical, Biological and Chemical Engineering, University of Missouri, Columbia, Missouri 65211, United States
| | - Xiaoqing He
- Electron
Microscopy Core, University of Missouri, Columbia, Missouri 65211, United States
- Department
of Mechanical & Aerospace Engineering, University of Missouri, Columbia, Missouri 65211, United States
| | - Yangchuan Xing
- Department
of Biomedical, Biological and Chemical Engineering, University of Missouri, Columbia, Missouri 65211, United States
- Department
of Mechanical & Aerospace Engineering, University of Missouri, Columbia, Missouri 65211, United States
| | - Tommi A. White
- Electron
Microscopy Core, University of Missouri, Columbia, Missouri 65211, United States
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Matthias J. Young
- Department
of Biomedical, Biological and Chemical Engineering, University of Missouri, Columbia, Missouri 65211, United States
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
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83
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Amphipathic environments for determining the structure of membrane proteins by single-particle electron cryo-microscopy. Q Rev Biophys 2021; 54:e6. [PMID: 33785082 DOI: 10.1017/s0033583521000044] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the past decade, the structural biology of membrane proteins (MPs) has taken a new turn thanks to epoch-making technical progress in single-particle electron cryo-microscopy (cryo-EM) as well as to improvements in sample preparation. The present analysis provides an overview of the extent and modes of usage of the various types of surfactants for cryo-EM studies. Digitonin, dodecylmaltoside, protein-based nanodiscs, lauryl maltoside-neopentyl glycol, glyco-diosgenin, and amphipols (APols) are the most popular surfactants at the vitrification step. Surfactant exchange is frequently used between MP purification and grid preparation, requiring extensive optimization each time the study of a new MP is undertaken. The variety of both the surfactants and experimental approaches used over the past few years bears witness to the need to continue developing innovative surfactants and optimizing conditions for sample preparation. The possibilities offered by novel APols for EM applications are discussed.
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84
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Abstract
The human microbiome encodes a second genome that dwarfs the genetic capacity of the host. Microbiota-derived small molecules can directly target human cells and their receptors or indirectly modulate host responses through functional interactions with other microbes in their ecological niche. Their biochemical complexity has profound implications for nutrition, immune system development, disease progression, and drug metabolism, as well as the variation in these processes that exists between individuals. While the species composition of the human microbiome has been deeply explored, detailed mechanistic studies linking specific microbial molecules to host phenotypes are still nascent. In this review, we discuss challenges in decoding these interaction networks, which require interdisciplinary approaches that combine chemical biology, microbiology, immunology, genetics, analytical chemistry, bioinformatics, and synthetic biology. We highlight important classes of microbiota-derived small molecules and notable examples. An understanding of these molecular mechanisms is central to realizing the potential of precision microbiome editing in health, disease, and therapeutic responses.
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Affiliation(s)
- Emilee E Shine
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06536, USA; .,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA.,Current affiliation: Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Jason M Crawford
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06536, USA; .,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA.,Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
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85
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Subramanian M, Kielar C, Tsushima S, Fahmy K, Oertel J. DNA-Mediated Stack Formation of Nanodiscs. Molecules 2021; 26:1647. [PMID: 33809519 PMCID: PMC8000961 DOI: 10.3390/molecules26061647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 03/05/2021] [Accepted: 03/12/2021] [Indexed: 11/16/2022] Open
Abstract
Membrane-scaffolding proteins (MSPs) derived from apolipoprotein A-1 have become a versatile tool in generating nano-sized discoidal membrane mimetics (nanodiscs) for membrane protein research. Recent efforts have aimed at exploiting their controlled lipid protein ratio and size distribution to arrange membrane proteins in regular supramolecular structures for diffraction studies. Thereby, direct membrane protein crystallization, which has remained the limiting factor in structure determination of membrane proteins, would be circumvented. We describe here the formation of multimers of membrane-scaffolding protein MSP1D1-bounded nanodiscs using the thiol reactivity of engineered cysteines. The mutated positions N42 and K163 in MSP1D1 were chosen to support chemical modification as evidenced by fluorescent labeling with pyrene. Minimal interference with the nanodisc formation and structure was demonstrated by circular dichroism spectroscopy, differential light scattering and size exclusion chromatography. The direct disulphide bond formation of nanodiscs formed by the MSP1D1_N42C variant led to dimers and trimers with low yield. In contrast, transmission electron microscopy revealed that the attachment of oligonucleotides to the engineered cysteines of MSP1D1 allowed the growth of submicron-sized tracts of stacked nanodiscs through the hybridization of nanodisc populations carrying complementary strands and a flexible spacer.
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Affiliation(s)
- Madhumalar Subramanian
- Biophysics Department, Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany; (M.S.); (C.K.); (S.T.)
- Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01062 Dresden, Germany
| | - Charlotte Kielar
- Biophysics Department, Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany; (M.S.); (C.K.); (S.T.)
| | - Satoru Tsushima
- Biophysics Department, Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany; (M.S.); (C.K.); (S.T.)
| | - Karim Fahmy
- Biophysics Department, Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany; (M.S.); (C.K.); (S.T.)
- Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01062 Dresden, Germany
| | - Jana Oertel
- Biophysics Department, Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany; (M.S.); (C.K.); (S.T.)
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86
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Balasco N, Diaferia C, Morelli G, Vitagliano L, Accardo A. Amyloid-Like Aggregation in Diseases and Biomaterials: Osmosis of Structural Information. Front Bioeng Biotechnol 2021; 9:641372. [PMID: 33748087 PMCID: PMC7966729 DOI: 10.3389/fbioe.2021.641372] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/05/2021] [Indexed: 11/13/2022] Open
Abstract
The discovery that the polypeptide chain has a remarkable and intrinsic propensity to form amyloid-like aggregates endowed with an extraordinary stability is one of the most relevant breakthroughs of the last decades in both protein/peptide chemistry and structural biology. This observation has fundamental implications, as the formation of these assemblies is systematically associated with the insurgence of severe neurodegenerative diseases. Although the ability of proteins to form aggregates rich in cross-β structure has been highlighted by recent studies of structural biology, the determination of the underlying atomic models has required immense efforts and inventiveness. Interestingly, the progressive molecular and structural characterization of these assemblies has opened new perspectives in apparently unrelated fields. Indeed, the self-assembling through the cross-β structure has been exploited to generate innovative biomaterials endowed with promising mechanical and spectroscopic properties. Therefore, this structural motif has become the fil rouge connecting these diversified research areas. In the present review, we report a chronological recapitulation, also performing a survey of the structural content of the Protein Data Bank, of the milestones achieved over the years in the characterization of cross-β assemblies involved in the insurgence of neurodegenerative diseases. A particular emphasis is given to the very recent successful elucidation of amyloid-like aggregates characterized by remarkable molecular and structural complexities. We also review the state of the art of the structural characterization of cross-β based biomaterials by highlighting the benefits of the osmosis of information between these two research areas. Finally, we underline the new promising perspectives that recent successful characterizations of disease-related amyloid-like assemblies can open in the biomaterial field.
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Affiliation(s)
- Nicole Balasco
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Carlo Diaferia
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples “Federico II”, Naples, Italy
| | - Giancarlo Morelli
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples “Federico II”, Naples, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Antonella Accardo
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples “Federico II”, Naples, Italy
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87
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Clabbers MTB, Xu H. Macromolecular crystallography using microcrystal electron diffraction. Acta Crystallogr D Struct Biol 2021; 77:313-324. [PMID: 33645535 PMCID: PMC7919406 DOI: 10.1107/s2059798320016368] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/16/2020] [Indexed: 11/10/2022] Open
Abstract
Microcrystal electron diffraction (MicroED) has recently emerged as a promising method for macromolecular structure determination in structural biology. Since the first protein structure was determined in 2013, the method has been evolving rapidly. Several protein structures have been determined and various studies indicate that MicroED is capable of (i) revealing atomic structures with charges, (ii) solving new protein structures by molecular replacement, (iii) visualizing ligand-binding interactions and (iv) determining membrane-protein structures from microcrystals embedded in lipidic mesophases. However, further development and optimization is required to make MicroED experiments more accurate and more accessible to the structural biology community. Here, we provide an overview of the current status of the field, and highlight the ongoing development, to provide an indication of where the field may be going in the coming years. We anticipate that MicroED will become a robust method for macromolecular structure determination, complementing existing methods in structural biology.
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Affiliation(s)
- Max T. B. Clabbers
- Department of Materials and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden
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88
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Danelius E, Halaby S, van der Donk WA, Gonen T. MicroED in natural product and small molecule research. Nat Prod Rep 2021; 38:423-431. [PMID: 32939523 PMCID: PMC7965795 DOI: 10.1039/d0np00035c] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Covering: 2013 to 2020The electron cryo-microscopy (cryo-EM) method Microcrystal Electron Diffraction (MicroED) allows the collection of high-resolution structural data from vanishingly small crystals that appear like amorphous powders or very fine needles. Since its debut in 2013, data collection and analysis schemes have been fine-tuned, and there are currently close to 100 structures determined by MicroED. Although originally developed to study proteins, MicroED is also very powerful for smaller systems, with some recent and very promising examples from the field of natural products. Herein, we review what has been achieved so far and provide examples of natural product structures, as well as demonstrate the expected future impact of MicroED to the field of natural product and small molecule research.
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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, CA 90095, USA.
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89
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Klenotic PA, Morgan CE, Yu EW. Cryo-EM as a tool to study bacterial efflux systems and the membrane proteome. Fac Rev 2021; 10:24. [PMID: 33718941 PMCID: PMC7946387 DOI: 10.12703/r/10-24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Antibiotic resistance is an emerging threat to global health. Current treatment regimens for these types of bacterial infections are becoming increasingly inadequate. Thus, new innovative technologies are needed to help identify and characterize novel drugs and drug targets which are critical in order to combat multidrug-resistant bacterial strains. Bacterial efflux systems have emerged as an attractive target for drug design, as blocking their export function significantly increases the potency of administered antibiotics. However, in order to develop potent and tolerable efflux pump inhibitors with high efficacy, detailed structural information is required for both the apo- and substrate-bound forms of these membrane proteins. The emergence of cryo-electron microscopy (cryo-EM) has greatly advanced the field of membrane protein structural biology. It has significantly enhanced the ability to solve large multi-protein complexes as well as extract meaningful data from a heterogeneous sample, such as identification of several assembly states of the bacterial ribosome, from a single data set. This technique can be expanded to solve the structures of substrate-bound efflux pumps and entire efflux systems from previously unusable membrane protein sample preparations. Subsequently, cryo-EM combined with other biophysical techniques has the potential to markedly advance the field of membrane protein structural biology. The ability to discern complete transport machineries, enzymatic signal transduction pathways, and other membrane-associated complexes will help us fully understand the complexities of the membrane proteome.
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Affiliation(s)
- Philip A Klenotic
- Department of Pharmacology, Case Western Reserve University School of Medicine, 2109 Adelbert Rd, Cleveland, OH 44106-4965, USA
| | - Christopher E Morgan
- Department of Pharmacology, Case Western Reserve University School of Medicine, 2109 Adelbert Rd, Cleveland, OH 44106-4965, USA
| | - Edward W Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, 2109 Adelbert Rd, Cleveland, OH 44106-4965, USA
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90
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Banerjee A, Bhakta S, Sengupta J. Integrative approaches in cryogenic electron microscopy: Recent advances in structural biology and future perspectives. iScience 2021; 24:102044. [PMID: 33532719 PMCID: PMC7829201 DOI: 10.1016/j.isci.2021.102044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cellular factories engage numerous highly complex "molecular machines" to perform pivotal biological functions. 3D structural visualization is an effective way to understand the functional mechanisms of these biomacromolecules. The "resolution revolution" has established cryogenic electron microscopy (cryo-EM) as a preferred structural biology tool. In parallel with the advances in cryo-EM methodologies aiming at atomic resolution, several innovative approaches have started emerging where other techniques are sensibly integrated with cryo-EM to obtain additional insights into the biological processes. For example, combining the time-resolved technique with high-resolution cryo-EM enables discerning structures of short-lived intermediates in the functional pathway of a biomolecule. Likewise, integrating mass spectrometry (MS) techniques with cryo-EM allows deciphering structural organizations of large molecular assemblies. Here, we discuss how the data generated upon combining either time resolve or MS techniques with cryo-EM supplement structural elucidations with in-depth understanding of the function of cellular macromolecules when they participate in fundamental biological processes.
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Affiliation(s)
- Aneek Banerjee
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sayan Bhakta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Jayati Sengupta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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91
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Cho HJ, Kim KS, Kim H, Kim T, Malyutin AG, Rees DC, Yoo BK, Song C. Microcrystal Electron Diffraction Elucidates Water-Specific Polymorphism-Induced Emission Enhancement of Bis-arylacylhydrazone. ACS APPLIED MATERIALS & INTERFACES 2021; 13:7546-7555. [PMID: 33544590 DOI: 10.1021/acsami.0c21248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Aggregation-induced emission (AIE) phenomena have gained intense interest over the last decades because of its importance in solid-state emission. However, the elucidation of a working mechanism is difficult owing to the limited characterization methods on solid-state molecules, further complicated if dynamic structural changes occur. Here, a series of bis-arylacylhydrazones (BAHs) were synthesized, for which their AIE properties are only turned on by the reversible adsorption of water molecules. We used microcrystal electron diffraction (MicroED) to determine the molecular structures of two BAHs directly from bulk powders (without attempting to grow crystals) prepared in the absence or presence of water adsorption. This study reveals the unambiguous characterization of the dependence of crystal packing on the specific cocrystallization with hydrates. The structural analysis demonstrates that water molecules form strong hydrogen bonds with three neighboring BAH-1, resulting in the almost complete planarization and restriction of the intramolecular rotation of the molecule. MicroED plays an important role in providing a decisive clue for the reversible polymorphism changes induced by the adsorption of water molecules, regulating emissive properties.
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Affiliation(s)
- Hye Jin Cho
- Department of Chemistry, Sungkyunkwan University, 2066 Seobu-ro, Janan-gu, Suwon-si, Gyeonggi-do 16419 Republic of Korea
| | - Kyung-Su Kim
- Department of Chemistry, Sungkyunkwan University, 2066 Seobu-ro, Janan-gu, Suwon-si, Gyeonggi-do 16419 Republic of Korea
| | - Hyunwoo Kim
- Department of Chemistry, Sungkyunkwan University, 2066 Seobu-ro, Janan-gu, Suwon-si, Gyeonggi-do 16419 Republic of Korea
| | - Taewoo Kim
- Department of Chemistry, Sungkyunkwan University, 2066 Seobu-ro, Janan-gu, Suwon-si, Gyeonggi-do 16419 Republic of Korea
| | - Andrey G Malyutin
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, United States
| | - Douglas C Rees
- HHMI, California Institute of Technology, Pasadena, CA 91125, United States
- Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Byung-Kuk Yoo
- HHMI, California Institute of Technology, Pasadena, CA 91125, United States
- Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Changsik Song
- Department of Chemistry, Sungkyunkwan University, 2066 Seobu-ro, Janan-gu, Suwon-si, Gyeonggi-do 16419 Republic of Korea
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92
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Spence JCH, Donatelli JJ. Inversion of dynamical Bragg intensities to complex structure factors by iterated projections. For Ultramic. 2020. ("Pico" Festschrift, May 2021). Ultramicroscopy 2021; 222:113214. [PMID: 33561601 DOI: 10.1016/j.ultramic.2021.113214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/16/2021] [Accepted: 01/19/2021] [Indexed: 10/22/2022]
Abstract
A method for recovering complex structure factors from many simultaneously excited Bragg beam in- tensities is described. The method is applied to simulated transmission electron diffraction data over a wide range of crystal thickness and beam energies. The method is based on iterated projections between structure and scattering matrices, which are related by a matrix unit ary transformation, exponential, which we invert. The algorithm removes multiple-scattering perturbations from diffraction data and might be extended to other fields, including X-ray and neutron diffraction and cryo-electron microscopy. Because coherent multiple scattering involves interference between Bragg beams, the method also solves the phase problem. Unlike dynamical inversion from electron microscope images or ptychography data, the method, which starts with Bragg beam intensities, provides complex structure factors unaffected by focusing errors or resolution limitations imposed by lenses. We provide inversions from simulated data with 441 simultaneously excited Bragg beams over a range of thickness and beam energy. We discuss the retrieval of chirality information from enantiomorphs, the efficient incorporation of symmetry information using the irreducible representation of the group of structure matrices, and the effect of HOLZ lines to provide three-dimensional information.
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Affiliation(s)
- John C H Spence
- Department of Physics, Arizona State University, Tempe, Arizona, 85287-1504 USA; Department of Applied Mathematics, Lawrence Berkeley Laboratory, Berkeley, CA 94720 USA; Center for Advanced Mathematics for Energy Research Applications, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA.
| | - Jeffrey J Donatelli
- Department of Physics, Arizona State University, Tempe, Arizona, 85287-1504 USA; Department of Applied Mathematics, Lawrence Berkeley Laboratory, Berkeley, CA 94720 USA; Center for Advanced Mathematics for Energy Research Applications, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
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93
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Beyond X-rays: an overview of emerging structural biology methods. Emerg Top Life Sci 2021; 5:221-230. [DOI: 10.1042/etls20200272] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/27/2020] [Accepted: 01/20/2021] [Indexed: 11/17/2022]
Abstract
Structural biologists rely on X-ray crystallography as the main technique for determining the three-dimensional structures of macromolecules; however, in recent years, new methods that go beyond X-ray-based technologies are broadening the selection of tools to understand molecular structure and function. Simultaneously, national facilities are developing programming tools and maintaining personnel to aid novice structural biologists in de novo structure determination. The combination of X-ray free electron lasers (XFELs) and serial femtosecond crystallography (SFX) now enable time-resolved structure determination that allows for capture of dynamic processes, such as reaction mechanism and conformational flexibility. XFEL and SFX, along with microcrystal electron diffraction (MicroED), help side-step the need for large crystals for structural studies. Moreover, advances in cryogenic electron microscopy (cryo-EM) as a tool for structure determination is revolutionizing how difficult to crystallize macromolecules and/or complexes can be visualized at the atomic scale. This review aims to provide a broad overview of these new methods and to guide readers to more in-depth literature of these methods.
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94
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Ghashghaei O, Pedrola M, Seghetti F, Martin VV, Zavarce R, Babiak M, Novacek J, Hartung F, Rolfes KM, Haarmann‐Stemmann T, Lavilla R. Extended Multicomponent Reactions with Indole Aldehydes: Access to Unprecedented Polyheterocyclic Scaffolds, Ligands of the Aryl Hydrocarbon Receptor. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ouldouz Ghashghaei
- Laboratory of Medicinal Chemistry Faculty of Pharmacy and Food Sciences and Institute of Biomedicine (IBUB) Universitat de Barcelona Av. Joan XXIII, 27–31 08028 Barcelona Spain
| | - Marina Pedrola
- Laboratory of Medicinal Chemistry Faculty of Pharmacy and Food Sciences and Institute of Biomedicine (IBUB) Universitat de Barcelona Av. Joan XXIII, 27–31 08028 Barcelona Spain
| | - Francesca Seghetti
- Laboratory of Medicinal Chemistry Faculty of Pharmacy and Food Sciences and Institute of Biomedicine (IBUB) Universitat de Barcelona Av. Joan XXIII, 27–31 08028 Barcelona Spain
| | - Victor V. Martin
- Laboratory of Medicinal Chemistry Faculty of Pharmacy and Food Sciences and Institute of Biomedicine (IBUB) Universitat de Barcelona Av. Joan XXIII, 27–31 08028 Barcelona Spain
| | - Ricardo Zavarce
- Laboratory of Medicinal Chemistry Faculty of Pharmacy and Food Sciences and Institute of Biomedicine (IBUB) Universitat de Barcelona Av. Joan XXIII, 27–31 08028 Barcelona Spain
| | - Michal Babiak
- CEITEC Masaryk University University Campus Bohunice 62500 Brno Czech Republic
| | - Jiri Novacek
- CEITEC Masaryk University University Campus Bohunice 62500 Brno Czech Republic
| | - Frederick Hartung
- IUF Leibniz Research Institute for Environmental Medicine 40225 Düsseldorf Germany
| | - Katharina M. Rolfes
- IUF Leibniz Research Institute for Environmental Medicine 40225 Düsseldorf Germany
| | | | - Rodolfo Lavilla
- Laboratory of Medicinal Chemistry Faculty of Pharmacy and Food Sciences and Institute of Biomedicine (IBUB) Universitat de Barcelona Av. Joan XXIII, 27–31 08028 Barcelona Spain
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95
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Gleason PR, Nannenga BL, Mills JH. Rapid Structural Analysis of a Synthetic Non-canonical Amino Acid by Microcrystal Electron Diffraction. Front Mol Biosci 2021; 7:609999. [PMID: 33490105 PMCID: PMC7821094 DOI: 10.3389/fmolb.2020.609999] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/07/2020] [Indexed: 02/03/2023] Open
Abstract
Structural characterization of small molecules is a crucial component of organic synthesis. In this work, we applied microcrystal electron diffraction (MicroED) to analyze the structure of the product of an enzymatic reaction that was intended to produce the unnatural amino acid 2,4-dihydroxyphenylalanine (24DHF). Characterization of our isolated product with nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS) suggested that an isomer of 24DHF had been formed. Microcrystals present in the isolated product were then used to determine its structure to 0.62 Å resolution, which confirmed its identity as 2-amino-2-(2,4-dihydroxyphenyl)propanoic acid (24DHPA). Moreover, the MicroED structural model indicated that both enantiomeric forms of 24DHPA were present in the asymmetric unit. Notably, the entire structure determination process including setup, data collection, and refinement was completed in ~1 h. The MicroED data not only bolstered previous results obtained using NMR and MS but also immediately provided information about the stereoisomers present in the product, which is difficult to achieve using NMR and MS alone. Our results therefore demonstrate that MicroED methods can provide useful structural information on timescales that are similar to many commonly used analytical methods and can be added to the existing suite of small molecule structure determination tools in future studies.
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Affiliation(s)
- Patrick R. Gleason
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States,Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Brent L. Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, United States,*Correspondence: Brent L. Nannenga
| | - Jeremy H. Mills
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States,Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States,Jeremy H. Mills
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96
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Seychell BC, Beck T. Molecular basis for protein-protein interactions. Beilstein J Org Chem 2021; 17:1-10. [PMID: 33488826 PMCID: PMC7801801 DOI: 10.3762/bjoc.17.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/07/2020] [Indexed: 01/11/2023] Open
Abstract
This minireview provides an overview on the current knowledge of protein-protein interactions, common characterisation methods to characterise them, and their role in protein complex formation with some examples. A deep understanding of protein-protein interactions and their molecular interactions is important for a number of applications, including drug design. Protein-protein interactions and their discovery are thus an interesting avenue for understanding how protein complexes, which make up the majority of proteins, work.
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Affiliation(s)
- Brandon Charles Seychell
- Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Grindelallee 117, 20146 Hamburg, Germany
| | - Tobias Beck
- Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Grindelallee 117, 20146 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
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97
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Ismail FMD, Nahar L, Sarker SD. Application of INADEQUATE NMR techniques for directly tracing out the carbon skeleton of a natural product. PHYTOCHEMICAL ANALYSIS : PCA 2021; 32:7-23. [PMID: 32671944 DOI: 10.1002/pca.2976] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 06/11/2023]
Abstract
INTRODUCTION Nuclear magnetic resonance (NMR) measurement of 1 JCC coupling by two-dimensional (2D) INADEQUATE (incredible natural abundance double quantum transfer experiment), which is a special case of double-quantum (DQ) spectroscopy that offers unambiguous determination of 13 C-13 C spin-spin connectivities through the DQ transitions of the spin system, is especially suited to solving structures rich in quaternary carbons and poor in hydrogen content (Crews rule). OBJECTIVE To review published literature on the application of NMR methods to determine structure in the liquid-state, which specifically considers the interaction of a pair of carbon-13 (13 C) nuclei adjacent to one another, to allow direct tracing out of contiguous carbon connectivity using 2D INADEQUATE. METHODOLOGY A comprehensive literature search was implemented with various databases: Web of Knowledge, PubMed and SciFinder, and other relevant published materials including published monographs. The keywords used, in various combinations, with INADEQUATE being present in all combinations, in the search were 2D NMR, 1 JCC coupling, natural product, structure elucidation, 13 C-13 C connectivity, cryoprobe and CASE (computer-assisted structure elucidation)/PANACEA (protons and nitrogen and carbon et alia). RESULTS The 2D INADEQUATE continues to solve "intractable" problems in natural product chemistry, and using milligram quantities with cryoprobe techniques combined with CASE/PANACEA experiments can increase machine time efficiency. The 13 C-13 C-based structural elucidation by dissolution single-scan dynamic nuclear polarisation NMR can overcome disadvantages of 13 C insensitivity at natural abundance. Selected examples have demonstrated the trajectory of INADEQUATE spectroscopy from structural determination to clarification of metabolomics analysis and use of DFT (density functional theory) and coupling constants to clarify the connectivity, hybridisation and stereochemistry within natural products. CONCLUSIONS Somewhat neglected over the years because of perceived lack of sensitivity, the 2D INADEQUATE NMR technique has re-emerged as a useful tool for solving natural products structures, which are rich in quaternary carbons and poor in hydrogen content.
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Affiliation(s)
- Fyaz M D Ismail
- Centre for Natural Products Discovery, School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, Merseyside, L3 3AF, UK
| | - Lutfun Nahar
- Centre for Natural Products Discovery, School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, Merseyside, L3 3AF, UK
- Laboratory of Growth Regulators, Institute of Experimental Botany ASCR & Palacký University, Olomouc, Czech Republic
| | - Satyajit D Sarker
- Centre for Natural Products Discovery, School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, Merseyside, L3 3AF, UK
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98
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Abstract
Microcrystal Electron Diffraction (MicroED) is the newest cryo-electron microscopy (cryo-EM) method, with over 70 protein, peptide, and several small organic molecule structures already determined. In MicroED, micro- or nanocrystalline samples in solution are deposited on electron microscopy grids and examined in a cryo-electron microscope, ideally under cryogenic conditions. Continuous rotation diffraction data are collected and then processed using conventional X-ray crystallography programs. The protocol outlined here details how to obtain and identify the nanocrystals, how to set up the microscope for screening and for MicroED data collection, and how to collect and process data to complete high-resolution structures. For well-behaving crystals with high-resolution diffraction in cryo-EM, the entire process can be achieved in less than an hour.
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99
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Abstract
Microcrystal electron diffraction (MicroED) is a technique for structure determination that relies on the strong interaction of electrons with a minuscule, crystalline sample. While some of the electrons used to probe the crystal interact without altering the crystal, others deposit energy which changes the sample through a series of damage events. It follows that the sample cannot be observed without damaging it, and the frames obtained at the beginning of data collection reflect a crystal that differs from the one that yields the last frames of the dataset. Data acquisition at cryogenic temperatures has been found to reduce the rate of damage progression and is routinely used to increase the dose tolerance of the crystal, allowing more useful data to be obtained before the sample is destroyed. Low-dose data collection can further prolong the lifetime of the crystal, such that less damage is inflicted over the course of data acquisition. Ideally, lower doses increase the measurable volume of a single-crystal lattice by reducing the damage caused by probing electrons. However, the information that can be recovered from a diffraction image is directly related to the number of electrons used to probe the sample. The signal from a weakly exposed crystal runs the risk of being lost in the noise contributed by solvent, crystal disorder, and the electron detection process. This work focuses on obtaining the best possible data from a MicroED measurement, which requires considering several aspects such as sample, dose, and camera type.
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100
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Abstract
Microcrystal Electron Diffraction (MicroED) enables structure determination of very small crystals that are much too small to be of use for other conventional diffraction techniques. MicroED has been used to determine the structures of many proteins and small organic molecules, and the technique can be performed on most standard cryo-TEM instruments equipped with high-speed detectors capable of collecting electron diffraction data. Here, we present protocols for MicroED sample preparation and data collection for protein microcrystals.
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Affiliation(s)
- Guanhong Bu
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA.
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
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