1
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Wankowicz SA, Fraser JS. Comprehensive encoding of conformational and compositional protein structural ensembles through the mmCIF data structure. IUCRJ 2024; 11:494-501. [PMID: 38958015 PMCID: PMC11220883 DOI: 10.1107/s2052252524005098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/29/2024] [Indexed: 07/04/2024]
Abstract
In the folded state, biomolecules exchange between multiple conformational states crucial for their function. However, most structural models derived from experiments and computational predictions only encode a single state. To represent biomolecules accurately, we must move towards modeling and predicting structural ensembles. Information about structural ensembles exists within experimental data from X-ray crystallography and cryo-electron microscopy. Although new tools are available to detect conformational and compositional heterogeneity within these ensembles, the legacy PDB data structure does not robustly encapsulate this complexity. We propose modifications to the macromolecular crystallographic information file (mmCIF) to improve the representation and interrelation of conformational and compositional heterogeneity. These modifications will enable the capture of macromolecular ensembles in a human and machine-interpretable way, potentially catalyzing breakthroughs for ensemble-function predictions, analogous to the achievements of AlphaFold with single-structure prediction.
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Affiliation(s)
- Stephanie A. Wankowicz
- Department of Bioengineering and Therapeutic ScienceUniversity of CaliforniaSan FranciscoCA94117USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic ScienceUniversity of CaliforniaSan FranciscoCA94117USA
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2
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Wankowicz SA, Ravikumar A, Sharma S, Riley B, Raju A, Hogan DW, Flowers J, van den Bedem H, Keedy DA, Fraser JS. Automated multiconformer model building for X-ray crystallography and cryo-EM. eLife 2024; 12:RP90606. [PMID: 38904665 PMCID: PMC11192534 DOI: 10.7554/elife.90606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024] Open
Abstract
In their folded state, biomolecules exchange between multiple conformational states that are crucial for their function. Traditional structural biology methods, such as X-ray crystallography and cryogenic electron microscopy (cryo-EM), produce density maps that are ensemble averages, reflecting molecules in various conformations. Yet, most models derived from these maps explicitly represent only a single conformation, overlooking the complexity of biomolecular structures. To accurately reflect the diversity of biomolecular forms, there is a pressing need to shift toward modeling structural ensembles that mirror the experimental data. However, the challenge of distinguishing signal from noise complicates manual efforts to create these models. In response, we introduce the latest enhancements to qFit, an automated computational strategy designed to incorporate protein conformational heterogeneity into models built into density maps. These algorithmic improvements in qFit are substantiated by superior Rfree and geometry metrics across a wide range of proteins. Importantly, unlike more complex multicopy ensemble models, the multiconformer models produced by qFit can be manually modified in most major model building software (e.g., Coot) and fit can be further improved by refinement using standard pipelines (e.g., Phenix, Refmac, Buster). By reducing the barrier of creating multiconformer models, qFit can foster the development of new hypotheses about the relationship between macromolecular conformational dynamics and function.
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Affiliation(s)
- Stephanie A Wankowicz
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Ashraya Ravikumar
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Shivani Sharma
- Structural Biology Initiative, CUNY Advanced Science Research CenterNew YorkUnited States
- Ph.D. Program in Biology, The Graduate Center, City University of New YorkNew YorkUnited States
| | - Blake Riley
- Structural Biology Initiative, CUNY Advanced Science Research CenterNew YorkUnited States
| | - Akshay Raju
- Structural Biology Initiative, CUNY Advanced Science Research CenterNew YorkUnited States
| | - Daniel W Hogan
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Jessica Flowers
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Henry van den Bedem
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
- Atomwise IncSan FranciscoUnited States
| | - Daniel A Keedy
- Structural Biology Initiative, CUNY Advanced Science Research CenterNew YorkUnited States
- Department of Chemistry and Biochemistry, City College of New YorkNew YorkUnited States
- Ph.D. Programs in Biochemistry, Biology and Chemistry, The Graduate Center, City University of New YorkNew YorkUnited States
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
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3
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Carlino E, Taurino A, Hasa D, Bučar DK, Polentarutti M, Chinchilla LE, Calvino Gamez JJ. Direct Imaging of Radiation-Sensitive Organic Polymer-Based Nanocrystals at Sub-Ångström Resolution. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:872. [PMID: 38786829 DOI: 10.3390/nano14100872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
Seeing the atomic configuration of single organic nanoparticles at a sub-Å spatial resolution by transmission electron microscopy has been so far prevented by the high sensitivity of soft matter to radiation damage. This difficulty is related to the need to irradiate the particle with a total dose of a few electrons/Å2, not compatible with the electron beam density necessary to search the low-contrast nanoparticle, to control its drift, finely adjust the electron-optical conditions and particle orientation, and finally acquire an effective atomic-resolution image. On the other hand, the capability to study individual pristine nanoparticles, such as proteins, active pharmaceutical ingredients, and polymers, with peculiar sensitivity to the variation in the local structure, defects, and strain, would provide advancements in many fields, including materials science, medicine, biology, and pharmacology. Here, we report the direct sub-ångström-resolution imaging at room temperature of pristine unstained crystalline polymer-based nanoparticles. This result is obtained by combining low-dose in-line electron holography and phase-contrast imaging on state-of-the-art equipment, providing an effective tool for the quantitative sub-ångström imaging of soft matter.
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Affiliation(s)
- Elvio Carlino
- Istituto di Cristallografia del Consiglio Nazionale delle Ricerche (IC-CNR), 70126 Bari, Italy
| | - Antonietta Taurino
- Istituto per la Microelettronica e i Microsistemi del Consiglio Nazionale delle Ricerche (IMM-CNR), 73100 Lecce, Italy
| | - Dritan Hasa
- Department of Chemical and Pharmaceutical Sciences University of Trieste, 34127 Trieste, Italy
| | | | | | - Lidia E Chinchilla
- Departamento de Ciencia de los Materiales, Ingeniería Metalúrgica y Química Inorgánica, Facultad de Ciencias, Universidad de Cádiz, 11519 Puerto Real, Cádiz, Spain
| | - Josè J Calvino Gamez
- Departamento de Ciencia de los Materiales, Ingeniería Metalúrgica y Química Inorgánica, Facultad de Ciencias, Universidad de Cádiz, 11519 Puerto Real, Cádiz, Spain
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4
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Wankowicz SA, Ravikumar A, Sharma S, Riley BT, Raju A, Flowers J, Hogan D, van den Bedem H, Keedy DA, Fraser JS. Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.28.546963. [PMID: 37425870 PMCID: PMC10327213 DOI: 10.1101/2023.06.28.546963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
In their folded state, biomolecules exchange between multiple conformational states that are crucial for their function. Traditional structural biology methods, such as X-ray crystallography and cryogenic electron microscopy (cryo-EM), produce density maps that are ensemble averages, reflecting molecules in various conformations. Yet, most models derived from these maps explicitly represent only a single conformation, overlooking the complexity of biomolecular structures. To accurately reflect the diversity of biomolecular forms, there is a pressing need to shift towards modeling structural ensembles that mirror the experimental data. However, the challenge of distinguishing signal from noise complicates manual efforts to create these models. In response, we introduce the latest enhancements to qFit, an automated computational strategy designed to incorporate protein conformational heterogeneity into models built into density maps. These algorithmic improvements in qFit are substantiated by superior R f r e e and geometry metrics across a wide range of proteins. Importantly, unlike more complex multicopy ensemble models, the multiconformer models produced by qFit can be manually modified in most major model building software (e.g. Coot) and fit can be further improved by refinement using standard pipelines (e.g. Phenix, Refmac, Buster). By reducing the barrier of creating multiconformer models, qFit can foster the development of new hypotheses about the relationship between macromolecular conformational dynamics and function.
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Affiliation(s)
- Stephanie A. Wankowicz
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Ashraya Ravikumar
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Shivani Sharma
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Ph.D. Program in Biology, The Graduate Center – City University of New York, New York, NY 10016
| | - Blake T. Riley
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
| | - Akshay Raju
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
| | - Jessica Flowers
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Daniel Hogan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Henry van den Bedem
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Atomwise, Inc., San Francisco, CA, United States
| | - Daniel A. Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031
- Ph.D. Programs in Biochemistry, Biology, and Chemistry, The Graduate Center – City University of New York, New York, NY 10016
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
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5
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Zhao X. Unlocking cryo-EM's multishot potential with square or rectangular beams. Nat Methods 2024; 21:555-557. [PMID: 38485741 DOI: 10.1038/s41592-024-02224-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Affiliation(s)
- Xiaowei Zhao
- Cryo-EM shared resource, Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA.
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6
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Bai XC, Zhang X. Applications of cryo-EM in drug development for STING. Curr Opin Struct Biol 2024; 84:102767. [PMID: 38183862 DOI: 10.1016/j.sbi.2023.102767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 01/08/2024]
Abstract
STING is a critical adaptor protein in the cGAS-mediated DNA-sensing innate immune pathway. Binding of the second messenger cGAMP generated by cGAS to STING induces the high-order oligomerization and activation of the STING dimer. STING is a promising target for diseases associated with the cGAS/STING pathway such as cancer and autoimmune diseases. Recent applications of cryo-EM to STING have led to exciting progress in the understanding of its regulatory mechanism. Cryo-EM structures of STING bound to either cGAMP mimetics or novel small molecule ligands not only revealed the action mechanisms of these ligands but also suggested new ways to modulate the activity of STING for therapeutic purposes. Some of these recent studies are highlighted here.
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Affiliation(s)
- Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Xuewu Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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7
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Zhu J, Zhang Q, Zhang H, Shi Z, Hu M, Bao C. A minority of final stacks yields superior amplitude in single-particle cryo-EM. Nat Commun 2023; 14:7822. [PMID: 38072910 PMCID: PMC10711021 DOI: 10.1038/s41467-023-43555-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Cryogenic electron microscopy (cryo-EM) is widely used to determine near-atomic resolution structures of biological macromolecules. Due to the low signal-to-noise ratio, cryo-EM relies on averaging many images. However, a crucial question in the field of cryo-EM remains unanswered: how close can we get to the minimum number of particles required to reach a specific resolution in practice? The absence of an answer to this question has impeded progress in understanding sample behavior and the performance of sample preparation methods. To address this issue, we develop an iterative particle sorting and/or sieving method called CryoSieve. Extensive experiments demonstrate that CryoSieve outperforms other cryo-EM particle sorting algorithms, revealing that most particles are unnecessary in final stacks. The minority of particles remaining in the final stacks yield superior high-resolution amplitude in reconstructed density maps. For some datasets, the size of the finest subset approaches the theoretical limit.
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Affiliation(s)
- Jianying Zhu
- Yau Mathematical Sciences Center, Tsinghua University, Beijing, China
| | - Qi Zhang
- Key Laboratory of Protein Sciences (Tsinghua University), Ministry of Education, Beijing, China
- School of Life Science, Tsinghua University, Beijing, China
- Beijing Advanced Innovation Center for Structural Biology, Beijing, China
- Beijing Frontier Research Center for Biological Structure, Beijing, China
| | - Hui Zhang
- Qiuzhen College, Tsinghua University, Beijing, China
| | - Zuoqiang Shi
- Yau Mathematical Sciences Center, Tsinghua University, Beijing, China.
- Yanqi Lake Beijing Institute of Mathematical Sciences and Applications, Beijing, China.
| | - Mingxu Hu
- Key Laboratory of Protein Sciences (Tsinghua University), Ministry of Education, Beijing, China.
- School of Life Science, Tsinghua University, Beijing, China.
- Beijing Advanced Innovation Center for Structural Biology, Beijing, China.
- Beijing Frontier Research Center for Biological Structure, Beijing, China.
- Shenzhen Academy of Research and Translation, Shenzhen, China.
| | - Chenglong Bao
- Yau Mathematical Sciences Center, Tsinghua University, Beijing, China.
- Yanqi Lake Beijing Institute of Mathematical Sciences and Applications, Beijing, China.
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, China.
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8
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de la Cruz MJ, Eng ET. Scaling up cryo-EM for biology and chemistry: The journey from niche technology to mainstream method. Structure 2023; 31:1487-1498. [PMID: 37820731 PMCID: PMC10841453 DOI: 10.1016/j.str.2023.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/31/2023] [Accepted: 09/14/2023] [Indexed: 10/13/2023]
Abstract
Cryoelectron microscopy (cryo-EM) methods have made meaningful contributions in a wide variety of scientific research fields. In structural biology, cryo-EM routinely elucidates molecular structure from isolated biological macromolecular complexes or in a cellular context by harnessing the high-resolution power of the electron in order to image samples in a frozen, hydrated environment. For structural chemistry, the cryo-EM method popularly known as microcrystal electron diffraction (MicroED) has facilitated atomic structure generation of peptides and small molecules from their three-dimensional crystal forms. As cryo-EM has grown from an emerging technology, it has undergone modernization to enable multimodal transmission electron microscopy (TEM) techniques becoming more routine, reproducible, and accessible to accelerate research across multiple disciplines. We review recent advances in modern cryo-EM and assess how they are contributing to the future of the field with an eye to the past.
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Affiliation(s)
- M Jason de la Cruz
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Edward T Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA.
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9
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Chari A, Stark H. Prospects and Limitations of High-Resolution Single-Particle Cryo-Electron Microscopy. Annu Rev Biophys 2023; 52:391-411. [PMID: 37159297 DOI: 10.1146/annurev-biophys-111622-091300] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Single particle cryo-electron microscopy (cryo-EM) has matured into a robust method for the determination of biological macromolecule structures in the past decade, complementing X-ray crystallography and nuclear magnetic resonance. Constant methodological improvements in both cryo-EM hardware and image processing software continue to contribute to an exponential growth in the number of structures solved annually. In this review, we provide a historical view of the many steps that were required to make cryo-EM a successful method for the determination of high-resolution protein complex structures. We further discuss aspects of cryo-EM methodology that are the greatest pitfalls challenging successful structure determination to date. Lastly, we highlight and propose potential future developments that would improve the method even further in the near future.
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Affiliation(s)
- Ashwin Chari
- Research Group for Structural Biochemistry and Mechanisms, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany;
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10
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Kumar R. Cryo-EM technique and its application: Structure of steroid hormone receptors. VITAMINS AND HORMONES 2023; 123:385-397. [PMID: 37717991 DOI: 10.1016/bs.vh.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
In recent years, cryo-electron microscopy (cryo-EM) has become one of the most powerful tools to solve the 3-D structure of macromolecules. Unlike X-ray crystallography, the cryo-EM method has advantage of providing an in-depth insight into the dynamic behavior of macromolecules, which is particularly useful to determine 3-D structural analyses of large protein complexes. Due to recent technical advancements, cryo-EM has become the method of choice for the determination of protein structures. Among other proteins, solving 3-D structure of steroid hormone receptors (SHRs) complexed with DNA and coactivators has been a challenge for decades. The limitations with X-ray crystallography and NMR to solve SHR protein structures prompted investigators to move towards cryo-EM technique. The cryo-EM structural analyses have been successful in revealing structural dynamics of several SHRs in recent years. Though, limited by low-resolution, the structural analyses of these SHRs may be useful in understanding many receptor functions as well as provide a platform to refine high-resolution structural analyses in future. This review article discusses the cryo-EM technique in general as well as structural information gained for SHRs using cryo-EM.
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Affiliation(s)
- Raj Kumar
- Department of Pharmaceutical and Biomedical Sciences, Touro College of Pharmacy, New York, NY, United States.
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11
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Lee S, Seok C, Park H. Benchmarking applicability of medium-resolution cryo-EM protein structures for structure-based drug design. J Comput Chem 2023; 44:1360-1368. [PMID: 36847771 DOI: 10.1002/jcc.27091] [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: 10/30/2022] [Revised: 01/18/2023] [Accepted: 02/05/2023] [Indexed: 03/01/2023]
Abstract
Cryo-electron microscopy (cryo-EM) is gaining large attention for high-resolution protein structure determination in solutions. However, a very high percentage of cryo-EM structures correspond to resolutions of 3-5 Å, making the structures difficult to be used in in silico drug design. In this study, we analyze how useful cryo-EM protein structures are for in silico drug design by evaluating ligand docking accuracy. From realistic cross-docking scenarios using medium resolution (3-5 Å) cryo-EM structures and a popular docking tool Autodock-Vina, only 20% of docking succeeded, when the success rate doubles in the same kind of cross-docking but using high-resolution (<2 Å) crystal structures instead. We decipher the reason for failures by decomposing the contribution from resolution-dependent and independent factors. The heterogeneity in the protein side-chain and backbone conformations is identified as the major resolution-dependent factor causing docking difficulty from our analysis, while intrinsic receptor flexibility mainly comprises the resolution-independent factor. We demonstrate the flexibility implementation in current ligand docking tools is able to rescue only a portion of failures (10%), and the limited performance was majorly due to potential structural errors than conformational changes. Our work suggests the strong necessity of more robust method developments on ligand docking and EM modeling techniques in order to fully utilize cryo-EM structures for in silico drug design.
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Affiliation(s)
- Seho Lee
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea.,Galux Inc., Seoul, Republic of Korea
| | - Hahnbeom Park
- Brain Science Institute, Korea Institute of Science and Technology, Seoul, Republic of Korea
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12
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Thorne RE. Determining biomolecular structures near room temperature using X-ray crystallography: concepts, methods and future optimization. Acta Crystallogr D Struct Biol 2023; 79:78-94. [PMID: 36601809 PMCID: PMC9815097 DOI: 10.1107/s2059798322011652] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/04/2022] [Indexed: 01/05/2023] Open
Abstract
For roughly two decades, cryocrystallography has been the overwhelmingly dominant method for determining high-resolution biomolecular structures. Competition from single-particle cryo-electron microscopy and micro-electron diffraction, increased interest in functionally relevant information that may be missing or corrupted in structures determined at cryogenic temperature, and interest in time-resolved studies of the biomolecular response to chemical and optical stimuli have driven renewed interest in data collection at room temperature and, more generally, at temperatures from the protein-solvent glass transition near 200 K to ∼350 K. Fischer has recently reviewed practical methods for room-temperature data collection and analysis [Fischer (2021), Q. Rev. Biophys. 54, e1]. Here, the key advantages and physical principles of, and methods for, crystallographic data collection at noncryogenic temperatures and some factors relevant to interpreting the resulting data are discussed. For room-temperature data collection to realize its potential within the structural biology toolkit, streamlined and standardized methods for delivering crystals prepared in the home laboratory to the synchrotron and for automated handling and data collection, similar to those for cryocrystallography, should be implemented.
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Affiliation(s)
- Robert E. Thorne
- Physics Department, Cornell University, Ithaca, NY 14853, USA
- MiTeGen LLC, PO Box 3867, Ithaca, NY 14850, USA
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13
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Liu N, Wang HW. Better Cryo-EM Specimen Preparation: How to Deal with the Air-Water Interface? J Mol Biol 2022; 435:167926. [PMID: 36563741 DOI: 10.1016/j.jmb.2022.167926] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/08/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
Cryogenic electron microscopy (cryo-EM) is now one of the most powerful and widely used methods to determine high-resolution structures of macromolecules. A major bottleneck of cryo-EM is to prepare high-quality vitrified specimen, which still faces many practical challenges. During the conventional vitrification process, macromolecules tend to adsorb at the air-water interface (AWI), which is known unfriendly to biological samples. In this review, we outline the nature of AWI and the problems caused by it, such as unpredictable or uneven particle distribution, protein denaturation, dissociation of complex and preferential orientation. We review and discuss the approaches and underlying mechanisms to deal with AWI: 1) Additives, exemplified by detergents, forming a protective layer at AWI and thus preserving the native folds of target macromolecules. 2) Fast vitrification devices based on the idea to freeze in-solution macromolecules before their touching of AWI. 3) Thin layer of continuous supporting films to adsorb macromolecules, and when functionalized with affinity ligands, to specifically anchor the target particles away from the AWI. Among these supporting films, graphene, together with its derivatives, with negligible background noise and mechanical robustness, has emerged as a new generation of support. These strategies have been proven successful in various cases and enable us a better handling of the problems caused by the AWI in cryo-EM specimen preparation.
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Affiliation(s)
- Nan Liu
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structures, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structures, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China.
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14
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Gureyev TE, Brown HG, Quiney HM, Allen LJ. Unified fast reconstruction algorithm for conventional, phase-contrast, and diffraction tomography. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2022; 39:C143-C155. [PMID: 36520754 DOI: 10.1364/josaa.468350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
A unified method for three-dimensional reconstruction of objects from transmission images collected at multiple illumination directions is described. The method may be applicable to experimental conditions relevant to absorption-based, phase-contrast, or diffraction imaging using x rays, electrons, and other forms of penetrating radiation or matter waves. Both the phase retrieval (also known as contrast transfer function correction) and the effect of Ewald sphere curvature (in the cases with a shallow depth of field and significant in-object diffraction) are incorporated in the proposed algorithm and can be taken into account. Multiple scattering is not treated explicitly but can be mitigated as a result of angular averaging that constitutes an essential feature of the method. The corresponding numerical algorithm is based on three-dimensional gridding which allows for fast computational implementation, including a straightforward parallelization. The algorithm can be used with any scanning geometry involving plane-wave illumination. A software code implementing the proposed algorithm has been developed, tested on simulated and experimental image data, and made publicly available.
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15
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Wang J, Liu J, Gisriel CJ, Wu S, Maschietto F, Flesher DA, Lolis E, Lisi GP, Brudvig GW, Xiong Y, Batista VS. How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM. J Struct Biol 2022; 214:107902. [PMID: 36202310 DOI: 10.1016/j.jsb.2022.107902] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/23/2022] [Accepted: 09/28/2022] [Indexed: 12/05/2022]
Abstract
The atomic coordinates derived from cryo-electron microscopy (cryo-EM) maps can be inaccurate when the voxel scaling factors are not properly calibrated. Here, we describe a method for correcting relative voxel scaling factors between pairs of cryo-EM maps for the same or similar structures that are expanded or contracted relative to each other. We find that the correction of scaling factors reduces the amplitude differences of Fourier-inverted structure factors from voxel-rescaled maps by up to 20-30%, as shown by two cryo-EM maps of the SARS-CoV-2 spike protein measured at pH 4.0 and pH 8.0. This allows for the calculation of the difference map after properly scaling, revealing differences between the two structures for individual amino acid residues. Unexpectedly, the analysis uncovers two previously overlooked differences of amino acid residues in structures and their local structural changes. Furthermore, we demonstrate the method as applied to two cryo-EM maps of monomeric apo-photosystem II from the cyanobacteria Synechocystis sp. PCC 6803 and Thermosynechococcus elongatus. The resulting difference maps reveal many changes in the peripheral transmembrane PsbX subunit between the two species.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536, USA.
| | - Jinchan Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536, USA
| | | | - Shenping Wu
- Department of Pharmacology, Yale University, New Haven, CT 06520-8066, USA
| | | | - David A Flesher
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536, USA
| | - Elias Lolis
- Department of Pharmacology, Yale University, New Haven, CT 06520-8066, USA
| | - George P Lisi
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Gary W Brudvig
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536, USA; Department of Chemistry, Yale University, New Haven, CT 06511-8499, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT 06511-8499, USA
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16
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Lovatt M, Leistner C, Frank RAW. Bridging length scales from molecules to the whole organism by cryoCLEM and cryoET. Faraday Discuss 2022; 240:114-126. [PMID: 35959706 PMCID: PMC9642002 DOI: 10.1039/d2fd00081d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Resolving atomic structures of isolated proteins has uncovered mechanisms and fundamental processes in biology. However, many functions can only be tested in the context of intact cells and tissues that are many orders of magnitude larger than the macromolecules on which they depend. Therefore, methods that interrogate macromolecular structure in situ provide a means of directly relating structure to function across length scales. Here, we developed several workflows using cryogenic correlated light and electron microscopy (cryoCLEM) and electron tomography (cryoET) that can bridge this gap to reveal the molecular infrastructure that underlies higher order functions within cells and tissues. We also describe experimental design considerations, including cryoCLEM labelling, sample preparation, and quality control, for determining the in situ molecular architectures within native, hydrated cells and tissues.
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Affiliation(s)
- Megan Lovatt
- Astbury Centre of Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of LeedsLS2 9JTUK
| | - Conny Leistner
- Astbury Centre of Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of LeedsLS2 9JTUK
| | - René A. W. Frank
- Astbury Centre of Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of LeedsLS2 9JTUK
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17
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Thangaratnarajah C, Rheinberger J, Paulino C. Cryo-EM studies of membrane proteins at 200 keV. Curr Opin Struct Biol 2022; 76:102440. [PMID: 36029606 DOI: 10.1016/j.sbi.2022.102440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 11/03/2022]
Abstract
Single-particle cryogenic electron-microscopy (cryo-EM) has emerged as a powerful technique for the structural characterisation of membrane proteins, especially for targets previously thought to be intractable. Taking advantage of the latest hard- and software developments, high-resolution three-dimensional (3D) reconstructions of membrane proteins by cryo-EM has become routine, with 300-kV transmission electron microscopes (TEMs) being the current standard. The use of 200-kV cryo-TEMs is gaining increasingly prominence, showing the capabilities of reaching better than 2 Å resolution for soluble proteins and better than 3 Å resolution for membrane proteins. Here, we highlight the challenges working with membrane proteins and the impact of cryo-EM, and review the technical and practical benefits, achievements and limitations of imaging at lower electron acceleration voltages.
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Affiliation(s)
- Chancievan Thangaratnarajah
- University of Groningen, Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy and Membrane Enzymology Group, Nijenborgh 4, 9747 AG, Groningen, Netherlands.
| | - Jan Rheinberger
- University of Groningen, Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy and Membrane Enzymology Group, Nijenborgh 4, 9747 AG, Groningen, Netherlands. https://twitter.com/rheinbergerj
| | - Cristina Paulino
- University of Groningen, Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy and Membrane Enzymology Group, Nijenborgh 4, 9747 AG, Groningen, Netherlands.
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18
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Vilas JL, Carazo JM, Sorzano COS. Emerging Themes in CryoEM─Single Particle Analysis Image Processing. Chem Rev 2022; 122:13915-13951. [PMID: 35785962 PMCID: PMC9479088 DOI: 10.1021/acs.chemrev.1c00850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cryo-electron microscopy (CryoEM) has become a vital technique in structural biology. It is an interdisciplinary field that takes advantage of advances in biochemistry, physics, and image processing, among other disciplines. Innovations in these three basic pillars have contributed to the boosting of CryoEM in the past decade. This work reviews the main contributions in image processing to the current reconstruction workflow of single particle analysis (SPA) by CryoEM. Our review emphasizes the time evolution of the algorithms across the different steps of the workflow differentiating between two groups of approaches: analytical methods and deep learning algorithms. We present an analysis of the current state of the art. Finally, we discuss the emerging problems and challenges still to be addressed in the evolution of CryoEM image processing methods in SPA.
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Affiliation(s)
- Jose Luis Vilas
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - Jose Maria Carazo
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - Carlos Oscar S Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
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19
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Conformational ensemble of the full-length SARS-CoV-2 nucleocapsid (N) protein based on molecular simulations and SAXS data. Biophys Chem 2022; 288:106843. [PMID: 35696898 PMCID: PMC9172258 DOI: 10.1016/j.bpc.2022.106843] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/10/2022] [Accepted: 06/02/2022] [Indexed: 11/02/2022]
Abstract
The nucleocapsid protein of the SARS-CoV-2 virus comprises two RNA-binding domains and three regions that are intrinsically disordered. While the structures of the RNA-binding domains have been solved using protein crystallography and NMR, current knowledge of the conformations of the full-length nucleocapsid protein is rather limited. To fill in this knowledge gap, we combined coarse-grained molecular simulations with data from small-angle X-ray scattering (SAXS) experiments using the ensemble refinement of SAXS (EROS) method. Our results show that the dimer of the full-length nucleocapsid protein exhibits large conformational fluctuations with its radius of gyration ranging from about 4 to 8 nm. The RNA-binding domains do not make direct contacts. The disordered region that links these two domains comprises a hydrophobic α-helix which makes frequent and nonspecific contacts with the RNA-binding domains. Each of the intrinsically disordered regions adopts conformations that are locally compact, yet on average, much more extended than Gaussian chains of equivalent lengths. We offer a detailed picture of the conformational ensemble of the nucleocapsid protein dimer under near-physiological conditions, which will be important for understanding the nucleocapsid assembly process.
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20
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Liu HF, Zhou Y, Bartesaghi A. High-resolution structure determination using high-throughput electron cryo-tomography. Acta Crystallogr D Struct Biol 2022; 78:817-824. [PMID: 35775981 PMCID: PMC9248845 DOI: 10.1107/s2059798322005010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/10/2022] [Indexed: 11/12/2022] Open
Abstract
In this article, it is shown that high-throughput strategies for tomographic data acquisition combined with unsupervised techniques for image analysis provide the foundation for closing the resolution gap between the high-resolution strategies used to study molecular assemblies reconstituted in vitro and techniques for in situ structure determination. Tomographic reconstruction of frozen-hydrated specimens followed by extraction and averaging of sub-tomograms has successfully been used to determine the structure of macromolecules in their native environment at resolutions that are high enough to reveal molecular level interactions. The low throughput characteristic of tomographic data acquisition combined with the complex data-analysis pipeline that is required to obtain high-resolution maps, however, has limited the applicability of this technique to favorable samples or to resolutions that are too low to provide useful mechanistic information. Recently, beam image-shift electron cryo-tomography (BISECT), a strategy to significantly accelerate the acquisition of tilt series without sacrificing image quality, was introduced. The ability to produce thousands of high-quality tilt series during a single microscope session, however, introduces significant bottlenecks in the downstream data analysis, which has so far relied on specialized pipelines. Here, recent advances in accurate estimation of the contrast transfer function and self-tuning exposure-weighting routines that contribute to improving the resolution and streamlining the structure-determination process using sub-volume averaging are reviewed. Ultimately, the combination of automated data-driven techniques for image analysis together with high-throughput strategies for tilt-series acquisition will pave the way for tomography to become the technique of choice for in situ structure determination.
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21
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Gureyev TE, Quiney HM, Allen LJ. Method for virtual optical sectioning and tomography utilizing shallow depth of field. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2022; 39:936-947. [PMID: 36215455 DOI: 10.1364/josaa.455682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/10/2022] [Indexed: 06/16/2023]
Abstract
A method is proposed for high-resolution, three-dimensional reconstruction of internal structures of objects from planar transmission images. The described approach can be used with any form of radiation or matter waves, in principle, provided that the depth of field is smaller than the thickness of the sample. The physical optics basis for the method is elucidated, and the reconstruction algorithm is presented in detail. A simulated example demonstrates an application of the method to three-dimensional electron transmission imaging of a nanoparticle under realistic radiation dose and spatial resolution constraints. It is envisaged that the method can be applicable in high-resolution transmission electron microscopy, soft x-ray microscopy, ultrasound imaging, and other areas.
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22
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Gureyev TE, Paganin DM, Brown HG, Quiney HM, Allen LJ. A Method for High-Resolution Three-Dimensional Reconstruction with Ewald Sphere Curvature Correction from Transmission Electron Images. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-17. [PMID: 35485646 DOI: 10.1017/s1431927622000630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A method for three-dimensional reconstruction of objects from defocused images collected at multiple illumination directions in high-resolution transmission electron microscopy is presented. The method effectively corrects for the Ewald sphere curvature by taking into account the in-particle propagation of the electron beam. Numerical simulations demonstrate that the proposed method is capable of accurately reconstructing biological molecules or nanoparticles from high-resolution defocused images under conditions achievable in single-particle electron cryo-microscopy or electron tomography with realistic radiation doses, non-trivial aberrations, multiple scattering, and other experimentally relevant factors. The physics of the method is based on the well-known Diffraction Tomography formalism, but with the phase-retrieval step modified to include a conjugation of the phase (i.e., multiplication of the phase by a negative constant). At each illumination direction, numerically backpropagating the beam with the conjugated phase produces maximum contrast at the location of individual atoms in the molecule or nanoparticle. The resultant algorithm, Conjugated Holographic Reconstruction, can potentially be incorporated into established software tools for single-particle analysis, such as, for example, RELION or FREALIGN, in place of the conventional contrast transfer function correction procedure, in order to account for the Ewald sphere curvature and improve the spatial resolution of the three-dimensional reconstruction.
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Affiliation(s)
- Timur E Gureyev
- ARC Centre in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Parkville, VIC3010, Australia
- School of Physics and Astronomy, Monash University, Clayton, VIC3800, Australia
| | - David M Paganin
- School of Physics and Astronomy, Monash University, Clayton, VIC3800, Australia
| | - Hamish G Brown
- ARC Centre in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Parkville, VIC3010, Australia
| | - Harry M Quiney
- ARC Centre in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Parkville, VIC3010, Australia
| | - Leslie J Allen
- ARC Centre in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Parkville, VIC3010, Australia
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23
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Ma H, Jia X, Zhang K, Su Z. Cryo-EM advances in RNA structure determination. Signal Transduct Target Ther 2022; 7:58. [PMID: 35197441 PMCID: PMC8864457 DOI: 10.1038/s41392-022-00916-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/27/2022] [Accepted: 01/30/2022] [Indexed: 02/08/2023] Open
Abstract
Cryo-electron microscopy (cryo-EM) has emerged as an unprecedented tool to resolve protein structures at atomic resolution. Structural insights of biological samples not accessible by conventional X-ray crystallography and NMR can be explored with cryo-EM because measurements are carried out under near-native crystal-free conditions, and large protein complexes with conformational and compositional heterogeneity are readily resolved. RNA has remained underexplored in cryo-EM, despite its essential role in various biological processes. This review highlights current challenges and recent progress in using cryo-EM single-particle analysis to determine protein-free RNA structures, enabled by improvement in sample preparation and integration of multiple structural and biochemical methods.
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Affiliation(s)
- Haiyun Ma
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610044, China
| | - Xinyu Jia
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610044, China
| | - Kaiming Zhang
- MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Zhaoming Su
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610044, China.
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24
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Pilsl M, Heiss FB, Pöll G, Höcherl M, Milkereit P, Engel C. Preparation of RNA Polymerase Complexes for Their Analysis by Single-Particle Cryo-Electron Microscopy. Methods Mol Biol 2022; 2533:81-96. [PMID: 35796984 PMCID: PMC9761500 DOI: 10.1007/978-1-0716-2501-9_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Recent technological progress revealed new prospects of high-resolution structure determination of macromolecular complexes using cryo-electron microscopy (cryo-EM) . In the field of RNA polymerase (Pol) I research, a number of cryo-EM studies contributed to understanding the highly specialized mechanisms underlying the transcription of ribosomal RNA genes . Despite a broad applicability of the cryo-EM method itself, preparation of samples for high-resolution data collection can be challenging. Here, we describe strategies for the purification and stabilization of Pol I complexes, exemplarily considering advantages and disadvantages of the methodology. We further provide an easy-to-implement protocol for the coating of EM-grids with self-made carbon support films. In sum, we present an efficient workflow for cryo-grid preparation and optimization, including early stage cryo-EM screening that can be adapted to a wide range of soluble samples for high-resolution structure determination .
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Affiliation(s)
- Michael Pilsl
- Regensburg Center for Biochemistry (RCB), University of Regensburg, Regensburg, Germany
| | - Florian B Heiss
- Regensburg Center for Biochemistry (RCB), University of Regensburg, Regensburg, Germany
| | - Gisela Pöll
- Regensburg Center for Biochemistry (RCB), University of Regensburg, Regensburg, Germany
| | - Mona Höcherl
- Regensburg Center for Biochemistry (RCB), University of Regensburg, Regensburg, Germany
| | - Philipp Milkereit
- Regensburg Center for Biochemistry (RCB), University of Regensburg, Regensburg, Germany
| | - Christoph Engel
- Regensburg Center for Biochemistry (RCB), University of Regensburg, Regensburg, Germany.
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25
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Foster B, Attwood M, Gibbs-Seymour I. Tools for Decoding Ubiquitin Signaling in DNA Repair. Front Cell Dev Biol 2021; 9:760226. [PMID: 34950659 PMCID: PMC8690248 DOI: 10.3389/fcell.2021.760226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/09/2021] [Indexed: 12/21/2022] Open
Abstract
The maintenance of genome stability requires dedicated DNA repair processes and pathways that are essential for the faithful duplication and propagation of chromosomes. These DNA repair mechanisms counteract the potentially deleterious impact of the frequent genotoxic challenges faced by cells from both exogenous and endogenous agents. Intrinsic to these mechanisms, cells have an arsenal of protein factors that can be utilised to promote repair processes in response to DNA lesions. Orchestration of the protein factors within the various cellular DNA repair pathways is performed, in part, by post-translational modifications, such as phosphorylation, ubiquitin, SUMO and other ubiquitin-like modifiers (UBLs). In this review, we firstly explore recent advances in the tools for identifying factors involved in both DNA repair and ubiquitin signaling pathways. We then expand on this by evaluating the growing repertoire of proteomic, biochemical and structural techniques available to further understand the mechanistic basis by which these complex modifications regulate DNA repair. Together, we provide a snapshot of the range of methods now available to investigate and decode how ubiquitin signaling can promote DNA repair and maintain genome stability in mammalian cells.
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Affiliation(s)
| | | | - Ian Gibbs-Seymour
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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26
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Engstrom T, Clinger JA, Spoth KA, Clarke OB, Closs DS, Jayne R, Apker BA, Thorne RE. High-resolution single-particle cryo-EM of samples vitrified in boiling nitro-gen. IUCRJ 2021; 8:867-877. [PMID: 34804541 PMCID: PMC8562666 DOI: 10.1107/s2052252521008095] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/05/2021] [Indexed: 05/24/2023]
Abstract
Based on work by Dubochet and others in the 1980s and 1990s, samples for single-particle cryo-electron microscopy (cryo-EM) have been vitrified using ethane, propane or ethane/propane mixtures. These liquid cryogens have a large difference between their melting and boiling temperatures and so can absorb substantial heat without formation of an insulating vapor layer adjacent to a cooling sample. However, ethane and propane are flammable, they must be liquified in liquid nitro-gen immediately before cryo-EM sample preparation, and cryocooled samples must be transferred to liquid nitro-gen for storage, complicating workflows and increasing the chance of sample damage during handling. Experiments over the last 15 years have shown that cooling rates required to vitrify pure water are only ∼250 000 K s-1, at the low end of earlier estimates, and that the dominant factor that has limited cooling rates of small samples in liquid nitro-gen is sample precooling in cold gas present above the liquid cryogen surface, not the Leidenfrost effect. Using an automated cryocooling instrument developed for cryocrystallography that combines high plunge speeds with efficient removal of cold gas, we show that single-particle cryo-EM samples on commercial grids can be routinely vitrified using only boiling nitro-gen and obtain apoferritin datasets and refined structures with 2.65 Å resolution. The use of liquid nitro-gen as the primary coolant may allow manual and automated workflows to be simplified and may reduce sample stresses that contribute to beam-induced motion.
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Affiliation(s)
| | | | - Katherine A. Spoth
- Cornell Center for Materials Research, Cornell University, Ithaca, NY 14853, USA
| | - Oliver B. Clarke
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
- Department of Anesthesiology, Columbia University, New York, NY 10032, USA
| | | | - Richard Jayne
- MiTeGen, LLC, PO Box 3867, Ithaca, NY 14850-3867, USA
| | | | - Robert E. Thorne
- MiTeGen, LLC, PO Box 3867, Ithaca, NY 14850-3867, USA
- Physics Department, Cornell University, Ithaca, NY 14853, USA
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27
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Ribet SM, Murthy AA, Roth EW, Dos Reis R, Dravid VP. Making the Most of your Electrons: Challenges and Opportunities in Characterizing Hybrid Interfaces with STEM. MATERIALS TODAY (KIDLINGTON, ENGLAND) 2021; 50:100-115. [PMID: 35241968 PMCID: PMC8887695 DOI: 10.1016/j.mattod.2021.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Inspired by the unique architectures composed of hard and soft materials in natural and biological systems, synthetic hybrid structures and associated soft-hard interfaces have recently evoked significant interest. Soft matter is typically dominated by fluctuations even at room temperature, while hard matter (which often serves as the substrate or anchor for the soft component) is governed by rigid mechanical behavior. This dichotomy offers considerable opportunities to leverage the disparate properties offered by these components across a wide spectrum spanning from basic science to engineering insights with significant technological overtones. Such hybrid structures, which include polymer nanocomposites, DNA functionalized nanoparticle superlattices and metal organic frameworks to name a few, have delivered promising insights into the areas of catalysis, environmental remediation, optoelectronics, medicine, and beyond. The interfacial structure between these hard and soft phases exists across a variety of length scales and often strongly influence the functionality of hybrid systems. While scanning/transmission electron microscopy (S/TEM) has proven to be a valuable tool for acquiring intricate molecular and nanoscale details of these interfaces, the unusual nature of hybrid composites presents a suite of challenges that make assessing or establishing the classical structure-property relationships especially difficult. These include challenges associated with preparing electron-transparent samples and obtaining sufficient contrast to resolve the interface between dissimilar materials given the dose sensitivity of soft materials. We discuss each of these challenges and supplement a review of recent developments in the field with additional experimental investigations and simulations to present solutions for attaining a nano or atomic-level understanding of these interfaces. These solutions present a host of opportunities for investigating and understanding the role interfaces play in this unique class of functional materials.
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Affiliation(s)
- Stephanie M Ribet
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL
| | - Akshay A Murthy
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL
- International Institute of Nanotechnology, Northwestern University, Evanston, IL
| | - Eric W Roth
- The NUANCE Center, Northwestern University, Evanston, IL
| | - Roberto Dos Reis
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL
- The NUANCE Center, Northwestern University, Evanston, IL
| | - Vinayak P Dravid
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL
- International Institute of Nanotechnology, Northwestern University, Evanston, IL
- The NUANCE Center, Northwestern University, Evanston, IL
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28
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García-Nafría J, Tate CG. Structure determination of GPCRs: cryo-EM compared with X-ray crystallography. Biochem Soc Trans 2021; 49:2345-2355. [PMID: 34581758 PMCID: PMC8589417 DOI: 10.1042/bst20210431] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 12/19/2022]
Abstract
G protein-coupled receptors (GPCRs) are the largest single family of cell surface receptors encoded by the human genome and they play pivotal roles in co-ordinating cellular systems throughout the human body, making them ideal drug targets. Structural biology has played a key role in defining how receptors are activated and signal through G proteins and β-arrestins. The application of structure-based drug design (SBDD) is now yielding novel compounds targeting GPCRs. There is thus significant interest from both academia and the pharmaceutical industry in the structural biology of GPCRs as currently only about one quarter of human non-odorant receptors have had their structure determined. Initially, all the structures were determined by X-ray crystallography, but recent advances in electron cryo-microscopy (cryo-EM) now make GPCRs tractable targets for single-particle cryo-EM with comparable resolution to X-ray crystallography. So far this year, 78% of the 99 GPCR structures deposited in the PDB (Jan-Jul 2021) were determined by cryo-EM. Cryo-EM has also opened up new possibilities in GPCR structural biology, such as determining structures of GPCRs embedded in a lipid nanodisc and multiple GPCR conformations from a single preparation. However, X-ray crystallography still has a number of advantages, particularly in the speed of determining many structures of the same receptor bound to different ligands, an essential prerequisite for effective SBDD. We will discuss the relative merits of cryo-EM and X-ray crystallography for the structure determination of GPCRs and the future potential of both techniques.
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Affiliation(s)
- Javier García-Nafría
- Institute for Biocomputation and Physics of Complex Systems (BIFI) and Laboratorio de Microscopías Avanzadas (LMA), University of Zaragoza, 50018 Zaragoza, Spain
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29
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Sanbonmatsu K. Getting to the bottom of lncRNA mechanism: structure-function relationships. Mamm Genome 2021; 33:343-353. [PMID: 34642784 PMCID: PMC8509902 DOI: 10.1007/s00335-021-09924-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/28/2021] [Indexed: 12/14/2022]
Abstract
While long non-coding RNAs are known to play key roles in disease and development, relatively few structural studies have been performed for this important class of RNAs. Here, we review functional studies of long non-coding RNAs and expose the need for high-resolution 3-D structural studies, discussing the roles of long non-coding RNAs in the cell and how structure–function relationships might be used to elucidate further understanding. We then describe structural studies of other classes of RNAs using chemical probing, nuclear magnetic resonance, small-angle X-ray scattering, X-ray crystallography, and cryogenic electron microscopy (cryo-EM). Next, we review early structural studies of long non-coding RNAs to date and describe the way forward for the structural biology of long non-coding RNAs in terms of cryo-EM.
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30
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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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31
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Gureyev TE, Quiney HM, Kozlov A, Paganin DM, Schmalz G, Brown HG, Allen LJ. Relative roles of multiple scattering and Fresnel diffraction in the imaging of small molecules using electrons, Part II: Differential Holographic Tomography. Ultramicroscopy 2021; 230:113311. [PMID: 34011462 DOI: 10.1016/j.ultramic.2021.113311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 04/29/2021] [Accepted: 05/02/2021] [Indexed: 11/30/2022]
Abstract
It has been argued that in atomic-resolution transmission electron microscopy (TEM) of sparse weakly scattering structures, such as small biological molecules, multiple electron scattering usually has only a small effect, while the in-molecule Fresnel diffraction can be significant due to the intrinsically shallow depth of focus. These facts suggest that the three-dimensional reconstruction of such structures from defocus image series collected at multiple rotational orientations of a molecule can be effectively performed for each atom separately, using the incoherent first Born approximation. The corresponding reconstruction method, termed here Differential Holographic Tomography, is developed theoretically and demonstrated computationally on several numerical models of biological molecules. It is shown that the method is capable of accurate reconstruction of the locations of atoms in a molecule from TEM data collected at a small number of random orientations of the molecule, with one or more defocus images per orientation. Possible applications to cryogenic electron microscopy and other areas are briefly discussed.
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Affiliation(s)
- T E Gureyev
- ARC Centre in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Parkville 3010, Australia; School of Physics and Astronomy, Monash University, Clayton 3800, Australia; School of Science and Technology, University of New England, Armidale 2351, Australia; Faculty of Health Science, The University of Sydney, Sydney 2006, Australia.
| | - H M Quiney
- ARC Centre in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Parkville 3010, Australia
| | - A Kozlov
- ARC Centre in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Parkville 3010, Australia
| | - D M Paganin
- School of Physics and Astronomy, Monash University, Clayton 3800, Australia
| | - G Schmalz
- School of Science and Technology, University of New England, Armidale 2351, Australia
| | - H G Brown
- ARC Centre in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Parkville 3010, Australia
| | - L J Allen
- ARC Centre in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Parkville 3010, Australia
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32
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Wang X, Alnabati E, Aderinwale TW, Maddhuri Venkata Subramaniya SR, Terashi G, Kihara D. Detecting protein and DNA/RNA structures in cryo-EM maps of intermediate resolution using deep learning. Nat Commun 2021; 12:2302. [PMID: 33863902 PMCID: PMC8052361 DOI: 10.1038/s41467-021-22577-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 03/19/2021] [Indexed: 12/21/2022] Open
Abstract
An increasing number of density maps of macromolecular structures, including proteins and DNA/RNA complexes, have been determined by cryo-electron microscopy (cryo-EM). Although lately maps at a near-atomic resolution are routinely reported, there are still substantial fractions of maps determined at intermediate or low resolutions, where extracting structure information is not trivial. Here, we report a new computational method, Emap2sec+, which identifies DNA or RNA as well as the secondary structures of proteins in cryo-EM maps of 5 to 10 Å resolution. Emap2sec+ employs the deep Residual convolutional neural network. Emap2sec+ assigns structural labels with associated probabilities at each voxel in a cryo-EM map, which will help structure modeling in an EM map. Emap2sec+ showed stable and high assignment accuracy for nucleotides in low resolution maps and improved performance for protein secondary structure assignments than its earlier version when tested on simulated and experimental maps.
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Affiliation(s)
- Xiao Wang
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Eman Alnabati
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Tunde W Aderinwale
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | | | - Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN, USA.
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
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33
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Chiu W, Schmid MF, Pintilie GD, Lawson CL. Evolution of standardization and dissemination of cryo-EM structures and data jointly by the community, PDB, and EMDB. J Biol Chem 2021; 296:100560. [PMID: 33744287 PMCID: PMC8050867 DOI: 10.1016/j.jbc.2021.100560] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/08/2021] [Accepted: 03/16/2021] [Indexed: 01/04/2023] Open
Abstract
Cryogenic electron microscopy (cryo-EM) methods began to be used in the mid-1970s to study thin and periodic arrays of proteins. Following a half-century of development in cryo-specimen preparation, instrumentation, data collection, data processing, and modeling software, cryo-EM has become a routine method for solving structures from large biological assemblies to small biomolecules at near to true atomic resolution. This review explores the critical roles played by the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) in partnership with the community to develop the necessary infrastructure to archive cryo-EM maps and associated models. Public access to cryo-EM structure data has in turn facilitated better understanding of structure–function relationships and advancement of image processing and modeling tool development. The partnership between the global cryo-EM community and PDB and EMDB leadership has synergistically shaped the standards for metadata, one-stop deposition of maps and models, and validation metrics to assess the quality of cryo-EM structures. The advent of cryo-electron tomography (cryo-ET) for in situ molecular cell structures at a broad resolution range and their correlations with other imaging data introduce new data archival challenges in terms of data size and complexity in the years to come.
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Affiliation(s)
- Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, California, USA; Division of CryoEM and Bioimaging, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California, USA.
| | - Michael F Schmid
- Division of CryoEM and Bioimaging, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California, USA
| | - Grigore D Pintilie
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Catherine L Lawson
- Institute for Quantitative Biomedicine and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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34
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Abstract
Cryo-electron microscopy (cryo-EM) has become the technique of choice for structural biology of macromolecular assemblies, after the 'resolution revolution' that has occurred in this field since 2012. With a suitable instrument, an appropriate electron detector and, last but not least, a cooperative sample it is now possible to collect images from which macromolecular structures can be determined to better than 2 Å resolution, where reliable atomic models can be built. By electron tomography and sub-tomogram averaging of cryo-samples, it is also possible to reconstruct subcellular structures to sub-nanometre resolution. This review describes the infrastructure that is needed to achieve this goal. Ideally, a cryo-EM lab will have a dedicated 300 kV electron microscope for data recording and a 200 kV instrument for screening cryo-samples, both with direct electron detectors, and at least one 120 kV EM for negative-stain screening at room temperature. Added to this should be ancillary equipment for specimen preparation, including a light microscope, carbon coater, plasma cleaner, glow discharge unit, a device for fast, robotic sample freezing, liquid nitrogen storage Dewars and a ready supply of clean liquid nitrogen. In practice, of course, the available budget will determine the number and types of microscopes and how elaborate the lab can be. The cryo-EM lab should be designed with adequate space for the electron microscopes and ancillary equipment, and should allow for sufficient storage space. Each electron microscope room should be connected to the image-processing computers by fibre-optic cables for the rapid transfer of large datasets. The cryo-EM lab should be overseen by a facility manager whose responsibilities include the day-to-day tasks to ensure that all microscopes are operating perfectly, organising service and repairs to minimise downtime, and controlling the budget. Large facilities will require additional support staff who help to oversee the operation of the facility and instruct new users.
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35
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Uchański T, Masiulis S, Fischer B, Kalichuk V, López-Sánchez U, Zarkadas E, Weckener M, Sente A, Ward P, Wohlkönig A, Zögg T, Remaut H, Naismith JH, Nury H, Vranken W, Aricescu AR, Pardon E, Steyaert J. Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM. Nat Methods 2021; 18:60-68. [PMID: 33408403 PMCID: PMC7611088 DOI: 10.1038/s41592-020-01001-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 10/22/2020] [Indexed: 01/28/2023]
Abstract
Nanobodies are popular and versatile tools for structural biology. They have a compact single immunoglobulin domain organization, bind target proteins with high affinities while reducing their conformational heterogeneity and stabilize multi-protein complexes. Here we demonstrate that engineered nanobodies can also help overcome two major obstacles that limit the resolution of single-particle cryo-electron microscopy reconstructions: particle size and preferential orientation at the water-air interfaces. We have developed and characterized constructs, termed megabodies, by grafting nanobodies onto selected protein scaffolds to increase their molecular weight while retaining the full antigen-binding specificity and affinity. We show that the megabody design principles are applicable to different scaffold proteins and recognition domains of compatible geometries and are amenable for efficient selection from yeast display libraries. Moreover, we demonstrate that megabodies can be used to obtain three-dimensional reconstructions for membrane proteins that suffer from severe preferential orientation or are otherwise too small to allow accurate particle alignment.
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Affiliation(s)
- Tomasz Uchański
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Simonas Masiulis
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Baptiste Fischer
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Valentina Kalichuk
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Uriel López-Sánchez
- CNRS, Université Grenoble Alpes, CEA, Institut de Biologie Structurale, Grenoble, France
| | - Eleftherios Zarkadas
- CNRS, Université Grenoble Alpes, CEA, Institut de Biologie Structurale, Grenoble, France
| | - Miriam Weckener
- Rosalind Franklin Institute, Rutherford Appleton Laboratory, Didcot, UK
| | - Andrija Sente
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Philip Ward
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Alexandre Wohlkönig
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Thomas Zögg
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Han Remaut
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - James H Naismith
- Rosalind Franklin Institute, Rutherford Appleton Laboratory, Didcot, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Hugues Nury
- CNRS, Université Grenoble Alpes, CEA, Institut de Biologie Structurale, Grenoble, France
| | - Wim Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium
| | - A Radu Aricescu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium.
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.
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36
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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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37
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Malac M, Hettler S, Hayashida M, Kano E, Egerton RF, Beleggia M. Phase plates in the transmission electron microscope: operating principles and applications. Microscopy (Oxf) 2020; 70:75-115. [DOI: 10.1093/jmicro/dfaa070] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/30/2020] [Accepted: 12/11/2020] [Indexed: 01/19/2023] Open
Abstract
Abstract
In this paper, we review the current state of phase plate imaging in a transmission electron microscope. We focus especially on the hole-free phase plate design, also referred to as the Volta phase plate. We discuss the implementation, operating principles and applications of phase plate imaging. We provide an imaging theory that accounts for inelastic scattering in both the sample and in the hole-free phase plate.
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Affiliation(s)
- Marek Malac
- NRC-NANO, National Research Council, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
- Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Simon Hettler
- Laboratorio de Microscopías Avanzadas (LMA), Instituto de Nanociencia y Materiales de Aragon (INMA), Universidad de Zaragoza, Campus Río Ebro, 50018 Zaragoza, España
| | - Misa Hayashida
- NRC-NANO, National Research Council, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
| | - Emi Kano
- Institute of Materials and Systems for Sustainability, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Ray F Egerton
- Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Marco Beleggia
- DTU Nanolab, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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38
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Relative roles of multiple scattering and Fresnel diffraction in the imaging of small molecules using electrons. Ultramicroscopy 2020; 218:113094. [DOI: 10.1016/j.ultramic.2020.113094] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 07/06/2020] [Accepted: 08/09/2020] [Indexed: 11/18/2022]
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39
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Wu M, Lander GC. Present and Emerging Methodologies in Cryo-EM Single-Particle Analysis. Biophys J 2020; 119:1281-1289. [PMID: 32919493 PMCID: PMC7567993 DOI: 10.1016/j.bpj.2020.08.027] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/22/2020] [Accepted: 08/26/2020] [Indexed: 11/25/2022] Open
Abstract
Over the past decade, technical and methodological improvements in cryogenic electron microscopy (cryo-EM) single-particle analysis have enabled routine high-resolution structural analyses of biological macromolecules, resulting in a flood of new molecular insights into protracted biological questions. However, despite the tremendous progress and success of the field in recent years, opportunities for improvement remain in various aspects of the cryo-EM single-particle analysis workflow (e.g., sample preparation, image acquisition and processing, and structure validation). Here, we review recent advances that have contributed to the principal methods in cryo-EM and identify persisting challenges and bottlenecks that will require further methodological and hardware development.
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Affiliation(s)
- Mengyu Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California.
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40
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Ravi RT, Leung MR, Zeev-Ben-Mordehai T. Looking back and looking forward: contributions of electron microscopy to the structural cell biology of gametes and fertilization. Open Biol 2020; 10:200186. [PMID: 32931719 PMCID: PMC7536082 DOI: 10.1098/rsob.200186] [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: 06/26/2020] [Accepted: 08/25/2020] [Indexed: 01/22/2023] Open
Abstract
Mammalian gametes-the sperm and the egg-represent opposite extremes of cellular organization and scale. Studying the ultrastructure of gametes is crucial to understanding their interactions, and how to manipulate them in order to either encourage or prevent their union. Here, we survey the prominent electron microscopy (EM) techniques, with an emphasis on considerations for applying them to study mammalian gametes. We review how conventional EM has provided significant insight into gamete ultrastructure, but also how the harsh sample preparation methods required preclude understanding at a truly molecular level. We present recent advancements in cryo-electron tomography that provide an opportunity to image cells in a near-native state and at unprecedented levels of detail. New and emerging cellular EM techniques are poised to rekindle exploration of fundamental questions in mammalian reproduction, especially phenomena that involve complex membrane remodelling and protein reorganization. These methods will also allow novel lines of enquiry into problems of practical significance, such as investigating unexplained causes of human infertility and improving assisted reproductive technologies for biodiversity conservation.
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Affiliation(s)
- Ravi Teja Ravi
- Cryo-Electron Microscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Miguel Ricardo Leung
- Cryo-Electron Microscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584CH Utrecht, The Netherlands
- Division of Structural Biology, Wellcome Centre for Human Genetics, The University of Oxford, Oxford OX3 7BN, UK
| | - Tzviya Zeev-Ben-Mordehai
- Cryo-Electron Microscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584CH Utrecht, The Netherlands
- Division of Structural Biology, Wellcome Centre for Human Genetics, The University of Oxford, Oxford OX3 7BN, UK
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41
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Mitochondrial F-ATP synthase as the permeability transition pore. Pharmacol Res 2020; 160:105081. [PMID: 32679179 DOI: 10.1016/j.phrs.2020.105081] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 07/06/2020] [Accepted: 07/10/2020] [Indexed: 12/27/2022]
Abstract
The current state of research on the mitochondrial permeability transition pore (PTP) can be described in terms of three major problems: molecular identity, atomic structure and gating mechanism. In this review these three problems are discussed in the light of recent findings with special emphasis on the discovery that the PTP is mitochondrial F-ATP synthase (mtFoF1). Novel features of the mitochondrial F-ATP synthase emerging from the success of single particle cryo electron microscopy (cryo-EM) to determine F-ATP synthase structures are surveyed along with their possible involvement in pore formation. Also, current findings from the gap junction field concerning the involvement of lipids in channel closure are examined. Finally, an earlier proposal denoted as the 'Death Finger' is discussed as a working model for PTP gating.
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42
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Abstract
Single-particle electron cryomicroscopy (cryo-EM) is an increasingly popular technique for elucidating the three-dimensional structure of proteins and other biologically significant complexes at near-atomic resolution. It is an imaging method that does not require crystallization and can capture molecules in their native states. In single-particle cryo-EM, the three-dimensional molecular structure needs to be determined from many noisy two-dimensional tomographic projections of individual molecules, whose orientations and positions are unknown. The high level of noise and the unknown pose parameters are two key elements that make reconstruction a challenging computational problem. Even more challenging is the inference of structural variability and flexible motions when the individual molecules being imaged are in different conformational states. This review discusses computational methods for structure determination by single-particle cryo-EM and their guiding principles from statistical inference, machine learning, and signal processing that also play a significant role in many other data science applications.
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Affiliation(s)
- Amit Singer
- Department of Mathematics and Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ 08544, USA
| | - Fred J Sigworth
- Departments of Cellular and Molecular Physiology, Biomedical Engineering, and Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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43
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Dokholyan NV. Experimentally-driven protein structure modeling. J Proteomics 2020; 220:103777. [PMID: 32268219 PMCID: PMC7214187 DOI: 10.1016/j.jprot.2020.103777] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/17/2020] [Accepted: 04/02/2020] [Indexed: 11/25/2022]
Abstract
Revolutions in natural and exact sciences started at the dawn of last century have led to the explosion of theoretical, experimental, and computational approaches to determine structures of molecules, complexes, as well as their rich conformational dynamics. Since different experimental methods produce information that is attributed to specific time and length scales, corresponding computational methods have to be tailored to these scales and experiments. These methods can be then combined and integrated in scales, hence producing a fuller picture of molecular structure and motion from the "puzzle pieces" offered by various experiments. Here, we describe a number of computational approaches to utilize experimental data to glance into structure of proteins and understand their dynamics. We will also discuss the limitations and the resolution of the constraints-based modeling approaches. SIGNIFICANCE: Experimentally-driven computational structure modeling and determination is a rapidly evolving alternative to traditional approaches for molecular structure determination. These new hybrid experimental-computational approaches are proving to be a powerful microscope to glance into the structural features of intrinsically or partially disordered proteins, dynamics of molecules and complexes. In this review, we describe various approaches in the field of experimentally-driven computational structure modeling.
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Affiliation(s)
- Nikolay V Dokholyan
- Department of Pharmacology, Penn State University College of Medicine, Hershey, PA 17033, USA; Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA.; Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.; Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
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44
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Danev R, Iijima H, Matsuzaki M, Motoki S. Fast and accurate defocus modulation for improved tunability of cryo-EM experiments. IUCRJ 2020; 7:566-574. [PMID: 32431839 PMCID: PMC7201282 DOI: 10.1107/s205225252000408x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/24/2020] [Indexed: 05/31/2023]
Abstract
Current data collection strategies in electron cryo-microscopy (cryo-EM) record multiframe movies with static optical settings. This limits the number of adjustable parameters that can be used to optimize the experiment. Here, a method for fast and accurate defocus (FADE) modulation during movie acquisition is proposed. It uses the objective lens aperture as an electrostatic pole that locally modifies the electron beam potential. The beam potential variation is converted to defocus change by the typically undesired chromatic aberration of the objective lens. The simplicity, electrostatic principle and low electrical impedance of the device allow fast switching speeds that will enable per-frame defocus modulation of cryo-EM movies. Researchers will be able to define custom defocus 'recipes' and tailor the experiment for optimal information extraction from the sample. The FADE method could help to convert the microscope into a more dynamic and flexible optical platform that delivers better performance in cryo-EM single-particle analysis and electron cryo-tomography.
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Affiliation(s)
- Radostin Danev
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Tokyo 113-0033, Japan
| | - Hirofumi Iijima
- JEOL Ltd, 1-2 Musashino 3-Chome, Akishima, Tokyo 196-8558, Japan
| | - Mizuki Matsuzaki
- JEOL Ltd, 1-2 Musashino 3-Chome, Akishima, Tokyo 196-8558, Japan
| | - Sohei Motoki
- JEOL Ltd, 1-2 Musashino 3-Chome, Akishima, Tokyo 196-8558, Japan
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45
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Akbar S, Mozumder S, Sengupta J. Retrospect and Prospect of Single Particle Cryo-Electron Microscopy: The Class of Integral Membrane Proteins as an Example. J Chem Inf Model 2020; 60:2448-2457. [DOI: 10.1021/acs.jcim.9b01015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shirin Akbar
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Sukanya Mozumder
- 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
| | - 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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46
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Randolph PS, Stagg SM. Reconstruction of Average Subtracted Tubular Regions (RASTR) enables structure determination of tubular filaments by cryo-EM. JOURNAL OF STRUCTURAL BIOLOGY-X 2020; 4:100023. [PMID: 32647826 PMCID: PMC7337063 DOI: 10.1016/j.yjsbx.2020.100023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 02/14/2020] [Accepted: 03/04/2020] [Indexed: 01/17/2023]
Abstract
Tubules (filaments, membrane tubules, etc) that stray from perfect symmetry or have decorations can be difficult to process. New method Reconstruction of Average Subtracted Tubular Regions (RASTR), provides a way to isolate small areas of tubular architecture. Upweighted and masked areas can be treated as single particles and the structure can be resolved using conventional refinement. Successfully reconstructed protein filaments and membrane tubule decorations.
As the field of electron microscopy advances, the increasing complexity of samples being produced demand more involved processing methods. In this study, we have developed a new processing method for generating 3D reconstructions of tubular structures. Tubular biomolecules are common throughout many cellular processes and are appealing targets for biophysical research. Processing of tubules with helical symmetry is relatively straightforward for electron microscopy if the helical parameters are known, but tubular structures that deviate from helical symmetry (asymmetrical components, local but no global order, etc) present myriad issues. Here we present a new processing technique called Reconstruction of Average Subtracted Tubular Regions (RASTR), which was developed to reconstruct tubular structures without applying symmetry. We explain the RASTR approach and quantify its performance using three examples: a simulated symmetrical tubular filament, a symmetrical tubular filament from cryo-EM data, and a membrane tubule coated with locally ordered but not globally ordered proteins.
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Affiliation(s)
- Peter S Randolph
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Scott M Stagg
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.,Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
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47
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Cianfrocco MA, Kellogg EH. What Could Go Wrong? A Practical Guide to Single-Particle Cryo-EM: From Biochemistry to Atomic Models. J Chem Inf Model 2020; 60:2458-2469. [PMID: 32078321 DOI: 10.1021/acs.jcim.9b01178] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cryo-electron microscopy (cryo-EM) has enjoyed explosive recent growth due to revolutionary advances in hardware and software, resulting in a steady stream of long-awaited, high-resolution structures with unprecedented atomic detail. With this comes an increased number of microscopes, cryo-EM facilities, and scientists eager to leverage the ability to determine protein structures without crystallization. However, numerous pitfalls and considerations beset the path toward high-resolution structures and are not necessarily obvious from literature surveys. Here, we detail the most common misconceptions when initiating a cryo-EM project and common technical hurdles, as well as their solutions, and we conclude with a vision for the future of this exciting field.
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Affiliation(s)
- Michael A Cianfrocco
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Elizabeth H Kellogg
- Department of Molecular Biology and Genetics,Cornell University, Ithaca, New York 14850, United States
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48
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Bücker R, Hogan-Lamarre P, Mehrabi P, Schulz EC, Bultema LA, Gevorkov Y, Brehm W, Yefanov O, Oberthür D, Kassier GH, Dwayne Miller RJ. Serial protein crystallography in an electron microscope. Nat Commun 2020; 11:996. [PMID: 32081905 PMCID: PMC7035385 DOI: 10.1038/s41467-020-14793-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/27/2020] [Indexed: 12/16/2022] Open
Abstract
Serial X-ray crystallography at free-electron lasers allows to solve biomolecular structures from sub-micron-sized crystals. However, beam time at these facilities is scarce, and involved sample delivery techniques are required. On the other hand, rotation electron diffraction (MicroED) has shown great potential as an alternative means for protein nano-crystallography. Here, we present a method for serial electron diffraction of protein nanocrystals combining the benefits of both approaches. In a scanning transmission electron microscope, crystals randomly dispersed on a sample grid are automatically mapped, and a diffraction pattern at fixed orientation is recorded from each at a high acquisition rate. Dose fractionation ensures minimal radiation damage effects. We demonstrate the method by solving the structure of granulovirus occlusion bodies and lysozyme to resolutions of 1.55 Å and 1.80 Å, respectively. Our method promises to provide rapid structure determination for many classes of materials with minimal sample consumption, using readily available instrumentation.
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Affiliation(s)
- Robert Bücker
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Pascal Hogan-Lamarre
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Pedram Mehrabi
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Eike C Schulz
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Lindsey A Bultema
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Yaroslav Gevorkov
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Institute of Vision Systems, Hamburg University of Technology, Harburger Schlossstrasse 20, 21079, Hamburg, Germany
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Günther H Kassier
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - R J Dwayne Miller
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany.
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada.
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49
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Yeates TO, Agdanowski MP, Liu Y. Development of imaging scaffolds for cryo-electron microscopy. Curr Opin Struct Biol 2020; 60:142-149. [PMID: 32066085 DOI: 10.1016/j.sbi.2020.01.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 12/14/2022]
Abstract
Following recent hardware and software developments, single particle cryo-electron microscopy (cryo-EM) has become one of the most popular structural biology tools. Many targets, such as viruses, large protein complexes and oligomeric membrane proteins, have been resolved to atomic resolution using single-particle cryo-EM, which relies on the accurate assignment of particle location and orientation from intrinsically noisy projection images. The same image processing procedures are more challenging for smaller proteins due to their lower signal-to-noise ratios. Consequently, though most cellular proteins are less than 50kDa, so far it has been possible to solve cryo-EM structures near that size range for only a few favorable cases. Here we highlight some of the challenges and recent efforts to break through this lower size limit by engineering large scaffolds to rigidly display multiple small proteins for imaging. Future design efforts are noted.
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Affiliation(s)
- Todd O Yeates
- UCLA Department of Chemistry and Biochemistry, United States; UCLA-DOE Institute for Genomics and Proteomics, United States; UCLA Molecular Biology Institute, United States.
| | | | - Yuxi Liu
- UCLA Department of Chemistry and Biochemistry, United States; UCLA Molecular Biology Institute, United States
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Alnabati E, Kihara D. Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps. Molecules 2019; 25:molecules25010082. [PMID: 31878333 PMCID: PMC6982917 DOI: 10.3390/molecules25010082] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 12/20/2019] [Accepted: 12/20/2019] [Indexed: 01/16/2023] Open
Abstract
Cryo-electron microscopy (cryo-EM) has now become a widely used technique for structure determination of macromolecular complexes. For modeling molecular structures from density maps of different resolutions, many algorithms have been developed. These algorithms can be categorized into rigid fitting, flexible fitting, and de novo modeling methods. It is also observed that machine learning (ML) techniques have been increasingly applied following the rapid progress of the ML field. Here, we review these different categories of macromolecule structure modeling methods and discuss their advances over time.
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Affiliation(s)
- Eman Alnabati
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
- Correspondence:
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