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Jonaid GM, Casasanta MA, Dearnaley WJ, Berry S, Kaylor L, Dressel-Dukes MJ, Spilman MS, Gray JL, Kelly DF. Automated Tools to Advance High-Resolution Imaging in Liquid. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-10. [PMID: 35048845 DOI: 10.1017/s1431927621013921] [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
Liquid-electron microscopy (EM), the room-temperature correlate to cryo-EM, is a rapidly growing field providing high-resolution insights of macromolecules in solution. Here, we describe how liquid-EM experiments can incorporate automated tools to propel the field to new heights. We demonstrate fresh workflows for specimen preparation, data collection, and computing processes to assess biological structures in liquid. Adeno-associated virus (AAV) and the SARS-CoV-2 nucleocapsid (N) were used as model systems to highlight the technical advances. These complexes were selected based on their major differences in size and natural symmetry. AAV is a highly symmetric, icosahedral assembly with a particle diameter of ~25 nm. At the other end of the spectrum, N protein is an asymmetric monomer or dimer with dimensions of approximately 5–7 nm, depending upon its oligomerization state. Equally important, both AAV and N protein are popular subjects in biomedical research due to their high value in vaccine development and therapeutic efforts against COVID-19. Overall, we demonstrate how automated practices in liquid-EM can be used to decode molecules of interest for human health and disease.
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Affiliation(s)
- G M Jonaid
- Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA16802, USA
| | - Michael A Casasanta
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA16802, USA
| | - William J Dearnaley
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA16802, USA
| | - Samantha Berry
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA16802, USA
| | - Liam Kaylor
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA16802, USA
- Molecular, Cellular, and Integrative Biosciences Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA16802, USA
| | | | | | - Jennifer L Gray
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
| | - Deborah F Kelly
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA16802, USA
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2
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Simpkin AJ, Winn MD, Rigden DJ, Keegan RM. Redeployment of automated MrBUMP search-model identification for map fitting in cryo-EM. Acta Crystallogr D Struct Biol 2021; 77:1378-1385. [PMID: 34726166 PMCID: PMC8561737 DOI: 10.1107/s2059798321009165] [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: 04/07/2021] [Accepted: 09/03/2021] [Indexed: 11/22/2022] Open
Abstract
In crystallography, the phase problem can often be addressed by the careful preparation of molecular-replacement search models. This has led to the development of pipelines such as MrBUMP that can automatically identify homologous proteins from an input sequence and edit them to focus on the areas that are most conserved. Many of these approaches can be applied directly to cryo-EM to help discover, prepare and correctly place models (here called cryo-EM search models) into electrostatic potential maps. This can significantly reduce the amount of manual model building that is required for structure determination. Here, MrBUMP is repurposed to fit automatically obtained PDB-derived chains and domains into cryo-EM maps. MrBUMP was successfully able to identify and place cryo-EM search models across a range of resolutions. Methods such as map segmentation are also explored as potential routes to improved performance. Map segmentation was also found to improve the effectiveness of the pipeline for higher resolution (<8 Å) data sets.
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Affiliation(s)
- Adam J. Simpkin
- Institute of Structural, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Martyn D. Winn
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Daniel J. Rigden
- Institute of Structural, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Ronan M. Keegan
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
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3
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Casasanta MA, Jonaid GM, Kaylor L, Luqiu WY, Solares MJ, Schroen ML, Dearnaley WJ, Wilson J, Dukes MJ, Kelly DF. Microchip-based structure determination of low-molecular weight proteins using cryo-electron microscopy. NANOSCALE 2021; 13:7285-7293. [PMID: 33889923 PMCID: PMC8135184 DOI: 10.1039/d1nr00388g] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Interest in cryo-Electron Microscopy (EM) imaging has skyrocketed in recent years due to its pristine views of macromolecules and materials. As advances in instrumentation and computing algorithms spurred this progress, there is renewed focus to address specimen-related challenges. Here we contribute a microchip-based toolkit to perform complementary structural and biochemical analysis on low-molecular weight proteins. As a model system, we used the SARS-CoV-2 nucleocapsid (N) protein (48 kDa) due to its stability and important role in therapeutic development. Cryo-EM structures of the N protein monomer revealed a flexible N-terminal "top hat" motif and a helical-rich C-terminal domain. To complement our structural findings, we engineered microchip-based immunoprecipitation assays that led to the discovery of the first antibody binding site on the N protein. The data also facilitated molecular modeling of a variety of pandemic and common cold-related coronavirus proteins. Such insights may guide future pandemic-preparedness protocols through immuno-engineering strategies to mitigate viral outbreaks.
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Affiliation(s)
- Michael A Casasanta
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
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4
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Solares MJ, Jonaid GM, Luqiu WY, Liang Y, Evans MC, Dearnaley WJ, Sheng Z, Kelly DF. Microchip-Based Structure Determination of Disease-Relevant p53. Anal Chem 2020; 92:15558-15564. [PMID: 33124814 PMCID: PMC7816086 DOI: 10.1021/acs.analchem.0c03599] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The tumor suppressor protein TP53 (p53) plays a multifaceted role in all cells of the human body. Mutations in the TP53 gene are often involved in cancer induction and disease progression. Despite its important role in health and development, structural information for p53 remains incomplete. Here, we present a microchip-based technology to facilitate structural studies of p53 assemblies derived from human cancer cells. These devices do not introduce foreign sequences to the p53 gene and maintain naturally occurring post-translational modifications. Using cryo-electron microscopy, structures for the p53 monomer (∼50 kDa) and tetramer (∼200 kDa) were resolved to ∼4.8 and ∼7 Å, respectively. These structures revealed new insights for flexible regions of p53 along with biologically relevant ubiquitination sites. Collectively, the convergence of nanotechnology tools and structural imaging builds a strong framework to understand the oncogenic impact of p53 in human tissues.
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Affiliation(s)
- Maria J Solares
- Molecular, Cellular, and Integrative Biosciences Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for Structural Oncology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - G M Jonaid
- Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for Structural Oncology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - William Y Luqiu
- Center for Structural Oncology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Electrical and Computer Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Yanping Liang
- Fralin Biomedical Research Institute at VTC, Roanoke, Virginia 24016, United States
| | - Madison C Evans
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - William J Dearnaley
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for Structural Oncology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Zhi Sheng
- Fralin Biomedical Research Institute at VTC, Roanoke, Virginia 24016, United States
| | - Deborah F Kelly
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for Structural Oncology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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5
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Penczek PA. Reliable cryo-EM resolution estimation with modified Fourier shell correlation. IUCRJ 2020; 7:995-1008. [PMID: 33209314 PMCID: PMC7642792 DOI: 10.1107/s2052252520011574] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/24/2020] [Indexed: 06/11/2023]
Abstract
A modified Fourier shell correlation (mFSC) methodology is introduced that is aimed at addressing two fundamental problems that mar the use of the FSC: the strong influence of mask-induced artifacts on resolution estimation and the lack of assessment of FSC uncertainties stemming from the inability to determine the associated number of degrees of freedom. It is shown that by simply changing the order of the steps in which the FSC is computed, the correlations induced by masking of the input data can be eliminated. In addition, to further reduce artifacts, a smooth Gaussian window function is used to outline the regions of reciprocal space within which the mFSC is computed. Next, it is shown that the number of degrees of freedom (ndf) of the system is approximated well by combining the ndf associated with the Gaussian window in reciprocal space with further reduction of the ndf owing to the use of the mask in real space. It is demonstrated through the application of the mFSC to both single-particle and helical structures that the mFSC yields reliable, mask-induced artifact-free results as a result of the introduced modifications. Since the adverse effect of the mask is eliminated, it also becomes possible to compute robust local resolutions both per voxel of a 3D map as well as, in a newly developed approach, per functional subunit, segment or even larger secondary element of the studied complex.
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Affiliation(s)
- Pawel A. Penczek
- Department of Biochemistry and Molecular Biology, The University of Texas – Houston Medical Center, 6431 Fannin Street, Houston, TX 77030, USA
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6
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Lü Y, Zeng X, Tian X, Shi X, Wang H, Zheng X, Liu X, Zhao X, Gao X, Xu M. Spark-based parallel calculation of 3D fourier shell correlation for macromolecule structure local resolution estimation. BMC Bioinformatics 2020; 21:391. [PMID: 32938398 PMCID: PMC7495889 DOI: 10.1186/s12859-020-03680-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Background Resolution estimation is the main evaluation criteria for the reconstruction of macromolecular 3D structure in the field of cryoelectron microscopy (cryo-EM). At present, there are many methods to evaluate the 3D resolution for reconstructed macromolecular structures from Single Particle Analysis (SPA) in cryo-EM and subtomogram averaging (SA) in electron cryotomography (cryo-ET). As global methods, they measure the resolution of the structure as a whole, but they are inaccurate in detecting subtle local changes of reconstruction. In order to detect the subtle changes of reconstruction of SPA and SA, a few local resolution methods are proposed. The mainstream local resolution evaluation methods are based on local Fourier shell correlation (FSC), which is computationally intensive. However, the existing resolution evaluation methods are based on multi-threading implementation on a single computer with very poor scalability. Results This paper proposes a new fine-grained 3D array partition method by key-value format in Spark. Our method first converts 3D images to key-value data (K-V). Then the K-V data is used for 3D array partitioning and data exchange in parallel. So Spark-based distributed parallel computing framework can solve the above scalability problem. In this distributed computing framework, all 3D local FSC tasks are simultaneously calculated across multiple nodes in a computer cluster. Through the calculation of experimental data, 3D local resolution evaluation algorithm based on Spark fine-grained 3D array partition has a magnitude change in computing speed compared with the mainstream FSC algorithm under the condition that the accuracy remains unchanged, and has better fault tolerance and scalability. Conclusions In this paper, we proposed a K-V format based fine-grained 3D array partition method in Spark to parallel calculating 3D FSC for getting a 3D local resolution density map. 3D local resolution density map evaluates the three-dimensional density maps reconstructed from single particle analysis and subtomogram averaging. Our proposed method can significantly increase the speed of the 3D local resolution evaluation, which is important for the efficient detection of subtle variations among reconstructed macromolecular structures.
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Affiliation(s)
- Yongchun Lü
- Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
| | - Xiangrui Zeng
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, USA
| | - Xinhui Tian
- Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China
| | - Xiao Shi
- Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China
| | - Hui Wang
- Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China
| | - Xiaohui Zheng
- Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaodong Liu
- Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China
| | - Xiaofang Zhao
- Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia
| | - Min Xu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, USA.
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7
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Abstract
A density-modification procedure for improving maps from single-particle electron cryogenic microscopy (cryo-EM) is presented. The theoretical basis of the method is identical to that of maximum-likelihood density modification, previously used to improve maps from macromolecular X-ray crystallography. Key differences from applications in crystallography are that the errors in Fourier coefficients are largely in the phases in crystallography but in both phases and amplitudes in cryo-EM, and that half-maps with independent errors are available in cryo-EM. These differences lead to a distinct approach for combination of information from starting maps with information obtained in the density-modification process. The density-modification procedure was applied to a set of 104 datasets and improved map-model correlation and increased the visibility of details in many of the maps. The procedure requires two unmasked half-maps and a sequence file or other source of information on the volume of the macromolecule that has been imaged.
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8
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Hughes TE, Del Rosario JS, Kapoor A, Yazici AT, Yudin Y, Fluck EC, Filizola M, Rohacs T, Moiseenkova-Bell VY. Structure-based characterization of novel TRPV5 inhibitors. eLife 2019; 8:49572. [PMID: 31647410 PMCID: PMC6834369 DOI: 10.7554/elife.49572] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 10/23/2019] [Indexed: 12/31/2022] Open
Abstract
Transient receptor potential vanilloid 5 (TRPV5) is a highly calcium selective ion channel that acts as the rate-limiting step of calcium reabsorption in the kidney. The lack of potent, specific modulators of TRPV5 has limited the ability to probe the contribution of TRPV5 in disease phenotypes such as hypercalcemia and nephrolithiasis. Here, we performed structure-based virtual screening (SBVS) at a previously identified TRPV5 inhibitor binding site coupled with electrophysiology screening and identified three novel inhibitors of TRPV5, one of which exhibits high affinity, and specificity for TRPV5 over other TRP channels, including its close homologue TRPV6. Cryo-electron microscopy of TRPV5 in the presence of the specific inhibitor and its parent compound revealed novel binding sites for this channel. Structural and functional analysis have allowed us to suggest a mechanism of action for the selective inhibition of TRPV5 and lay the groundwork for rational design of new classes of TRPV5 modulators.
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Affiliation(s)
- Taylor Et Hughes
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - John Smith Del Rosario
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, United States
| | - Abhijeet Kapoor
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Aysenur Torun Yazici
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, United States
| | - Yevgen Yudin
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, United States
| | - Edwin C Fluck
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Tibor Rohacs
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, United States
| | - Vera Y Moiseenkova-Bell
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
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Chen L, He J. A Histogram-based Outlier Profile for Atomic Structures Derived from Cryo-Electron Microscopy. ACM-BCB ... ... : THE ... ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE. ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE 2019; 2019:586-591. [PMID: 35838364 PMCID: PMC9279010 DOI: 10.1145/3307339.3343865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
As more atomic structures are determined from cryo-electron microscopy (cryo-EM) density maps, validation of such structures is an important task. We report findings after analyzing the change of cryo-EM structures in a comparison between those released by December 2016 and those released between 2017 and 2019. The cryo-EM models created from density maps with resolution better than 6 Å were divided into six data sets. A histogram-based outlier score (HBOS) was implemented and validation reports were collected from the Protein Data Bank. The results suggest that the overall quality of EM structures released after December 2016 is better than that of structures released before 2017. The conformation qualities of most residue types might have been improved, except for Leucine, Phenylalanine, and Serine in high-resolution datasets (higher than 4 Å). We observe that structures solved from 0-4 Å resolution density maps have an almost identical HBOS profile as that of structures derived from density maps with 4-6 Å resolution.
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Affiliation(s)
| | - Jing He
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529
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10
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Chen L, Baker B, Santos E, Sheep M, Daftarian D. A Visualization Tool for Cryo-EM Protein Validation with an Unsupervised Machine Learning Model in Chimera Platform. MEDICINES (BASEL, SWITZERLAND) 2019; 6:E86. [PMID: 31390767 PMCID: PMC6789601 DOI: 10.3390/medicines6030086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 11/22/2022]
Abstract
Background: Cryo-electron microscopy (cryo-EM) has become a major technique for protein structure determination. However, due to the low quality of cryo-EM density maps, many protein structures derived from cryo-EM contain outliers introduced during the modeling process. The current protein model validation system lacks identification features for cryo-EM proteins making it not enough to identify outliers in cryo-EM proteins. Methods: This study introduces an efficient unsupervised outlier detection model for validating protein models built from cryo-EM technique. The current model uses a high-resolution X-ray dataset (<1.5 Å) as the reference dataset. The distal block distance, side-chain length, phi, psi, and first chi angle of the residues in the reference dataset are collected and saved as a database of the histogram-based outlier score (HBOS). The HBOS value of the residues in target cryo-EM proteins can be read from this HBOS database. Results: Protein residues with a HBOS value greater than ten are labeled as outliers by default. Four datasets containing proteins derived from cryo-EM density maps were tested with this probabilistic anomaly detection model. Conclusions: According to the proposed model, a visualization assistant tool was designed for Chimera, a protein visualization platform.
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Affiliation(s)
- Lin Chen
- Department of Computer Science, Valdosta State University, Valdosta, GA 31693, USA.
| | - Brandon Baker
- Department of Natural Science, Elizabeth City State University, Elizabeth City, NC 27909, USA
| | - Eduardo Santos
- Department of Natural Science, Elizabeth City State University, Elizabeth City, NC 27909, USA
| | - Michell Sheep
- Department of Mathematics & Computer Science, Elizabeth City State University, Elizabeth City, NC 27909, USA
| | - Darius Daftarian
- Department of Mathematics & Computer Science, Elizabeth City State University, Elizabeth City, NC 27909, USA
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11
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Hauser M, Dearnaley WJ, Varano AC, Casasanta M, McDonald SM, Kelly DF. Cryo-EM Reveals Architectural Diversity in Active Rotavirus Particles. Comput Struct Biotechnol J 2019; 17:1178-1183. [PMID: 31467657 PMCID: PMC6710475 DOI: 10.1016/j.csbj.2019.07.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/26/2019] [Accepted: 07/27/2019] [Indexed: 12/04/2022] Open
Abstract
Rotavirus is a well-studied RNA virus that causes severe gastroenteritis in children. During viral entry, the outer layer of the virion is shed, creating a double-layered particle (DLP) that is competent to perform viral transcription (i.e., mRNA synthesis) and launch infection. While inactive forms of rotavirus DLPs have been structurally characterized in detail, information about the transcriptionally-active DLP remains limited. Here, we used cryo-Electron Microscopy (cryo-EM) and 3D image reconstructions to compare the structures of internal protein components in transcriptionally-active versus inactive DLPs. Our findings showed that transcriptionally-active DLPs gained internal order as mRNA synthesis unfolded, while inactive DLPs remained dynamically disordered. Regions of viral protein/RNA constituents were analyzed across two different axes of symmetry to provide a more comprehensive view of moving components. Taken together, our results bring forth a new view of active DLPs, which may enable future pharmacological strategies aimed at obliterating rotavirus transcription as a therapeutic approach.
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Affiliation(s)
| | - William J. Dearnaley
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
| | - A. Cameron Varano
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
| | - Michael Casasanta
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
| | - Sarah M. McDonald
- Department of Biology, Wake Forest University, Winston-Salem, NC 27109, USA
| | - Deborah F. Kelly
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
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12
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A Local Agreement Filtering Algorithm for Transmission EM Reconstructions. J Struct Biol 2018; 205:30-40. [PMID: 30502495 PMCID: PMC6351148 DOI: 10.1016/j.jsb.2018.11.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 11/14/2018] [Accepted: 11/25/2018] [Indexed: 12/04/2022]
Abstract
We propose an algorithm, LAFTER, that recovers features with more signal than noise from half maps. LAFTER is shown to recover features over a wide range of FSCs and local signal-to-noise ratios. We suggest effective local noise suppression be evaluated by comparing the filter-sum xFSC to Cref.
We present LAFTER, an algorithm for de-noising single particle reconstructions from cryo-EM. Single particle analysis entails the reconstruction of high-resolution volumes from tens of thousands of particle images with low individual signal-to-noise. Imperfections in this process result in substantial variations in the local signal-to-noise ratio within the resulting reconstruction, complicating the interpretation of molecular structure. An effective local de-noising filter could therefore improve interpretability and maximise the amount of useful information obtained from cryo-EM maps. LAFTER is a local de-noising algorithm based on a pair of serial real-space filters. It compares independent half-set reconstructions to identify and retain shared features that have power greater than the noise. It is capable of recovering features across a wide range of signal-to-noise ratios, and we demonstrate recovery of the strongest features at Fourier shell correlation (FSC) values as low as 0.144 over a 2563-voxel cube. A fast and computationally efficient implementation of LAFTER is freely available. We also propose a new way to evaluate the effectiveness of real-space filters for noise suppression, based on the correspondence between two FSC curves: 1) the FSC between the filtered and unfiltered volumes, and 2) Cref, the FSC between the unfiltered volume and a hypothetical noiseless volume, which can readily be estimated from the FSC between two half-set reconstructions.
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13
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Mendez JH, Stagg SM. Assessing the quality of single particle reconstructions by atomic model building. J Struct Biol 2018; 204:276-282. [PMID: 30213768 PMCID: PMC6201253 DOI: 10.1016/j.jsb.2018.09.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 09/05/2018] [Accepted: 09/08/2018] [Indexed: 10/28/2022]
Abstract
The 2015/2016 Map Challenge challenged cryo-EM practitioners to process a series of publicly available cryo-EM datasets. As part of the challenge, metrics needed to be developed to assess and compare the quality of the different map submissions. The most common metric for assessing maps is determining the resolution by Fourier shell correlation (FSC), but there are well known instances where the resolution can be misleading. In this manuscript, we present a new approach for assessing the quality of a map by determining the map "modelability" rather than on resolution. We used the automated map tracing and modeling algorithms in Rosetta to generate populations of models, and then compared the populations between different map entries by the Rosetta score, RMSD to a reference model provided by the map challenge, and by pair-wise RMSDs between different models in the population. These metrics were used to determine statistically significant rankings for the map challengers for each dataset. The rankings revealed inconsistencies between the resolution by FSC, emphasized the importance of the interplay between number of particles contributing to a map and map quality, and revealed the importance of software familiarity on single particle reconstruction results. However, because multiple variables changed between map entries, it was challenging to derive best practices from the map challenge results.
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Affiliation(s)
- Joshua H Mendez
- Department of Physics, 77 Chieftan Way, Tallahassee, FL 32306, United States
| | - Scott M Stagg
- Institute of Molecular Biophysics, 91 Chieftain Way, Florida State University, Tallahassee, FL 32306, United States; Department of Chemistry and Biochemistry, 95 Chieftain Way, Florida State University, Tallahassee, FL 32306, United States.
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14
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The structure of a β 2-microglobulin fibril suggests a molecular basis for its amyloid polymorphism. Nat Commun 2018; 9:4517. [PMID: 30375379 PMCID: PMC6207761 DOI: 10.1038/s41467-018-06761-6] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 09/20/2018] [Indexed: 11/08/2022] Open
Abstract
All amyloid fibrils contain a cross-β fold. How this structure differs in fibrils formed from proteins associated with different diseases remains unclear. Here, we combine cryo-EM and MAS-NMR to determine the structure of an amyloid fibril formed in vitro from β2-microglobulin (β2m), the culprit protein of dialysis-related amyloidosis. The fibril is composed of two identical protofilaments assembled from subunits that do not share β2m's native tertiary fold, but are formed from similar β-strands. The fibrils share motifs with other amyloid fibrils, but also contain unique features including π-stacking interactions perpendicular to the fibril axis and an intramolecular disulfide that stabilises the subunit fold. We also describe a structural model for a second fibril morphology and show that it is built from the same subunit fold. The results provide insights into the mechanisms of fibril formation and the commonalities and differences within the amyloid fold in different protein sequences.
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15
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Hughes TET, Pumroy RA, Yazici AT, Kasimova MA, Fluck EC, Huynh KW, Samanta A, Molugu SK, Zhou ZH, Carnevale V, Rohacs T, Moiseenkova-Bell VY. Structural insights on TRPV5 gating by endogenous modulators. Nat Commun 2018; 9:4198. [PMID: 30305626 PMCID: PMC6179994 DOI: 10.1038/s41467-018-06753-6] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/14/2018] [Indexed: 11/10/2022] Open
Abstract
TRPV5 is a transient receptor potential channel involved in calcium reabsorption. Here we investigate the interaction of two endogenous modulators with TRPV5. Both phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) and calmodulin (CaM) have been shown to directly bind to TRPV5 and activate or inactivate the channel, respectively. Using cryo-electron microscopy (cryo-EM), we determined TRPV5 structures in the presence of dioctanoyl PI(4,5)P2 and CaM. The PI(4,5)P2 structure reveals a binding site between the N-linker, S4-S5 linker and S6 helix of TRPV5. These interactions with PI(4,5)P2 induce conformational rearrangements in the lower gate, opening the channel. The CaM structure reveals two TRPV5 C-terminal peptides anchoring a single CaM molecule and that calcium inhibition is mediated through a cation-π interaction between Lys116 on the C-lobe of calcium-activated CaM and Trp583 at the intracellular gate of TRPV5. Overall, this investigation provides insight into the endogenous modulation of TRPV5, which has the potential to guide drug discovery.
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Affiliation(s)
- Taylor E T Hughes
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ruth A Pumroy
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Aysenur Torun Yazici
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Marina A Kasimova
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, 19122, USA
| | - Edwin C Fluck
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kevin W Huynh
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - Amrita Samanta
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sudheer K Molugu
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Z Hong Zhou
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, 19122, USA
| | - Tibor Rohacs
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Vera Y Moiseenkova-Bell
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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16
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Yang YJ, Wang S, Zhang B, Shen HB. Resolution Measurement from a Single Reconstructed Cryo-EM Density Map with Multiscale Spectral Analysis. J Chem Inf Model 2018; 58:1303-1311. [DOI: 10.1021/acs.jcim.8b00149] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Yu-Jiao Yang
- Institute of Image Processing and Pattern Recognition and MOE Key Laboratory of System Control and Information Processing, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shuai Wang
- Institute of Image Processing and Pattern Recognition and MOE Key Laboratory of System Control and Information Processing, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Biao Zhang
- Institute of Image Processing and Pattern Recognition and MOE Key Laboratory of System Control and Information Processing, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong-Bin Shen
- Institute of Image Processing and Pattern Recognition and MOE Key Laboratory of System Control and Information Processing, Shanghai Jiao Tong University, Shanghai 200240, China
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17
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Abstract
Structural studies of biocomplexes using single-particle cryo-electron microscopy (cryo-EM) is now a well-established technique in structural biology and has become competitive with X-ray crystallography. The latest advances in EM enable us to determine structures of protein complexes at 3-5 Å resolution for an extremely broad range of sizes from ~200 kDa up to hundreds of megadaltons (Bartesaghi et al., Science 348(6239):1147-1151, 2051; Bai et al., Nature 525(7568):212-217, 2015; Vinothkumar et al., Nature 515(7525):80-84, 2014; Grigorieff and Harrison, Curr Opin Struct Biol 21(2):265-273, 2011). The majority of biocomplexes comprise a number of different components and are not amenable to crystallisation. Secretion systems are typical examples of such multi-protein complexes, and structural studies of them are extremely challenging. The only feasible approach to revealing their spatial organisation and functional modification is cryo-EM. The development of systems for digital registration of images and algorithms for the fast and efficient processing of recorded images and subsequent analysis facilitated the determination of structures at near-atomic resolution. In this review we will describe sample preparation for cryo-EM, how data are collected by new detectors, and the logistics of image analysis through the basic steps required for reconstructions of both small and large biological complexes and their refinement to nearly atomic resolution. The processing workflow is illustrated using examples of EM analysis of a Type IV Secretion System.
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18
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Vilas JL, Gómez-Blanco J, Conesa P, Melero R, Miguel de la Rosa-Trevín J, Otón J, Cuenca J, Marabini R, Carazo JM, Vargas J, Sorzano COS. MonoRes: Automatic and Accurate Estimation of Local Resolution for Electron Microscopy Maps. Structure 2018; 26:337-344.e4. [PMID: 29395788 DOI: 10.1016/j.str.2017.12.018] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 10/06/2017] [Accepted: 12/29/2017] [Indexed: 11/29/2022]
Abstract
Since the beginning of electron microscopy, resolution has been a critical parameter. In this article, we propose a fully automatic, accurate method for determining the local resolution of a 3D map (MonoRes). The foundation of this algorithm is an extension of the concept of analytic signal, termed monogenic signal. The map is filtered at different frequencies and the amplitude of the monogenic signal is calculated, after which a criterion is applied to determine the resolution at each voxel. MonoRes is fully automatic without compulsory user parameters, with great accuracy in all tests, and is computationally more rapid than existing methods in the field. In addition, MonoRes offers the option of local filtering of the original map based on the calculated local resolution.
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Affiliation(s)
- Jose Luis Vilas
- Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain.
| | - Josué Gómez-Blanco
- Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
| | - Pablo Conesa
- Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
| | - Roberto Melero
- Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
| | | | - Joaquin Otón
- Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
| | - Jesús Cuenca
- Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
| | - Roberto Marabini
- Escuela Politécnica Superior, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - José María Carazo
- Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain.
| | - Javier Vargas
- Department of Anatomy and Cell Biology, McGill University, University Street Strathcona Anatomy Building, 3640 Montreal, Canada
| | - Carlos Oscar S Sorzano
- Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain; Department of Engineering of Electronic and Telecommunication Systems, Universidad San Pablo-CEU, Campus Urbanización Montepríncipe, Boadilla del Monte, 28668 Madrid, Spain.
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19
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Liang Y, Dearnaley WJ, Varano AC, Winton CE, Gilmore BL, Alden NA, Sheng Z, Kelly DF. Structural analysis of BRCA1 reveals modification hotspot. SCIENCE ADVANCES 2017; 3:e1701386. [PMID: 28948225 PMCID: PMC5606707 DOI: 10.1126/sciadv.1701386] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 08/30/2017] [Indexed: 05/21/2023]
Abstract
Cancer cells afflicted with mutations in the breast cancer susceptibility protein (BRCA1) often suffer from increased DNA damage and genomic instability. The precise manner in which physical changes to BRCA1 influence its role in DNA maintenance remains unclear. We used single-particle electron microscopy to study the three-dimensional properties of BRCA1 naturally produced in breast cancer cells. Structural studies revealed new information for full-length BRCA1, engaging its nuclear binding partner, the BRCA1-associated RING domain protein (BARD1). Equally important, we identified a region in mutated BRCA1 that was highly susceptible to ubiquitination. We refer to this site as a modification "hotspot." Ubiquitin adducts in the hotspot region proved to be biochemically reversible. Collectively, we show how key changes to BRCA1 affect its structure-function relationship, and present new insights to potentially modulate mutated BRCA1 in human cancer cells.
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Affiliation(s)
- Yanping Liang
- Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, VA 24016, USA
| | - William J. Dearnaley
- Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, VA 24016, USA
| | - A. Cameron Varano
- Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, VA 24016, USA
- Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Blacksburg, VA 24061, USA
| | - Carly E. Winton
- Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, VA 24016, USA
- School of Biomedical Engineering and Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Brian L. Gilmore
- Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, VA 24016, USA
| | - Nick A. Alden
- Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, VA 24016, USA
| | - Zhi Sheng
- Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, VA 24016, USA
- Virginia Tech Carilion School of Medicine, Virginia Tech, Roanoke, VA 24016, USA
| | - Deborah F. Kelly
- Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, VA 24016, USA
- School of Biomedical Engineering and Science, Virginia Tech, Blacksburg, VA 24061, USA
- Virginia Tech Carilion School of Medicine, Virginia Tech, Roanoke, VA 24016, USA
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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20
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Sorzano C, Vargas J, Otón J, Abrishami V, de la Rosa-Trevín J, Gómez-Blanco J, Vilas J, Marabini R, Carazo J. A review of resolution measures and related aspects in 3D Electron Microscopy. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 124:1-30. [DOI: 10.1016/j.pbiomolbio.2016.09.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 08/22/2016] [Accepted: 09/18/2016] [Indexed: 12/21/2022]
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21
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Hoffmann NA, Jakobi AJ, Vorländer MK, Sachse C, Müller CW. Transcribing RNA polymerase III observed by electron cryomicroscopy. FEBS J 2016; 283:2811-9. [PMID: 27059519 PMCID: PMC5053293 DOI: 10.1111/febs.13732] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 03/26/2016] [Accepted: 04/04/2016] [Indexed: 12/21/2022]
Abstract
Electron cryomicroscopy reconstructions of elongating RNA polymerase (Pol) III at 3.9 Å resolution and of unbound Pol III (apo Pol III) in two distinct conformations at 4.6 Å and 4.7 Å resolution allow the construction of complete atomic models of Pol III and provide new functional insights into the adaption of Pol III to fulfill its specific transcription tasks.
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Affiliation(s)
- Niklas A Hoffmann
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Arjen J Jakobi
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Matthias K Vorländer
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Carsten Sachse
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Christoph W Müller
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
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22
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Vemu A, Atherton J, Spector JO, Szyk A, Moores CA, Roll-Mecak A. Structure and Dynamics of Single-isoform Recombinant Neuronal Human Tubulin. J Biol Chem 2016; 291:12907-15. [PMID: 27129203 PMCID: PMC4933209 DOI: 10.1074/jbc.c116.731133] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Indexed: 12/31/2022] Open
Abstract
Microtubules are polymers that cycle stochastically between polymerization and depolymerization, i.e. they exhibit "dynamic instability." This behavior is crucial for cell division, motility, and differentiation. Although studies in the last decade have made fundamental breakthroughs in our understanding of how cellular effectors modulate microtubule dynamics, analysis of the relationship between tubulin sequence, structure, and dynamics has been held back by a lack of dynamics measurements with and structural characterization of homogeneous isotypically pure engineered tubulin. Here, we report for the first time the cryo-EM structure and in vitro dynamics parameters of recombinant isotypically pure human tubulin. α1A/βIII is a purely neuronal tubulin isoform. The 4.2-Å structure of post-translationally unmodified human α1A/βIII microtubules shows overall similarity to that of heterogeneous brain microtubules, but it is distinguished by subtle differences at polymerization interfaces, which are hot spots for sequence divergence between tubulin isoforms. In vitro dynamics assays show that, like mosaic brain microtubules, recombinant homogeneous microtubules undergo dynamic instability, but they polymerize slower and have fewer catastrophes. Interestingly, we find that epitaxial growth of α1A/βIII microtubules from heterogeneous brain seeds is inefficient but can be fully rescued by incorporating as little as 5% of brain tubulin into the homogeneous α1A/βIII lattice. Our study establishes a system to examine the structure and dynamics of mammalian microtubules with well defined tubulin species and is a first and necessary step toward uncovering how tubulin genetic and chemical diversity is exploited to modulate intrinsic microtubule dynamics.
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Affiliation(s)
| | - Joseph Atherton
- the Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London WC1E, United Kingdom
| | | | | | - Carolyn A Moores
- the Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London WC1E, United Kingdom
| | - Antonina Roll-Mecak
- From the Cell Biology and Biophysics Unit, NINDS, and Biophysics Center, NHLBI, National Institutes of Health, Bethesda, Maryland 20892 and
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23
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Zhao H, Speir JA, Matsui T, Lin Z, Liang L, Lynn AY, Varnado B, Weiss TM, Tang L. Structure of a Bacterial Virus DNA-Injection Protein Complex Reveals a Decameric Assembly with a Constricted Molecular Channel. PLoS One 2016; 11:e0149337. [PMID: 26882199 PMCID: PMC4755594 DOI: 10.1371/journal.pone.0149337] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 01/29/2016] [Indexed: 12/18/2022] Open
Abstract
The multi-layered cell envelope structure of Gram-negative bacteria represents significant physical and chemical barriers for short-tailed phages to inject phage DNA into the host cytoplasm. Here we show that a DNA-injection protein of bacteriophage Sf6, gp12, forms a 465-kDa, decameric assembly in vitro. The electron microscopic structure of the gp12 assembly shows a ~150-Å, mushroom-like architecture consisting of a crown domain and a tube-like domain, which embraces a 25-Å-wide channel that could precisely accommodate dsDNA. The constricted channel suggests that gp12 mediates rapid, uni-directional injection of phage DNA into host cells by providing a molecular conduit for DNA translocation. The assembly exhibits a 10-fold symmetry, which may be a common feature among DNA-injection proteins of P22-like phages and may suggest a symmetry mismatch with respect to the 6-fold symmetric phage tail. The gp12 monomer is highly flexible in solution, supporting a mechanism for translocation of the protein through the conduit of the phage tail toward the host cell envelope, where it assembles into a DNA-injection device.
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Affiliation(s)
- Haiyan Zhao
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas, United States of America
| | - Jeffrey A. Speir
- National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, California, United States of America
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 14 2575 Sand Hill Road, MS69, Menlo Park, California, United States of America
| | - Zihan Lin
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas, United States of America
| | - Lingfei Liang
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas, United States of America
| | - Anna Y. Lynn
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas, United States of America
| | - Brittany Varnado
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas, United States of America
| | - Thomas M. Weiss
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 14 2575 Sand Hill Road, MS69, Menlo Park, California, United States of America
| | - Liang Tang
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas, United States of America
- * E-mail:
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24
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Kuijper M, van Hoften G, Janssen B, Geurink R, De Carlo S, Vos M, van Duinen G, van Haeringen B, Storms M. FEI’s direct electron detector developments: Embarking on a revolution in cryo-TEM. J Struct Biol 2015; 192:179-87. [DOI: 10.1016/j.jsb.2015.09.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/23/2015] [Accepted: 09/25/2015] [Indexed: 10/23/2022]
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25
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Rosenthal PB, Rubinstein JL. Validating maps from single particle electron cryomicroscopy. Curr Opin Struct Biol 2015; 34:135-44. [DOI: 10.1016/j.sbi.2015.07.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/30/2015] [Accepted: 07/03/2015] [Indexed: 01/10/2023]
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26
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Rahimi A, Varano AC, Demmert AC, Melanson LA, McDonald SM, Kelly DF. A Non-Symmetric Reconstruction Technique for Transcriptionally-Active Viral Assemblies. ACTA ACUST UNITED AC 2015; 2. [PMID: 27819069 PMCID: PMC5094455 DOI: 10.13188/2474-1914.1000004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The molecular mechanisms by which RNA viruses coordinate their transcriptional activities are not fully understood. For rotavirus, an important pediatric gastroenteric pathogen, transcription occurs within a double-layered particle that encloses the viral genome. To date, there remains very little structural information available for actively-transcribing rotavirus double-layered particles, which could provide new insights for antiviral development. To improve our vision of these viral assemblies, we developed a new combinatorial strategy that utilizes currently available high-resolution image processing tools. First, we employed a 3D classification routine that allowed us to sort transcriptionally-active rotavirus assemblies on the basis of their internal density. Next, we implemented an additional 3D refinement procedure using the most active class of DLPs. For comparison, the refined structures were computed in parallel by (1) enforcing icosahedral symmetry, and by (2) using no symmetry operators. Comparing the resulting structures, we were able to visualize the continuum that exists between viral capsid proteins and the viral RNA for the first time.
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Affiliation(s)
- Amina Rahimi
- Virginia Tech Carilion Research Institute, Roanoke, VA, USA
| | | | - Andrew C Demmert
- Virginia Tech Carilion Research Institute, Roanoke, VA, USA; Virginia Tech Carilion School of Medicine, Roanoke, VA, USA
| | | | - Sarah M McDonald
- Virginia Tech Carilion Research Institute, Roanoke, VA, USA; Virginia Tech Carilion School of Medicine, Roanoke, VA, USA; Department of Biomedical Sciences and Pathology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - Deborah F Kelly
- Virginia Tech Carilion Research Institute, Roanoke, VA, USA; Virginia Tech Carilion School of Medicine, Roanoke, VA, USA; Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
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27
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Ramia NF, Spilman M, Tang L, Shao Y, Elmore J, Hale C, Cocozaki A, Bhattacharya N, Terns RM, Terns MP, Li H, Stagg SM. Essential structural and functional roles of the Cmr4 subunit in RNA cleavage by the Cmr CRISPR-Cas complex. Cell Rep 2014; 9:1610-1617. [PMID: 25482566 DOI: 10.1016/j.celrep.2014.11.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 10/14/2014] [Accepted: 11/05/2014] [Indexed: 10/24/2022] Open
Abstract
The Cmr complex is the multisubunit effector complex of the type III-B clustered regularly interspaced short palindromic repeats (CRISPR)-Cas immune system. The Cmr complex recognizes a target RNA through base pairing with the integral CRISPR RNA (crRNA) and cleaves the target at multiple regularly spaced locations within the complementary region. To understand the molecular basis of the function of this complex, we have assembled information from electron microscopic and X-ray crystallographic structural studies and mutagenesis of a complete Pyrococcus furiosus Cmr complex. Our findings reveal that four helically packed Cmr4 subunits, which make up the backbone of the Cmr complex, act as a platform to support crRNA binding and target RNA cleavage. Interestingly, we found a hook-like structural feature associated with Cmr4 that is likely the site of target RNA binding and cleavage. Our results also elucidate analogies in the mechanisms of crRNA and target molecule binding by the distinct Cmr type III-A and Cascade type I-E complexes.
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Affiliation(s)
- Nancy F Ramia
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Michael Spilman
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Li Tang
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Yaming Shao
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Joshua Elmore
- Departments of Biochemistry and Molecular Biology, Genetics, and Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Caryn Hale
- Departments of Biochemistry and Molecular Biology, Genetics, and Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Alexis Cocozaki
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | | | - Rebecca M Terns
- Departments of Biochemistry and Molecular Biology, Genetics, and Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Michael P Terns
- Departments of Biochemistry and Molecular Biology, Genetics, and Microbiology, University of Georgia, Athens, GA 30602, USA.
| | - Hong Li
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA; Department of Chemistry and Biochemistry, 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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28
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Atherton J, Farabella I, Yu IM, Rosenfeld SS, Houdusse A, Topf M, Moores CA. Conserved mechanisms of microtubule-stimulated ADP release, ATP binding, and force generation in transport kinesins. eLife 2014; 3:e03680. [PMID: 25209998 PMCID: PMC4358365 DOI: 10.7554/elife.03680] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 09/08/2014] [Indexed: 01/21/2023] Open
Abstract
Kinesins are a superfamily of microtubule-based ATP-powered motors, important for multiple, essential cellular functions. How microtubule binding stimulates their ATPase and controls force generation is not understood. To address this fundamental question, we visualized microtubule-bound kinesin-1 and kinesin-3 motor domains at multiple steps in their ATPase cycles—including their nucleotide-free states—at ∼7 Å resolution using cryo-electron microscopy. In both motors, microtubule binding promotes ordered conformations of conserved loops that stimulate ADP release, enhance microtubule affinity and prime the catalytic site for ATP binding. ATP binding causes only small shifts of these nucleotide-coordinating loops but induces large conformational changes elsewhere that allow force generation and neck linker docking towards the microtubule plus end. Family-specific differences across the kinesin–microtubule interface account for the distinctive properties of each motor. Our data thus provide evidence for a conserved ATP-driven mechanism for kinesins and reveal the critical mechanistic contribution of the microtubule interface. DOI:http://dx.doi.org/10.7554/eLife.03680.001 The interior of a cell is a hive of activity, filled with proteins and other items moving from one location to another. A network of filaments called microtubules forms tracks along which so-called motor proteins carry these items. Kinesins are one group of motor proteins, and a typical kinesin protein has one end (called the ‘motor domain’) that can attach itself to the microtubules. The other end links to the cargo being carried, and a ‘neck’ connects the two. When two of these proteins work together, flexible regions of the neck allow the two motor domains to move past one another, which enable the kinesin to essentially walk along a microtubule in a stepwise manner. To take these steps along microtubules, each kinesin motor domain in the pair must undergo alternating cycles of tight association and release from their tracks. This cycle is coordinated by binding and breaking down a molecule called ATP, which also provides the energy needed to take the next step. How the cycle of loose and tight microtubule attachment is coordinated with the release of the breakdown products of ATP, and how the energy from the ATP molecule is converted into the force that moves the motor along the microtubule, has been unclear. Atherton et al. use a technique called cryo-electron microscopy to study—in more detail than previously seen—the structure of the motor domains of two types of kinesin called kinesin-1 and kinesin-3. Images were taken at different stages of the cycle used by the motor domains to extract the energy from ATP molecules. Although the two kinesins have been thought to move along the microtubule tracks in different ways, Atherton et al. find that the core mechanism used by their motor domains is the same. When a motor domain binds to the microtubule, its shape changes, first stimulating release of the breakdown products of ATP from the previous cycle. This release makes room for a new ATP molecule to bind. The structural changes caused by ATP binding are relatively small but produce larger changes in the flexible neck region that enable individual motor domains within a kinesin pair to co-ordinate their movement and move in a consistent direction. This mechanism involves tight coupling between track binding and fuel usage and makes kinesins highly efficient motors. The structures uncovered by Atherton et al. reveal a mechanism that links microtubule binding, the energy supplied to the motor domain and the force that moves the kinesin along a microtubule. Future work will clarify whether the key features observed in the motor domains of kinesin-1 and kinesin-3 are also found in other types of kinesin motors. DOI:http://dx.doi.org/10.7554/eLife.03680.002
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Affiliation(s)
- Joseph Atherton
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, United Kingdom
| | - Irene Farabella
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, United Kingdom
| | - I-Mei Yu
- Structural Motility, Institut Curie, Centre National de la Recherche Scientifique, Paris, France
| | - Steven S Rosenfeld
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Anne Houdusse
- Structural Motility, Institut Curie, Centre National de la Recherche Scientifique, Paris, France
| | - Maya Topf
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, United Kingdom
| | - Carolyn A Moores
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, United Kingdom
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Lu A, Magupalli VG, Ruan J, Yin Q, Atianand MK, Vos MR, Schröder GF, Fitzgerald KA, Wu H, Egelman EH. Unified polymerization mechanism for the assembly of ASC-dependent inflammasomes. Cell 2014; 156:1193-1206. [PMID: 24630722 DOI: 10.1016/j.cell.2014.02.008] [Citation(s) in RCA: 944] [Impact Index Per Article: 94.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Revised: 12/04/2013] [Accepted: 02/03/2014] [Indexed: 12/27/2022]
Abstract
Inflammasomes elicit host defense inside cells by activating caspase-1 for cytokine maturation and cell death. AIM2 and NLRP3 are representative sensor proteins in two major families of inflammasomes. The adaptor protein ASC bridges the sensor proteins and caspase-1 to form ternary inflammasome complexes, achieved through pyrin domain (PYD) interactions between sensors and ASC and through caspase activation and recruitment domain (CARD) interactions between ASC and caspase-1. We found that PYD and CARD both form filaments. Activated AIM2 and NLRP3 nucleate PYD filaments of ASC, which, in turn, cluster the CARD of ASC. ASC thus nucleates CARD filaments of caspase-1, leading to proximity-induced activation. Endogenous NLRP3 inflammasome is also filamentous. The cryoelectron microscopy structure of ASC(PYD) filament at near-atomic resolution provides a template for homo- and hetero-PYD/PYD associations, as confirmed by structure-guided mutagenesis. We propose that ASC-dependent inflammasomes in both families share a unified assembly mechanism that involves two successive steps of nucleation-induced polymerization. PAPERFLICK:
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Affiliation(s)
- Alvin Lu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Venkat Giri Magupalli
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Jianbin Ruan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Qian Yin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Maninjay K Atianand
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Matthijn R Vos
- FEI Company, Nanoport Europe, 5651 GG Eindhoven, the Netherlands
| | - Gunnar F Schröder
- Institute of Complex Systems, Forschungszentrum Jülich, 52425 Jülich, Germany; Physics Department, Heinrich-Heine Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Katherine A Fitzgerald
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
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Dukes MJ, Thomas R, Damiano J, Klein KL, Balasubramaniam S, Kayandan S, Riffle JS, Davis RM, McDonald SM, Kelly DF. Improved microchip design and application for in situ transmission electron microscopy of macromolecules. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2014; 20:338-345. [PMID: 24331164 DOI: 10.1017/s1431927613013858] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Understanding the fundamental properties of macromolecules has enhanced the development of emerging technologies used to improve biomedical research. Currently, there is a critical need for innovative platforms that can illuminate the function of biomedical reagents in a native environment. To address this need, we have developed an in situ approach to visualize the dynamic behavior of biomedically relevant macromolecules at the nanoscale. Newly designed silicon nitride devices containing integrated "microwells" were used to enclose active macromolecular specimens in liquid for transmission electron microscopy imaging purposes.We were able to successfully examine novel magnetic resonance imaging contrast reagents, micelle suspensions, liposome carrier vehicles, and transcribing viral assemblies. With each specimen tested, the integrated microwells adequately maintained macromolecules in discrete local environments while enabling thin liquid layers to be produced.
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Affiliation(s)
| | | | | | - Kate L Klein
- 2 Department of Mechanical Engineering, University of the District of Columbia, Washington, DC 20008, USA
| | | | - Sanem Kayandan
- 3 Macromolecules and Interfaces Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Judy S Riffle
- 3 Macromolecules and Interfaces Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Richey M Davis
- 3 Macromolecules and Interfaces Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Sarah M McDonald
- 6 Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, VA 24016, USA
| | - Deborah F Kelly
- 3 Macromolecules and Interfaces Institute, Virginia Tech, Blacksburg, VA 24061, USA
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31
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Kucukelbir A, Sigworth FJ, Tagare HD. Quantifying the local resolution of cryo-EM density maps. Nat Methods 2014; 11:63-5. [PMID: 24213166 PMCID: PMC3903095 DOI: 10.1038/nmeth.2727] [Citation(s) in RCA: 1385] [Impact Index Per Article: 138.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 10/02/2013] [Indexed: 01/11/2023]
Abstract
We propose a definition of local resolution for three-dimensional electron cryo-microscopy (cryo-EM) density maps that uses local sinusoidal features. Our algorithm has no free parameters and is applicable to other imaging modalities, including tomography. By evaluating the local resolution of single-particle reconstructions and subtomogram averages for four example data sets, we report variable resolution across a 4- to 40-Å range.
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Affiliation(s)
- Alp Kucukelbir
- Department of Biomedical Engineering, Yale University, New Haven, United States
| | - Fred J. Sigworth
- Department of Biomedical Engineering, Yale University, New Haven, United States
- Department of Cellular and Molecular Physiology, Yale University, New Haven, United States
| | - Hemant D. Tagare
- Department of Biomedical Engineering, Yale University, New Haven, United States
- Department of Diagnostic Radiology, Yale University, New Haven, United States
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32
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ResLog plots as an empirical metric of the quality of cryo-EM reconstructions. J Struct Biol 2013; 185:418-26. [PMID: 24384117 DOI: 10.1016/j.jsb.2013.12.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 12/19/2013] [Accepted: 12/23/2013] [Indexed: 12/13/2022]
Abstract
Compared to the field of X-ray crystallography, the field of single particle three-dimensional electron microscopy has few reliable metrics for assessing the quality of 3D reconstructions. New metrics are needed that can determine whether a given 3D reconstruction accurately reflects the structure of the particles from which it was derived or instead depicts a plausible though incorrect structure due to coarse misalignment of particles. Here an empirical procedure is presented for differentiating between a reconstruction with well-aligned particles and a reconstruction with grossly misclassified particles. For a given dataset, 3D reconstructions are computed from subsets of particles with decreasing numbers of particles contributing to the reconstruction. A plot of inverse resolution vs. the logarithm of the number of particles (a "ResLog" plot) provides metrics for the reliability of the reconstruction and the overall quality of the dataset and processing. Specifically, the y-intercept of a regression line provides a measure of the relative accuracy of the particle alignment and classification, and the slope is an indicator of the overall data quality including the imaging conditions and processing steps. ResLog plots can also be used to optimize conditions for data collection and reconstruction parameters. Although resolution estimates can vary by method of calculation, ResLog-derived parameters are consistent whether calculated by Fourier shell correlation or Fourier neighbor correlation, or a new coordinate-based metric that serves as a yardstick for structures where atomic coordinates are available. ResLog plots could become part of a standard set of parameters to be included in 3D reconstruction reports.
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33
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Lyumkis D, Julien JP, de Val N, Cupo A, Potter CS, Klasse PJ, Burton DR, Sanders RW, Moore JP, Carragher B, Wilson IA, Ward AB. Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer. Science 2013; 342:1484-90. [PMID: 24179160 PMCID: PMC3954647 DOI: 10.1126/science.1245627] [Citation(s) in RCA: 586] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The HIV-1 envelope glycoprotein (Env) trimer contains the receptor binding sites and membrane fusion machinery that introduce the viral genome into the host cell. As the only target for broadly neutralizing antibodies (bnAbs), Env is a focus for rational vaccine design. We present a cryo-electron microscopy reconstruction and structural model of a cleaved, soluble Env trimer (termed BG505 SOSIP.664 gp140) in complex with a CD4 binding site (CD4bs) bnAb, PGV04, at 5.8 angstrom resolution. The structure reveals the spatial arrangement of Env components, including the V1/V2, V3, HR1, and HR2 domains, as well as shielding glycans. The structure also provides insights into trimer assembly, gp120-gp41 interactions, and the CD4bs epitope cluster for bnAbs, which covers a more extensive area and defines a more complex site of vulnerability than previously described.
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Affiliation(s)
- Dmitry Lyumkis
- National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, California, 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Jean-Philippe Julien
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Natalia de Val
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Albert Cupo
- Weill Medical College of Cornell University, New York, New York 10021, USA
| | - Clinton S. Potter
- National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, California, 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Per Johan Klasse
- Weill Medical College of Cornell University, New York, New York 10021, USA
| | - Dennis R. Burton
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02129, USA
| | - Rogier W. Sanders
- Weill Medical College of Cornell University, New York, New York 10021, USA
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, Netherlands
| | - John P. Moore
- Weill Medical College of Cornell University, New York, New York 10021, USA
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, California, 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, USA
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Xie Q, Spilman M, Meyer NL, Lerch TF, Stagg SM, Chapman MS. Electron microscopy analysis of a disaccharide analog complex reveals receptor interactions of adeno-associated virus. J Struct Biol 2013; 184:129-35. [PMID: 24036405 DOI: 10.1016/j.jsb.2013.09.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 09/02/2013] [Accepted: 09/04/2013] [Indexed: 12/19/2022]
Abstract
Mechanistic studies of macromolecular complexes often feature X-ray structures of complexes with bound ligands. The attachment of adeno-associated virus (AAV) to cell surface glycosaminoglycans (GAGs) is an example that has not proven amenable to crystallography, because the binding of GAG analogs disrupts lattice contacts. The interactions of AAV with GAGs are of interest in mediating the cell specificity of AAV-based gene therapy vectors. Previous electron microscopy led to differing conclusions on the exact binding site and the existence of large ligand-induced conformational changes in the virus. Conformational changes are expected during cell entry, but it has remained unclear whether the electron microscopy provided evidence of their induction by GAG-binding. Taking advantage of automated data collection, careful processing and new methods of structure refinement, the structure of AAV-DJ complexed with sucrose octasulfate is determined by electron microscopy difference map analysis to 4.8Å resolution. At this higher resolution, individual sulfate groups are discernible, providing a stereochemical validation of map interpretation, and highlighting interactions with two surface arginines that have been implicated in genetic studies. Conformational changes induced by the SOS are modest and limited to the loop most directly interacting with the ligand. While the resolution attainable will depend on sample order and other factors, there are an increasing number of macromolecular complexes that can be studied by cryo-electron microscopy at resolutions beyond 5Å, for which the approaches used here could be used to characterize the binding of inhibitors and other small molecule effectors when crystallography is not tractable.
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Affiliation(s)
- Qing Xie
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health &v Science University, Portland, OR 97239-3098, USA
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35
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Cardone G, Heymann JB, Steven AC. One number does not fit all: mapping local variations in resolution in cryo-EM reconstructions. J Struct Biol 2013; 184:226-36. [PMID: 23954653 DOI: 10.1016/j.jsb.2013.08.002] [Citation(s) in RCA: 252] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 07/31/2013] [Accepted: 08/07/2013] [Indexed: 12/26/2022]
Abstract
The resolution of density maps from single particle analysis is usually measured in terms of the highest spatial frequency to which consistent information has been obtained. This calculation represents an average over the entire reconstructed volume. In practice, however, substantial local variations in resolution may occur, either from intrinsic properties of the specimen or for technical reasons such as a non-isotropic distribution of viewing orientations. To address this issue, we propose the use of a space-frequency representation, the short-space Fourier transform, to assess the quality of a density map, voxel-by-voxel, i.e. by local resolution mapping. In this approach, the experimental volume is divided into small subvolumes and the resolution determined for each of them. It is illustrated in applications both to model data and to experimental density maps. Regions with lower-than-average resolution may be mobile components or ones with incomplete occupancy or result from multiple conformational states. To improve the interpretability of reconstructions, we propose an adaptive filtering approach that reconciles the resolution to which individual features are calculated with the results of the local resolution map.
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Affiliation(s)
- Giovanni Cardone
- Laboratory of Structural Biology, National Institute for Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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36
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Abstract
Single-particle cryo-EM is a powerful approach to determine the structure of large macromolecules and assemblies thereof in many cases at subnanometer resolution. It has become popular to refine or flexibly fit atomic models into density maps derived from cryo-EM experiments. These density maps are typically significantly lower in resolution than electron density maps obtained from X-ray diffraction experiments, such that the number of parameters that need to be determined is much larger than the number of experimental observables. Overfitting and misinterpretation of the density, thus, become a serious problem. For diffraction data, a cross-validation approach was introduced almost 20 y ago; however, no such approach has been described yet for structure refinement against cryo-EM density maps, although the overfitting problem is, because of the lower resolution, significantly larger. We present a cross-validation approach for real-space refinement against cryo-EM density maps in analogy to cross-validation typically used in crystallography. Our approach is able to detect overfitting and allows for optimizing the choice of restraints used in the refinement. The approach is shown on three protein structures with simulated data and experimental data of the rotavirus double-layer particle. Because cross-validation requires splitting the dataset into at least two independent sets, we further present an approach to quantify correlations between the structure factor sets. This analysis is also helpful for other cross-validation applications, such as refinements against diffraction data or 3D reconstructions of cryo-EM density maps.
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Abstract
Single particle electron microscopy is a versatile technique for the structural analysis of protein complexes in near-native conditions. While tremendous progress has been made during the past few decades in techniques for specimen preparation, imaging, and image analysis, the field is still in development. In the context of this volume on electron crystallography, the following chapter gives practical guidelines on how to begin single particle EM studies, including preparing specimens, selecting imaging conditions, and choosing which of the many approaches to image analysis are appropriate for a specific sample.
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Affiliation(s)
- Wilson C Y Lau
- Molecular Structure and Function Program, Departments of Biochemistry and Medical Biophysics, The Hospital for Sick Children, The University of Toronto, Toronto, ON, Canada
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Shen QT, Hsiue PP, Sindelar CV, Welch MD, Campellone KG, Wang HW. Structural insights into WHAMM-mediated cytoskeletal coordination during membrane remodeling. ACTA ACUST UNITED AC 2013; 199:111-24. [PMID: 23027905 PMCID: PMC3461504 DOI: 10.1083/jcb.201204010] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Structural analysis of the WHAMM–microtubule interaction provides insight into WHAMM’s coordination of microtubule binding, membrane association, and actin nucleation. The microtubule (MT) and actin cytoskeletons drive many essential cellular processes, yet fairly little is known about how their functions are coordinated. One factor that mediates important cross talk between these two systems is WHAMM, a Golgi-associated protein that utilizes MT binding and actin nucleation activities to promote membrane tubulation during intracellular transport. Using cryoelectron microscopy and other biophysical and biochemical approaches, we unveil the underlying mechanisms for how these activities are coordinated. We find that WHAMM bound to the outer surface of MT protofilaments via a novel interaction between its central coiled-coil region and tubulin heterodimers. Upon the assembly of WHAMM onto MTs, its N-terminal membrane-binding domain was exposed at the MT periphery, where it can recruit vesicles and remodel them into tubular structures. In contrast, MT binding masked the C-terminal portion of WHAMM and prevented it from promoting actin nucleation. These results give rise to a model whereby distinct MT-bound and actin-nucleating populations of WHAMM collaborate during membrane tubulation.
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Affiliation(s)
- Qing-Tao Shen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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39
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HCV IRES manipulates the ribosome to promote the switch from translation initiation to elongation. Nat Struct Mol Biol 2012; 20:150-8. [PMID: 23262488 PMCID: PMC3864654 DOI: 10.1038/nsmb.2465] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 11/12/2012] [Indexed: 12/11/2022]
Abstract
The hepatitis C virus (HCV) internal ribosome entry site (IRES) drives non-canonical initiation of protein synthesis necessary for viral replication. HCV IRES functional studies have focused on 80S ribosome formation, but have not explored roles after the 80S ribosome is poised at the start codon. Here, we report that mutations of an IRES domain that docks in the 40S subunit’s decoding groove and cause only a local perturbation in IRES structure result in conformational changes in the IRES-rabbit 40S subunit complex. Functionally, we find the mutation decreases IRES activity by inhibiting the first ribosome translocation event, and modeling suggests that this effect is through an interaction with a single ribosomal protein. The HCV IRES’ ability to manipulate the ribosome provides insight into how the ribosome’s structure and function can be altered by bound RNAs, including those derived from cellular invaders.
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40
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Benlekbir S, Bueler SA, Rubinstein JL. Structure of the vacuolar-type ATPase from Saccharomyces cerevisiae at 11-Å resolution. Nat Struct Mol Biol 2012; 19:1356-62. [PMID: 23142977 DOI: 10.1038/nsmb.2422] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 09/21/2012] [Indexed: 11/09/2022]
Abstract
Vacuolar-type ATPases (V-type ATPases) in eukaryotic cells are large membrane protein complexes that acidify various intracellular compartments. The enzymes are regulated by dissociation of the V(1) and V(O) regions of the complex. Here we present the structure of the Saccharomyces cerevisiae V-type ATPase at 11-Å resolution by cryo-EM of protein particles in ice. The structure explains many cross-linking and protein interaction studies. Docking of crystal structures suggests that inhibition of ATPase activity by the dissociated V(1) region involves rearrangement of the N- and C-terminal domains of subunit H and also suggests how this inhibition is triggered upon dissociation. We provide support for this model by demonstrating that mutation of subunit H to increase the rigidity of the linker between its two domains decreases its ability to inhibit ATPase activity.
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Affiliation(s)
- Samir Benlekbir
- Molecular Structure and Function Program, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
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Goulet A, Behnke-Parks WM, Sindelar CV, Major J, Rosenfeld SS, Moores CA. The structural basis of force generation by the mitotic motor kinesin-5. J Biol Chem 2012; 287:44654-66. [PMID: 23135273 DOI: 10.1074/jbc.m112.404228] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Kinesin-5 is required for forming the bipolar spindle during mitosis. Its motor domain, which contains nucleotide and microtubule binding sites and mechanical elements to generate force, has evolved distinct properties for its spindle-based functions. In this study, we report subnanometer resolution cryoelectron microscopy reconstructions of microtubule-bound human kinesin-5 before and after nucleotide binding and combine this information with studies of the kinetics of nucleotide-induced neck linker and cover strand movement. These studies reveal coupled, nucleotide-dependent conformational changes that explain many of this motor's properties. We find that ATP binding induces a ratchet-like docking of the neck linker and simultaneous, parallel docking of the N-terminal cover strand. Loop L5, the binding site for allosteric inhibitors of kinesin-5, also undergoes a dramatic reorientation when ATP binds, suggesting that it is directly involved in controlling nucleotide binding. Our structures indicate that allosteric inhibitors of human kinesin-5, which are being developed as anti-cancer therapeutics, bind to a motor conformation that occurs in the course of normal function. However, due to evolutionarily defined sequence variations in L5, this conformation is not adopted by invertebrate kinesin-5s, explaining their resistance to drug inhibition. Together, our data reveal the precision with which the molecular mechanism of kinesin-5 motors has evolved for force generation.
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Affiliation(s)
- Adeline Goulet
- Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom
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Berry JL, Phelan MM, Collins RF, Adomavicius T, Tønjum T, Frye SA, Bird L, Owens R, Ford RC, Lian LY, Derrick JP. Structure and assembly of a trans-periplasmic channel for type IV pili in Neisseria meningitidis. PLoS Pathog 2012; 8:e1002923. [PMID: 23028322 PMCID: PMC3441751 DOI: 10.1371/journal.ppat.1002923] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2012] [Accepted: 08/07/2012] [Indexed: 01/24/2023] Open
Abstract
Type IV pili are polymeric fibers which protrude from the cell surface and play a critical role in adhesion and invasion by pathogenic bacteria. The secretion of pili across the periplasm and outer membrane is mediated by a specialized secretin protein, PilQ, but the way in which this large channel is formed is unknown. Using NMR, we derived the structures of the periplasmic domains from N. meningitidis PilQ: the N-terminus is shown to consist of two β-domains, which are unique to the type IV pilus-dependent secretins. The structure of the second β-domain revealed an eight-stranded β-sandwich structure which is a novel variant of the HSP20-like fold. The central part of PilQ consists of two α/β fold domains: the structure of the first of these is similar to domains from other secretins, but with an additional α-helix which links it to the second α/β domain. We also determined the structure of the entire PilQ dodecamer by cryoelectron microscopy: it forms a cage-like structure, enclosing a cavity which is approximately 55 Å in internal diameter at its largest extent. Specific regions were identified in the density map which corresponded to the individual PilQ domains: this allowed us to dock them into the cryoelectron microscopy density map, and hence reconstruct the entire PilQ assembly which spans the periplasm. We also show that the C-terminal domain from the lipoprotein PilP, which is essential for pilus assembly, binds specifically to the first α/β domain in PilQ and use NMR chemical shift mapping to generate a model for the PilP:PilQ complex. We conclude that passage of the pilus fiber requires disassembly of both the membrane-spanning and the β-domain regions in PilQ, and that PilP plays an important role in stabilising the PilQ assembly during secretion, through its anchorage in the inner membrane.
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Affiliation(s)
- Jamie-Lee Berry
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Manchester, United Kingdom
| | - Marie M. Phelan
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Richard F. Collins
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Manchester, United Kingdom
| | - Tomas Adomavicius
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Manchester, United Kingdom
| | - Tone Tønjum
- Centre for Molecular Biology and Neuroscience, University of Oslo, Oslo, Norway
| | - Stefan A. Frye
- Centre for Molecular Biology and Neuroscience, University of Oslo, Oslo, Norway
| | - Louise Bird
- Oxford Protein Production Facility, Research Complex at Harwell, Harwell, Oxford, United Kingdom
| | - Ray Owens
- Oxford Protein Production Facility, Research Complex at Harwell, Harwell, Oxford, United Kingdom
| | - Robert C. Ford
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Manchester, United Kingdom
| | - Lu-Yun Lian
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Jeremy P. Derrick
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Manchester, United Kingdom
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43
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Lerch TF, O’Donnell JK, Meyer NL, Xie Q, Taylor KA, Stagg SM, Chapman MS. Structure of AAV-DJ, a retargeted gene therapy vector: cryo-electron microscopy at 4.5 Å resolution. Structure 2012; 20:1310-20. [PMID: 22727812 PMCID: PMC3418430 DOI: 10.1016/j.str.2012.05.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 05/10/2012] [Accepted: 05/11/2012] [Indexed: 12/19/2022]
Abstract
AAV-DJ, a leading candidate vector for liver gene therapy, was created through random homologous recombination followed by directed evolution, selecting for in vivo liver tropism and resistance to in vitro immune neutralization. Here, the 4.5 Å resolution cryo-EM structure is determined for the engineered AAV vector, revealing structural features that illuminate its phenotype. The heparan sulfate receptor-binding site is little changed from AAV-2, and heparin-binding affinity is similar. A loop that is antigenic in other serotypes has a unique conformation in AAV-DJ that would conflict with the binding of an AAV-2 neutralizing monoclonal antibody. This is consistent with increased resistance to neutralization by human polyclonal sera, raising the possibility that changed tropism may be a secondary effect of altered immune interactions. The reconstruction exemplifies analysis of fine structural changes and the potential of cryo-EM, in favorable cases, to characterize mutant or ligand-bound complexes.
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Affiliation(s)
- Thomas F. Lerch
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jason K. O’Donnell
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Nancy L. Meyer
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Qing Xie
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Kenneth A. Taylor
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Scott M. Stagg
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Michael S. Chapman
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
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Arrangement of subunits in intact mammalian mitochondrial ATP synthase determined by cryo-EM. Proc Natl Acad Sci U S A 2012; 109:11675-80. [PMID: 22753497 DOI: 10.1073/pnas.1204935109] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Mitochondrial ATP synthase is responsible for the synthesis of ATP, a universal energy currency in cells. Whereas X-ray crystallography has revealed the structure of the soluble region of the complex and the membrane-intrinsic c-subunits, little is known about the structure of the six other proteins (a, b, f, A6L, e, and g) that comprise the membrane-bound region of the complex in animal mitochondria. Here, we present the structure of intact bovine mitochondrial ATP synthase at ∼18 Å resolution by electron cryomicroscopy of single particles in amorphous ice. The map reveals that the a-subunit and c(8)-ring of the complex interact with a small contact area and that the b-subunit spans the membrane without contacting the c(8)-ring. The e- and g-subunits extend from the a-subunit density distal to the c(8)-ring. The map was calculated from images of a preparation of the enzyme solubilized with the detergent dodecyl maltoside, which is visible in electron cryomicroscopy maps. The structure shows that the micelle surrounding the complex is curved. The observed bend in the micelle of the detergent-solubilized complex is consistent with previous electron tomography experiments and suggests that monomers of ATP synthase are sufficient to produce curvature in lipid bilayers.
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45
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Lander GC, Baudoux AC, Azam F, Potter CS, Carragher B, Johnson JE. Capsomer dynamics and stabilization in the T = 12 marine bacteriophage SIO-2 and its procapsid studied by CryoEM. Structure 2012; 20:498-503. [PMID: 22405008 DOI: 10.1016/j.str.2012.01.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 12/30/2011] [Accepted: 01/10/2012] [Indexed: 10/28/2022]
Abstract
We report the subnanometer cryo-electron microscopy (cryoEM) reconstruction of a marine siphovirus, the Vibrio phage SIO-2. This phage is lytic for related Vibrio species with significant ecological importance, including the broadly antagonistic bacterium Vibrio sp. SWAT3. The three-dimensional structure of the 800 Å SIO-2, icosahedrally averaged head of the tailed particle revealed a T = 12 quasi-symmetry not previously described in a bacteriophage. Two morphologically distinct types of auxiliary proteins were also identified; one species bound to the surface of hexamers, and the other bound to pentamers. The secondary structure, evident in the electron density, shows that the major capsid protein has the HK97-like fold. The three-dimensional structure of the procapsid form, also presented here, has no "decoration" proteins and reveals a capsomer organization due to the constraints of the T = 12 symmetry.
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Affiliation(s)
- Gabriel C Lander
- National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, CA 92037, USA
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46
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De Carlo S, Lin SC, Taatjes DJ, Hoenger A. Molecular basis of transcription initiation in Archaea. Transcription 2012; 1:103-11. [PMID: 21326901 DOI: 10.4161/trns.1.2.13189] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2010] [Revised: 07/19/2010] [Accepted: 07/27/2010] [Indexed: 01/24/2023] Open
Abstract
Compared with eukaryotes, the archaeal transcription initiation machinery-commonly known as the Pre-Initiation Complex-is relatively simple. The archaeal PIC consists of the TFIIB ortholog TFB, TBP, and an 11-subunit RNA polymerase (RNAP). The relatively small size of the entire archaeal PIC makes it amenable to structural analysis. Using purified RNAP, TFB, and TBP from the thermophile Pyrococcus furiosus, we assembled the biochemically active PIC at 65ºC. The intact archaeal PIC was isolated by implementing a cross-linking technique followed by size-exclusion chromatography, and the structure of this 440 kDa assembly was determined using electron microscopy and single-particle reconstruction techniques. Combining difference maps with crystal structure docking of various sub-domains, TBP and TFB were localized within the macromolecular PIC. TBP/TFB assemble near the large RpoB subunit and the RpoD/L "foot" domain behind the RNAP central cleft. This location mimics that of yeast TBP and TFIIB in complex with yeast RNAP II. Collectively, these results define the structural organization of the archaeal transcription machinery and suggest a conserved core PIC architecture.
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Affiliation(s)
- Sacha De Carlo
- Department of Chemistry, City College of the City University of New York, NY, USA.
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Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL. Outcome of the first electron microscopy validation task force meeting. Structure 2012; 20:205-14. [PMID: 22325770 PMCID: PMC3328769 DOI: 10.1016/j.str.2011.12.014] [Citation(s) in RCA: 361] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 12/29/2011] [Accepted: 12/29/2011] [Indexed: 11/10/2022]
Abstract
This Meeting Review describes the proceedings and conclusions from the inaugural meeting of the Electron Microscopy Validation Task Force organized by the Unified Data Resource for 3DEM (http://www.emdatabank.org) and held at Rutgers University in New Brunswick, NJ on September 28 and 29, 2010. At the workshop, a group of scientists involved in collecting electron microscopy data, using the data to determine three-dimensional electron microscopy (3DEM) density maps, and building molecular models into the maps explored how to assess maps, models, and other data that are deposited into the Electron Microscopy Data Bank and Protein Data Bank public data archives. The specific recommendations resulting from the workshop aim to increase the impact of 3DEM in biology and medicine.
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Affiliation(s)
- Richard Henderson
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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48
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Mim C, Cui H, Gawronski-Salerno JA, Frost A, Lyman E, Voth GA, Unger VM. Structural basis of membrane bending by the N-BAR protein endophilin. Cell 2012; 149:137-45. [PMID: 22464326 DOI: 10.1016/j.cell.2012.01.048] [Citation(s) in RCA: 178] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2011] [Revised: 07/29/2011] [Accepted: 01/25/2012] [Indexed: 10/28/2022]
Abstract
Functioning as key players in cellular regulation of membrane curvature, BAR domain proteins bend bilayers and recruit interaction partners through poorly understood mechanisms. Using electron cryomicroscopy, we present reconstructions of full-length endophilin and its N-terminal N-BAR domain in their membrane-bound state. Endophilin lattices expose large areas of membrane surface and are held together by promiscuous interactions between endophilin's amphipathic N-terminal helices. Coarse-grained molecular dynamics simulations reveal that endophilin lattices are highly dynamic and that the N-terminal helices are required for formation of a stable and regular scaffold. Furthermore, endophilin accommodates different curvatures through a quantized addition or removal of endophilin dimers, which in some cases causes dimerization of endophilin's SH3 domains, suggesting that the spatial presentation of SH3 domains, rather than affinity, governs the recruitment of downstream interaction partners.
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Affiliation(s)
- Carsten Mim
- Department of Molecular Biosciences, Northwestern University, 2205 Campus Drive, Evanston, IL 60208, USA
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49
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Alloyeau D. Transmission Electron Microscopy: A Multifunctional Tool for the Atomic-scale Characterization of Nanoalloys. NANOALLOYS 2012. [DOI: 10.1007/978-1-4471-4014-6_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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50
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Subnanometre-resolution structure of the intact Thermus thermophilus H+-driven ATP synthase. Nature 2011; 481:214-8. [DOI: 10.1038/nature10699] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 11/03/2011] [Indexed: 01/15/2023]
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