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Serysheva II. Toward a high-resolution structure of IP₃R channel. Cell Calcium 2014; 56:125-32. [PMID: 25159857 DOI: 10.1016/j.ceca.2014.08.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 08/01/2014] [Accepted: 08/02/2014] [Indexed: 12/11/2022]
Abstract
The ability of cells to maintain low levels of Ca(2+) under resting conditions and to create rapid and transient increases in Ca(2+) upon stimulation is a fundamental property of cellular Ca(2+) signaling mechanism. An increase of cytosolic Ca(2+) level in response to diverse stimuli is largely accounted for by the inositol 1,4,5-trisphosphate receptor (IP3R) present in the endoplasmic reticulum membranes of virtually all eukaryotic cells. Extensive information is currently available on the function of IP3Rs and their interaction with modulators. Very little, however, is known about their molecular architecture and therefore most critical issues surrounding gating of IP3R channels are still ambiguous, including the central question of how opening of the IP3R pore is initiated by IP3 and Ca(2+). Membrane proteins such as IP3R channels have proven to be exceptionally difficult targets for structural analysis due to their large size, their location in the membrane environment, and their dynamic nature. To date, a 3D structure of complete IP3R channel is determined by single-particle cryo-EM at intermediate resolution, and the best crystal structures of IP3R are limited to a soluble portion of the cytoplasmic region representing ∼15% of the entire channel protein. Together these efforts provide the important structural information for this class of ion channels and serve as the basis for further studies aiming at understanding of the IP3R function.
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Affiliation(s)
- Irina I Serysheva
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School at Houston, 6431 Fannin Street, Houston, TX 77030, USA.
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52
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Elaid S, Libersou S, Ouldali M, Morellet N, Desbat B, Alves ID, Lepault J, Bouaziz S. A peptide derived from the rotavirus outer capsid protein VP7 permeabilizes artificial membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2026-35. [DOI: 10.1016/j.bbamem.2014.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 04/02/2014] [Accepted: 04/07/2014] [Indexed: 01/02/2023]
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Structure of β-galactosidase at 3.2-Å resolution obtained by cryo-electron microscopy. Proc Natl Acad Sci U S A 2014; 111:11709-14. [PMID: 25071206 DOI: 10.1073/pnas.1402809111] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report the solution structure of Escherichia coli β-galactosidase (∼465 kDa), solved at ∼3.2-Å resolution by using single-particle cryo-electron microscopy (cryo-EM). Densities for most side chains, including those of residues in the active site, and a catalytic Mg(2+) ion can be discerned in the map obtained by cryo-EM. The atomic model derived from our cryo-EM analysis closely matches the 1.7-Å crystal structure with a global rmsd of ∼0.66 Å. There are significant local differences throughout the protein, with clear evidence for conformational changes resulting from contact zones in the crystal lattice. Inspection of the map reveals that although densities for residues with positively charged and neutral side chains are well resolved, systematically weaker densities are observed for residues with negatively charged side chains. We show that the weaker densities for negatively charged residues arise from their greater sensitivity to radiation damage from electron irradiation as determined by comparison of density maps obtained by using electron doses ranging from 10 to 30 e(-)/Å(2). In summary, we establish that it is feasible to use cryo-EM to determine near-atomic resolution structures of protein complexes (<500 kDa) with low symmetry, and that the residue-specific radiation damage that occurs with increasing electron dose can be monitored by using dose fractionation tools available with direct electron detector technology.
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Predicted structure and domain organization of rotavirus capping enzyme and innate immune antagonist VP3. J Virol 2014; 88:9072-85. [PMID: 24899176 DOI: 10.1128/jvi.00923-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
UNLABELLED Rotaviruses and orbiviruses are nonturreted Reoviridae members. The rotavirus VP3 protein is a multifunctional capping enzyme and antagonist of the interferon-induced cellular oligoadenylate synthetase-RNase L pathway. Despite mediating important processes, VP3 is the sole protein component of the rotavirus virion whose structure remains unknown. In the current study, we used sequence alignment and homology modeling to identify features common to nonturreted Reoviridae capping enzymes and to predict the domain organization, structure, and active sites of rotavirus VP3. Our results suggest that orbivirus and rotavirus capping enzymes share a domain arrangement similar to that of the bluetongue virus capping enzyme. Sequence alignments revealed conserved motifs and suggested that rotavirus and orbivirus capping enzymes contain a variable N-terminal domain, a central guanine-N7-methyltransferase domain that contains an additional inserted domain, and a C-terminal guanylyltransferase and RNA 5'-triphosphatase domain. Sequence conservation and homology modeling suggested that the insertion in the guanine-N7-methyltransferase domain is a ribose-2'-O-methyltransferase domain for most rotavirus species. Our analyses permitted putative identification of rotavirus VP3 active-site residues, including those that form the ribose-2'-O-methyltransferase catalytic tetrad, interact with S-adenosyl-l-methionine, and contribute to autoguanylation. Previous reports have indicated that group A rotavirus VP3 contains a C-terminal 2H-phosphodiesterase domain that can cleave 2'-5' oligoadenylates, thereby preventing RNase L activation. Our results suggest that a C-terminal phosphodiesterase domain is present in the capping enzymes from two additional rotavirus species. Together, these findings provide insight into a poorly understood area of rotavirus biology and are a springboard for future biochemical and structural studies of VP3. IMPORTANCE Rotaviruses are an important cause of severe diarrheal disease. The rotavirus VP3 protein caps viral mRNAs and helps combat cellular innate antiviral defenses, but little is known about its structure or enzymatic mechanisms. In this study, we used sequence- and structure-based alignments with related proteins to predict the structure of VP3 and identify enzymatic domains and active sites therein. This work provides insight into the mechanisms of rotavirus transcription and evasion of host innate immune defenses. An improved understanding of these processes may aid our ability to develop rotavirus vaccines and therapeutics.
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New insights into rotavirus entry machinery: stabilization of rotavirus spike conformation is independent of trypsin cleavage. PLoS Pathog 2014; 10:e1004157. [PMID: 24873828 PMCID: PMC4038622 DOI: 10.1371/journal.ppat.1004157] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 04/16/2014] [Indexed: 12/31/2022] Open
Abstract
The infectivity of rotavirus, the main causative agent of childhood diarrhea, is dependent on activation of the extracellular viral particles by trypsin-like proteases in the host intestinal lumen. This step entails proteolytic cleavage of the VP4 spike protein into its mature products, VP8* and VP5*. Previous cryo-electron microscopy (cryo-EM) analysis of trypsin-activated particles showed well-resolved spikes, although no density was identified for the spikes in uncleaved particles; these data suggested that trypsin activation triggers important conformational changes that give rise to the rigid, entry-competent spike. The nature of these structural changes is not well understood, due to lack of data relative to the uncleaved spike structure. Here we used cryo-EM and cryo-electron tomography (cryo-ET) to characterize the structure of the uncleaved virion in two model rotavirus strains. Cryo-EM three-dimensional reconstruction of uncleaved virions showed spikes with a structure compatible with the atomic model of the cleaved spike, and indistinguishable from that of digested particles. Cryo-ET and subvolume average, combined with classification methods, resolved the presence of non-icosahedral structures, providing a model for the complete structure of the uncleaved spike. Despite the similar rigid structure observed for uncleaved and cleaved particles, trypsin activation is necessary for successful infection. These observations suggest that the spike precursor protein must be proteolytically processed, not to achieve a rigid conformation, but to allow the conformational changes that drive virus entry. Rotavirus is responsible for more than 400,000 annual infant deaths worldwide. Its viral particle bears 60 protuberant spikes that constitute the machinery responsible for virus binding to and entry into the host cell. For efficient infection, the protein molecules that build the spike must be cleaved. Despite the importance of this activation step, the nature of the changes induced in the spike structure is unknown. According to the current hypothesis, the uncleaved spike is very flexible, and activation stabilizes the spike in an entry-competent conformation. Here we used distinct electron microscopy techniques to determine the structure of the uncleaved particle in two model rotavirus strains. Our results provide a complete structure of the uncleaved spike and demonstrate that cleaved and uncleaved spikes have similar conformations, indicating that proteolytic processing is not involved in stabilization of the spike. We suggest that spike processing is important for infection since it is necessary to allow the spike domain movements involved in rotavirus entry.
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Rohou A, Grigorieff N. Frealix: model-based refinement of helical filament structures from electron micrographs. J Struct Biol 2014; 186:234-44. [PMID: 24657230 DOI: 10.1016/j.jsb.2014.03.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 03/12/2014] [Accepted: 03/13/2014] [Indexed: 12/20/2022]
Abstract
The structures of many helical protein filaments can be derived from electron micrographs of their suspensions in thin films of vitrified aqueous solutions. The most successful and generally-applicable approach treats short segments of these filaments as independent "single particles", yielding near-atomic resolution for rigid and well-ordered filaments. The single-particle approach can also accommodate filament deformations, yielding sub-nanometer resolution for more flexible filaments. However, in the case of thin and flexible filaments, such as some amyloid-β (Aβ) fibrils, the single-particle approach may fail because helical segments can be curved or otherwise distorted and their alignment can be inaccurate due to low contrast in the micrographs. We developed new software called Frealix that allows the use of arbitrarily short filament segments during alignment to approximate even high curvatures. All segments in a filament are aligned simultaneously with constraints that ensure that they connect to each other in space to form a continuous helical structure. In this paper, we describe the algorithm and benchmark it against datasets of Aβ(1-40) fibrils and tobacco mosaic virus (TMV), both analyzed in earlier work. In the case of TMV, our algorithm achieves similar results to single-particle analysis. In the case of Aβ(1-40) fibrils, we match the previously-obtained resolution but we are also able to obtain reliable alignments and ∼8-Å reconstructions from curved filaments. Our algorithm also offers a detailed characterization of filament deformations in three dimensions and enables a critical evaluation of the worm-like chain model for biological filaments.
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Affiliation(s)
- Alexis Rohou
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA; Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Nikolaus Grigorieff
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA; Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.
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Workshop on the validation and modeling of electron cryo-microscopy structures of biological nanomachines. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2013. [PMID: 21121065 DOI: 10.1142/9789814335058_0039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Electron cryo-microscopy (cryoEM) is a rapidly maturing methodology in structural biology, which now enables the determination of 3D structures of molecules, macromolecular complexes and cellular components at resolutions as high as 3.5Å, bridging the gap between light microscopy and X-ray crystallography/NMR. In recent years structures of many complex molecular machines have been visualized using this method. Single particle reconstruction, the most widely used technique in cryoEM, has recently demonstrated the capability of producing structures at resolutions approaching those of X-ray crystallography, with over a dozen structures at better than 5 Å resolution published to date. This method represents a significant new source of experimental data for molecular modeling and simulation studies. CryoEM derived maps and models are archived through EMDataBank.org joint deposition services to the EM Data Bank (EMDB) and Protein Data Bank (PDB), respectively. CryoEM maps are now being routinely produced over the 3 - 30 Å resolution range, and a number of computational groups are developing software for building coordinate models based on this data and developing validation techniques to better assess map and model accuracy. In this workshop we will present the results of the first cryoEM modeling challenge, in which computational groups were asked to apply their tools to a selected set of published cryoEM structures. We will also compare the results of the various applied methods, and discuss the current state of the art and how we can most productively move forward.
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58
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High-resolution 3D structures reveal the biological functions of reoviruses. Virol Sin 2013; 28:318-25. [PMID: 24254888 DOI: 10.1007/s12250-013-3341-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Accepted: 09/30/2013] [Indexed: 02/07/2023] Open
Abstract
Viruses in the family Reoviridae are non-enveloped particles comprising a segmented double-stranded RNA genome surrounded by a two-layered or multi-layered icosahedral protein capsid. These viruses are classified into two sub-families based on their particle structural organization. Recent studies have focused on high-resolution three-dimensional structures of reovirus particles by using cryo-electron microscopy (cryo-EM) to approach the resolutions seen in X-ray crystallographic structures. The results of cryo-EM image reconstructions allow tracing of most of the protein side chains, and thus permit integration of structural and functional information into a coherent mechanism for reovirus assembly and entry.
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59
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Li X, Zheng SQ, Egami K, Agard DA, Cheng Y. Influence of electron dose rate on electron counting images recorded with the K2 camera. J Struct Biol 2013; 184:251-60. [PMID: 23968652 PMCID: PMC3854003 DOI: 10.1016/j.jsb.2013.08.005] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 08/12/2013] [Accepted: 08/13/2013] [Indexed: 11/24/2022]
Abstract
A recent technological breakthrough in electron cryomicroscopy (cryoEM) is the development of direct electron detection cameras for data acquisition. By bypassing the traditional phosphor scintillator and fiber optic coupling, these cameras have greatly enhanced sensitivity and detective quantum efficiency (DQE). Of the three currently available commercial cameras, the Gatan K2 Summit was designed specifically for counting individual electron events. Counting further enhances the DQE, allows for practical doubling of detector resolution and eliminates noise arising from the variable deposition of energy by each primary electron. While counting has many advantages, undercounting of electrons happens when more than one electron strikes the same area of the detector within the analog readout period (coincidence loss), which influences image quality. In this work, we characterized the K2 Summit in electron counting mode, and studied the relationship of dose rate and coincidence loss and its influence on the quality of counted images. We found that coincidence loss reduces low frequency amplitudes but has no significant influence on the signal-to-noise ratio of the recorded image. It also has little influence on high frequency signals. Images of frozen hydrated archaeal 20S proteasome (~700 kDa, D7 symmetry) recorded at the optimal dose rate retained both high-resolution signal and low-resolution contrast and enabled calculating a 3.6 Å three-dimensional reconstruction from only 10,000 particles.
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Affiliation(s)
- Xueming Li
- The Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158, United States
| | - Shawn Q. Zheng
- The Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158, United States
- The Howard Hughes Medical Institute, University of California San Francisco, 600 16th Street, San Francisco, CA 94158, United States
| | - Kiyoshi Egami
- The Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158, United States
- Graduate Group in Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158, United States
| | - David A. Agard
- The Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158, United States
- The Howard Hughes Medical Institute, University of California San Francisco, 600 16th Street, San Francisco, CA 94158, United States
| | - Yifan Cheng
- The Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158, United States
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60
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Wentzel JF, Yuan L, Rao S, van Dijk AA, O'Neill HG. Consensus sequence determination and elucidation of the evolutionary history of a rotavirus Wa variant reveal a close relationship to various Wa variants derived from the original Wa strain. INFECTION GENETICS AND EVOLUTION 2013; 20:276-83. [PMID: 24056015 DOI: 10.1016/j.meegid.2013.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 08/14/2013] [Accepted: 09/03/2013] [Indexed: 10/26/2022]
Abstract
The consensus nucleotide sequence of a human rotavirus Wa strain, with only a partially known passage history, was determined with sequence-independent amplification and next generation 454® pyrosequencing. This rotavirus Wa strain had the expected genome constellation of G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 and was designated RVA/Human-tc/USA/WaCS/1974/G1P[8]. Phylogenetic analyses revealed a close relationship to four human rotavirus Wa variants (Wag5re, Wag7/8re, ParWa and VirWa) derived from the original 1974 human isolate. There were rearrangements in the Wag5re- and Wag7/8re variants in genome segments 5 (Wag5re) and 7 and 8 (Wag7/8re), which were not present in WaCS. Pairwise comparisons and a combined molecular clock for the Wa rotavirus genome indicated a close relationship between WaCS and ParWa and VirWa. These results suggest that WaCS is most probably an early cell culture adapted variant from the initial gnotobiotic pig passaged Wa isolate. Evolutionary pressure analysis identified a possible negative selected amino acid site in VP1 (genome segment 1) and a likely positive selected site in VP4 (genome segment 4). The WaCS may be more appropriate as a rotavirus Wa reference sequence than the current composite Wa reference genome.
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Affiliation(s)
- Johannes F Wentzel
- Biochemistry Division, North-West University, Potchefstroom, South Africa
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61
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Veesler D, Campbell MG, Cheng A, Fu CY, Murez Z, Johnson JE, Potter CS, Carragher B. Maximizing the potential of electron cryomicroscopy data collected using direct detectors. J Struct Biol 2013; 184:193-202. [PMID: 24036281 DOI: 10.1016/j.jsb.2013.09.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Revised: 08/28/2013] [Accepted: 09/03/2013] [Indexed: 11/26/2022]
Abstract
Single-particle electron cryomicroscopy is undergoing a technical revolution due to the recent developments of direct detectors. These new recording devices detect electrons directly (i.e. without conversion into light) and feature significantly improved detective quantum efficiencies and readout rates as compared to photographic films or CCDs. We evaluated here the potential of one such detector (Gatan K2 Summit) to enable the achievement of near-atomic resolution reconstructions of biological specimens when coupled to a widely used, mid-range transmission electron microscope (FEI TF20 Twin). Compensating for beam-induced motion and stage drift provided a 4.4Å resolution map of Sulfolobus turreted icosahedral virus (STIV), which we used as a test particle in this study. Several motion correction and dose fractionation procedures were explored and we describe their influence on the resolution of the final reconstruction. We also compared the quality of this data to that collected with a FEI Titan Krios microscope equipped with a Falcon I direct detector, which provides a benchmark for data collected using a high-end electron microscope.
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Affiliation(s)
- David Veesler
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037.,National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, CA 92037
| | - Melody G Campbell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037.,National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, CA 92037
| | - Anchi Cheng
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037.,National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, CA 92037
| | - Chi-Yu Fu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Zachary Murez
- Department of Computer Science and Engineering, University of California, San Diego, CA 92093
| | - John E Johnson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Clinton S Potter
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037.,National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, CA 92037
| | - Bridget Carragher
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037.,National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, CA 92037
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Rotavirus NSP4 Triggers Secretion of Proinflammatory Cytokines from Macrophages via Toll-Like Receptor 2. J Virol 2013; 87:11160-7. [PMID: 23926349 DOI: 10.1128/jvi.03099-12] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Nonstructural protein 4 (NSP4), encoded by rotavirus, exhibits various properties linked to viral pathogenesis, including enterotoxic activity. A recent study (O. V. Kavanagh et al., Vaccine 28:3106-3111, 2010) indicated that NSP4 also has adjuvant properties, suggesting a possible role in the innate immune response to rotavirus infection. We report here that NSP4 purified from the medium of rotavirus-infected Caco-2 cells triggers the secretion of proinflammatory cytokines from macrophage-like THP-1 cells and nitric oxide from murine RAW 264.7 cells. Secretion is accompanied by the stimulation of p38 and JNK mitogen-activated protein kinases (MAPKs) and nuclear factor NF-κB. NSP4 triggered the secretion of cytokines from murine macrophages derived from wild-type but not MyD88(-/-) or Toll-like receptor 2 (TLR2(-/-)) mice and induced secretion of interleukin-8 (IL-8) from human embryonic kidney cells transfected with TLR2 but not TLR4. Our studies identify NSP4 as a pathogen-associated molecular pattern (PAMP) encoded by rotavirus and provide a mechanism for the production of proinflammatory cytokines associated with the clinical symptoms of infection in humans and animals.
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63
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Lyumkis D, Brilot AF, Theobald DL, Grigorieff N. Likelihood-based classification of cryo-EM images using FREALIGN. J Struct Biol 2013; 183:377-388. [PMID: 23872434 DOI: 10.1016/j.jsb.2013.07.005] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 07/03/2013] [Accepted: 07/09/2013] [Indexed: 10/26/2022]
Abstract
We describe an implementation of maximum likelihood classification for single particle electron cryo-microscopy that is based on the FREALIGN software. Particle alignment parameters are determined by maximizing a joint likelihood that can include hierarchical priors, while classification is performed by expectation maximization of a marginal likelihood. We test the FREALIGN implementation using a simulated dataset containing computer-generated projection images of three different 70S ribosome structures, as well as a publicly available dataset of 70S ribosomes. The results show that the mixed strategy of the new FREALIGN algorithm yields performance on par with other maximum likelihood implementations, while remaining computationally efficient.
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Affiliation(s)
- Dmitry Lyumkis
- National Resource for Automated Molecular Microscopy, Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Axel F Brilot
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, MS029, 415 South Street, Waltham, MA 02454, USA
| | - Douglas L Theobald
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, MS029, 415 South Street, Waltham, MA 02454, USA
| | - Nikolaus Grigorieff
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, MS029, 415 South Street, Waltham, MA 02454, USA; Howard Hughes Medical Institute, Brandeis University, MS029, 415 South Street, Waltham, MA 02454, USA.
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64
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Carreño-Fuentes L, Ascencio JA, Medina A, Aguila S, Palomares LA, Ramírez OT. Strategies for specifically directing metal functionalization of protein nanotubes: constructing protein coated silver nanowires. NANOTECHNOLOGY 2013; 24:235602. [PMID: 23676195 DOI: 10.1088/0957-4484/24/23/235602] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Biological molecules that self-assemble in the nanoscale range are useful multifunctional materials. Rotavirus VP6 protein self-assembles into tubular structures in the absence of other rotavirus proteins. Here, we present strategies for selectively directing metal functionalization to the lumen of VP6 nanotubes. The specific in situ metal reduction in the inner surface of nanotube walls was achieved by the simple modification of a method previously reported to functionalize the nanotube outer surface. Silver nanorods and nanowires as long as 1.5 μm were formed inside the nanotubes by coalescence of nanoparticles. Such one-dimensional structures were longer than others previously obtained using bioscaffolds. The interactions between silver ions and the nanotube were simulated to understand the conditions that allowed nanowire formation. Molecular docking showed that a naturally occurring arrangement of aspartate residues enabled the stabilization of silver ions on the internal surface of the VP6 nanotubes. This is the first time that such a spatial arrangement has been proposed for the nucleation of silver nanoparticles, opening the possibility of using such an array to direct functionalization of other biomolecules. These results demonstrate the natural capabilities of VP6 nanotubes to function as a versatile biotemplate for nanomaterials.
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Affiliation(s)
- Liliana Carreño-Fuentes
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, AP 510-3, CP 62250, Cuernavaca, Morelos, Mexico
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65
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Aiyegbo MS, Sapparapu G, Spiller BW, Eli IM, Williams DR, Kim R, Lee DE, Liu T, Li S, Woods VL, Nannemann DP, Meiler J, Stewart PL, Crowe JE. Human rotavirus VP6-specific antibodies mediate intracellular neutralization by binding to a quaternary structure in the transcriptional pore. PLoS One 2013; 8:e61101. [PMID: 23671563 PMCID: PMC3650007 DOI: 10.1371/journal.pone.0061101] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 03/05/2013] [Indexed: 11/17/2022] Open
Abstract
Several live attenuated rotavirus (RV) vaccines have been licensed, but the mechanisms of protective immunity are still poorly understood. The most frequent human B cell response is directed to the internal protein VP6 on the surface of double-layered particles, which is normally exposed only in the intracellular environment. Here, we show that the canonical VP6 antibodies secreted by humans bind to such particles and inhibit viral transcription. Polymeric IgA RV antibodies mediated an inhibitory effect against virus replication inside cells during IgA transcytosis. We defined the recognition site on VP6 as a quaternary epitope containing a high density of charged residues. RV human mAbs appear to bind to a negatively-charged patch on the surface of the Type I channel in the transcriptionally active particle, and they sterically block the channel. This unique mucosal mechanism of viral neutralization, which is not apparent from conventional immunoassays, may contribute significantly to human immunity to RV.
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Affiliation(s)
- Mohammed S Aiyegbo
- Department of Pathology, Microbiology and Immunology, Vanderbilt Medical Center, Nashville, Tennessee, USA
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Li X, Mooney P, Zheng S, Booth CR, Braunfeld MB, Gubbens S, Agard DA, Cheng Y. Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat Methods 2013; 10:584-90. [PMID: 23644547 PMCID: PMC3684049 DOI: 10.1038/nmeth.2472] [Citation(s) in RCA: 1389] [Impact Index Per Article: 126.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Accepted: 04/03/2013] [Indexed: 11/21/2022]
Abstract
In recent work with large high symmetry viruses, single particle electron cryomicroscopy (cryoEM) has reached the milestone of determining near atomic resolution structures by allowing direct fitting of atomic models into experimental density maps. However, achieving this goal with smaller particles of lower symmetry remains extraordinarily challenging. Using a newly developed single electron counting detector, we confirm that electron beam induced motion significantly degrades resolution and, importantly, show how the combination of rapid readout and nearly noiseless electron counting allow image blurring to be corrected to subpixel accuracy. Thus, intrinsic image information can be restored to high resolution (Thon rings visible to ~3 Å). Using this approach we determined a 3.3 Å resolution structure of a ~700 kDa protein with D7 symmetry showing clear side chain density. Our method greatly enhances image quality and data acquisition efficiency - key bottlenecks in applying near atomic resolution cryoEM to a broad range of protein samples.
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67
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Schenk AD, Philippsen A, Engel A, Walz T. A pipeline for comprehensive and automated processing of electron diffraction data in IPLT. J Struct Biol 2013; 182:173-85. [PMID: 23500887 DOI: 10.1016/j.jsb.2013.02.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 02/27/2013] [Indexed: 11/25/2022]
Abstract
Electron crystallography of two-dimensional crystals allows the structural study of membrane proteins in their native environment, the lipid bilayer. Determining the structure of a membrane protein at near-atomic resolution by electron crystallography remains, however, a very labor-intense and time-consuming task. To simplify and accelerate the data processing aspect of electron crystallography, we implemented a pipeline for the processing of electron diffraction data using the Image Processing Library and Toolbox (IPLT), which provides a modular, flexible, integrated, and extendable cross-platform, open-source framework for image processing. The diffraction data processing pipeline is organized as several independent modules implemented in Python. The modules can be accessed either from a graphical user interface or through a command line interface, thus meeting the needs of both novice and expert users. The low-level image processing algorithms are implemented in C++ to achieve optimal processing performance, and their interface is exported to Python using a wrapper. For enhanced performance, the Python processing modules are complemented with a central data managing facility that provides a caching infrastructure. The validity of our data processing algorithms was verified by processing a set of aquaporin-0 diffraction patterns with the IPLT pipeline and comparing the resulting merged data set with that obtained by processing the same diffraction patterns with the classical set of MRC programs.
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Affiliation(s)
- Andreas D Schenk
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, USA.
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68
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Estrozi LF, Settembre EC, Goret G, McClain B, Zhang X, Chen JZ, Grigorieff N, Harrison SC. Location of the dsRNA-dependent polymerase, VP1, in rotavirus particles. J Mol Biol 2013; 425:124-32. [PMID: 23089332 PMCID: PMC3540981 DOI: 10.1016/j.jmb.2012.10.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 10/07/2012] [Accepted: 10/11/2012] [Indexed: 10/27/2022]
Abstract
Double-stranded RNA (dsRNA) viruses transcribe and replicate RNA within an assembled, inner capsid particle; only plus-sense mRNA emerges into the intracellular milieu. During infectious entry of a rotavirus particle, the outer layer of its three-layer structure dissociates, delivering the inner double-layered particle (DLP) into the cytosol. DLP structures determined by X-ray crystallography and electron cryomicroscopy (cryoEM) show that the RNA coils uniformly into the particle interior, avoiding a "fivefold hub" of more structured density projecting inward from the VP2 shell of the DLP along each of the twelve 5-fold axes. Analysis of the X-ray crystallographic electron density map suggested that principal contributors to the hub are the N-terminal arms of VP2, but reexamination of the cryoEM map has shown that many features come from a molecule of VP1, randomly occupying five equivalent and partly overlapping positions. We confirm here that the electron density in the X-ray map leads to the same conclusion, and we describe the functional implications of the orientation and position of the polymerase. The exit channel for the nascent transcript directs the nascent transcript toward an opening along the 5-fold axis. The template strand enters from within the particle, and the dsRNA product of the initial replication step exits in a direction tangential to the inner surface of the VP2 shell, allowing it to coil optimally within the DLP. The polymerases of reoviruses appear to have similar positions and functional orientations.
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Affiliation(s)
- Leandro F Estrozi
- European Molecular Biology Laboratory, Grenoble Outstation, 6 Rue Jules Horowitz, Grenoble 38042, France.
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69
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Movies of ice-embedded particles enhance resolution in electron cryo-microscopy. Structure 2012; 20:1823-8. [PMID: 23022349 DOI: 10.1016/j.str.2012.08.026] [Citation(s) in RCA: 216] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 08/25/2012] [Accepted: 08/30/2012] [Indexed: 11/23/2022]
Abstract
Low-dose images obtained by electron cryo-microscopy (cryo-EM) are often affected by blurring caused by sample motion during electron beam exposure, degrading signal especially at high resolution. We show here that we can align frames of movies, recorded with a direct electron detector during beam exposure of rotavirus double-layered particles, thereby greatly reducing image blurring caused by beam-induced motion and sample stage instabilities. This procedure increases the efficiency of cryo-EM imaging and enhances the resolution obtained in three-dimensional reconstructions of the particle. Using movies in this way is generally applicable to all cryo-EM samples and should also improve the performance of midrange electron microscopes that may have limited mechanical stability and beam coherence.
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70
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Scheres SHW. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol 2012; 180:519-30. [PMID: 23000701 PMCID: PMC3690530 DOI: 10.1016/j.jsb.2012.09.006] [Citation(s) in RCA: 3671] [Impact Index Per Article: 305.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 09/03/2012] [Accepted: 09/06/2012] [Indexed: 11/17/2022]
Abstract
RELION, for REgularized LIkelihood OptimizatioN, is an open-source computer program for the refinement of macromolecular structures by single-particle analysis of electron cryo-microscopy (cryo-EM) data. Whereas alternative approaches often rely on user expertise for the tuning of parameters, RELION uses a Bayesian approach to infer parameters of a statistical model from the data. This paper describes developments that reduce the computational costs of the underlying maximum a posteriori (MAP) algorithm, as well as statistical considerations that yield new insights into the accuracy with which the relative orientations of individual particles may be determined. A so-called gold-standard Fourier shell correlation (FSC) procedure to prevent overfitting is also described. The resulting implementation yields high-quality reconstructions and reliable resolution estimates with minimal user intervention and at acceptable computational costs.
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Affiliation(s)
- Sjors H W Scheres
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.
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71
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Baker ML, Baker MR, Hryc CF, Ju T, Chiu W. Gorgon and pathwalking: macromolecular modeling tools for subnanometer resolution density maps. Biopolymers 2012; 97:655-68. [PMID: 22696403 PMCID: PMC3899894 DOI: 10.1002/bip.22065] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The complex interplay of proteins and other molecules, often in the form of large transitory assemblies, are critical to cellular function. Today, X-ray crystallography and electron cryo-microscopy (cryo-EM) are routinely used to image these macromolecular complexes, though often at limited resolutions. Despite the rapidly growing number of macromolecular structures, few tools exist for modeling and annotating structures in the range of 3-10 Å resolution. To address this need, we have developed a number of utilities specifically targeting subnanometer resolution density maps. As part of the 2010 Cryo-EM Modeling Challenge, we demonstrated two of our latest de novo modeling tools, Pathwalking and Gorgon, as well as a tool for secondary structure identification (SSEHunter) and a new rigid-body/flexible fitting tool in Gorgon. In total, we submitted 30 structural models from ten different subnanometer resolution data sets in four of the six challenge categories. Each of our utlities produced accurate structural models and annotations across the various density maps. In the end, the utilities that we present here offer users a robust toolkit for analyzing and modeling protein structure in macromolecular assemblies at non-atomic resolutions.
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Affiliation(s)
- Matthew L Baker
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA.
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72
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Abstract
Electron cryo-microscopy (cryo-EM) is a technique in structural biology that is widely used to solve the three-dimensional structures of macromolecular assemblies, close to their biological and solution conditions. Recent improvements in cryo-EM and single-particle reconstruction methodologies have led to the determination of several virus structures at near-atomic resolution (3.3 - 4.6 Å). These cryo-EM structures not only resolve the Cα backbones and side-chain densities of viral capsid proteins, but also suggest functional roles that the protein domains and some key amino acid residues play. This paper reviews the recent advances in near-atomic-resolution cryo-EM for probing the mechanisms of virus assembly and morphogenesis.
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73
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Ghosh A, Chattopadhyay S, Chawla-Sarkar M, Nandy P, Nandy A. In silico study of rotavirus VP7 surface accessible conserved regions for antiviral drug/vaccine design. PLoS One 2012; 7:e40749. [PMID: 22844409 PMCID: PMC3406019 DOI: 10.1371/journal.pone.0040749] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 06/12/2012] [Indexed: 11/23/2022] Open
Abstract
Background Rotaviral diarrhoea kills about half a million children annually in developing countries and accounts for one third of diarrhea related hospitalizations. Drugs and vaccines against the rotavirus are handicapped, as in all viral diseases, by the rapid mutational changes that take place in the DNA and protein sequences rendering most of these ineffective. As of now only two vaccines are licensed and approved by the WHO (World Health Organization), but display reduced efficiencies in the underdeveloped countries where the disease is more prevalent. We approached this issue by trying to identify regions of surface exposed conserved segments on the surface glycoproteins of the virion, which may then be targeted by specific peptide vaccines. We had developed a bioinformatics protocol for these kinds of problems with reference to the influenza neuraminidase protein, which we have refined and expanded to analyze the rotavirus issue. Results Our analysis of 433 VP7 (Viral Protein 7 from rotavirus) surface protein sequences across 17 subtypes encompassing mammalian hosts using a 20D Graphical Representation and Numerical Characterization method, identified four possible highly conserved peptide segments. Solvent accessibility prediction servers were used to identify that these are predominantly surface situated. These regions analyzed through selected epitope prediction servers for their epitopic properties towards possible T-cell and B-cell activation showed good results as epitopic candidates (only dry lab confirmation). Conclusions The main reasons for the development of alternative vaccine strategies for the rotavirus are the failure of current vaccines and high production costs that inhibit their application in developing countries. We expect that it would be possible to use the protein surface exposed regions identified in our study as targets for peptide vaccines and drug designs for stable immunity against divergent strains of the rotavirus. Though this study is fully dependent on computational prediction algorithms, it provides a platform for wet lab experiments.
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Affiliation(s)
- Ambarnil Ghosh
- Physics Department, Jadavpur University, Kolkata, West Bengal, India
| | - Shiladitya Chattopadhyay
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Mamta Chawla-Sarkar
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Papiya Nandy
- Physics Department, Jadavpur University, Kolkata, West Bengal, India
| | - Ashesh Nandy
- Centre for Interdisciplinary Research and Education, Kolkata, West Bengal, India
- * E-mail:
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74
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Lander GC, Saibil HR, Nogales E. Go hybrid: EM, crystallography, and beyond. Curr Opin Struct Biol 2012; 22:627-35. [PMID: 22835744 DOI: 10.1016/j.sbi.2012.07.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 06/21/2012] [Accepted: 07/09/2012] [Indexed: 01/30/2023]
Abstract
A mechanistic understanding of the molecular transactions that govern cellular function requires knowledge of the dynamic organization of the macromolecular machines involved in these processes. Structural biologists employ a variety of biophysical methods to study large macromolecular complexes, but no single technique is likely to provide a complete description of the structure-function relationship of all the constituent components. Since structural studies generally only provide snapshots of these dynamic machines as they accomplish their molecular functions, combining data from many methodologies is crucial to our understanding of molecular function.
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Affiliation(s)
- Gabriel C Lander
- Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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75
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Nagaoka Y, Tatsumi M, Tsugawa T, Yoto Y, Tsutsumi H. Phylogenetic and computational structural analysis of VP7 gene of group a human rotavirus G1P[8] strains obtained in Sapporo, Japan from 1987 to 2000. J Med Virol 2012; 84:832-8. [PMID: 22431033 DOI: 10.1002/jmv.23247] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Many studies indicate that G1P[8] genotypes are the most prevalent rotavirus strains worldwide. Although two vaccines have been licensed and their value proven in many countries, continuous surveillance for genetic evolution of circulating rotavirus strains before and after the introduction of the vaccines is desirable. G and P typing were carried out on all field strains isolated during 1987-2000 in Sapporo, Japan. Phylogenetic analysis for the VP7 gene of rotavirus G1P[8] strains was performed. Amino acid substitutions were mapped on the predicted three-dimensional VP7 protein image. G1P[8] genotype predominated. One hundred thirteen strains with G1P[8] genotype were analyzed. Phylogenetic studies of the VP7 gene classified these strains into three lineages. The mean estimated substitution rate was 7.25 × 10(-4) nucleotide substitutions per site per year. One predominant lineage contained the mutant strains which had VP7 amino acid substitutions at residue 91 and 212 that is in the neutralization domains. They were estimated to locate in or near intersubunit boundary of VP7 trimer. It is suggested that the most prevalent G1P[8] lineage strains in Sapporo obtained some survival advantages by changing the neutralization domains of VP7.
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Affiliation(s)
- Yoshinobu Nagaoka
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan.
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76
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De Lorenzo G, Eichwald C, Schraner EM, Nicolin V, Bortul R, Mano M, Burrone OR, Arnoldi F. Production of in vivo-biotinylated rotavirus particles. J Gen Virol 2012; 93:1474-1482. [DOI: 10.1099/vir.0.040089-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although inserting exogenous viral genome segments into rotavirus particles remains a hard challenge, this study describes the in vivo incorporation of a recombinant viral capsid protein (VP6) into newly assembled rotavirus particles. In vivo biotinylation technology was exploited to biotinylate a recombinant VP6 protein fused to a 15 aa biotin-acceptor peptide (BAP) by the bacterial biotin ligase BirA contextually co-expressed in mammalian cells. To avoid toxicity of VP6 overexpression, a stable HEK293 cell line was constructed with tetracycline-inducible expression of VP6–BAP and constitutive expression of BirA. Following tetracycline induction and rotavirus infection, VP6–BAP was biotinylated, recruited into viroplasms and incorporated into newly assembled virions. The biotin molecules in the capsid allowed the use of streptavidin-coated magnetic beads as a purification technique instead of CsCl gradient ultracentrifugation. Following transfection, double-layered particles attached to beads were able to induce viroplasm formation and to generate infective viral progeny.
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Affiliation(s)
- G. De Lorenzo
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - C. Eichwald
- Institute of Virology, University of Zürich, Winterthurerstrasse 260, CH-8057 Zürich, Switzerland
| | - E. M. Schraner
- Institute of Veterinary Anatomy, University of Zürich, Winterthurerstrasse 260, CH-8057 Zürich, Switzerland
- Institute of Virology, University of Zürich, Winterthurerstrasse 260, CH-8057 Zürich, Switzerland
| | - V. Nicolin
- Dipartimento Universitario Clinico di Scienze Mediche, Chirurgiche e della Salute, Strada di Fiume 447, 34149 Trieste, Italy
| | - R. Bortul
- Dipartimento Universitario Clinico di Scienze Mediche, Chirurgiche e della Salute, Strada di Fiume 447, 34149 Trieste, Italy
| | - M. Mano
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - O. R. Burrone
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - F. Arnoldi
- Dipartimento Universitario Clinico di Scienze Mediche, Chirurgiche e della Salute, Strada di Fiume 447, 34149 Trieste, Italy
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
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77
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Abstract
African horsesickness (AHS) is a devastating disease of horses. The disease is caused by the double-stranded RNA-containing African horsesickness virus (AHSV). Using electron cryomicroscopy and three-dimensional image reconstruction, we determined the architecture of an AHSV serotype 4 (AHSV-4) reference strain. The structure revealed triple-layered AHS virions enclosing the segmented genome and transcriptase complex. The innermost protein layer contains 120 copies of VP3, with the viral polymerase, capping enzyme, and helicase attached to the inner surface of the VP3 layer on the 5-fold axis, surrounded by double-stranded RNA. VP7 trimers form a second, T=13 layer on top of VP3. Comparative analyses of the structures of bluetongue virus and AHSV-4 confirmed that VP5 trimers form globular domains and VP2 trimers form triskelions, on the virion surface. We also identified an AHSV-7 strain with a truncated VP2 protein (AHSV-7 tVP2) which outgrows AHSV-4 in culture. Comparison of AHSV-7 tVP2 to bluetongue virus and AHSV-4 allowed mapping of two domains in AHSV-4 VP2, and one in bluetongue virus VP2, that are important in infection. We also revealed a protein plugging the 5-fold vertices in AHSV-4. These results shed light on virus-host interactions in an economically important orbivirus to help the informed design of new vaccines.
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78
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Trask SD, Ogden KM, Patton JT. Interactions among capsid proteins orchestrate rotavirus particle functions. Curr Opin Virol 2012; 2:373-9. [PMID: 22595300 DOI: 10.1016/j.coviro.2012.04.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 04/23/2012] [Accepted: 04/24/2012] [Indexed: 11/16/2022]
Abstract
Rotaviruses are members of the Reoviridae family of non-enveloped viruses and important etiologic agents of acute gastroenteritis in infants and young children. In recent years, high-resolution structures of triple-layered rotavirus virions and the constituent proteins have provided valuable insights into functions. Of note, structural studies have revealed the position of the viral RNA-dependent RNA polymerase, VP1, within the inner capsid, which in turn provides clues about the location of the viral capping machinery and the route of viral transcript egress. Mechanisms by which the viral spike protein, VP4, mediates receptor binding and membrane penetration have also been aided by high-resolution structural studies. Future work may serve to fill the remaining gaps in understanding of rotavirus particle structure and function.
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Affiliation(s)
- Shane D Trask
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-8026, USA
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79
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Chavez JD, Cilia M, Weisbrod CR, Ju HJ, Eng JK, Gray SM, Bruce JE. Cross-linking measurements of the Potato leafroll virus reveal protein interaction topologies required for virion stability, aphid transmission, and virus-plant interactions. J Proteome Res 2012; 11:2968-81. [PMID: 22390342 PMCID: PMC3402239 DOI: 10.1021/pr300041t] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein interactions are critical determinants of insect transmission for viruses in the family Luteoviridae. Two luteovirid structural proteins, the capsid protein (CP) and the readthrough protein (RTP), contain multiple functional domains that regulate virus transmission. There is no structural information available for these economically important viruses. We used Protein Interaction Reporter (PIR) technology, a strategy that uses chemical cross-linking and high resolution mass spectrometry, to discover topological features of the Potato leafroll virus (PLRV) CP and RTP that are required for the diverse biological functions of PLRV virions. Four cross-linked sites were repeatedly detected, one linking CP monomers, two within the RTP, and one linking the RTP and CP. Virus mutants with triple amino acid deletions immediately adjacent to or encompassing the cross-linked sites were defective in virion stability, RTP incorporation into the capsid, and aphid transmission. Plants infected with a new, infectious PLRV mutant lacking 26 amino acids encompassing a cross-linked site in the RTP exhibited a delay in the appearance of systemic infection symptoms. PIR technology provided the first structural insights into luteoviruses which are crucially lacking and are involved in vector-virus and plant-virus interactions. These are the first cross-linking measurements on any infectious, insect-transmitted virus.
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Affiliation(s)
- Juan D. Chavez
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98109
| | - Michelle Cilia
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture, Agricultural Research Service, Ithaca, New York, 14853
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853
| | - Chad R. Weisbrod
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98109
| | - Ho-Jong Ju
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853
- Department of Agricultural Biology and Plant Medicinal Research Center, College of Agricultural & Life Sciences, Chonbuk National University, 664-14 Deokjin-Dong 1Ga Deokjin-Gu Jeonju Jeonbuk 561-756, South Korea
| | - Jimmy K. Eng
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98109
| | - Stewart M. Gray
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture, Agricultural Research Service, Ithaca, New York, 14853
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853
| | - James E. Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98109
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80
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Inka Borchers AM, Gonzalez-Rabade N, Gray JC. Increased accumulation and stability of rotavirus VP6 protein in tobacco chloroplasts following changes to the 5' untranslated region and the 5' end of the coding region. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:422-34. [PMID: 22257338 DOI: 10.1111/j.1467-7652.2011.00675.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Rotavirus is the main cause of gastroenteritis in children worldwide, and the World Health Organisation has recommended that a rotavirus vaccine should be included in all infant immunization programmes. VP6 is the most immunogenic rotavirus subunit and is a potential target for an oral subunit vaccine. VP6 accumulated at up to 3% of total soluble protein in the young leaves of transplastomic tobacco plants, but the protein was unstable and was lost as the leaves aged. The aim of this study was to alter the 5'-untranslated region (5'-UTR) and the 5' end of the coding region of VP6 cDNA in an attempt to increase the expression and stability of VP6 protein in tobacco chloroplasts. The inclusion of the 5'-UTR from gene 10 of bacteriophage T7 (T7g10) and the addition of 15 nucleotides, encoding five additional amino acid residues, at the 5' end of the coding region increased the expression to >15% of total leaf protein and stabilized the protein in ageing leaves. Plants containing VP6 expression constructs with the rbcL 5'-UTR and with the native VP6 5' end of the coding region produced VP6 protein at only 1.9% of total leaf protein. Both the T7g10 5'-UTR and the additional 15 nucleotides increased transcript accumulation and translational efficiency compared with VP6 constructs containing the rbcL 5'-UTR. The VP6 protein produced from all gene constructs appeared to be susceptible to proteolytic processing at its N-terminal region. However, in all transplastomic lines, VP6 proteins assembled into the trimeric form found in the rotavirus capsid.
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Affiliation(s)
- A-M Inka Borchers
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
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81
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Wu S, Avila-Sakar A, Kim J, Booth DS, Greenberg CH, Rossi A, Liao M, Li X, Alian A, Griner SL, Juge N, Yu Y, Mergel CM, Chaparro-Riggers J, Strop P, Tampé R, Edwards RH, Stroud RM, Craik CS, Cheng Y. Fabs enable single particle cryoEM studies of small proteins. Structure 2012; 20:582-92. [PMID: 22483106 PMCID: PMC3322386 DOI: 10.1016/j.str.2012.02.017] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2011] [Revised: 01/31/2012] [Accepted: 02/17/2012] [Indexed: 01/08/2023]
Abstract
In spite of its recent achievements, the technique of single particle electron cryomicroscopy (cryoEM) has not been widely used to study proteins smaller than 100 kDa, although it is a highly desirable application of this technique. One fundamental limitation is that images of small proteins embedded in vitreous ice do not contain adequate features for accurate image alignment. We describe a general strategy to overcome this limitation by selecting a fragment antigen binding (Fab) to form a stable and rigid complex with a target protein, thus providing a defined feature for accurate image alignment. Using this approach, we determined a three-dimensional structure of an ∼65 kDa protein by single particle cryoEM. Because Fabs can be readily generated against a wide range of proteins by phage display, this approach is generally applicable to study many small proteins by single particle cryoEM.
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Affiliation(s)
- Shenping Wu
- The W.M. Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158
| | - Agustin Avila-Sakar
- The W.M. Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158
| | - JungMin Kim
- Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, San Francisco, CA 94158
| | - David S. Booth
- The W.M. Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158
- Graduate Group in Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158
| | - Charles H. Greenberg
- The W.M. Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158
- Graduate Group in Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158
| | - Andrea Rossi
- Rinat Labs, Pfizer Inc., 230 East Grand Ave, South San Francisco, CA 94080
| | - Maofu Liao
- The W.M. Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158
| | - Xueming Li
- The W.M. Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158
| | - Akram Alian
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Sarah L. Griner
- Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158
| | - Narinobu Juge
- Department of Physiology and Department of Neurology, University of California San Francisco, 600 16th Street, San Francisco, CA 94158
| | - Yadong Yu
- The W.M. Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158
| | - Claudia M. Mergel
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | | | - Pavel Strop
- Rinat Labs, Pfizer Inc., 230 East Grand Ave, South San Francisco, CA 94080
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Robert H. Edwards
- Department of Physiology and Department of Neurology, University of California San Francisco, 600 16th Street, San Francisco, CA 94158
- California Institute of Quantitative Biosciences (QB3), University of California San Francisco, 600 16th Street, San Francisco, CA 94158
| | - Robert M. Stroud
- Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158
- California Institute of Quantitative Biosciences (QB3), University of California San Francisco, 600 16th Street, San Francisco, CA 94158
| | - Charles S. Craik
- Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, San Francisco, CA 94158
- California Institute of Quantitative Biosciences (QB3), University of California San Francisco, 600 16th Street, San Francisco, CA 94158
| | - Yifan Cheng
- The W.M. Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158
- California Institute of Quantitative Biosciences (QB3), University of California San Francisco, 600 16th Street, San Francisco, CA 94158
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82
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Beam-induced motion of vitrified specimen on holey carbon film. J Struct Biol 2012; 177:630-7. [PMID: 22366277 DOI: 10.1016/j.jsb.2012.02.003] [Citation(s) in RCA: 278] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 02/06/2012] [Accepted: 02/07/2012] [Indexed: 11/21/2022]
Abstract
The contrast observed in images of frozen-hydrated biological specimens prepared for electron cryo-microscopy falls significantly short of theoretical predictions. In addition to limits imposed by the current instrumentation, it is widely acknowledged that motion of the specimen during its exposure to the electron beam leads to significant blurring in the recorded images. We have studied the amount and direction of motion of virus particles suspended in thin vitrified ice layers across holes in perforated carbon films using exposure series. Our data show that the particle motion is correlated within patches of 0.3-0.5 μm, indicating that the whole ice layer is moving in a drum-like motion, with accompanying particle rotations of up to a few degrees. Support films with smaller holes, as well as lower electron dose rates tend to reduce beam-induced specimen motion, consistent with a mechanical effect. Finally, analysis of movies showing changes in the specimen during beam exposure show that the specimen moves significantly more at the start of an exposure than towards its end. We show how alignment and averaging of movie frames can be used to restore high-resolution detail in images affected by beam-induced motion.
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83
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Roldão A, Mellado MCM, Lima JC, Carrondo MJT, Alves PM, Oliveira R. On the effect of thermodynamic equilibrium on the assembly efficiency of complex multi-layered virus-like particles (VLP): the case of rotavirus VLP. PLoS Comput Biol 2012; 8:e1002367. [PMID: 22359487 PMCID: PMC3280969 DOI: 10.1371/journal.pcbi.1002367] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Accepted: 12/17/2011] [Indexed: 11/18/2022] Open
Abstract
Previous studies have reported the production of malformed virus-like-particles (VLP) in recombinant host systems. Here we computationally investigate the case of a large triple-layered rotavirus VLP (RLP). In vitro assembly, disassembly and reassembly data provides strong evidence of microscopic reversibility of RLP assembly. Light scattering experimental data also evidences a slow and reversible assembly untypical of kinetic traps, thus further strengthening the fidelity of a thermodynamically controlled assembly. In silico analysis further reveals that under favourable conditions particles distribution is dominated by structural subunits and completely built icosahedra, while other intermediates are present only at residual concentrations. Except for harshly unfavourable conditions, assembly yield is maximised when proteins are provided in the same VLP protein mass composition. The assembly yield decreases abruptly due to thermodynamic equilibrium when the VLP protein mass composition is not obeyed. The latter effect is more pronounced the higher the Gibbs free energy of subunit association is and the more complex the particle is. Overall this study shows that the correct formation of complex multi-layered VLPs is restricted to a narrow range of association energies and protein concentrations, thus the choice of the host system is critical for successful assembly. Likewise, the dynamic control of intracellular protein expression rates becomes very important to minimize wasted proteins.
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Affiliation(s)
- António Roldão
- Instituto de Tecnologia Química e Biológica-Universidade Nova de Lisboa (ITQB-UNL), Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica (IBET), Oeiras, Portugal
| | - Maria Candida M. Mellado
- Instituto de Tecnologia Química e Biológica-Universidade Nova de Lisboa (ITQB-UNL), Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica (IBET), Oeiras, Portugal
| | - J. C. Lima
- REQUIMTE, Faculdade de Ciências e Tecnologia/Universidade Nova de Lisboa (FCT/UNL), Caparica, Portugal
| | - Manuel J. T. Carrondo
- Instituto de Tecnologia Química e Biológica-Universidade Nova de Lisboa (ITQB-UNL), Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica (IBET), Oeiras, Portugal
- Faculdade de Ciências e Tecnologia/Universidade Nova de Lisboa (FCT/UNL), Monte de Caparica, Portugal
| | - Paula M. Alves
- Instituto de Tecnologia Química e Biológica-Universidade Nova de Lisboa (ITQB-UNL), Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica (IBET), Oeiras, Portugal
| | - R. Oliveira
- Instituto de Biologia Experimental e Tecnológica (IBET), Oeiras, Portugal
- REQUIMTE, Faculdade de Ciências e Tecnologia/Universidade Nova de Lisboa (FCT/UNL), Caparica, Portugal
- * E-mail:
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84
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Structural insights into the coupling of virion assembly and rotavirus replication. Nat Rev Microbiol 2012; 10:165-77. [PMID: 22266782 DOI: 10.1038/nrmicro2673] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Viral replication is rapid and robust, but it is far from a chaotic process. Instead, successful production of infectious progeny requires that events occur in the correct place and at the correct time. Rotaviruses (segmented double-stranded RNA viruses of the Reoviridae family) seem to govern their replication through ordered disassembly and assembly of a triple-layered icosahedral capsid. In recent years, high-resolution structural data have provided unprecedented insight into these events. In this Review, we explore the current understanding of rotavirus replication and how it compares to replication of other Reoviridae family members.
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85
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Reconstructing virus structures from nanometer to near-atomic resolutions with cryo-electron microscopy and tomography. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 726:49-90. [PMID: 22297510 DOI: 10.1007/978-1-4614-0980-9_4] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The past few decades have seen tremendous advances in single-particle electron -cryo-microscopy (cryo-EM). The field has matured to the point that near-atomic resolution density maps can be generated for icosahedral viruses without the need for crystallization. In parallel, substantial progress has been made in determining the structures of nonicosahedrally arranged proteins in viruses by employing either single-particle cryo-EM or cryo-electron tomography (cryo-ET). Implicit in this course have been the availability of a new generation of electron cryo-microscopes and the development of the computational tools that are essential for generating these maps and models. This methodology has enabled structural biologists to analyze structures in increasing detail for virus particles that are in different morphogenetic states. Furthermore, electron imaging of frozen, hydrated cells, in the process of being infected by viruses, has also opened up a new avenue for studying virus structures "in situ". Here we present the common techniques used to acquire and process cryo-EM and cryo-ET data and discuss their implications for structural virology both now and in the future.
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86
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Rochat R, Chiu W. 1.16 Cryo-Electron Microscopy and Tomography of Virus Particles. COMPREHENSIVE BIOPHYSICS 2012. [PMCID: PMC7151817 DOI: 10.1016/b978-0-12-374920-8.00120-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Human infectious disease is classified into five etiologies: bacterial, viral, parasitic, fungal, and prion. Viral infections are unique in that they recruit human cellular machinery to replicate themselves and spread infection. The number of viruses causing human disease is vast, and viruses can be broadly categorized by their structures. Many viruses, such as influenza, appear to be amorphous particles, whereas others, such as herpes simplex virus, rhinovirus, dengue virus, and adenovirus, have roughly symmetric structural components. Icosahedral viruses have been a target of electron microscopists for years, and they were some of the first objects to be reconstructed three-dimensionally from electron micrographs. The ease with which highly purified and conformationally uniform virus samples can be produced makes them an ideal target structural studies. Apart from their biological significance, these virus samples have played a pivotal role in the development of new methodologies in the field of molecular biology as well as in cryo-electron microscopy and cryo-electron tomography.
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87
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Lasker K, Velázquez-Muriel JA, Webb BM, Yang Z, Ferrin TE, Sali A. Macromolecular assembly structures by comparative modeling and electron microscopy. Methods Mol Biol 2012; 857:331-350. [PMID: 22323229 DOI: 10.1007/978-1-61779-588-6_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Advances in electron microscopy allow for structure determination of large biological machines at increasingly higher resolutions. A key step in this process is fitting component structures into the electron microscopy-derived density map of their assembly. Comparative modeling can contribute by providing atomic models of the components, via fold assignment, sequence-structure alignment, model building, and model assessment. All four stages of comparative modeling can also benefit from consideration of the density map. In this chapter, we describe numerous types of modeling problems restrained by a density map and available protocols for finding solutions. In particular, we provide detailed instructions for density map-guided modeling using the Integrative Modeling Platform (IMP), MODELLER, and UCSF Chimera.
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Affiliation(s)
- Keren Lasker
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
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88
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Yip CW, Hon CC, Zeng F, Leung FCC. Cell culture-adapted IBDV uses endocytosis for entry in DF-1 chicken embryonic fibroblasts. Virus Res 2011; 165:9-16. [PMID: 22230315 DOI: 10.1016/j.virusres.2011.12.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 12/20/2011] [Accepted: 12/23/2011] [Indexed: 11/19/2022]
Abstract
Although membrane perforation was suggested as the means of penetration mediated by IBDV, the cellular mechanism being hijacked to facilitate its entry is largely unknown. In this study, the entry pathway of cell culture adapted IBDV (caIBDV) was characterized in DF-1 chicken embryonic fibroblasts. We observed that the entry of caIBDV was inhibited by bafilomycin A1 and CaEGTA which interfere with the function of vacuolar H(+)-ATPase (V-ATPase) and retain endosomal Ca(2+). This result suggests that the intact caIBDV particle was transported to the V-ATPase positive vesicles for uncoating and implicates an essential role of endocytosis during the viral entry. The IBDV-mediated endocytosis was demonstrated to be clathrin-independent. Instead, the entry of caIBDV in DF-1 was reduced under the inhibitions or depletions of lipid raft, c-Src tyrosine kinase, dynamin and actin polymerization. In summary, this study confirmed the role of endocytosis in caIBDV entry and characterized the route of its endocytosis.
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Affiliation(s)
- Chi Wai Yip
- The School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region, China
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89
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Bajaj C, Goswami S, Zhang Q. Detection of secondary and supersecondary structures of proteins from cryo-electron microscopy. J Struct Biol 2011; 177:367-81. [PMID: 22186625 DOI: 10.1016/j.jsb.2011.11.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 11/09/2011] [Accepted: 11/15/2011] [Indexed: 11/30/2022]
Abstract
Recent advances in three-dimensional electron microscopy (3D EM) have enabled the quantitative visualization of the structural building blocks of proteins at improved resolutions. We provide algorithms to detect the secondary structures (α-helices and β-sheets) from proteins for which the volumetric maps are reconstructed at 6-10Å resolution. Additionally, we show that when the resolution is coarser than 10Å, some of the supersecondary structures can be detected from 3D EM maps. For both these algorithms, we employ tools from computational geometry and differential topology, specifically the computation of stable/unstable manifolds of certain critical points of the distance function induced by the molecular surface. Our results connect mathematically well-defined constructions with bio-chemically induced structures observed in proteins.
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Affiliation(s)
- Chandrajit Bajaj
- Center for Computational Visualization, The Institute for Computational Engineering and Sciences, Department of Computer Science, The University of Texas at Austin, University Station C0200, Austin, TX 78712, USA.
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90
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Tjioe E, Lasker K, Webb B, Wolfson HJ, Sali A. MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map. Nucleic Acids Res 2011; 39:W167-70. [PMID: 21715383 PMCID: PMC3125811 DOI: 10.1093/nar/gkr490] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Advances in electron microscopy (EM) allow for structure determination of large biological assemblies at increasingly higher resolutions. A key step in this process is fitting multiple component structures into an EM-derived density map of their assembly. Here, we describe a web server for this task. The server takes as input a set of protein structures in the PDB format and an EM density map in the MRC format. The output is an ensemble of models ranked by their quality of fit to the density map. The models can be viewed online or downloaded from the website. The service is available at; http://salilab.org/multifit/ and http://bioinfo3d.cs.tau.ac.il/.
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Affiliation(s)
- Elina Tjioe
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
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91
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Milazzo AC, Cheng A, Moeller A, Lyumkis D, Jacovetty E, Polukas J, Ellisman MH, Xuong NH, Carragher B, Potter CS. Initial evaluation of a direct detection device detector for single particle cryo-electron microscopy. J Struct Biol 2011; 176:404-8. [PMID: 21933715 DOI: 10.1016/j.jsb.2011.09.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Revised: 09/04/2011] [Accepted: 09/07/2011] [Indexed: 11/18/2022]
Abstract
We report on initial results of using a new direct detection device (DDD) for single particle reconstruction of vitreous ice embedded specimens. Images were acquired on a Tecnai F20 at 200keV and a nominal magnification of 29,000×. This camera has a significantly improved signal to noise ratio and modulation transfer function (MTF) at 200keV compared to a standard CCD camera installed on the same microscope. Control of the DDD has been integrated into Leginon, an automated data collection system. Using GroEL as a test specimen, we obtained images of ∼30K particles with the CCD and the DDD from the same specimen sample using essentially identical imaging conditions. Comparison of the maps reconstructed from the CCD images and the DDD images demonstrates the improved performance of the DDD. We also obtained a 3D reconstruction from ∼70K GroEL particles acquired using the DDD; the quality of the density map demonstrates the potential of this new recording device for cryoEM data acquisition.
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Affiliation(s)
- Anna-Clare Milazzo
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
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92
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Glaeser RM, Hall RJ. Reaching the information limit in cryo-EM of biological macromolecules: experimental aspects. Biophys J 2011; 100:2331-7. [PMID: 21575566 DOI: 10.1016/j.bpj.2011.04.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 03/29/2011] [Accepted: 04/07/2011] [Indexed: 01/19/2023] Open
Abstract
Although cryo-electron microscopy (cryo-EM) of biological macromolecules has made important advances in the past few years, the level of current technical performance is still well below what the physics of electron scattering would allow. It should be possible, for example, to use cryo-EM to solve protein structures at atomic resolution for particle sizes well below 80 kDa, but currently this has been achieved only for particles at least 10 times larger than that. In this review, we first examine some of the reasons for this large gap in performance. We then give an overview of work that is currently in progress to 1), improve the signal/noise ratio for area detectors; 2), improve the signal transfer between the scattered electrons and the corresponding images; and 3), reduce the extent to which beam-induced movement causes a steep fall-off of signal at high resolution. In each case, there is substantial reason to think that cryo-EM can indeed be made to approach the estimated physical limits.
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Affiliation(s)
- Robert M Glaeser
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, USA.
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93
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Zhang X, Zhou ZH. Limiting factors in atomic resolution cryo electron microscopy: no simple tricks. J Struct Biol 2011; 175:253-63. [PMID: 21627992 PMCID: PMC3710782 DOI: 10.1016/j.jsb.2011.05.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Revised: 05/03/2011] [Accepted: 05/05/2011] [Indexed: 01/25/2023]
Abstract
To bring cryo electron microscopy (cryoEM) of large biological complexes to atomic resolution, several factors--in both cryoEM image acquisition and 3D reconstruction--that may be neglected at low resolution become significantly limiting. Here we present thorough analyses of four limiting factors: (a) electron-beam tilt, (b) inaccurate determination of defocus values, (c) focus gradient through particles, and (d) particularly for large particles, dynamic (multiple) scattering of electrons. We also propose strategies to cope with these factors: (a) the divergence and direction tilt components of electron-beam tilt could be reduced by maintaining parallel illumination and by using a coma-free alignment procedure, respectively. Moreover, the effect of all beam tilt components, including spiral tilt, could be eliminated by use of a spherical aberration corrector. (b) More accurate measurement of defocus value could be obtained by imaging areas adjacent to the target area at high electron dose and by measuring the image shift induced by tilting the electron beam. (c) Each known Fourier coefficient in the Fourier transform of a cryoEM image is the sum of two Fourier coefficients of the 3D structure, one on each of two curved 'characteristic surfaces' in 3D Fourier space. We describe a simple model-based iterative method that could recover these two Fourier coefficients on the two characteristic surfaces. (d) The effect of dynamic scattering could be corrected by deconvolution of a transfer function. These analyses and our proposed strategies offer useful guidance for future experimental designs targeting atomic resolution cryoEM reconstruction.
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Affiliation(s)
- Xing Zhang
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, 237 BSRB, 615 Charles E. Young Dr. S., Los Angeles, CA 90095-7364, USA California NanoSystems Institute, University of California, Los Angeles, Box 957227, 570 Westwood Plaza, Bldg 114, Los Angeles, CA 90095-7227, USA
| | - Z. Hong Zhou
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, 237 BSRB, 615 Charles E. Young Dr. S., Los Angeles, CA 90095-7364, USA California NanoSystems Institute, University of California, Los Angeles, Box 957227, 570 Westwood Plaza, Bldg 114, Los Angeles, CA 90095-7227, USA
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94
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Cross-linking of rotavirus outer capsid protein VP7 by antibodies or disulfides inhibits viral entry. J Virol 2011; 85:10509-17. [PMID: 21849465 DOI: 10.1128/jvi.00234-11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Antibodies that neutralize rotavirus infection target outer coat proteins VP4 and VP7 and inhibit viral entry. The structure of a VP7-Fab complex (S. T. Aoki, et al., Science 324:1444-1447, 2009) led us to reclassify epitopes into two binding regions at inter- and intrasubunit boundaries of the calcium-dependent trimer. It further led us to show that antibodies binding at the intersubunit boundary inhibit uncoating of the virion outer layer. We have now tested representative antibodies for each of the defined structural epitope regions and find that antibodies recognizing epitopes in either binding region neutralize by cross-linking VP7 trimers. Antibodies that bind at the intersubunit junction neutralize as monovalent Fabs, while those that bind at the intrasubunit region require divalency. The VP7 structure has also allowed us to design a disulfide cross-linked VP7 mutant which recoats double-layered particles (DLPs) as efficiently as does wild-type VP7 but which yields particles defective in cell entry as determined both by lack of infectivity and by loss of α-sarcin toxicity in the presence of recoated particles. We conclude that dissociation of the VP7 trimer is an essential step in viral penetration into cells.
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95
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Discrete fracture patterns of virus shells reveal mechanical building blocks. Proc Natl Acad Sci U S A 2011; 108:12611-6. [PMID: 21768340 DOI: 10.1073/pnas.1105586108] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Viral shells are self-assembled protein nanocontainers with remarkable material properties. They combine simplicity of construction with toughness and complex functionality. These properties make them interesting for bionanotechnology. To date we know little about how virus structure determines assembly pathways and shell mechanics. We have here used atomic force microscopy to study structural failure of the shells of the bacteriophage Φ29. We observed rigidity patterns following the symmetry of the capsid proteins. Under prolonged force exertion, we observed fracture along well-defined lines of the 2D crystal lattice. The mechanically most stable building block of the shells was a trimer. Our approach of "reverse engineering" the virus shells thus made it possible to identify stable structural intermediates. Such stable intermediates point to a hierarchy of interactions among equal building blocks correlated with distinct next-neighbor interactions. The results also demonstrate that concepts from macroscopic materials science, such as fracture, can be usefully employed in molecular engineering.
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96
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Fändrich M, Schmidt M, Grigorieff N. Recent progress in understanding Alzheimer's β-amyloid structures. Trends Biochem Sci 2011; 36:338-45. [PMID: 21411326 DOI: 10.1016/j.tibs.2011.02.002] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 02/09/2011] [Accepted: 02/09/2011] [Indexed: 01/22/2023]
Abstract
The formation of amyloid fibrils, protofibrils and oligomers from the β-amyloid (Aβ) peptide represents a hallmark of Alzheimer's disease. Aβ-peptide-derived assemblies might be crucial for disease onset, but determining their atomic structures has proven to be a major challenge. Progress over the past 5 years has yielded substantial new data obtained with improved methodologies including electron cryo-microscopy and NMR. It is now possible to resolve the global fibril topology and the cross-β sheet organization within protofilaments, and to identify residues that are crucial for stabilizing secondary structural elements and peptide conformations within specific assemblies. These data have significantly enhanced our understanding of the mechanism of Aβ aggregation and have illuminated the possible relevance of specific conformers for neurodegenerative pathologies.
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Affiliation(s)
- Marcus Fändrich
- Max-Planck Research Unit for Enzymology of Protein Folding & Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany.
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97
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Grigorieff N, Harrison SC. Near-atomic resolution reconstructions of icosahedral viruses from electron cryo-microscopy. Curr Opin Struct Biol 2011; 21:265-73. [PMID: 21333526 DOI: 10.1016/j.sbi.2011.01.008] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 12/22/2010] [Accepted: 01/19/2011] [Indexed: 01/19/2023]
Abstract
Nine different near-atomic resolution structures of icosahedral viruses, determined by electron cryo-microscopy and published between early 2008 and late 2010, fulfil predictions made 15 years ago that single-particle cryo-EM techniques could visualize molecular detail at 3-4Å resolution. This review summarizes technical developments, both in instrumentation and in computation, that have led to the new structures, which advance our understanding of virus assembly and cell entry.
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Affiliation(s)
- Nikolaus Grigorieff
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02154, USA
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98
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Baker ML, Abeysinghe SS, Schuh S, Coleman RA, Abrams A, Marsh MP, Hryc CF, Ruths T, Chiu W, Ju T. Modeling protein structure at near atomic resolutions with Gorgon. J Struct Biol 2011; 174:360-73. [PMID: 21296162 DOI: 10.1016/j.jsb.2011.01.015] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 01/27/2011] [Accepted: 01/31/2011] [Indexed: 11/29/2022]
Abstract
Electron cryo-microscopy (cryo-EM) has played an increasingly important role in elucidating the structure and function of macromolecular assemblies in near native solution conditions. Typically, however, only non-atomic resolution reconstructions have been obtained for these large complexes, necessitating computational tools for integrating and extracting structural details. With recent advances in cryo-EM, maps at near-atomic resolutions have been achieved for several macromolecular assemblies from which models have been manually constructed. In this work, we describe a new interactive modeling toolkit called Gorgon targeted at intermediate to near-atomic resolution density maps (10-3.5 Å), particularly from cryo-EM. Gorgon's de novo modeling procedure couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques to generate initial protein backbone models. Beyond model building, Gorgon is an extensible interactive visualization platform with a variety of computational tools for annotating a wide variety of 3D volumes. Examples from cryo-EM maps of Rotavirus and Rice Dwarf Virus are used to demonstrate its applicability to modeling protein structure.
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Affiliation(s)
- Matthew L Baker
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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99
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Abstract
A universal goal in studying the structures of macromolecules and macromolecular complexes by means of electron cryo-microscopy (cryo-TEM) and three-dimensional (3D) image reconstruction is the derivation of a reliable atomic or pseudoatomic model. Such a model provides the foundation for exploring in detail the mechanisms by which biomolecules function. Though a variety of highly ordered, symmetric specimens such as 2D crystals, helices, and icosahedral virus capsids have been studied by these methods at near-atomic resolution, until recently, numerous challenges have made it difficult to achieve sub-nanometer resolution with large (≥~500Å), asymmetric molecules such as the tailed bacteriophages. After briefly reviewing some of the history behind the development of asymmetric virus reconstructions, we use recent structural studies of the prolate phage ϕ29 as an example to illustrate the step-by-step procedures used to compute an asymmetric reconstruction at sub-nanometer resolution. In contrast to methods that have been employed to study other asymmetric complexes, we demonstrate how symmetries in the head and tail components of the phage can be exploited to obtain the structure of the entire phage in an expedited, stepwise process. Prospects for future enhancements to the procedures currently employed are noted in the concluding section.
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Zhou ZH. Atomic resolution cryo electron microscopy of macromolecular complexes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2011; 82:1-35. [PMID: 21501817 PMCID: PMC3698602 DOI: 10.1016/b978-0-12-386507-6.00001-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Single-particle cryo electron microscopy (cryoEM) is a technique for determining three-dimensional (3D) structures from projection images of molecular complexes preserved in their "native," noncrystalline state. Recently, atomic or near-atomic resolution structures of several viruses and protein assemblies have been determined by single-particle cryoEM, allowing ab initio atomic model building by following the amino acid side chains or nucleic acid bases identifiable in their cryoEM density maps. In particular, these cryoEM structures have revealed extended arms contributing to molecular interactions that are otherwise not resolved by the conventional structural method of X-ray crystallography at similar resolutions. High-resolution cryoEM requires careful consideration of a number of factors, including proper sample preparation to ensure structural homogeneity, optimal configuration of electron imaging conditions to record high-resolution cryoEM images, accurate determination of image parameters to correct image distortions, efficient refinement and computation to reconstruct a 3D density map, and finally appropriate choice of modeling tools to construct atomic models for functional interpretation. This progress illustrates the power of cryoEM and ushers it into the arsenal of structural biology, alongside conventional techniques of X-ray crystallography and NMR, as a major tool (and sometimes the preferred one) for the studies of molecular interactions in supramolecular assemblies or machines.
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Affiliation(s)
- Z Hong Zhou
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, California, USA
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