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Yang K, Wang C, White KI, Pfuetzner RA, Esquivies L, Brunger AT. Structural conservation among variants of the SARS-CoV-2 spike postfusion bundle. Proc Natl Acad Sci U S A 2022; 119:e2119467119. [PMID: 35363556 PMCID: PMC9169775 DOI: 10.1073/pnas.2119467119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 02/22/2022] [Indexed: 01/10/2023] Open
Abstract
Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available COVID-19 vaccines and monoclonal antibody therapies due to structural and dynamic changes of the viral spike glycoprotein (S). The heptad repeat 1 (HR1) and heptad repeat 2 (HR2) domains of S drive virus–host membrane fusion by assembly into a six-helix bundle, resulting in delivery of viral RNA into the host cell. We surveyed mutations of currently reported SARS-CoV-2 variants and selected eight mutations, including Q954H, N969K, and L981F from the Omicron variant, in the postfusion HR1HR2 bundle for functional and structural studies. We designed a molecular scaffold to determine cryogenic electron microscopy (cryo-EM) structures of HR1HR2 at 2.2–3.8 Å resolution by linking the trimeric N termini of four HR1 fragments to four trimeric C termini of the Dps4 dodecamer from Nostoc punctiforme. This molecular scaffold enables efficient sample preparation and structure determination of the HR1HR2 bundle and its mutants by single-particle cryo-EM. Our structure of the wild-type HR1HR2 bundle resolves uncertainties in previously determined structures. The mutant structures reveal side-chain positions of the mutations and their primarily local effects on the interactions between HR1 and HR2. These mutations do not alter the global architecture of the postfusion HR1HR2 bundle, suggesting that the interfaces between HR1 and HR2 are good targets for developing antiviral inhibitors that should be efficacious against all known variants of SARS-CoV-2 to date. We also note that this work paves the way for similar studies in more distantly related viruses.
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Affiliation(s)
- Kailu Yang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| | - Chuchu Wang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| | - K. Ian White
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| | - Richard A. Pfuetzner
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| | - Luis Esquivies
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| | - Axel T. Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
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2
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Jagota M, Townshend RJL, Kang LW, Bushnell DA, Dror RO, Kornberg RD, Azubel M. Gold nanoparticles and tilt pairs to assess protein flexibility by cryo-electron microscopy. Ultramicroscopy 2021; 227:113302. [PMID: 34062386 DOI: 10.1016/j.ultramic.2021.113302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 01/24/2023]
Abstract
A computational method was developed to recover the three-dimensional coordinates of gold nanoparticles specifically attached to a protein complex from tilt-pair images collected by electron microscopy. The program was tested on a simulated dataset and applied to a real dataset comprising tilt-pair images recorded by cryo electron microscopy of RNA polymerase II in a complex with four gold-labeled single-chain antibody fragments. The positions of the gold nanoparticles were determined, and comparison of the coordinates among the tetrameric particles revealed the range of motion within the protein complexes.
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Affiliation(s)
- Milind Jagota
- Department of Computer Science, Stanford University, Stanford, CA, USA; Department of Electrical Engineering, Stanford University, Stanford, CA, USA
| | | | - Lin-Woo Kang
- Department of Biological Sciences, Konkuk University, Seoul, Korea
| | - David A Bushnell
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA; Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Maia Azubel
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
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3
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Yao Q, Weaver SJ, Mock JY, Jensen GJ. Fusion of DARPin to Aldolase Enables Visualization of Small Protein by Cryo-EM. Structure 2019; 27:1148-1155.e3. [PMID: 31080120 PMCID: PMC6610650 DOI: 10.1016/j.str.2019.04.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 03/04/2019] [Accepted: 04/05/2019] [Indexed: 12/21/2022]
Abstract
Solving protein structures by single-particle cryoelectron microscopy (cryo-EM) has become a crucial tool in structural biology. While exciting progress is being made toward the visualization of small macromolecules, the median protein size in both eukaryotes and bacteria is still beyond the reach of cryo-EM. To overcome this problem, we implemented a platform strategy in which a small protein target was rigidly attached to a large, symmetric base via a selectable adapter. Of our seven designs, the best construct used a designed ankyrin repeat protein (DARPin) rigidly fused to tetrameric rabbit muscle aldolase through a helical linker. The DARPin retained its ability to bind its target: GFP. We solved the structure of this complex to 3.0 Å resolution overall, with 5-8 Å resolution in the GFP region. As flexibility in the DARPin position limited the overall resolution of the target, we describe strategies to rigidify this element.
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Affiliation(s)
- Qing Yao
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Sara J Weaver
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Jee-Young Mock
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, 1200 E. California Boulevard, Pasadena, CA 91125, USA.
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4
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Takizawa Y, Binshtein E, Erwin AL, Pyburn TM, Mittendorf KF, Ohi MD. While the revolution will not be crystallized, biochemistry reigns supreme. Protein Sci 2016; 26:69-81. [PMID: 27673321 DOI: 10.1002/pro.3054] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 09/22/2016] [Indexed: 12/14/2022]
Abstract
Single-particle cryo-electron microscopy (EM) is currently gaining attention for the ability to calculate structures that reach sub-5 Å resolutions; however, the technique is more than just an alternative approach to X-ray crystallography. Molecular machines work via dynamic conformational changes, making structural flexibility the hallmark of function. While the dynamic regions in molecules are essential, they are also the most challenging to structurally characterize. Single-particle EM has the distinct advantage of being able to directly visualize purified molecules without the formation of ordered arrays of molecules locked into identical conformations. Additionally, structures determined using single-particle EM can span resolution ranges from very low- to atomic-levels (>30-1.8 Å), sometimes even in the same structure. The ability to accommodate various resolutions gives single-particle EM the unique capacity to structurally characterize dynamic regions of biological molecules, thereby contributing essential structural information needed for the development of molecular models that explain function. Further, many important molecular machines are intrinsically dynamic and compositionally heterogeneous. Structures of these complexes may never reach sub-5 Å resolutions due to this flexibility required for function. Thus, the biochemical quality of the sample, as well as, the calculation and interpretation of low- to mid-resolution cryo-EM structures (30-8 Å) remains critical for generating insights into the architecture of many challenging biological samples that cannot be visualized using alternative techniques.
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Affiliation(s)
- Yoshimasa Takizawa
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, 37232.,Center for Structural Biology Vanderbilt University, Nashville, Tennessee, 37232
| | - Elad Binshtein
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, 37232.,Center for Structural Biology Vanderbilt University, Nashville, Tennessee, 37232
| | - Amanda L Erwin
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, 37232.,Center for Structural Biology Vanderbilt University, Nashville, Tennessee, 37232
| | - Tasia M Pyburn
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, 37232.,Center for Structural Biology Vanderbilt University, Nashville, Tennessee, 37232
| | - Kathleen F Mittendorf
- Vanderbilt-Ingram Cancer Center Vanderbilt University Medical Center, Nashville, Tennessee, 37232
| | - Melanie D Ohi
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, 37232.,Center for Structural Biology Vanderbilt University, Nashville, Tennessee, 37232
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Anthony KC, You C, Piehler J, Pomeranz Krummel DA. High-affinity gold nanoparticle pin to label and localize histidine-tagged protein in macromolecular assemblies. Structure 2014; 22:628-35. [PMID: 24560806 DOI: 10.1016/j.str.2014.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 01/08/2014] [Accepted: 01/16/2014] [Indexed: 10/25/2022]
Abstract
There is significant demand for experimental approaches to aid protein localization in electron microscopy micrographs and ultimately in three-dimensional reconstructions of macromolecular assemblies. We report preparation and use of a reagent consisting of tris-nitrilotriacetic acid (tris-NTA) conjugated with a monofunctional gold nanoparticle ((AuNP)tris-NTA) for site-specific, non-covalent labeling of protein termini fused to a histidine-tag (His-tag). Multivalent binding of tris-NTA to a His-tag via complexed Ni(II) ions results in subnanomolar affinity and a defined 1:1 stoichiometry. Precise localization of (AuNP)tris-NTA labeled proteins by electron microscopy is further ensured by the reagent's short conformationally restricted linker. We used (AuNP)tris-NTA to localize His-tagged proteins in an oligomeric ATPase and in the bacterial 50S ribosomal subunit. (AuNP)tris-NTA can specifically bind to the target proteins in these assemblies and is clearly discernible. Our labeling reagent should find broad application in noncovalent, site-specific labeling of protein termini to pinpoint their location in macromolecular assemblies.
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Affiliation(s)
- Kelsey C Anthony
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | - Changjiang You
- Department of Biology, University of Osnabrück, Barbarastraße 11, Osnabrück 49076, Germany
| | - Jacob Piehler
- Department of Biology, University of Osnabrück, Barbarastraße 11, Osnabrück 49076, Germany.
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6
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Hybrid electron microscopy-FRET imaging localizes the dynamical C-terminus of Tfg2 in RNA polymerase II-TFIIF with nanometer precision. J Struct Biol 2013; 184:52-62. [PMID: 23732819 DOI: 10.1016/j.jsb.2013.05.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 05/06/2013] [Accepted: 05/21/2013] [Indexed: 01/23/2023]
Abstract
TFIIF-a general transcription factor comprising two conserved subunits can associate with RNA polymerase II (RNAPII) tightly to regulate the synthesis of messenger RNA in eukaryotes. Herein, a hybrid method that combines electron microscopy (EM) and Förster resonance energy transfer (FRET) is described and used to localize the C-terminus of the second TFIIF subunit (Tfg2) in the architecture of RNAPII-TFIIF. In the first stage, a poly-histidine tag appended to the Tfg2 C-terminus was labeled with nickel-NTA nanogold and a seven-step single particle EM protocol was devised to obtain the region accessible by the nanogold in 3D, suggesting the Tfg2 C-terminus is proximal to the clamp of RNAPII. Next, the C-termini of the Rpb2 and the Rpb4 subunits of RNAPII, adjacent to the clamp, were selected for placing FRET satellites to enable the nano-positioning (NP) analysis, by which the localization precision was improved such that the Tfg2 C-terminus was found to dwell on the clamp ridge but could move to the clamp top during transcription. Because the tag receptive to the EM or FRET probes can be readily introduced to any protein subunit, this hybrid approach is generally applicable to complement cryo-EM study of many protein complexes to nanometer precision.
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7
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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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Levi-Kalisman Y, Jadzinsky PD, Kalisman N, Tsunoyama H, Tsukuda T, Bushnell DA, Kornberg RD. Synthesis and Characterization of Au102(p-MBA)44 Nanoparticles. J Am Chem Soc 2011; 133:2976-82. [DOI: 10.1021/ja109131w] [Citation(s) in RCA: 200] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yael Levi-Kalisman
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Pablo D. Jadzinsky
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Nir Kalisman
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Hironori Tsunoyama
- Section of Catalytic Assemblies, Catalysis Research Center, Hokkaido University, Sapporo 001-0021, Japan
| | - Tatsuya Tsukuda
- Section of Catalytic Assemblies, Catalysis Research Center, Hokkaido University, Sapporo 001-0021, Japan
| | - David A. Bushnell
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Roger D. Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, United States
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Sexton JZ, Ackerson CJ. Determination of Rigidity of Protein Bound Au(144) Clusters by Electron Cryomicroscopy. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2010; 114:16037-16042. [PMID: 21116473 PMCID: PMC2992337 DOI: 10.1021/jp101970x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A method for estimating the positional displacement of protein bound gold nanoparticles is presented and used to estimate the rigidity of linkage of Au(144) nanoparticles bound to a tetrameric model protein. We observe a distribution of displacement values where most Au(144) clusters are immobilized to within 3Å relative to the protein center of mass. The shape of the distribution suggests two physical processes of thermal motion and protein deformation. The application of this and similar rigid gold nanoparticle/protein conjugates in high resolution single particle electron cryo-microscopy is discussed.
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Affiliation(s)
- Jonathan Z. Sexton
- Department of Structural Biology, 299 Campus Drive West, Stanford, CA 94305
- Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC
| | - Christopher J. Ackerson
- Department of Structural Biology, 299 Campus Drive West, Stanford, CA 94305
- Department of Chemistry, Colorado State University, Fort Collins, CO 80521
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10
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Ackerson CJ, Jadzinsky PD, Sexton JZ, Bushnell DA, Kornberg RD. Synthesis and bioconjugation of 2 and 3 nm-diameter gold nanoparticles. Bioconjug Chem 2010; 21:214-8. [PMID: 20099843 PMCID: PMC3113727 DOI: 10.1021/bc900135d] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
By adjustment of solvent conditions for synthesis, virtually monodisperse 4-mercaptobenzoic acid (p-MBA) monolayer-protected gold nanoparticles, 2 and 3 nm in diameter, were obtained. Large single crystals of the 2 nm particles could be grown from the reaction mixture. Uniformity was also demonstrated by the formation of two-dimensional arrays and by quantitative high-angle annular dark-field scanning transmission electron microscopy. The 2 and 3 nm particles were spontaneously reactive for conjugation with proteins and DNA, and further reaction could be prevented by repassivation with glutathione. Conjugates with antibody Fc fragment could be used to identify TAP-tagged proteins of interest in electron micrographs, through the binding of a pair of particles to the pair of protein A domains in the TAP tag.
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Affiliation(s)
- Christopher J Ackerson
- Department of Structural Biology, Stanford School of Medicine, 299 Campus Drive West, Stanford, California 94305, USA
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11
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Kruschel D, Zagrovic B. Conformational averaging in structural biology: issues, challenges and computational solutions. MOLECULAR BIOSYSTEMS 2009; 5:1606-16. [PMID: 20023721 DOI: 10.1039/b917186j] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Most experimental methods in structural biology provide time- and ensemble-averaged signals and, consequently, molecular structures based on such signals often exhibit only idealized, average features. Second, most experimental signals are only indirectly related to real, molecular geometries, and solving a structure typically involves a complicated procedure, which may not always result in a unique solution. To what extent do such conformationally-averaged, non-linear experimental signals and structural models derived from them accurately represent the underlying microscopic reality? Are there some structural motifs that are actually artificially more likely to be "seen" in an experiment simply due to the averaging artifact? Finally, what are the practical consequences of ignoring the averaging effects when it comes to functional and mechanistic implications that we try to glean from experimentally-based structural models? In this review, we critically address the work that has been aimed at studying such questions. We summarize the details of experimental methods typically used in structural biology (most notably nuclear magnetic resonance, X-ray crystallography and different types of spectroscopy), discuss their individual susceptibility to conformational (motional) averaging, and review several theoretical approaches, most importantly molecular dynamics simulations that are increasingly being used to aid experimentalists in interpreting structural biology experiments.
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Affiliation(s)
- Daniela Kruschel
- Laboratory of Computational Biophysics, Mediterranean Institute for Life Sciences, Mestrovicevo setaliste bb, Split, HR-21000, Croatia
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12
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An autobiographic conversation with Roger D Kornberg on his work on transcription regulation. Cell Death Differ 2007; 14:1977-80. [DOI: 10.1038/sj.cdd.4402250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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13
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Gold nanoparticle-protein arrays improve resolution for cryo-electron microscopy. J Struct Biol 2007; 161:83-91. [PMID: 18006331 DOI: 10.1016/j.jsb.2007.09.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Revised: 09/19/2007] [Accepted: 09/20/2007] [Indexed: 11/23/2022]
Abstract
Cryo-electron microscopy single particle analysis shows limited resolution due to poor alignment precision of noisy images taken under low electron exposure. Certain advantages can be obtained by assembling proteins into two-dimensional (2D) arrays since protein particles are locked into repetitive orientation, thus improving alignment precision. We present a labeling method to prepare protein 2D arrays using gold nanoparticles (NPs) interconnecting genetic tag sites on proteins. As an example, mycobacterium tuberculosis 20S proteasomes tagged with 6x-histidine were assembled into 2D arrays using 3.9-nm Au NPs functionalized with nickel-nitrilotriacetic acid. The averaged top-view images from the array particles showed higher resolution (by 6-8A) compared to analysis of single particles. The correct 7-fold symmetry was also evident by using array particles whereas it was not clear by analysis of a comparable number of single particles. The applicability of this labeling method for three-dimensional reconstruction of biological macromolecules is discussed.
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14
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Affiliation(s)
- Jesper Q Svejstrup
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, EN6 3LD, United Kingdom
| | - Ronald C Conaway
- Stowers Institute for Medical Research, Kansas City, Missouri 64112
| | - Joan W Conaway
- Stowers Institute for Medical Research, Kansas City, Missouri 64112.
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15
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Abstract
To determine the structure of a biological particle to high resolution by electron microscopy, image averaging is required to combine information from different views and to increase the signal-to-noise ratio. Starting from the number of noiseless views necessary to resolve features of a given size, four general factors are considered that increase the number of images actually needed: (1) the physics of electron scattering introduces shot noise, (2) thermal motion and particle inhomogeneity cause the scattered electrons to describe a mixture of structures, (3) the microscope system fails to usefully record all the information carried by the scattered electrons, and (4) image misalignment leads to information loss through incoherent averaging. The compound effect of factors 2-4 is approximated by the product of envelope functions. The problem of incoherent image averaging is developed in detail through derivation of five envelope functions that account for small errors in 11 "alignment" parameters describing particle location, orientation, defocus, magnification, and beam tilt. The analysis provides target error tolerances for single particle analysis to near-atomic (3.5 A) resolution, and this prospect is shown to depend critically on image quality, defocus determination, and microscope alignment.
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Affiliation(s)
- G J Jensen
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720-0001, USA.
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