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Oda T, Kikkawa M. Novel structural labeling method using cryo-electron tomography and biotin–streptavidin system. J Struct Biol 2013; 183:305-311. [DOI: 10.1016/j.jsb.2013.07.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Revised: 07/02/2013] [Accepted: 07/03/2013] [Indexed: 10/26/2022]
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2
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Goulet A, Behnke-Parks WM, Sindelar CV, Major J, Rosenfeld SS, Moores CA. The structural basis of force generation by the mitotic motor kinesin-5. J Biol Chem 2012; 287:44654-66. [PMID: 23135273 DOI: 10.1074/jbc.m112.404228] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Kinesin-5 is required for forming the bipolar spindle during mitosis. Its motor domain, which contains nucleotide and microtubule binding sites and mechanical elements to generate force, has evolved distinct properties for its spindle-based functions. In this study, we report subnanometer resolution cryoelectron microscopy reconstructions of microtubule-bound human kinesin-5 before and after nucleotide binding and combine this information with studies of the kinetics of nucleotide-induced neck linker and cover strand movement. These studies reveal coupled, nucleotide-dependent conformational changes that explain many of this motor's properties. We find that ATP binding induces a ratchet-like docking of the neck linker and simultaneous, parallel docking of the N-terminal cover strand. Loop L5, the binding site for allosteric inhibitors of kinesin-5, also undergoes a dramatic reorientation when ATP binds, suggesting that it is directly involved in controlling nucleotide binding. Our structures indicate that allosteric inhibitors of human kinesin-5, which are being developed as anti-cancer therapeutics, bind to a motor conformation that occurs in the course of normal function. However, due to evolutionarily defined sequence variations in L5, this conformation is not adopted by invertebrate kinesin-5s, explaining their resistance to drug inhibition. Together, our data reveal the precision with which the molecular mechanism of kinesin-5 motors has evolved for force generation.
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Affiliation(s)
- Adeline Goulet
- Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom
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3
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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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Barat C, Datta PP, Raj VS, Sharma MR, Kaji H, Kaji A, Agrawal RK. Progression of the Ribosome Recycling Factor through the Ribosome Dissociates the Two Ribosomal Subunits. Mol Cell 2007; 27:250-261. [PMID: 17643374 DOI: 10.1016/j.molcel.2007.06.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2007] [Revised: 04/18/2007] [Accepted: 06/05/2007] [Indexed: 11/23/2022]
Abstract
After the termination step of translation, the posttermination complex (PoTC), composed of the ribosome, mRNA, and a deacylated tRNA, is processed by the concerted action of the ribosome-recycling factor (RRF), elongation factor G (EF-G), and GTP to prepare the ribosome for a fresh round of protein synthesis. However, the sequential steps of dissociation of the ribosomal subunits, and release of mRNA and deacylated tRNA from the PoTC, are unclear. Using three-dimensional cryo-electron microscopy, in conjunction with undecagold-labeled RRF, we show that RRF is capable of spontaneously moving from its initial binding site on the 70S Escherichia coli ribosome to a site exclusively on the large 50S ribosomal subunit. This movement leads to disruption of crucial intersubunit bridges and thereby to the dissociation of the two ribosomal subunits, the central event in ribosome recycling. Results of this study allow us to propose a model of ribosome recycling.
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Affiliation(s)
- Chandana Barat
- Division of Molecular Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, USA
| | - Partha P Datta
- Division of Molecular Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, USA
| | - V Samuel Raj
- Department of Microbiology, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Manjuli R Sharma
- Division of Molecular Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, USA
| | - Hideko Kaji
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Akira Kaji
- Department of Microbiology, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rajendra K Agrawal
- Division of Molecular Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, USA; Department of Biomedical Sciences, School of Public Health, State University of New York at Albany, Albany, NY 12201, USA.
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Chui SSY, Chen R, Che CM. A Chiral [2]Catenane Precursor of the Antiarthritic Gold(I) Drug Auranofin. Angew Chem Int Ed Engl 2006; 45:1621-4. [PMID: 16444789 DOI: 10.1002/anie.200503431] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Stephen Sin-Yin Chui
- Department of Chemistry and Open Laboratory of Chemical Biology, Institute of Molecular Technology for Drug Discovery and Synthesis, University of Hong Kong, Pokfulam, Hong Kong, China
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6
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Chui SSY, Chen R, Che CM. A Chiral [2]Catenane Precursor of the Antiarthritic Gold(I) Drug Auranofin. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200503431] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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7
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Datta PP, Sharma MR, Qi L, Frank J, Agrawal RK. Interaction of the G′ Domain of Elongation Factor G and the C-Terminal Domain of Ribosomal Protein L7/L12 during Translocation as Revealed by Cryo-EM. Mol Cell 2005; 20:723-31. [PMID: 16337596 DOI: 10.1016/j.molcel.2005.10.028] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2005] [Revised: 09/30/2005] [Accepted: 10/25/2005] [Indexed: 10/25/2022]
Abstract
During tRNA translocation on the ribosome, an arc-like connection (ALC) is formed between the G' domain of elongation factor G (EF-G) and the L7/L12-stalk base of the large ribosomal subunit in the GDP state. To delineate the boundary of EF-G within the ALC, we tagged an amino acid residue near the tip of the G' domain of EF-G with undecagold, which was then visualized with three-dimensional cryo-electron microscopy (cryo-EM). Two distinct positions for the undecagold, observed in the GTP-state and GDP-state cryo-EM maps of the ribosome bound EF-G, allowed us to determine the movement of the labeled amino acid. Molecular analyses of the cryo-EM maps show: (1) that three structural components, the N-terminal domain of ribosomal protein L11, the C-terminal domain of ribosomal protein L7/L12, and the G' domain of EF-G, participate in formation of the ALC; and (2) that both EF-G and the ribosomal protein L7/L12 undergo large conformational changes to form the ALC.
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Affiliation(s)
- Partha P Datta
- Division of Molecular Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, P.O. Box 509, Albany, New York 12201, USA
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Al-Bassam J, Ozer RS, Safer D, Halpain S, Milligan RA. MAP2 and tau bind longitudinally along the outer ridges of microtubule protofilaments. J Cell Biol 2002; 157:1187-96. [PMID: 12082079 PMCID: PMC2173547 DOI: 10.1083/jcb.200201048] [Citation(s) in RCA: 243] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
MAP2 and tau exhibit microtubule-stabilizing activities that are implicated in the development and maintenance of neuronal axons and dendrites. The proteins share a homologous COOH-terminal domain, composed of three or four microtubule binding repeats separated by inter-repeats (IRs). To investigate how MAP2 and tau stabilize microtubules, we calculated 3D maps of microtubules fully decorated with MAP2c or tau using cryo-EM and helical image analysis. Comparing these maps with an undecorated microtubule map revealed additional densities along protofilament ridges on the microtubule exterior, indicating that MAP2c and tau form an ordered structure when they bind microtubules. Localization of undecagold attached to the second IR of MAP2c showed that IRs also lie along the ridges, not between protofilaments. The densities attributable to the microtubule-associated proteins lie in close proximity to helices 11 and 12 and the COOH terminus of tubulin. Our data further suggest that the evolutionarily maintained differences observed in the repeat domain may be important for the specific targeting of different repeats to either alpha or beta tubulin. These results provide strong evidence suggesting that MAP2c and tau stabilize microtubules by binding along individual protofilaments, possibly by bridging the tubulin interfaces.
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Affiliation(s)
- Jawdat Al-Bassam
- Department of Cell Biology, Scripps Research Institute, La Jolla, CA 92037, USA
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Tao Y, Zhang W. Recent developments in cryo-electron microscopy reconstruction of single particles. Curr Opin Struct Biol 2000; 10:616-22. [PMID: 11042462 DOI: 10.1016/s0959-440x(00)00139-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cryo-electron microscopy and single-particle 3D image reconstruction techniques have been used to examine a broad spectrum of samples ranging from 500 kDa protein complexes to large subcellular organelles. The attainable resolution has improved rapidly over the past few years. Structures of both symmetric and asymmetric assemblies at approximately 7.5 A have been reported. Together with X-ray crystallography, three-dimensional cryo-electron microscopy reconstruction has provided important insights into the function of many biological systems in their native biochemical contexts.
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Affiliation(s)
- Y Tao
- Department of Molecular and Cellular Biology, 7 Divinity Avenue, Harvard University, Cambridge, MA 02138, USA.
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Rice S, Lin AW, Safer D, Hart CL, Naber N, Carragher BO, Cain SM, Pechatnikova E, Wilson-Kubalek EM, Whittaker M, Pate E, Cooke R, Taylor EW, Milligan RA, Vale RD. A structural change in the kinesin motor protein that drives motility. Nature 1999; 402:778-84. [PMID: 10617199 DOI: 10.1038/45483] [Citation(s) in RCA: 570] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Kinesin motors power many motile processes by converting ATP energy into unidirectional motion along microtubules. The force-generating and enzymatic properties of conventional kinesin have been extensively studied; however, the structural basis of movement is unknown. Here we have detected and visualized a large conformational change of an approximately 15-amino-acid region (the neck linker) in kinesin using electron paramagnetic resonance, fluorescence resonance energy transfer, pre-steady state kinetics and cryo-electron microscopy. This region becomes immobilized and extended towards the microtubule 'plus' end when kinesin binds microtubules and ATP, and reverts to a more mobile conformation when gamma-phosphate is released after nucleotide hydrolysis. This conformational change explains both the direction of kinesin motion and processive movement by the kinesin dimer.
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Affiliation(s)
- S Rice
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco 94143, USA
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