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Rangan R, Feathers R, Khavnekar S, Lerer A, Johnston JD, Kelley R, Obr M, Kotecha A, Zhong ED. CryoDRGN-ET: deep reconstructing generative networks for visualizing dynamic biomolecules inside cells. Nat Methods 2024; 21:1537-1545. [PMID: 39025970 DOI: 10.1038/s41592-024-02340-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 06/06/2024] [Indexed: 07/20/2024]
Abstract
Advances in cryo-electron tomography (cryo-ET) have produced new opportunities to visualize the structures of dynamic macromolecules in native cellular environments. While cryo-ET can reveal structures at molecular resolution, image processing algorithms remain a bottleneck in resolving the heterogeneity of biomolecular structures in situ. Here, we introduce cryoDRGN-ET for heterogeneous reconstruction of cryo-ET subtomograms. CryoDRGN-ET learns a deep generative model of three-dimensional density maps directly from subtomogram tilt-series images and can capture states diverse in both composition and conformation. We validate this approach by recovering the known translational states in Mycoplasma pneumoniae ribosomes in situ. We then perform cryo-ET on cryogenic focused ion beam-milled Saccharomyces cerevisiae cells. CryoDRGN-ET reveals the structural landscape of S. cerevisiae ribosomes during translation and captures continuous motions of fatty acid synthase complexes inside cells. This method is openly available in the cryoDRGN software.
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Affiliation(s)
- Ramya Rangan
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Ryan Feathers
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | | | | | - Jake D Johnston
- Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Ron Kelley
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Eindhoven, the Netherlands
| | - Martin Obr
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Eindhoven, the Netherlands
| | - Abhay Kotecha
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Eindhoven, the Netherlands.
| | - Ellen D Zhong
- Department of Computer Science, Princeton University, Princeton, NJ, USA.
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2
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Xu D, Zhao J, Jiang L, Song J, Zong S, Yan X, Liu H, Zhang H, Hu S, Bu Z. Comparison of transcriptional change of B. melitensis M5-90 after macrophage infection highlights the role of ribosome gene L31 in virulence. Vet Microbiol 2020; 253:108951. [PMID: 33373884 DOI: 10.1016/j.vetmic.2020.108951] [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: 07/29/2019] [Accepted: 12/07/2020] [Indexed: 01/11/2023]
Abstract
Brucella, a facultative intracellular bacterium, can survive and replicate in various cell types such as epithelial cell, fibroblasts and macrophage. Macrophage is the most important sites for the survival of Brucella in vivo. The mechanisms of pathogenesis are difficult to address, since the unknown virulence genes are still exist. RNA-seq is available to study transcriptional changes that occur during disease as a way to identify important virulence-related genes. Here we described and analyzed the transcriptional change of avirulent strain Brucella melitensis M5-90 (B. melitensis M5-90) during macrophage infection using RNA-seq technology. We detected 601 significant changed genes of which 428 were upregulated after infection. The upregulated gene L31 which involved in ribosome KEGG pathway was selected to illustrate its effect on virulence in a vaccine strain B. melitensis M5-90 and a virulent strain B. melitensis M28. Deletion of L31 significant attenuates the spleen colonization in model of M5-90 or M28 infection mouse at 7, 21 and 35 days post-infection (P < 0.05). We further examine the role of L31 in a macrophage cell infection model, and the result showed a significant reduction of intracellular M28ΔL31 cells at 48 h post-infection (P < 0.001). In total, our study provided a view of transcriptional landscape of B. melitensis M5-90 intracellular, and found L31 gene is required for the full virulence of B. melitensis.
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Affiliation(s)
- Da Xu
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China; State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Jianlong Zhao
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
| | - Liying Jiang
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
| | - Jiabao Song
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
| | - Shucheng Zong
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
| | - Xin Yan
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
| | - Haican Liu
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Huitong Zhang
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
| | - Sen Hu
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
| | - Zhigao Bu
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
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Créchet JB, Agbo'Saga FK, Baouz S, Hountondj C. RpbL12 Assists Catalysis by Correctly Positioning the Incoming Aminoacyl-tRNA in the A-Site of E. coli 70S Ribosomes. Open Biochem J 2018; 12:113-129. [PMID: 30197688 PMCID: PMC6110070 DOI: 10.2174/1874091x01812010113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/26/2018] [Accepted: 07/02/2018] [Indexed: 11/30/2022] Open
Abstract
Introduction: We have recently demonstrated that Lys-65 of the 62GANK65 motif of E. coli RpbL12 was affinity labeled with a tRNA analogue, resulting in the loss of activity. Materials and Methods: In this report, we show that mutations operated at the position of Lys-65 led to an impairment in the activity of the mutant ribosomes, except the K65R or K65H bL12 mutants, suggesting that the only requirement of the reaction catalyzed or facilitated by RpbL12is the positive charge of the side chain of Lys-65. We also demonstrate that Lys-65 did not play any role in the peptidyl transferase reaction with respect to puromycin, but rather assisted the binding of the incoming aminoacyl-tRNA to the ribosomal A-site. Results & Discussions The protonated, positively charged εNH3+ form of Lys-65 is likely to participate to the binding of aa-tRNA through ionic bonds with phosphate groups, in order to insure the accurate positioning required for the nucleophilic attack of its α-amino group on the carbonyl carbone of peptidyl-tRNA. Conclusion This α-NH2 group is likely to be generated by the unprotonated εNH2 form of Lys-65 which is capable of withdrawing a proton from the α-NH3+ group of aa-tRNA.
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Affiliation(s)
| | - Fulbert K Agbo'Saga
- Sorbonne Université, Campus Pierre et Marie Curie, Unité de Recherche SUUR6 "Enzymologie de l'ARN", 7 Quai Saint-Bernard, F-75252 Paris Cedex 05, France
| | - Soria Baouz
- Sorbonne Université, Campus Pierre et Marie Curie, Unité de Recherche SUUR6 "Enzymologie de l'ARN", 7 Quai Saint-Bernard, F-75252 Paris Cedex 05, France
| | - Codjo Hountondj
- Sorbonne Université, Campus Pierre et Marie Curie, Unité de Recherche SUUR6 "Enzymologie de l'ARN", 7 Quai Saint-Bernard, F-75252 Paris Cedex 05, France
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4
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Hountondji C, Créchet JB, Le Caër JP, Lancelot V, Cognet JAH, Baouz S. Affinity labelling in situ of the bL12 protein on E. coli 70S ribosomes by means of a tRNA dialdehyde derivative. J Biochem 2017; 162:437-448. [DOI: 10.1093/jb/mvx055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 06/29/2017] [Indexed: 11/14/2022] Open
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Yu G, Yan R, Zhang C, Mao C, Jiang W. Single-Particle Cryo-EM and 3D Reconstruction of Hybrid Nanoparticles with Electron-Dense Components. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:5157-5163. [PMID: 26179326 DOI: 10.1002/smll.201500531] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 06/13/2015] [Indexed: 06/04/2023]
Abstract
Single-particle cryo-electron microscopy (cryo-EM), accompanied with 3D reconstruction, is a broadly applicable tool for the structural characterization of macromolecules and nanoparticles. Recently, the cryo-EM field has pushed the limits of this technique to higher resolutions and samples of smaller molecular mass, however, some samples still present hurdles to this technique. Hybrid particles with electron-dense components, which have been studied using single-particle cryo-EM yet with limited success in 3D reconstruction due to the interference caused by electron-dense elements, constitute one group of such challenging samples. To process such hybrid particles, a masking method is developed in this work to adaptively remove pixels arising from electron-dense portions in individual projection images while maintaining maximal biomass signals for subsequent 2D alignment, 3D reconstruction, and iterative refinements. As demonstrated by the success in 3D reconstruction of an octahedron DNA/gold hybrid particle, which has been previously published without a 3D reconstruction, the devised strategy that combines adaptive masking and standard single-particle 3D reconstruction approach has overcome the hurdle of electron-dense elements interference, and is generally applicable to cryo-EM structural characterization of most, if not all, hybrid nanomaterials with electron-dense components.
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Affiliation(s)
- Guimei Yu
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, 240 S Martin Jischke Dr, West Lafayette, IN, 47907, USA
| | - Rui Yan
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, 240 S Martin Jischke Dr, West Lafayette, IN, 47907, USA
| | - Chuan Zhang
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA
| | - Wen Jiang
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, 240 S Martin Jischke Dr, West Lafayette, IN, 47907, USA
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6
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Waudby CA, Launay H, Cabrita LD, Christodoulou J. Protein folding on the ribosome studied using NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 74:57-75. [PMID: 24083462 PMCID: PMC3991860 DOI: 10.1016/j.pnmrs.2013.07.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 07/17/2013] [Accepted: 07/17/2013] [Indexed: 05/11/2023]
Abstract
NMR spectroscopy is a powerful tool for the investigation of protein folding and misfolding, providing a characterization of molecular structure, dynamics and exchange processes, across a very wide range of timescales and with near atomic resolution. In recent years NMR methods have also been developed to study protein folding as it might occur within the cell, in a de novo manner, by observing the folding of nascent polypeptides in the process of emerging from the ribosome during synthesis. Despite the 2.3 MDa molecular weight of the bacterial 70S ribosome, many nascent polypeptides, and some ribosomal proteins, have sufficient local flexibility that sharp resonances may be observed in solution-state NMR spectra. In providing information on dynamic regions of the structure, NMR spectroscopy is therefore highly complementary to alternative methods such as X-ray crystallography and cryo-electron microscopy, which have successfully characterized the rigid core of the ribosome particle. However, the low working concentrations and limited sample stability associated with ribosome-nascent chain complexes means that such studies still present significant technical challenges to the NMR spectroscopist. This review will discuss the progress that has been made in this area, surveying all NMR studies that have been published to date, and with a particular focus on strategies for improving experimental sensitivity.
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Abstract
Nanoparticle-protein conjugates hold great promise in biomedical applications. Diverse strategies have been developed to link nanoparticles to proteins. This chapter describes a method to assemble and purify nanoparticle-protein conjugates. First, stable and biocompatible 1.5 nm gold nanoparticles are synthesized. Conjugation of the nanoparticle to the protein is then achieved via two different approaches that do not require heavy chemical modifications or cloning: cysteine-gold covalent bonding, or electrostatic attachment of the nanoparticle to charged groups of the protein. Co-functionalization of the nanoparticle with PEG thiols is recommended to help protein folding. Finally, structural characterization is performed with circular dichroism, as this spectroscopy technique has proven to be effective at examining protein secondary structure in nanoparticle-protein conjugates.
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8
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Parent KN, Deedas CT, Egelman EH, Casjens SR, Baker TS, Teschke CM. Stepwise molecular display utilizing icosahedral and helical complexes of phage coat and decoration proteins in the development of robust nanoscale display vehicles. Biomaterials 2012; 33:5628-37. [PMID: 22575828 DOI: 10.1016/j.biomaterials.2012.04.026] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Accepted: 04/08/2012] [Indexed: 01/18/2023]
Abstract
A stepwise addition protocol was developed to display cargo using bacteriophage P22 capsids and the phage decoration (Dec) protein. Three-dimensional image reconstructions of frozen-hydrated samples of P22 particles with nanogold-labeled Dec bound to them revealed the locations of the N- and C-termini of Dec. Each terminus is readily accessible for molecular display through affinity tags such as nickel-nitrilotriacetic acid, providing a total of 240 cargo-binding sites. Dec was shown by circular dichroism to be a β-sheet rich protein, and fluorescence anisotropy binding experiments demonstrated that Dec binds to P22 heads with high (~110 nm) affinity. Dec also binds to P22 nanotubes, which are helically symmetric assemblies that form when the P22 coat protein contains the F170A amino acid substitution. Several classes of tubes with Dec bound to them were visualized by cryo-electron microscopy and their three-dimensional structures were determined by helical reconstruction methods. In all instances, Dec trimers bound to P22 capsids and nanotubes at positions where three neighboring capsomers (oligomers of six coat protein subunits) lie in close proximity to one another. Stable interactions between Dec and P22 allow for the development of robust, nanoscale size, display vehicles.
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Affiliation(s)
- Kristin N Parent
- Department of Chemistry & Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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Parent KN, Khayat R, Tu LH, Suhanovsky MM, Cortines JR, Teschke CM, Johnson JE, Baker TS. P22 coat protein structures reveal a novel mechanism for capsid maturation: stability without auxiliary proteins or chemical crosslinks. Structure 2010; 18:390-401. [PMID: 20223221 DOI: 10.1016/j.str.2009.12.014] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Revised: 12/15/2009] [Accepted: 12/29/2009] [Indexed: 11/30/2022]
Abstract
Viral capsid assembly and stability in tailed, dsDNA phage and Herpesviridae are achieved by various means including chemical crosslinks (unique to HK97), or auxiliary proteins (lambda, T4, phi29, and herpesviruses). All these viruses have coat proteins (CP) with a conserved, HK97-like core structure. We used a combination of trypsin digestion, gold labeling, cryo-electron microscopy, 3D image reconstruction, and comparative modeling to derive two independent, pseudoatomic models of bacteriophage P22 CP: before and after maturation. P22 capsid stabilization results from intersubunit interactions among N-terminal helices and an extensive "P loop," which obviate the need for crosslinks or auxiliary proteins. P22 CP also has a telokin-like Ig domain that likely stabilizes the monomer fold so that assembly may proceed via individual subunit addition rather than via preformed capsomers as occurs in HK97. Hence, the P22 CP structure may be a paradigm for understanding how monomers assemble in viruses like phi29 and HSV-1.
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Affiliation(s)
- Kristin N Parent
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
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10
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He Y, Jensen GJ, Bjorkman PJ. Nanogold as a specific marker for electron cryotomography. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2009; 15:183-188. [PMID: 19460172 PMCID: PMC2785728 DOI: 10.1017/s1431927609090424] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
While electron cryotomography (ECT) provides "molecular" resolution, three-dimensional images of unique biological specimens, sample crowdedness, and/or resolution limitations can make it difficult to identify specific macromolecular components. Here we used a 1.4 nm Nanogold cluster specifically attached to the Fc fragment of IgG to monitor its interaction with the neonatal Fc receptor (FcRn), a membrane-bound receptor that transports IgG across cells in acidic intracellular vesicles. ECT was used to image complexes formed by Nanogold-labeled Fc bound to FcRn attached to the outer surface of synthetic liposomes. In the resulting three-dimensional reconstructions, 1.4 nm Nanogold particles were distributed predominantly along the interfaces where 2:1 FcRn-Fc complexes bridged adjacent lipid bilayers. These results demonstrate that the 1.4 nm Nanogold cluster is visible in tomograms of typically thick samples (approximately 250 nm) recorded with defocuses appropriate for large macromolecules and is thus an effective marker.
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Affiliation(s)
- Yongning He
- Division of Biology, California Institute of Technology, 114-96, 1200 East California Blvd., Pasadena, CA 91125
| | - Grant J. Jensen
- Division of Biology, California Institute of Technology, 114-96, 1200 East California Blvd., Pasadena, CA 91125
- Howard Hughes Medical Institute, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125
| | - Pamela J. Bjorkman
- Division of Biology, California Institute of Technology, 114-96, 1200 East California Blvd., Pasadena, CA 91125
- Howard Hughes Medical Institute, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125
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Aubin-Tam ME, Hwang W, Hamad-Schifferli K. Site-directed nanoparticle labeling of cytochrome c. Proc Natl Acad Sci U S A 2009; 106:4095-100. [PMID: 19251670 PMCID: PMC2657428 DOI: 10.1073/pnas.0807299106] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Indexed: 11/18/2022] Open
Abstract
Although nanoparticle-protein conjugates have been synthesized for numerous applications, bioconjugation remains a challenge, often resulting in denaturation or loss of protein function. This is partly because the protein-nanoparticle interface is poorly understood, which impedes the use of nanoparticles in nanomedicine. Although the effects of nanoparticle ligand and material on protein structure have been explored, the choice of the labeling site on the protein has not yet been systematically studied. To address this issue, we label cytochrome c site-specifically with a negatively charged Au nanoparticle via a covalent thiol-Au bond. The attachment site is controlled by cysteine mutations of surface residues. The effect of labeling on protein structure is probed by circular dichroism. Protein unfolding is the most severe when the nanoparticle is attached to the N- and C-terminal foldon, the core motif of cytochrome c. Also, when the nanoparticle is attached in the vicinity of charged residues, the amount of structural damage is greater because of salt-dependent electrostatic interactions with charged ligand bis(p-sulfonatophenyl) phenylphosphine on the nanoparticle. Molecular dynamics simulations also elucidate local to global structural perturbation depending on labeling site. These results suggest that the labeling site must be considered as one of the main design criteria for nanoparticle-protein conjugates.
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Affiliation(s)
- Marie-Eve Aubin-Tam
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843; and
| | - Kimberly Hamad-Schifferli
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
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12
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Kurkcuoglu O, Doruker P, Sen TZ, Kloczkowski A, Jernigan RL. The ribosome structure controls and directs mRNA entry, translocation and exit dynamics. Phys Biol 2008; 5:046005. [PMID: 19029596 DOI: 10.1088/1478-3975/5/4/046005] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The protein-synthesizing ribosome undergoes large motions to effect the translocation of tRNAs and mRNA; here, the domain motions of this system are explored with a coarse-grained elastic network model using normal mode analysis. Crystal structures are used to construct various model systems of the 70S complex with/without tRNA, elongation factor Tu and the ribosomal proteins. Computed motions reveal the well-known ratchet-like rotational motion of the large subunits, as well as the head rotation of the small subunit and the high flexibility of the L1 and L7/L12 stalks, even in the absence of ribosomal proteins. This result indicates that these experimentally observed motions during translocation are inherently controlled by the ribosomal shape and only partially dependent upon GTP hydrolysis. Normal mode analysis further reveals the mobility of A- and P-tRNAs to increase in the absence of the E-tRNA. In addition, the dynamics of the E-tRNA is affected by the absence of the ribosomal protein L1. The mRNA in the entrance tunnel interacts directly with helicase proteins S3 and S4, which constrain the mRNA in a clamp-like fashion, as well as with protein S5, which likely orients the mRNA to ensure correct translation. The ribosomal proteins S7, S11 and S18 may also be involved in assuring translation fidelity by constraining the mRNA at the exit site of the channel. The mRNA also interacts with the 16S 3' end forming the Shine-Dalgarno complex at the initiation step; the 3' end may act as a 'hook' to reel in the mRNA to facilitate its exit.
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Affiliation(s)
- Ozge Kurkcuoglu
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, 34342 Bebek, Istanbul, Turkey
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13
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Abstract
The assignment of specific ribosomal functions to individual ribosomal proteins is difficult due to the enormous cooperativity of the ribosome; however, important roles for distinct ribosomal proteins are becoming evident. Although rRNA has a major role in certain aspects of ribosomal function, such as decoding and peptidyl-transferase activity, ribosomal proteins are nevertheless essential for the assembly and optimal functioning of the ribosome. This is particularly true in the context of interactions at the entrance pore for mRNA, for the translation-factor binding site and at the tunnel exit, where both chaperones and complexes associated with protein transport through membranes bind.
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14
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Soman P, Rice Z, Siedlecki CA. Immunological identification of fibrinogen in dual-component protein films by AFM imaging. Micron 2008; 39:832-42. [PMID: 18294855 PMCID: PMC2637371 DOI: 10.1016/j.micron.2007.12.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Revised: 12/18/2007] [Accepted: 12/21/2007] [Indexed: 11/16/2022]
Abstract
The success of long-term blood-contacting implanted devices is largely dependent upon the interaction of the blood components with the device biomaterial surface. The ability to study these interactions has been hindered by a lack of methods to measure single-molecule interactions in complex multi-protein environments similar to the environment found in vivo. In this paper, we demonstrate the use of atomic force microscopy (AFM) in conjunction with gold nanolabels to detect the protein fibrinogen under aqueous conditions without the topographical clues usually necessary for high resolution visualization. BSA was patterned onto both muscovite mica and plasma-treated polydimethylsiloxane (PDMS) substrates and these test substrates were subsequently backfilled with fibrinogen to yield a featureless protein layer. The fibrinogen in this dual-protein layer was detected using high resolution AFM imaging following infusion of anti-fibrinogen conjugated with nanogold particles. This AFM immuno-detection technique will potentially be applicable to complex multi-component protein films adsorbed on clinically relevant polymers used in medical devices.
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Affiliation(s)
- Pranav Soman
- Department of Bioengineering, Biomedical Engineering Institute, The Pennsylvania State University, College of Medicine, Hershey, PA, 17033
| | - Zachary Rice
- Department of Surgery, Biomedical Engineering Institute, The Pennsylvania State University, College of Medicine, Hershey, PA, 17033
| | - Christopher A. Siedlecki
- Department of Bioengineering, Biomedical Engineering Institute, The Pennsylvania State University, College of Medicine, Hershey, PA, 17033
- Department of Surgery, Biomedical Engineering Institute, The Pennsylvania State University, College of Medicine, Hershey, PA, 17033
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15
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Aubin-Tam ME, Hamad-Schifferli K. Structure and function of nanoparticle–protein conjugates. Biomed Mater 2008; 3:034001. [DOI: 10.1088/1748-6041/3/3/034001] [Citation(s) in RCA: 205] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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16
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Miyoshi T, Uchiumi T. Functional interaction between bases C1049 in domain II and G2751 in domain VI of 23S rRNA in Escherichia coli ribosomes. Nucleic Acids Res 2008; 36:1783-91. [PMID: 18252772 PMCID: PMC2330231 DOI: 10.1093/nar/gkm1171] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The factor-binding center within the Escherichia coli ribosome is comprised of two discrete domains of 23S rRNA: the GTPase-associated region (GAR) in domain II and the sarcin-ricin loop in domain VI. These two regions appear to collaborate in the factor-dependent events that occur during protein synthesis. Current X-ray crystallography of the ribosome shows an interaction between C1049 in the GAR and G2751 in domain VI. We have confirmed this interaction by site-directed mutagenesis and chemical probing. Disruption of this base pair affected not only the chemical modification of some bases in domains II and VI and in helix H89 of domain V, but also ribosome function dependent on both EF-G and EF-Tu. Mutant ribosomes carrying the C1049 to G substitution, which show enhancement of chemical modification at G2751, were used to probe the interactions between the regions around 1049 and 2751. Binding of EF-G-GDP-fusidic acid, but not EF-G-GMP-PNP, to the ribosome protected G2751 from modification. The G2751 protection was also observed after tRNA binding to the ribosomal P and E sites. The results suggest that the interactions between the bases around 1049 and 2751 alter during different stages of the translation process.
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Affiliation(s)
- Tomohiro Miyoshi
- Department of Biology, Faculty of Science, Niigata University, Niigata 950-2181, Japan
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Abstract
YsxC is a small GTPase of Bacillus subtilis with essential but still unknown function, although recent works have suggested that it might be involved in ribosome biogenesis. Here, purified YsxC overexpressed in Escherichia coli was found to be partly associated with high-molecular-weight material, most likely rRNA, and thus eluted from gel filtration as a large complex. In addition, purification of ribosomes from an E. coli strain overexpressing YsxC allowed the copurification of the YsxC protein. Purified YsxC was shown to bind preferentially to the 50S subunit of B. subtilis ribosomes; this interaction was modulated by nucleotides and was stronger in the presence of a nonhydrolyzable GTP analogue than with GTP. Far-Western blotting analysis performed with His(6)-YsxC and ribosomal proteins separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed that YsxC interacted with at least four ribosomal proteins from the 50S subunit. Two of these putative protein partners were identified by mass spectrometry as L1 and L3, while the third reactive band in the one-dimensional gel contained L6 and L10. The fourth band that reacted with YsxC contained a mixture of three proteins, L7/L12, L23, and L27, suggesting that at least one of them binds to YsxC. Coimmobilization assays confirmed that L1, L6, and L7/L12 interact with YsxC. Together, these results suggest that YsxC plays a role in ribosome assembly.
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18
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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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19
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Hu M, Qian L, Briñas RP, Lymar ES, Hainfeld JF. Assembly of Nanoparticle–Protein Binding Complexes: From Monomers to Ordered Arrays. Angew Chem Int Ed Engl 2007; 46:5111-4. [PMID: 17538920 DOI: 10.1002/anie.200701180] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Minghui Hu
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
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20
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Hu M, Qian L, Briñas R, Lymar E, Hainfeld J. Assembly of Nanoparticle–Protein Binding Complexes: From Monomers to Ordered Arrays. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200701180] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Shcherbakov D, Dontsova M, Tribus M, Garber M, Piendl W. Stability of the 'L12 stalk' in ribosomes from mesophilic and (hyper)thermophilic Archaea and Bacteria. Nucleic Acids Res 2006; 34:5800-14. [PMID: 17053098 PMCID: PMC1635324 DOI: 10.1093/nar/gkl751] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2006] [Revised: 09/23/2006] [Accepted: 09/23/2006] [Indexed: 11/12/2022] Open
Abstract
The ribosomal stalk complex, consisting of one molecule of L10 and four or six molecules of L12, is attached to 23S rRNA via protein L10. This complex forms the so-called 'L12 stalk' on the 50S ribosomal subunit. Ribosomal protein L11 binds to the same region of 23S rRNA and is located at the base of the 'L12 stalk'. The 'L12 stalk' plays a key role in the interaction of the ribosome with translation factors. In this study stalk complexes from mesophilic and (hyper)thermophilic species of the archaeal genus Methanococcus and from the Archaeon Sulfolobus solfataricus, as well as from the Bacteria Escherichia coli, Geobacillus stearothermophilus and Thermus thermophilus, were overproduced in E.coli and purified under non-denaturing conditions. Using filter-binding assays the affinities of the archaeal and bacterial complexes to their specific 23S rRNA target site were analyzed at different pH, ionic strength and temperature. Affinities of both archaeal and bacterial complexes for 23S rRNA vary by more than two orders of magnitude, correlating very well with the growth temperatures of the organisms. A cooperative effect of binding to 23S rRNA of protein L11 and the L10/L12(4) complex from mesophilic and thermophilic Archaea was shown to be temperature-dependent.
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Affiliation(s)
- D Shcherbakov
- Biocenter, Division of Medical Biochemistry, Innsbruck Medical University, Fritz-Pregl-Strasse 3, 6020, Innsbruck, Austria.
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22
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Mitra K, Schaffitzel C, Fabiola F, Chapman MS, Ban N, Frank J. Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements. Mol Cell 2006; 22:533-43. [PMID: 16713583 DOI: 10.1016/j.molcel.2006.05.003] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2005] [Revised: 02/21/2006] [Accepted: 05/03/2006] [Indexed: 11/18/2022]
Abstract
In E. coli, the SecM nascent polypeptide causes elongation arrest, while interacting with 23S RNA bases A2058 and A749-753 in the exit tunnel of the large ribosomal subunit. We compared atomic models fitted by real-space refinement into cryo-electron microscopy reconstructions of a pretranslocational and SecM-stalled E. coli ribosome complex. A cascade of RNA rearrangements propagates from the exit tunnel throughout the large subunit, affecting intersubunit bridges and tRNA positions, which in turn reorient small subunit RNA elements. Elongation arrest could result from the inhibition of mRNA.(tRNAs) translocation, E site tRNA egress, and perhaps translation factor activation at the GTPase-associated center. Our study suggests that the specific secondary and tertiary arrangement of ribosomal RNA provides the basis for internal signal transduction within the ribosome. Thus, the ribosome may itself have the ability to regulate its progression through translation by modulating its structure and consequently its receptivity to activation by cofactors.
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MESH Headings
- Cryoelectron Microscopy
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Macromolecular Substances
- Models, Molecular
- Nucleic Acid Conformation
- Peptide Chain Elongation, Translational
- Protein Conformation
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- Ribosomes/metabolism
- Transcription Factors/chemistry
- Transcription Factors/genetics
- Transcription Factors/metabolism
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Affiliation(s)
- Kakoli Mitra
- Howard Hughes Medical Institute, Health Research, Inc., at the Wadsworth Center, Empire State Plaza, Albany, New York 12201, USA
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23
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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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24
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Sullivan L, Bennett GN. Proteome analysis and comparison of Clostridium acetobutylicum ATCC 824 and Spo0A strain variants. J Ind Microbiol Biotechnol 2005; 33:298-308. [PMID: 16308714 DOI: 10.1007/s10295-005-0050-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Accepted: 10/01/2005] [Indexed: 11/24/2022]
Abstract
The proteomic profiles of several Clostridium acetobutylicum strains were compared by two-dimensional gel electrophoresis and mass spectroscopy. The proteomic profile of C. acetobutylicum wild type strain ATCC 824 with and without a commonly used control plasmid and with a spo0A overexpression plasmid pMSPOA was compared. A total of 2,081 protein spots were analyzed; 23 proteins were chosen to be identified of which 18 were unique and 5 were proteins located in more than one location. The proteins identified were classified into heat shock stress response, acid and solvent formation, and transcription and translation proteins. Spo0A was identified and its protein expression was confirmed to be absent in the spo0A knockout SKO1 strain as expected, as was the protein Adc, which is known to be regulated by Spo0A. The expression of six proteins was not detected in strain SKO1 indicating these proteins require Spo0A. Spo0A overexpression affected the abundance of proteins involved in glycolysis, translation, heat shock stress response, and energy production. Two features were identified: five of the 23 proteins identified were located in more than one position and clusters of protein spots resembled fingers of a straightened hand. Normally a protein localizes to only one spot on the gel; localization of a protein to more than one spot is indicative of post-translational modifications, suggesting that such modification of proteins may be a more prevalent mechanism in C. acetobutylicum than previously thought. The clusters of protein spots resembling fingers of a straightened hand were in the acidic high molecular weight areas. Two such protein spots were identified as variants of the same protein, GroEL.
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Affiliation(s)
- Leighann Sullivan
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA
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25
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Uversky VN, Oldfield CJ, Dunker AK. Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling. J Mol Recognit 2005; 18:343-84. [PMID: 16094605 DOI: 10.1002/jmr.747] [Citation(s) in RCA: 660] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Regulation, recognition and cell signaling involve the coordinated actions of many players. To achieve this coordination, each participant must have a valid identification (ID) that is easily recognized by the others. For proteins, these IDs are often within intrinsically disordered (also ID) regions. The functions of a set of well-characterized ID regions from a diversity of proteins are presented herein to support this view. These examples include both more recently described signaling proteins, such as p53, alpha-synuclein, HMGA, the Rieske protein, estrogen receptor alpha, chaperones, GCN4, Arf, Hdm2, FlgM, measles virus nucleoprotein, RNase E, glycogen synthase kinase 3beta, p21(Waf1/Cip1/Sdi1), caldesmon, calmodulin, BRCA1 and several other intriguing proteins, as well as historical prototypes for signaling, regulation, control and molecular recognition, such as the lac repressor, the voltage gated potassium channel, RNA polymerase and the S15 peptide associating with the RNA polymerase S-protein. The frequent occurrence and the common use of ID regions in important protein functions raise the possibility that the relationship between amino acid sequence, disordered ensemble and function might be the dominant paradigm for the molecular recognition that serves as the basis for signaling and regulation by protein molecules.
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Affiliation(s)
- Vladimir N Uversky
- Molecular Kinetics, 6201 La Pas Trail, Suite 160, Indianapolis, IN 46268, USA
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26
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Diaconu M, Kothe U, Schlünzen F, Fischer N, Harms JM, Tonevitsky AG, Stark H, Rodnina MV, Wahl MC. Structural basis for the function of the ribosomal L7/12 stalk in factor binding and GTPase activation. Cell 2005; 121:991-1004. [PMID: 15989950 DOI: 10.1016/j.cell.2005.04.015] [Citation(s) in RCA: 316] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2004] [Revised: 03/04/2005] [Accepted: 04/14/2005] [Indexed: 11/23/2022]
Abstract
The L7/12 stalk of the large subunit of bacterial ribosomes encompasses protein L10 and multiple copies of L7/12. We present crystal structures of Thermotoga maritima L10 in complex with three L7/12 N-terminal-domain dimers, refine the structure of an archaeal L10E N-terminal domain on the 50S subunit, and identify these elements in cryo-electron-microscopic reconstructions of Escherichia coli ribosomes. The mobile C-terminal helix alpha8 of L10 carries three L7/12 dimers in T. maritima and two in E. coli, in concordance with the different length of helix alpha8 of L10 in these organisms. The stalk is organized into three elements (stalk base, L10 helix alpha8-L7/12 N-terminal-domain complex, and L7/12 C-terminal domains) linked by flexible connections. Highly mobile L7/12 C-terminal domains promote recruitment of translation factors to the ribosome and stimulate GTP hydrolysis by the ribosome bound factors through stabilization of their active GTPase conformation.
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Affiliation(s)
- Mihaela Diaconu
- Röntgenkristallographie, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, D-37077 Göttingen, Germany
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27
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Allen GS, Zavialov A, Gursky R, Ehrenberg M, Frank J. The Cryo-EM Structure of a Translation Initiation Complex from Escherichia coli. Cell 2005; 121:703-12. [PMID: 15935757 DOI: 10.1016/j.cell.2005.03.023] [Citation(s) in RCA: 242] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Revised: 03/14/2005] [Accepted: 03/22/2005] [Indexed: 11/22/2022]
Abstract
The 70S ribosome and its complement of factors required for initiation of translation in E. coli were purified separately and reassembled in vitro with GDPNP, producing a stable initiation complex (IC) stalled after 70S assembly. We have obtained a cryo-EM reconstruction of the IC showing IF2*GDPNP at the intersubunit cleft of the 70S ribosome. IF2*GDPNP contacts the 30S and 50S subunits as well as fMet-tRNA(fMet). IF2 here adopts a conformation radically different from that seen in the recent crystal structure of IF2. The C-terminal domain of IF2 binds to the single-stranded portion of fMet-tRNA(fMet), thereby forcing the tRNA into a novel orientation at the P site. The GTP binding domain of IF2 binds to the GTPase-associated center of the 50S subunit in a manner similar to EF-G and EF-Tu. Additionally, we present evidence for the localization of IF1, IF3, one C-terminal domain of L7/L12, and the N-terminal domain of IF2 in the initiation complex.
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Affiliation(s)
- Gregory S Allen
- Howard Hughes Medical Institute, Health Research, Inc. at the Wadsworth Center, Albany, New York 12201, USA
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28
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Asturias FJ, Chadick JZ, Cheung IK, Stark H, Witkowski A, Joshi AK, Smith S. Structure and molecular organization of mammalian fatty acid synthase. Nat Struct Mol Biol 2005; 12:225-32. [PMID: 15711565 DOI: 10.1038/nsmb899] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2004] [Accepted: 01/19/2005] [Indexed: 11/09/2022]
Abstract
De novo synthesis of fatty acids in the cytosol of animal cells is carried out by the multifunctional, homodimeric fatty acid synthase (FAS). Cryo-EM analysis of single FAS particles imaged under conditions that limit conformational variability, combined with gold labeling of the N termini and structural analysis of the FAS monomers, reveals two coiled monomers in an overlapping arrangement. Comparison of dimeric FAS structures related to different steps in the fatty acid synthesis process indicates that only limited local rearrangements are required for catalytic interaction among different functional domains. Monomer coiling probably contributes to FAS efficiency and provides a structural explanation for the reported activity of a FAS monomer dimerized to a catalytically inactive partner. The new FAS structure provides a new paradigm for understanding the architecture of FAS and the related modular polyketide synthases.
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Affiliation(s)
- Francisco J Asturias
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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29
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Zhao Q, Ofverstedt LG, Skoglund U, Isaksson LA. Morphological variation of individual Escherichia coli 50S ribosomal subunits in situ, as revealed by cryo-electron tomography. Exp Cell Res 2004; 300:190-201. [PMID: 15383326 DOI: 10.1016/j.yexcr.2004.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2004] [Revised: 07/08/2004] [Indexed: 10/26/2022]
Abstract
Electron tomography (ET) has been used to reconstruct in situ individual 50S ribosomal subunits in Escherichia coli rifampicin-treated cells. Rifampicin inhibits transcription initiation. As a result, rapid degradation of preformed mRNA and dissociation of 70S ribosomes give accumulation of free subunits. In the 50S subunit, the L1 stalk, the L7/L12 stalk, the central protuberance (CP), and the peptidyl transferase center (PTC) cleft are the most dynamic and flexible parts in the reconstructed structures with clear movements indicated. Different locations of the tunnel in the central cross-sections through the in situ 50S subunits indicate the flexible nature of the pathway inside the large ribosomal subunit. In addition, gross morphological heterogeneity was observed in the reconstructions. Our results demonstrate a considerable structural variability among individual 50S subunits in the intracellular environment.
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Affiliation(s)
- Qing Zhao
- Department of Genetics, Microbiology and Toxicology, Stockholm University, S-106 91 Stockholm, Sweden
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30
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Christodoulou J, Larsson G, Fucini P, Connell SR, Pertinhez TA, Hanson CL, Redfield C, Nierhaus KH, Robinson CV, Schleucher J, Dobson CM. Heteronuclear NMR investigations of dynamic regions of intact Escherichia coli ribosomes. Proc Natl Acad Sci U S A 2004; 101:10949-54. [PMID: 15263071 PMCID: PMC503724 DOI: 10.1073/pnas.0400928101] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
15N-(1)H NMR spectroscopy has been used to probe the dynamic properties of uniformly (15)N labeled Escherichia coli ribosomes. Despite the high molecular weight of the complex ( approximately 2.3 MDa), [(1)H-(15)N] heteronuclear single-quantum correlation spectra contain approximately 100 well resolved resonances, the majority of which arise from two of the four C-terminal domains of the stalk proteins, L7/L12. Heteronuclear pulse-field gradient NMR experiments show that the resonances arise from species with a translational diffusion constant consistent with that of the intact ribosome. Longitudinal relaxation time (T(1)) and T(1 rho) (15)N-spin relaxation measurements show that the observable domains tumble anisotropically, with an apparent rotational correlation time significantly longer than that expected for a free L7/L12 domain but much shorter than expected for a protein rigidly incorporated within the ribosomal particle. The relaxation data allow the ribosomally bound C-terminal domains to be oriented relative to the rotational diffusion tensor. Binding of elongation factor G to the ribosome results in the disappearance of the resonances of the L7/L12 domains, indicating a dramatic reduction in their mobility. This result is in agreement with cryoelectron microscopy studies showing that the ribosomal stalk assumes a single rigid orientation upon elongation factor G binding. As well as providing information about the dynamical properties of L7/L12, these results demonstrate the utility of heteronuclear NMR in the study of mobile regions of large biological complexes and form the basis for further NMR studies of functional ribosomal complexes in the context of protein synthesis.
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Affiliation(s)
- John Christodoulou
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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31
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Bocharov EV, Sobol AG, Pavlov KV, Korzhnev DM, Jaravine VA, Gudkov AT, Arseniev AS. From structure and dynamics of protein L7/L12 to molecular switching in ribosome. J Biol Chem 2004; 279:17697-706. [PMID: 14960595 DOI: 10.1074/jbc.m313384200] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Based on the (1)H-(15)N NMR spectroscopy data, the three-dimensional structure and internal dynamic properties of ribosomal protein L7 from Escherichia coli were derived. The structure of L7 dimer in solution can be described as a set of three distinct domains, tumbling rather independently and linked via flexible hinge regions. The dimeric N-terminal domain (residues 1-32) consists of two antiparallel alpha-alpha-hairpins forming a symmetrical four-helical bundle, whereas the two identical C-terminal domains (residues 52-120) adopt a compact alpha/beta-fold. There is an indirect evidence of the existence of transitory helical structures at least in the first part (residues 33-43) of the hinge region. Combining structural data for the ribosomal protein L7/L12 from NMR spectroscopy and x-ray crystallography, it was suggested that its hinge region acts as a molecular switch, initiating "ratchet-like" motions of the L7/L12 stalk with respect to the ribosomal surface in response to elongation factor binding and GTP hydrolysis. This hypothesis allows an explanation of events observed during the translation cycle and provides useful insights into the role of protein L7/L12 in the functioning of the ribosome.
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Affiliation(s)
- Eduard V Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow 117997, Russia
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32
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Nomura T, Mochizuki R, Dabbs ER, Shimizu Y, Ueda T, Hachimori A, Uchiumi T. A point mutation in ribosomal protein L7/L12 reduces its ability to form a compact dimer structure and to assemble into the GTPase center. Biochemistry 2003; 42:4691-8. [PMID: 12705832 DOI: 10.1021/bi027087g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An Escherichia coli mutant, LL103, harboring a mutation (Ser15 to Phe) in ribosomal protein L7/L12 was isolated among revertants of a streptomycin-dependent strain. In the crystal structure of the L7/L12 dimer, residue 15 within the N-terminal domain contacts the C-terminal domain of the partner monomer. We tested effects of the mutation on molecular assembly by biochemical approaches. Gel electrophoretic analysis showed that the Phe15-L7/L12 variant had reduced ability in binding to L10, an effect enhanced in the presence of 0.05% of nonionic detergent. Mobility of Phe15-L7/L12 on gel containing the detergent was very low compared to the wild-type proteins, presumably because of an extended structural state of the mutant L7/L12. Ribosomes isolated from LL103 cells contained a reduced amount of L7/L12 and showed low levels (15-30% of wild-type ribosomes) of activities dependent on elongation factors and in translation of natural mRNA. The ribosomal activity was completely recovered by addition of an excess amount of Phe15-L7/L12 to the ribosomes, suggesting that the mutant L7/L12 exerts normal functions when bound on the ribosome. The interaction of Ser15 with the C-terminal domain of the partner molecule seems to contribute to formation of the compact dimer structure and its efficient assembly into the ribosomal GTPase center. We propose a model relating compact and elongated forms of L7/L12 dimers. Phe15-L7/L12 provides a new tool for studying the functional structure of the homodimer.
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Affiliation(s)
- Takaomi Nomura
- Institute of High Polymer Research, Faculty of Textile Science and Technology, Shinshu University, Ueda 386-8567, Japan
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33
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Hanson CL, Fucini P, Ilag LL, Nierhaus KH, Robinson CV. Dissociation of intact Escherichia coli ribosomes in a mass spectrometer. Evidence for conformational change in a ribosome elongation factor G complex. J Biol Chem 2003; 278:1259-67. [PMID: 12409297 DOI: 10.1074/jbc.m208966200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We used mass spectrometry to identify proteins that are released in the gas phase from Escherichia coli ribosomes in response to a range of different solution conditions and cofactor binding. From solution at neutral pH the spectra are dominated by just 4 of the 54 ribosomal proteins (L7/L12, L11, and L10). Lowering the pH of the solution leads to the gas phase dissociation of four additional proteins as well as the 5 S RNA. Replacement of Mg(2+) by Li(+) ions in solutions of ribosomes induced the dissociation of 17 ribosomal proteins. Correlation of these results with available structural information for ribosomes revealed that a relatively high interaction surface area of the protein with RNA was the major force in preventing dissociation. By using the proteins that dissociate to probe their interactions with RNA, we examined different complexes of the ribosome formed with the elongation factor G and inhibited by fusidic acid or thiostrepton. Mass spectra recorded for the fusidic acid-inhibited complex reveal subtle changes in peak intensity of the proteins that dissociate. By contrast gas phase dissociation from the thiostrepton-inhibited complex is markedly different and demonstrates the presence of L5 and L18, two proteins that interact exclusively with the 5 S RNA. These results allow us to propose that the ribosome elongation factor-G complex inhibited by thiostrepton, but not fusidic acid, involves destabilization of 5 S RNA-protein interactions.
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Affiliation(s)
- Charlotte L Hanson
- Department of Chemistry, University of Cambridge, Lensfield Road, United Kingdom
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34
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Uchiumi T, Honma S, Nomura T, Dabbs ER, Hachimori A. Translation elongation by a hybrid ribosome in which proteins at the GTPase center of the Escherichia coli ribosome are replaced with rat counterparts. J Biol Chem 2002; 277:3857-62. [PMID: 11729183 DOI: 10.1074/jbc.m107730200] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ribosomal L10-L7/L12 protein complex and L11 bind to a highly conserved RNA region around position 1070 in domain II of 23 S rRNA and constitute a part of the GTPase-associated center in Escherichia coli ribosomes. We replaced these ribosomal proteins in vitro with the rat counterparts P0-P1/P2 complex and RL12, and tested them for ribosomal activities. The core 50 S subunit lacking the proteins on the 1070 RNA domain was prepared under gentle conditions from a mutant deficient in ribosomal protein L11. The rat proteins bound to the core 50 S subunit through their interactions with the 1070 RNA domain. The resultant hybrid ribosome was insensitive to thiostrepton and showed poly(U)-programmed polyphenylalanine synthesis dependent on the actions of both eukaryotic elongation factors 1alpha (eEF-1alpha) and 2 (eEF-2) but not of the prokaryotic equivalent factors EF-Tu and EF-G. The results from replacement of either the L10-L7/L12 complex or L11 with rat protein showed that the P0-P1/P2 complex, and not RL12, was responsible for the specificity of the eukaryotic ribosomes to eukaryotic elongation factors and for the accompanying GTPase activity. The presence of either E. coli L11 or rat RL12 considerably stimulated the polyphenylalanine synthesis by the hybrid ribosome, suggesting that L11/RL12 proteins play an important role in post-GTPase events of translation elongation.
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Affiliation(s)
- Toshio Uchiumi
- Institute of High Polymer Research, Faculty of Textile Science and Technology, Shinshu University, Ueda 386-8567, Japan.
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Metzler DE, Metzler CM, Sauke DJ. Ribosomes and the Synthesis of Proteins. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50032-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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