1
|
Chamberlain SR, Moore S, Grant TD. Fitting high-resolution electron density maps from atomic models to solution scattering data. Biophys J 2023; 122:4567-4581. [PMID: 37924208 PMCID: PMC10719074 DOI: 10.1016/j.bpj.2023.10.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/29/2023] [Accepted: 10/31/2023] [Indexed: 11/06/2023] Open
Abstract
Solution scattering techniques, such as small- and wide-angle X-ray scattering (SWAXS), provide valuable insights into the structure and dynamics of biological macromolecules in solution. In this study, we present an approach to accurately predict solution X-ray scattering profiles at wide angles from atomic models by generating high-resolution electron density maps. Our method accounts for the excluded volume of bulk solvent by calculating unique adjusted atomic volumes directly from the atomic coordinates. This approach eliminates the need for one of the free fitting parameters commonly used in existing algorithms, resulting in improved accuracy of the calculated SWAXS profile. An implicit model of the hydration shell is generated that uses the form factor of water. Two parameters, namely the bulk solvent density and the mean hydration shell contrast, are adjusted to best fit the data. Results using eight publicly available SWAXS profiles show high-quality fits to the data. In each case, the optimized parameter values show small adjustments demonstrating that the default values are close to the true solution. Disabling parameter optimization produces significantly more accurate predicted scattering profiles compared to the leading software. The algorithm is computationally efficient, comparable to the leading software and up to 10 times faster for large molecules. The algorithm is encoded in a command line script called denss.pdb2mrc.py and is available open source as part of the DENSS v1.7.0 software package. In addition to improving the ability to compare atomic models to experimental SWAXS data, these developments pave the way for increasing the accuracy of modeling algorithms using SWAXS data and decreasing the risk of overfitting.
Collapse
Affiliation(s)
- Sarah R Chamberlain
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, New York
| | - Stephen Moore
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, New York
| | - Thomas D Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, New York.
| |
Collapse
|
2
|
Krupnik L, Joshi P, Kappler A, Flühmann B, Alston AB, Digigow R, Wick P, Neels A. Critical nanomaterial attributes of iron-carbohydrate nanoparticles: Leveraging orthogonal methods to resolve the 3-dimensional structure. Eur J Pharm Sci 2023; 188:106521. [PMID: 37423578 DOI: 10.1016/j.ejps.2023.106521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 06/08/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
Abstract
Intravenous iron-carbohydrate nanomedicines are widely used to treat iron deficiency and iron deficiency anemia across a wide breadth of patient populations. These colloidal solutions of nanoparticles are complex drugs which inherently makes physicochemical characterization more challenging than small molecule drugs. There have been advancements in physicochemical characterization techniques such as dynamic light scattering and zeta potential measurement, that have provided a better understanding of the physical structure of these drug products in vitro. However, establishment and validation of complementary and orthogonal approaches are necessary to better understand the 3-dimensional physical structure of the iron-carbohydrate complexes, particularly with regard to their physical state in the context of the nanoparticle interaction with biological components such as whole blood (i.e. the nano-bio interface).
Collapse
Affiliation(s)
- Leonard Krupnik
- Laboratory for Particles-Biology Interactions, Materials meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), St. Gallen, Switzerland; Center for X-ray Analytics, Materials meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), St. Gallen, Switzerland; Department of Chemistry, University of Fribourg, Fribourg 1700, Switzerland
| | - Prachi Joshi
- Geomicrobiology, Department of Geosciences, University of Tuebingen, Tuebingen 72076, Germany
| | - Andreas Kappler
- Geomicrobiology, Department of Geosciences, University of Tuebingen, Tuebingen 72076, Germany; Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, Tuebingen 72076, Germany
| | - Beat Flühmann
- CSL Vifor, Flughofstrasse 61, Glattbrug 8152, Switzerland
| | | | | | - Peter Wick
- Laboratory for Particles-Biology Interactions, Materials meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), St. Gallen, Switzerland
| | - Antonia Neels
- Center for X-ray Analytics, Materials meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), St. Gallen, Switzerland; Department of Chemistry, University of Fribourg, Fribourg 1700, Switzerland
| |
Collapse
|
3
|
Chamberlain SR, Moore S, Grant TD. Fitting high-resolution electron density maps from atomic models to solution scattering data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543451. [PMID: 37398274 PMCID: PMC10312546 DOI: 10.1101/2023.06.02.543451] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Solution scattering techniques, such as small and wide-angle X-ray scattering (SWAXS), provide valuable insights into the structure and dynamics of biological macromolecules in solution. In this study, we present an approach to accurately predict solution X-ray scattering profiles at wide angles from atomic models by generating high-resolution electron density maps. Our method accounts for the excluded volume of bulk solvent by calculating unique adjusted atomic volumes directly from the atomic coordinates. This approach eliminates the need for a free fitting parameter commonly used in existing algorithms, resulting in improved accuracy of the calculated SWAXS profile. An implicit model of the hydration shell is generated which uses the form factor of water. Two parameters, namely the bulk solvent density and the mean hydration shell contrast, are adjusted to best fit the data. Results using eight publicly available SWAXS profiles show high quality fits to the data. In each case, the optimized parameter values show small adjustments demonstrating that the default values are close to the true solution. Disabling parameter optimization results in a significant improvement of the calculated scattering profiles compared to the leading software. The algorithm is computationally efficient, showing more than tenfold reduction in execution time compared to the leading software. The algorithm is encoded in a command line script called denss.pdb2mrc.py and is available open source as part of the DENSS v1.7.0 software package (https://github.com/tdgrant1/denss). In addition to improving the ability to compare atomic models to experimental SWAXS data, these developments pave the way for increasing the accuracy of modeling algorithms utilizing SWAXS data while decreasing the risk of overfitting.
Collapse
Affiliation(s)
- Sarah R. Chamberlain
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, USA
| | - Stephen Moore
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, USA
| | - Thomas D. Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, USA
| |
Collapse
|
4
|
Ge X, Oliveira A, Hjort K, Bergfors T, Gutiérrez-de-Terán H, Andersson DI, Sanyal S, Åqvist J. Inhibition of translation termination by small molecules targeting ribosomal release factors. Sci Rep 2019; 9:15424. [PMID: 31659219 PMCID: PMC6817905 DOI: 10.1038/s41598-019-51977-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/10/2019] [Indexed: 11/18/2022] Open
Abstract
The bacterial ribosome is an important drug target for antibiotics that can inhibit different stages of protein synthesis. Among the various classes of compounds that impair translation there are, however, no known small-molecule inhibitors that specifically target ribosomal release factors (RFs). The class I RFs are essential for correct termination of translation and they differ considerably between bacteria and eukaryotes, making them potential targets for inhibiting bacterial protein synthesis. We carried out virtual screening of a large compound library against 3D structures of free and ribosome-bound RFs in order to search for small molecules that could potentially inhibit termination by binding to the RFs. Here, we report identification of two such compounds which are found both to bind free RFs in solution and to inhibit peptide release on the ribosome, without affecting peptide bond formation.
Collapse
Affiliation(s)
- Xueliang Ge
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Ana Oliveira
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Karin Hjort
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Terese Bergfors
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Hugo Gutiérrez-de-Terán
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden.
| |
Collapse
|
5
|
Hura GL, Hodge CD, Rosenberg D, Guzenko D, Duarte JM, Monastyrskyy B, Grudinin S, Kryshtafovych A, Tainer JA, Fidelis K, Tsutakawa SE. Small angle X-ray scattering-assisted protein structure prediction in CASP13 and emergence of solution structure differences. Proteins 2019; 87:1298-1314. [PMID: 31589784 DOI: 10.1002/prot.25827] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 09/27/2019] [Accepted: 09/27/2019] [Indexed: 12/14/2022]
Abstract
Small angle X-ray scattering (SAXS) measures comprehensive distance information on a protein's structure, which can constrain and guide computational structure prediction algorithms. Here, we evaluate structure predictions of 11 monomeric and oligomeric proteins for which SAXS data were collected and provided to predictors in the 13th round of the Critical Assessment of protein Structure Prediction (CASP13). The category for SAXS-assisted predictions made gains in certain areas for CASP13 compared to CASP12. Improvements included higher quality data with size exclusion chromatography-SAXS (SEC-SAXS) and better selection of targets and communication of results by CASP organizers. In several cases, we can track improvements in model accuracy with use of SAXS data. For hard multimeric targets where regular folding algorithms were unsuccessful, SAXS data helped predictors to build models better resembling the global shape of the target. For most models, however, no significant improvement in model accuracy at the domain level was registered from use of SAXS data, when rigorously comparing SAXS-assisted models to the best regular server predictions. To promote future progress in this category, we identify successes, challenges, and opportunities for improved strategies in prediction, assessment, and communication of SAXS data to predictors. An important observation is that, for many targets, SAXS data were inconsistent with crystal structures, suggesting that these proteins adopt different conformation(s) in solution. This CASP13 result, if representative of PDB structures and future CASP targets, may have substantive implications for the structure training databases used for machine learning, CASP, and use of prediction models for biology.
Collapse
Affiliation(s)
- Greg L Hura
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California.,Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California
| | - Curtis D Hodge
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Daniel Rosenberg
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Dmytro Guzenko
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, California
| | - Jose M Duarte
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, California
| | - Bohdan Monastyrskyy
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, California
| | - Sergei Grudinin
- Univ. Grenoble Alpes, CNRS, Inria, Grenoble INP, LJK, 38000, Grenoble, France
| | - Andriy Kryshtafovych
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, California
| | - John A Tainer
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California.,Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | - Krzysztof Fidelis
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, California
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California
| |
Collapse
|
6
|
The structural basis for release-factor activation during translation termination revealed by time-resolved cryogenic electron microscopy. Nat Commun 2019; 10:2579. [PMID: 31189921 PMCID: PMC6561943 DOI: 10.1038/s41467-019-10608-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 05/14/2019] [Indexed: 11/08/2022] Open
Abstract
When the ribosome encounters a stop codon, it recruits a release factor (RF) to hydrolyze the ester bond between the peptide chain and tRNA. RFs have structural motifs that recognize stop codons in the decoding center and a GGQ motif for induction of hydrolysis in the peptidyl transfer center 70 Å away. Surprisingly, free RF2 is compact, with only 20 Å between its codon-reading and GGQ motifs. Cryo-EM showed that ribosome-bound RFs have extended structures, suggesting that RFs are compact when entering the ribosome and then extend their structures upon stop codon recognition. Here we use time-resolved cryo-EM to visualize transient compact forms of RF1 and RF2 at 3.5 and 4 Å resolution, respectively, in the codon-recognizing ribosome complex on the native pathway. About 25% of complexes have RFs in the compact state at 24 ms reaction time, and within 60 ms virtually all ribosome-bound RFs are transformed to their extended forms. Translation termination is under strong selection pressure for high speed and accuracy. Here the authors provide a 3D view of the dynamics of a translating bacterial ribosome as it recruits a class-1 release factor (RF1 or RF2) upon encountering a stop codon, and propose a structure-based kinetic model for the early steps in bacterial translation termination.
Collapse
|
7
|
Sutton EJ, Bradshaw RT, Orr CM, Frendéus B, Larsson G, Teige I, Cragg MS, Tews I, Essex JW. Evaluating Anti-CD32b F(ab) Conformation Using Molecular Dynamics and Small-Angle X-Ray Scattering. Biophys J 2018; 115:289-299. [PMID: 30021105 PMCID: PMC6050753 DOI: 10.1016/j.bpj.2018.03.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 02/16/2018] [Accepted: 03/27/2018] [Indexed: 11/04/2022] Open
Abstract
Complementary strategies of small-angle x-ray scattering (SAXS) and crystallographic analysis are often used to determine atomistic three-dimensional models of macromolecules and their variability in solution. This combination of techniques is particularly valuable when applied to macromolecular complexes to detect changes within the individual binding partners. Here, we determine the x-ray crystallographic structure of a F(ab) fragment in complex with CD32b, the only inhibitory Fc-γ receptor in humans, and compare the structure of the F(ab) from the crystal complex to SAXS data for the F(ab) alone in solution. We investigate changes in F(ab) structure by predicting theoretical scattering profiles for atomistic structures extracted from molecular dynamics (MD) simulations of the F(ab) and assessing the agreement of these structures to our experimental SAXS data. Through principal component analysis, we are able to extract principal motions observed during the MD trajectory and evaluate the influence of these motions on the agreement of structures to the F(ab) SAXS data. Changes in the F(ab) elbow angle were found to be important to reach agreement with the experimental data; however, further discrepancies were apparent between our F(ab) structure from the crystal complex and SAXS data. By analyzing multiple MD structures observed in similar regions of the principal component analysis, we were able to pinpoint these discrepancies to a specific loop region in the F(ab) heavy chain. This method, therefore, not only allows determination of global changes but also allows identification of localized motions important for determining the agreement between atomistic structures and SAXS data. In this particular case, the findings allowed us to discount the hypothesis that structural changes were induced upon complex formation, a significant find informing the drug development process. The methodology described here is generally applicable to deconvolute global and local changes of macromolecular structures and is well suited to other systems.
Collapse
Affiliation(s)
- Emma J Sutton
- Antibody & Vaccine Group, Cancer Sciences Unit, Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom; Department of Chemistry, University of Southampton, Highfield Campus, Southampton, United Kingdom; Department of Biological Sciences, Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton, United Kingdom
| | - Richard T Bradshaw
- Department of Chemistry, University of Southampton, Highfield Campus, Southampton, United Kingdom
| | - Christian M Orr
- Antibody & Vaccine Group, Cancer Sciences Unit, Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom; Department of Biological Sciences, Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton, United Kingdom
| | | | | | | | - Mark S Cragg
- Antibody & Vaccine Group, Cancer Sciences Unit, Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
| | - Ivo Tews
- Department of Biological Sciences, Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton, United Kingdom
| | - Jonathan W Essex
- Department of Chemistry, University of Southampton, Highfield Campus, Southampton, United Kingdom.
| |
Collapse
|
8
|
Abstract
Codon usage depends on mutation bias, tRNA-mediated selection, and the need for high efficiency and accuracy in translation. One codon in a synonymous codon family is often strongly over-used, especially in highly expressed genes, which often leads to a high dN/dS ratio because dS is very small. Many different codon usage indices have been proposed to measure codon usage and codon adaptation. Sense codon could be misread by release factors and stop codons misread by tRNAs, which also contribute to codon usage in rare cases. This chapter outlines the conceptual framework on codon evolution, illustrates codon-specific and gene-specific codon usage indices, and presents their applications. A new index for codon adaptation that accounts for background mutation bias (Index of Translation Elongation) is presented and contrasted with codon adaptation index (CAI) which does not consider background mutation bias. They are used to re-analyze data from a recent paper claiming that translation elongation efficiency matters little in protein production. The reanalysis disproves the claim.
Collapse
|
9
|
Conformational Control of Translation Termination on the 70S Ribosome. Structure 2018; 26:821-828.e3. [PMID: 29731232 DOI: 10.1016/j.str.2018.04.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/07/2018] [Accepted: 04/05/2018] [Indexed: 11/20/2022]
Abstract
Translation termination ensures proper lengths of cellular proteins. During termination, release factor (RF) recognizes a stop codon and catalyzes peptide release. Conformational changes in RF are thought to underlie accurate translation termination. However, structural studies of ribosome termination complexes have only captured RFs in a conformation that is consistent with the catalytically active state. Here, we employ a hyper-accurate RF1 variant to obtain crystal structures of 70S termination complexes that suggest a structural pathway for RF1 activation. We trapped RF1 conformations with the catalytic domain outside of the peptidyl-transferase center, while the codon-recognition domain binds the stop codon. Stop-codon recognition induces 30S decoding-center rearrangements that precede accommodation of the catalytic domain. The separation of codon recognition from the opening of the catalytic domain suggests how rearrangements in RF1 and in the ribosomal decoding center coordinate stop-codon recognition with peptide release, ensuring accurate translation termination.
Collapse
|
10
|
Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem Rev 2018; 118:4177-4338. [PMID: 29297679 PMCID: PMC5920944 DOI: 10.1021/acs.chemrev.7b00427] [Citation(s) in RCA: 327] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 12/14/2022]
Abstract
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.
Collapse
Affiliation(s)
- Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory, Department of Biology , University of Copenhagen , Copenhagen 2200 , Denmark
| | - Richard A Cunha
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Alejandro Gil-Ley
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Giovanni Pinamonti
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Simón Poblete
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| |
Collapse
|
11
|
Recent developments in small-angle X-ray scattering and hybrid method approaches for biomacromolecular solutions. Emerg Top Life Sci 2018; 2:69-79. [PMID: 33525782 DOI: 10.1042/etls20170138] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 02/01/2018] [Accepted: 02/05/2018] [Indexed: 01/05/2023]
Abstract
Small-angle X-ray scattering (SAXS) has become a streamline method to characterize biological macromolecules, from small peptides to supramolecular complexes, in near-native solutions. Modern SAXS requires limited amounts of purified material, without the need for labelling, crystallization, or freezing. Dedicated beamlines at modern synchrotron sources yield high-quality data within or below several milliseconds of exposure time and are highly automated, allowing for rapid structural screening under different solutions and ambient conditions but also for time-resolved studies of biological processes. The advanced data analysis methods allow one to meaningfully interpret the scattering data from monodisperse systems, from transient complexes as well as flexible and heterogeneous systems in terms of structural models. Especially powerful are hybrid approaches utilizing SAXS with high-resolution structural techniques, but also with biochemical, biophysical, and computational methods. Here, we review the recent developments in the experimental SAXS practice and in analysis methods with a specific focus on the joint use of SAXS with complementary methods.
Collapse
|
12
|
Demo G, Svidritskiy E, Madireddy R, Diaz-Avalos R, Grant T, Grigorieff N, Sousa D, Korostelev AA. Mechanism of ribosome rescue by ArfA and RF2. eLife 2017; 6. [PMID: 28300532 PMCID: PMC5378476 DOI: 10.7554/elife.23687] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 03/14/2017] [Indexed: 11/13/2022] Open
Abstract
ArfA rescues ribosomes stalled on truncated mRNAs by recruiting release factor RF2, which normally binds stop codons to catalyze peptide release. We report two 3.2 Å resolution cryo-EM structures – determined from a single sample – of the 70S ribosome with ArfA•RF2 in the A site. In both states, the ArfA C-terminus occupies the mRNA tunnel downstream of the A site. One state contains a compact inactive RF2 conformation. Ordering of the ArfA N-terminus in the second state rearranges RF2 into an extended conformation that docks the catalytic GGQ motif into the peptidyl-transferase center. Our work thus reveals the structural dynamics of ribosome rescue. The structures demonstrate how ArfA ‘senses’ the vacant mRNA tunnel and activates RF2 to mediate peptide release without a stop codon, allowing stalled ribosomes to be recycled. DOI:http://dx.doi.org/10.7554/eLife.23687.001
Collapse
Affiliation(s)
- Gabriel Demo
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
| | - Egor Svidritskiy
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
| | - Rohini Madireddy
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Ruben Diaz-Avalos
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Timothy Grant
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Nikolaus Grigorieff
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Duncan Sousa
- Department of Biological Science, Florida State University, Tallahassee, United States
| | - Andrei A Korostelev
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| |
Collapse
|
13
|
Kim JS, Afsari B, Chirikjian GS. Cross-Validation of Data Compatibility Between Small Angle X-ray Scattering and Cryo-Electron Microscopy. J Comput Biol 2017; 24:13-30. [PMID: 27710115 PMCID: PMC5220572 DOI: 10.1089/cmb.2016.0139] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cryo-electron microscopy (EM) and small angle X-ray scattering (SAXS) are two different data acquisition modalities often used to glean information about the structure of large biomolecular complexes in their native states. A SAXS experiment is generally considered fast and easy but unveils the structure at very low resolution, whereas a cryo-EM experiment needs more extensive preparation and postacquisition computation to yield a three-dimensional (3D) density map at higher resolution. In certain applications, we may need to verify whether the data acquired in the SAXS and cryo-EM experiments correspond to the same structure (e.g., before reconstructing the 3D density map in EM). In this article, a simple and fast method is proposed to verify the compatibility of the SAXS and EM experimental data. The method is based on averaging the two-dimensional correlation of EM images and the Abel transform of the SAXS data. Orientational preferences are known to exist in cryo-EM experiments, and we also consider these effects on our method. The results are verified on simulations of conformational states of large biomolecular complexes.
Collapse
Affiliation(s)
- Jin Seob Kim
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Bijan Afsari
- Center for Imaging Science, Johns Hopkins University, Baltimore, Maryland
| | | |
Collapse
|
14
|
James NR, Brown A, Gordiyenko Y, Ramakrishnan V. Translational termination without a stop codon. Science 2016; 354:1437-1440. [PMID: 27934701 PMCID: PMC5351859 DOI: 10.1126/science.aai9127] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/17/2016] [Indexed: 11/02/2022]
Abstract
Ribosomes stall when they encounter the end of messenger RNA (mRNA) without an in-frame stop codon. In bacteria, these "nonstop" complexes can be rescued by alternative ribosome-rescue factor A (ArfA). We used electron cryomicroscopy to determine structures of ArfA bound to the ribosome with 3'-truncated mRNA, at resolutions ranging from 3.0 to 3.4 angstroms. ArfA binds within the ribosomal mRNA channel and substitutes for the absent stop codon in the A site by specifically recruiting release factor 2 (RF2), initially in a compact preaccommodated state. A similar conformation of RF2 may occur on stop codons, suggesting a general mechanism for release-factor-mediated translational termination in which a conformational switch leads to peptide release only when the appropriate signal is present in the A site.
Collapse
Affiliation(s)
- Nathan R James
- Medical Research Council (MRC) Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Alan Brown
- Medical Research Council (MRC) Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Yuliya Gordiyenko
- Medical Research Council (MRC) Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - V Ramakrishnan
- Medical Research Council (MRC) Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| |
Collapse
|
15
|
Vestergaard B. Analysis of biostructural changes, dynamics, and interactions – Small-angle X-ray scattering to the rescue. Arch Biochem Biophys 2016; 602:69-79. [DOI: 10.1016/j.abb.2016.02.029] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 02/17/2016] [Accepted: 02/26/2016] [Indexed: 12/27/2022]
|
16
|
Venditti V, Egner TK, Clore GM. Hybrid Approaches to Structural Characterization of Conformational Ensembles of Complex Macromolecular Systems Combining NMR Residual Dipolar Couplings and Solution X-ray Scattering. Chem Rev 2016; 116:6305-22. [PMID: 26739383 PMCID: PMC5590664 DOI: 10.1021/acs.chemrev.5b00592] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Solving structures or structural ensembles of large macromolecular systems in solution poses a challenging problem. While NMR provides structural information at atomic resolution, increased spectral complexity, chemical shift overlap, and short transverse relaxation times (associated with slow tumbling) render application of the usual techniques that have been so successful for medium sized systems (<50 kDa) difficult. Solution X-ray scattering, on the other hand, is not limited by molecular weight but only provides low resolution structural information related to the overall shape and size of the system under investigation. Here we review how combining atomic resolution structures of smaller domains with sparse experimental data afforded by NMR residual dipolar couplings (which yield both orientational and shape information) and solution X-ray scattering data in rigid-body simulated annealing calculations provides a powerful approach for investigating the structural aspects of conformational dynamics in large multidomain proteins. The application of this hybrid methodology is illustrated for the 128 kDa dimer of bacterial Enzyme I which exists in a variety of open and closed states that are sampled at various points in the catalytic cycles, and for the capsid protein of the human immunodeficiency virus.
Collapse
Affiliation(s)
- Vincenzo Venditti
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Timothy K. Egner
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| |
Collapse
|
17
|
Wei Y, Gao Z, Zhang H, Dong Y. Structural characterizations of phage antitoxin Dmd and its interactions with bacterial toxin RnlA. Biochem Biophys Res Commun 2016; 472:592-7. [PMID: 26972252 DOI: 10.1016/j.bbrc.2016.03.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 03/07/2016] [Indexed: 10/22/2022]
Abstract
Toxin-antitoxin (TA) loci are widespread in bacteria plasmids and chromosomes, and target various cellular functions to regulate cell growth and death. A type II TA system RnlA-RnlB from Escherichia coli is associated with phage-resistance. After the infection of bacteriophage T4 with Dmd defection, RnlA is activated by the disappearance of RnlB, resulting in the rapid degradation of T4 mRNAs. Dmd can bind to RnlA directly and neutralize RnlA toxicity to allow phage reproduction. Dmd represent a heterogenous antitoxin of RnlA replacing antitoxin RnlB. Here, we reported two structures of Dmd from T4 phage and RB69 phage. Both Dmd structures are high similar with a compacted domain composed of a four-stranded anti-parallel β-sheet and an α-helix. Chromatography and SAXS suggest Dmd forms a dimer in solution consistent with that in crystal. Structure-based mutagenesis of Dmd reveals key residues involved in RnlA-binding. Possibility cavities in Dmd used for compounds design were modeled. Our structural study revealed the recognition and inhibition mechanism of RnlA by Dmd and providing a potential laboratory phage prevention target for drug design.
Collapse
Affiliation(s)
- Yong Wei
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Zengqiang Gao
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Heng Zhang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuhui Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
18
|
Trappl K, Joseph S. Ribosome Induces a Closed to Open Conformational Change in Release Factor 1. J Mol Biol 2016; 428:1333-1344. [PMID: 26827724 DOI: 10.1016/j.jmb.2016.01.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 01/15/2016] [Accepted: 01/22/2016] [Indexed: 11/19/2022]
Abstract
Bacterial translation termination is triggered when a stop codon arrives at the ribosomal A site. Stop codons are recognized by class I release factors (RF1 and RF2 in Escherichia coli), which bind to the ribosome and catalyze the release of the newly synthesized protein. Crystal structures showed that RF1 and RF2 are in an open conformation when bound to the ribosome but are in a closed conformation when not bound to the ribosome. It is not clear whether only the open form of RF1 and RF2 binds to the ribosome. Alternatively, the closed form of RF1 and RF2 may bind to the ribosome and undergo a conformational change to the open state upon binding. We used transition metal ion fluorescence resonance energy transfer experiments to monitor precisely the conformation of RF1 in the absence and presence of the ribosome. Our results indicate that RF1 undergoes a large conformational change from a closed to an open form upon binding to the ribosome. Our results are consistent with the mechanism, in which high termination fidelity is achieved by linking stop codon recognition by RF1 to the change in conformation from closed to open state.
Collapse
Affiliation(s)
- Krista Trappl
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0314, USA
| | - Simpson Joseph
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0314, USA.
| |
Collapse
|
19
|
Abstract
The hydrodynamic parameters measured in an AUC experiment, s(20,w) and D(t)(20,w)(0), can be used to gain information on the solution structure of (bio)macromolecules and their assemblies. This entails comparing the measured parameters with those that can be computed from usually "dry" structures by "hydrodynamic modeling." In this chapter, we will first briefly put hydrodynamic modeling in perspective and present the basic physics behind it as implemented in the most commonly used methods. The important "hydration" issue is also touched upon, and the distinction between rigid bodies versus those for which flexibility must be considered in the modeling process is then made. The available hydrodynamic modeling/computation programs, HYDROPRO, BEST, SoMo, AtoB, and Zeno, the latter four all implemented within the US-SOMO suite, are described and their performance evaluated. Finally, some literature examples are presented to illustrate the potential applications of hydrodynamics in the expanding field of multiresolution modeling.
Collapse
Affiliation(s)
- Mattia Rocco
- Biopolimeri e Proteomica, IRCCS AOU San Martino-IST, Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy.
| | - Olwyn Byron
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, United Kingdom.
| |
Collapse
|
20
|
Indrisiunaite G, Pavlov MY, Heurgué-Hamard V, Ehrenberg M. On the pH dependence of class-1 RF-dependent termination of mRNA translation. J Mol Biol 2015; 427:1848-60. [PMID: 25619162 DOI: 10.1016/j.jmb.2015.01.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 01/05/2015] [Accepted: 01/09/2015] [Indexed: 10/24/2022]
Abstract
We have studied the pH dependence of the rate of termination of bacterial protein synthesis catalyzed by a class-1 release factor (RF1 or RF2). We used a classical quench-flow technique and a newly developed stopped-flow technique that relies on the use of fluorescently labeled peptides. We found the termination rate to increase with increasing pH and, eventually, to saturate at about 70 s(-1) with an apparent pKa value of about 7.6. From our data, we suggest that class-1 RF termination is rate limited by the chemistry of ester bond hydrolysis at low pH and by a stop-codon-dependent and pH-independent conformational change of RFs at high pH. We propose that RF-dependent termination depends on the participation of a hydroxide ion rather than a water molecule in the hydrolysis of the ester bond between the P-site tRNA and its peptide chain. We provide a simple explanation for why the rate of termination saturated at high pH in our experiments but not in those of others.
Collapse
Affiliation(s)
- Gabriele Indrisiunaite
- Department of Cell and Molecular Biology, Uppsala University, Biomedicinskt Centrum, Box 596, 75124 Uppsala, Sweden
| | - Michael Y Pavlov
- Department of Cell and Molecular Biology, Uppsala University, Biomedicinskt Centrum, Box 596, 75124 Uppsala, Sweden
| | - Valérie Heurgué-Hamard
- Centre National de la Recherche Scientifique, FRE3630, University Paris Diderot Sorbonne Paris Cité Institut de Biologie Physico-Chimique, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Måns Ehrenberg
- Department of Cell and Molecular Biology, Uppsala University, Biomedicinskt Centrum, Box 596, 75124 Uppsala, Sweden.
| |
Collapse
|
21
|
Acosta-Silva C, Bertran J, Branchadell V, Oliva A. Quantum Mechanical Study on the Mechanism of Peptide Release in the Ribosome. J Phys Chem B 2013; 117:3503-15. [DOI: 10.1021/jp3110248] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Carles Acosta-Silva
- Departament de Química, Universitat Autònoma
de Barcelona, 08193 Bellaterra, Spain
| | - Joan Bertran
- Departament de Química, Universitat Autònoma
de Barcelona, 08193 Bellaterra, Spain
| | - Vicenç Branchadell
- Departament de Química, Universitat Autònoma
de Barcelona, 08193 Bellaterra, Spain
| | - Antoni Oliva
- Departament de Química, Universitat Autònoma
de Barcelona, 08193 Bellaterra, Spain
| |
Collapse
|
22
|
Zhou J, Korostelev A, Lancaster L, Noller HF. Crystal structures of 70S ribosomes bound to release factors RF1, RF2 and RF3. Curr Opin Struct Biol 2012; 22:733-42. [PMID: 22999888 DOI: 10.1016/j.sbi.2012.08.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 08/22/2012] [Accepted: 08/22/2012] [Indexed: 11/29/2022]
Abstract
Termination is a crucial step in translation, most notably because premature termination can lead to toxic truncated polypeptides. Most interesting is the fact that stop codons are read by a completely different mechanism from that of sense codons. In recent years, rapid progress has been made in the structural biology of complexes of bacterial ribosomes bound to translation termination factors, much of which has been discussed in earlier reviews [1-5]. Here, we present a brief overview of the structures of bacterial translation termination complexes. The first part summarizes what has been learned from crystal structures of complexes containing the class I release factors RF1 and RF2. In the second part, we discuss the results and implications of two recent X-ray structures of complexes of ribosomes bound to the translational GTPase RF3. These structures have provided many insights and a number of surprises. While structures alone do not tell us how these complicated molecular assemblies work, is it nevertheless clear that it will not be possible to understand their mechanisms without detailed structural information.
Collapse
Affiliation(s)
- Jie Zhou
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | | | | | | |
Collapse
|
23
|
Low-resolution solution structures of Munc18:Syntaxin protein complexes indicate an open binding mode driven by the Syntaxin N-peptide. Proc Natl Acad Sci U S A 2012; 109:9816-21. [PMID: 22670057 DOI: 10.1073/pnas.1116975109] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
When nerve cells communicate, vesicles from one neuron fuse with the presynaptic membrane releasing chemicals that signal to the next. Similarly, when insulin binds its receptor on adipocytes or muscle, glucose transporter-4 vesicles fuse with the cell membrane, allowing glucose to be imported. These essential processes require the interaction of SNARE proteins on vesicle and cell membranes, as well as the enigmatic protein Munc18 that binds the SNARE protein Syntaxin. Here, we show that in solution the neuronal protein Syntaxin1a interacts with Munc18-1 whether or not the Syntaxin1a N-peptide is present. Conversely, the adipocyte protein Syntaxin4 does not bind its partner Munc18c unless the N-peptide is present. Solution-scattering data for the Munc18-1:Syntaxin1a complex in the absence of the N-peptide indicates that this complex adopts the inhibitory closed binding mode, exemplified by a crystal structure of the complex. However, when the N-peptide is present, the solution-scattering data indicate both Syntaxin1a and Syntaxin4 adopt extended conformations in complexes with their respective Munc18 partners. The low-resolution solution structure of the open Munc18:Syntaxin binding mode was modeled using data from cross-linking/mass spectrometry, small-angle X-ray scattering, and small-angle neutron scattering with contrast variation, indicating significant differences in Munc18:Syntaxin interactions compared with the closed binding mode. Overall, our results indicate that the neuronal Munc18-1:Syntaxin1a proteins can adopt two alternate and functionally distinct binding modes, closed and open, depending on the presence of the N-peptide, whereas Munc18c:Syntaxin4 adopts only the open binding mode.
Collapse
|
24
|
Petoukhov MV, Franke D, Shkumatov AV, Tria G, Kikhney AG, Gajda M, Gorba C, Mertens HDT, Konarev PV, Svergun DI. New developments in the ATSAS program package for small-angle scattering data analysis. J Appl Crystallogr 2012; 45:342-350. [PMID: 25484842 PMCID: PMC4233345 DOI: 10.1107/s0021889812007662] [Citation(s) in RCA: 1368] [Impact Index Per Article: 114.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 02/20/2012] [Indexed: 11/26/2022] Open
Abstract
New developments in the program package ATSAS (version 2.4) for the processing and analysis of isotropic small-angle X-ray and neutron scattering data are described. They include (i) multiplatform data manipulation and display tools, (ii) programs for automated data processing and calculation of overall parameters, (iii) improved usage of high- and low-resolution models from other structural methods, (iv) new algorithms to build three-dimensional models from weakly interacting oligomeric systems and complexes, and (v) enhanced tools to analyse data from mixtures and flexible systems. The new ATSAS release includes installers for current major platforms (Windows, Linux and Mac OSX) and provides improved indexed user documentation. The web-related developments, including a user discussion forum and a widened online access to run ATSAS programs, are also presented.
Collapse
Affiliation(s)
- Maxim V. Petoukhov
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Daniel Franke
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Alexander V. Shkumatov
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Giancarlo Tria
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Alexey G. Kikhney
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Michal Gajda
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Christian Gorba
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Haydyn D. T. Mertens
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Petr V. Konarev
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| |
Collapse
|
25
|
Brélivet Y, Rochel N, Moras D. Structural analysis of nuclear receptors: from isolated domains to integral proteins. Mol Cell Endocrinol 2012; 348:466-73. [PMID: 21888944 DOI: 10.1016/j.mce.2011.08.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 07/28/2011] [Accepted: 08/12/2011] [Indexed: 11/26/2022]
Abstract
Nuclear receptors (NRs) are ligand dependent transcription factors that regulate gene expression. A number of in depth structure-function relationship studies have been performed, in particular with drug design perspectives. Recent structural results concerning integral receptors in diverse functional states, obtained using a combination of different methods, now allow a better understanding of the mechanisms involved in molecular regulation. The structural data highlight the importance of DNA sequences for binding selectivity and the role of promoter response elements in the spatial organization of the protein domains into functional complexes. The solution structures of several heterodimer complexes reveal how the DNA directs the positioning of coactivators. In the case of PPARγ-RXRα the comparison with the crystal structure reveals two different conformational states that illustrate the flexibility of the receptors. The results shed light on the dynamics of the molecular recognition process.
Collapse
Affiliation(s)
- Yann Brélivet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Institut National de la Santé et de la Recherche Médicale U964/Centre National de Recherche Scientifique UMR7104/Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch, France
| | | | | |
Collapse
|
26
|
Graille M, Figaro S, Kervestin S, Buckingham RH, Liger D, Heurgué-Hamard V. Methylation of class I translation termination factors: structural and functional aspects. Biochimie 2012; 94:1533-43. [PMID: 22266024 DOI: 10.1016/j.biochi.2012.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 01/07/2012] [Indexed: 12/23/2022]
Abstract
During protein synthesis, release of polypeptide from the ribosome occurs when an in frame termination codon is encountered. Contrary to sense codons, which are decoded by tRNAs, stop codons present in the A-site are recognized by proteins named class I release factors, leading to the release of newly synthesized proteins. Structures of these factors bound to termination ribosomal complexes have recently been obtained, and lead to a better understanding of stop codon recognition and its coordination with peptidyl-tRNA hydrolysis in bacteria. Release factors contain a universally conserved GGQ motif which interacts with the peptidyl-transferase centre to allow peptide release. The Gln side chain from this motif is methylated, a feature conserved from bacteria to man, suggesting an important biological role. However, methylation is catalysed by completely unrelated enzymes. The function of this motif and its post-translational modification will be discussed in the context of recent structural and functional studies.
Collapse
Affiliation(s)
- Marc Graille
- IBBMC, Université Paris-Sud 11, CNRS UMR8619, Orsay Cedex, F-91405, France.
| | | | | | | | | | | |
Collapse
|
27
|
Ahmed A, Whitford PC, Sanbonmatsu KY, Tama F. Consensus among flexible fitting approaches improves the interpretation of cryo-EM data. J Struct Biol 2011; 177:561-70. [PMID: 22019767 DOI: 10.1016/j.jsb.2011.10.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Revised: 10/05/2011] [Accepted: 10/06/2011] [Indexed: 12/31/2022]
Abstract
Cryo-elecron microscopy (cryo-EM) can provide important structural information of large macromolecular assemblies in different conformational states. Recent years have seen an increase in structures deposited in the Protein Data Bank (PDB) by fitting a high-resolution structure into its low-resolution cryo-EM map. A commonly used protocol for accommodating the conformational changes between the X-ray structure and the cryo-EM map is rigid body fitting of individual domains. With the emergence of different flexible fitting approaches, there is a need to compare and revise these different protocols for the fitting. We have applied three diverse automated flexible fitting approaches on a protein dataset for which rigid domain fitting (RDF) models have been deposited in the PDB. In general, a consensus is observed in the conformations, which indicates a convergence from these theoretically different approaches to the most probable solution corresponding to the cryo-EM map. However, the result shows that the convergence might not be observed for proteins with complex conformational changes or with missing densities in cryo-EM map. In contrast, RDF structures deposited in the PDB can represent conformations that not only differ from the consensus obtained by flexible fitting but also from X-ray crystallography. Thus, this study emphasizes that a "consensus" achieved by the use of several automated flexible fitting approaches can provide a higher level of confidence in the modeled configurations. Following this protocol not only increases the confidence level of fitting, but also highlights protein regions with uncertain fitting. Hence, this protocol can lead to better interpretation of cryo-EM data.
Collapse
Affiliation(s)
- Aqeel Ahmed
- Department of Chemistry and Biochemistry, The University of Arizona, 1041 E. Lowell Street, Tucson, AZ 85721, USA.
| | | | | | | |
Collapse
|
28
|
Korostelev AA. Structural aspects of translation termination on the ribosome. RNA (NEW YORK, N.Y.) 2011; 17:1409-1421. [PMID: 21700725 PMCID: PMC3153966 DOI: 10.1261/rna.2733411] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Translation of genetic information encoded in messenger RNAs into polypeptide sequences is carried out by ribosomes in all organisms. When a full protein is synthesized, a stop codon positioned in the ribosomal A site signals termination of translation and protein release. Translation termination depends on class I release factors. Recently, atomic-resolution crystal structures were determined for bacterial 70S ribosome termination complexes bound with release factors RF1 or RF2. In combination with recent biochemical studies, the structures resolve long-standing questions about translation termination. They bring insights into the mechanisms of recognition of all three stop codons, peptidyl-tRNA hydrolysis, and coordination of stop-codon recognition with peptidyl-tRNA hydrolysis. In this review, the structural aspects of these mechanisms are discussed.
Collapse
Affiliation(s)
- Andrei A Korostelev
- RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
| |
Collapse
|
29
|
Klaholz BP. Molecular recognition and catalysis in translation termination complexes. Trends Biochem Sci 2011; 36:282-92. [DOI: 10.1016/j.tibs.2011.02.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 02/01/2011] [Accepted: 02/04/2011] [Indexed: 11/16/2022]
|
30
|
Rochel N, Ciesielski F, Godet J, Moman E, Roessle M, Peluso-Iltis C, Moulin M, Haertlein M, Callow P, Mély Y, Svergun DI, Moras D. Common architecture of nuclear receptor heterodimers on DNA direct repeat elements with different spacings. Nat Struct Mol Biol 2011; 18:564-70. [DOI: 10.1038/nsmb.2054] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 01/27/2011] [Indexed: 11/09/2022]
|
31
|
Nakamura Y, Ito K. tRNA mimicry in translation termination and beyond. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:647-68. [DOI: 10.1002/wrna.81] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
32
|
O'Connor M, Gregory ST. Inactivation of the RluD pseudouridine synthase has minimal effects on growth and ribosome function in wild-type Escherichia coli and Salmonella enterica. J Bacteriol 2011; 193:154-62. [PMID: 21037010 PMCID: PMC3019933 DOI: 10.1128/jb.00970-10] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 10/18/2010] [Indexed: 11/20/2022] Open
Abstract
The Escherichia coli rluD gene encodes a pseudouridine synthase responsible for the pseudouridine (Ψ) modifications at positions 1911, 1915, and 1917 in helix 69 of 23S rRNA. It has been reported that deletion of rluD in K-12 strains of E. coli is associated with extremely slow growth, increased readthrough of stop codons, and defects in 50S ribosomal subunit assembly and 30S-50S subunit association. Suppressor mutations in the prfB and prfC genes encoding release factor 2 (RF2) and RF3 that restore the wild type-growth rate and also correct the ribosomal defects have now been isolated. These suppressors link helix 69 Ψ residues with the termination phase of protein synthesis. However, further genetic analysis reported here also reveals that the slow growth and other defects associated with inactivation of rluD in E. coli K-12 strains are due to a defective RF2 protein, with a threonine at position 246, which is present in all K-12 strains. This is in contrast to the more typical alanine found at this position in most bacterial RF2s, including those of other E. coli strains. Inactivation of rluD in E. coli strains containing the prfB allele from E. coli B or in Salmonella enterica, both carrying an RF2 with Ala246, has negligible effects on growth, termination, or ribosome function. The results indicate that, in contrast to those in wild bacteria, termination functions in E. coli K-12 strains carrying a partially defective RF2 protein are especially susceptible to perturbation of ribosome-RF interactions, such as that caused by loss of h69 Ψ modifications.
Collapse
Affiliation(s)
- Michael O'Connor
- School of Biological Sciences, University of Missouri-Kansas City, 5007 Rockhill Rd, Kansas City, Missouri 64110, USA.
| | | |
Collapse
|
33
|
Miyashita O, Gorba C, Tama F. Structure modeling from small angle X-ray scattering data with elastic network normal mode analysis. J Struct Biol 2010; 173:451-60. [PMID: 20850542 DOI: 10.1016/j.jsb.2010.09.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 09/08/2010] [Accepted: 09/10/2010] [Indexed: 11/24/2022]
Abstract
Computational algorithms to construct structural models from SAXS experimental data are reviewed. SAXS data provides a wealth of information to study the structure and dynamics of biological molecules, however it does not provide atomic details of structures. Thus combining the low-resolution data with already known X-ray structure is a common approach to study conformational transitions of biological molecules. This review provides a survey of SAXS modeling approaches. In addition, we will discuss theoretical backgrounds and performance of our approach, in which elastic network normal mode analysis is used to predict reasonable conformational transitions from known X-ray structures, and find alternative conformations that are consistent with SAXS data.
Collapse
Affiliation(s)
- Osamu Miyashita
- Department of Chemistry and Biochemistry, The University of Arizona, 1041 E. Lowell Street, Tucson, AZ 85721, USA
| | | | | |
Collapse
|
34
|
Recognition of the amber UAG stop codon by release factor RF1. EMBO J 2010; 29:2577-85. [PMID: 20588254 DOI: 10.1038/emboj.2010.139] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Accepted: 05/28/2010] [Indexed: 11/08/2022] Open
Abstract
We report the crystal structure of a termination complex containing release factor RF1 bound to the 70S ribosome in response to an amber (UAG) codon at 3.6-A resolution. The amber codon is recognized in the 30S subunit-decoding centre directly by conserved elements of domain 2 of RF1, including T186 of the PVT motif. Together with earlier structures, the mechanisms of recognition of all three stop codons by release factors RF1 and RF2 can now be described. Our structure confirms that the backbone amide of Q230 of the universally conserved GGQ motif is positioned to contribute directly to the catalysis of the peptidyl-tRNA hydrolysis reaction through stabilization of the leaving group and/or transition state. We also observe synthetic-negative interactions between mutations in the switch loop of RF1 and in helix 69 of 23S rRNA, revealing that these structural features interact functionally in the termination process. These findings are consistent with our proposal that structural rearrangements of RF1 and RF2 are critical to accurate translation termination.
Collapse
|
35
|
Gorba C, Tama F. Normal Mode Flexible Fitting of High-Resolution Structures of Biological Molecules Toward SAXS Data. Bioinform Biol Insights 2010; 4:43-54. [PMID: 20634984 PMCID: PMC2901630 DOI: 10.4137/bbi.s4551] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
We present a method to reconstruct a three-dimensional protein structure from an atomic pair distribution function derived from the scattering intensity profile from SAXS data by flexibly fitting known x-ray structures. This method uses a linear combination of low-frequency normal modes from an elastic network description of the molecule in an iterative manner to deform the structure to conform optimally to the target pair distribution function derived from SAXS data. For computational efficiency, the protein and water molecules included in the protein first hydration shell are coarse-grained. In this paper, we demonstrate the validity of our coarse-graining approach to study SAXS data. Illustrative results of our flexible fitting studies on simulated SAXS data from five different proteins are presented.
Collapse
Affiliation(s)
- Christian Gorba
- Department of Chemistry and Biochemistry, The University of Arizona, 1041 E. Lowell Street, Tucson, AZ, 85721
| | | |
Collapse
|
36
|
Mertens HDT, Svergun DI. Structural characterization of proteins and complexes using small-angle X-ray solution scattering. J Struct Biol 2010; 172:128-41. [PMID: 20558299 DOI: 10.1016/j.jsb.2010.06.012] [Citation(s) in RCA: 384] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Revised: 06/08/2010] [Accepted: 06/10/2010] [Indexed: 01/27/2023]
Abstract
Small-angle scattering of X-rays (SAXS) is an established method for the low-resolution structural characterization of biological macromolecules in solution. The technique provides three-dimensional low-resolution structures, using ab initio and rigid body modeling, and allow one to assess the oligomeric state of proteins and protein complexes. In addition, SAXS is a powerful tool for structure validation and the quantitative analysis of flexible systems, and is highly complementary to the high resolution methods of X-ray crystallography and NMR. At present, SAXS analysis methods have reached an advanced state, allowing for automated and rapid characterization of protein solutions in terms of low-resolution models, quaternary structure and oligomeric composition. In this communication, main approaches to the characterization of proteins and protein complexes using SAXS are reviewed. The tools for the analysis of proteins in solution are presented, and the impact that these tools have made in modern structural biology is discussed.
Collapse
Affiliation(s)
- Haydyn D T Mertens
- European Molecular Biology Laboratory-Hamburg Outstation, c/o DESY, Notkestrasse 85, Hamburg, Germany
| | | |
Collapse
|
37
|
Jacques DA, Trewhella J. Small-angle scattering for structural biology--expanding the frontier while avoiding the pitfalls. Protein Sci 2010; 19:642-57. [PMID: 20120026 PMCID: PMC2867006 DOI: 10.1002/pro.351] [Citation(s) in RCA: 303] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 01/17/2010] [Accepted: 01/19/2010] [Indexed: 12/18/2022]
Abstract
The last decade has seen a dramatic increase in the use of small-angle scattering for the study of biological macromolecules in solution. The drive for more complete structural characterization of proteins and their interactions, coupled with the increasing availability of instrumentation and easy-to-use software for data analysis and interpretation, is expanding the utility of the technique beyond the domain of the biophysicist and into the realm of the protein scientist. However, the absence of publication standards and the ease with which 3D models can be calculated against the inherently 1D scattering data means that an understanding of sample quality, data quality, and modeling assumptions is essential to have confidence in the results. This review is intended to provide a road map through the small-angle scattering experiment, while also providing a set of guidelines for the critical evaluation of scattering data. Examples of current best practice are given that also demonstrate the power of the technique to advance our understanding of protein structure and function.
Collapse
Affiliation(s)
| | - Jill Trewhella
- School of Molecular and Microbial Biosciences, The University of SydneySydney, New South Wales 2006, Australia
| |
Collapse
|
38
|
Hetrick B, Lee K, Joseph S. Kinetics of stop codon recognition by release factor 1. Biochemistry 2009; 48:11178-84. [PMID: 19874047 DOI: 10.1021/bi901577d] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recognition of stop codons by class I release factors is a fundamental step in the termination phase of protein synthesis. Since premature termination is costly to the cell, release factors have to efficiently discriminate between stop and sense codons. To understand the mechanism of discrimination between stop and sense codons, we developed a new, pre-steady state kinetic assay to monitor the interaction of RF1 with the ribosome. Our results show that RF1 associates with similar association rate constants with ribosomes programmed with stop or sense codons. However, dissociation of RF1 from sense codons is as much as 3 orders of magnitude faster than from stop codons. Interestingly, the affinity of RF1 for ribosomes programmed with different sense codons does not correlate with the defects in peptide release. Thus, discrimination against sense codons is achieved with both an increase in the dissociation rates and a decrease in the rate of peptide release. These results suggest that sense codons inhibit conformational changes necessary for RF1 to stably bind to the ribosome and catalyze peptide release.
Collapse
Affiliation(s)
- Byron Hetrick
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0314, USA
| | | | | |
Collapse
|
39
|
Trobro S, Åqvist J. Mechanism of the Translation Termination Reaction on the Ribosome. Biochemistry 2009; 48:11296-303. [DOI: 10.1021/bi9017297] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stefan Trobro
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| |
Collapse
|
40
|
Pelikan M, Hura GL, Hammel M. Structure and flexibility within proteins as identified through small angle X-ray scattering. Gen Physiol Biophys 2009; 28:174-89. [PMID: 19592714 DOI: 10.4149/gpb_2009_02_174] [Citation(s) in RCA: 335] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Flexibility between domains of proteins is often critical for function. These motions and proteins with large scale flexibility in general are often not readily amenable to conventional structural analysis such as X-ray crystallography, nuclear magnetic resonance spectroscopy (NMR) or electron microscopy. A common evolution of a crystallography project, once a high resolution structure has been determined, is to postulate possible sights of flexibility. Here we describe an analysis tool using relatively inexpensive small angle X-ray scattering (SAXS) measurements to identify flexibility and validate a constructed minimal ensemble of models, which represent highly populated conformations in solution. The resolution of these results is sufficient to address the questions being asked: what kinds of conformations do the domains sample in solution? In our rigid body modeling strategy BILBOMD, molecular dynamics (MD) simulations are used to explore conformational space. A common strategy is to perform the MD simulation on the domains connections at very high temperature, where the additional kinetic energy prevents the molecule from becoming trapped in a local minimum. The MD simulations provide an ensemble of molecular models from which a SAXS curve is calculated and compared to the experimental curve. A genetic algorithm is used to identify the minimal ensemble (minimal ensemble search, MES) required to best fit the experimental data. We demonstrate the use of MES in several model and in four experimental examples.
Collapse
Affiliation(s)
- Martin Pelikan
- Department of Mathematics and Computer Science, University of Missouri in St. Louis, St. Louis, Missouri 63121, USA
| | | | | |
Collapse
|
41
|
Andér M, Åqvist J. Does Glutamine Methylation Affect the Intrinsic Conformation of the Universally Conserved GGQ Motif in Ribosomal Release Factors? Biochemistry 2009; 48:3483-9. [DOI: 10.1021/bi900117r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martin Andér
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| |
Collapse
|
42
|
Weixlbaumer A, Jin H, Neubauer C, Voorhees RM, Petry S, Kelley AC, Ramakrishnan V. Insights into translational termination from the structure of RF2 bound to the ribosome. Science 2008; 322:953-6. [PMID: 18988853 DOI: 10.1126/science.1164840] [Citation(s) in RCA: 221] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The termination of protein synthesis occurs through the specific recognition of a stop codon in the A site of the ribosome by a release factor (RF), which then catalyzes the hydrolysis of the nascent protein chain from the P-site transfer RNA. Here we present, at a resolution of 3.5 angstroms, the crystal structure of RF2 in complex with its cognate UGA stop codon in the 70S ribosome. The structure provides insight into how RF2 specifically recognizes the stop codon; it also suggests a model for the role of a universally conserved GGQ motif in the catalysis of peptide release.
Collapse
Affiliation(s)
- Albert Weixlbaumer
- Medical Research Council (MRC) Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | | | | | | | | | | | | |
Collapse
|
43
|
Youngman EM, McDonald ME, Green R. Peptide release on the ribosome: mechanism and implications for translational control. Annu Rev Microbiol 2008; 62:353-73. [PMID: 18544041 DOI: 10.1146/annurev.micro.61.080706.093323] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Peptide release, the reaction that hydrolyzes a completed protein from the peptidyl-tRNA upon completion of translation, is catalyzed in the active site of the large subunit of the ribosome and requires a class I release factor protein. The ribosome and release factor protein cooperate to accomplish two tasks: recognition of the stop codon and catalysis of peptidyl-tRNA hydrolysis. Although many fundamental questions remain, substantial progress has been made in the past several years. This review summarizes those advances and presents current models for the mechanisms of stop codon specificity and catalysis of peptide release. Finally, we discuss how these views fit into a larger emerging theme in the translation field: the importance of induced fit and conformational changes for progression through the translation cycle.
Collapse
Affiliation(s)
- Elaine M Youngman
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
| | | | | |
Collapse
|
44
|
Diago-Navarro E, Mora L, Buckingham RH, Díaz-Orejas R, Lemonnier M. Novel Escherichia coli RF1 mutants with decreased translation termination activity and increased sensitivity to the cytotoxic effect of the bacterial toxins Kid and RelE. Mol Microbiol 2008; 71:66-78. [PMID: 19019162 PMCID: PMC2680264 DOI: 10.1111/j.1365-2958.2008.06510.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Novel mutations in prfA, the gene for the polypeptide release factor RF1 of Escherichia coli, were isolated using a positive genetic screen based on the parD (kis, kid) toxin–antitoxin system. This original approach allowed the direct selection of mutants with altered translational termination efficiency at UAG codons. The isolated prfA mutants displayed a ∼10-fold decrease in UAG termination efficiency with no significant changes in RF1 stability in vivo. All three mutations, G121S, G301S and R303H, were situated close to the nonsense codon recognition site in RF1:ribosome complexes. The prfA mutants displayed increased sensitivity to the RelE toxin encoded by the relBE system of E. coli, thus providing in vivo support for the functional interaction between RF1 and RelE. The prfA mutants also showed increased sensitivity to the Kid toxin. Since this toxin can cleave RNA in a ribosome-independent manner, this result was not anticipated and provided first evidence for the involvement of RF1 in the pathway of Kid toxicity. The sensitivity of the prfA mutants to RelE and Kid was restored to normal levels upon overproduction of the wild-type RF1 protein. We discuss these results and their utility for the design of novel antibacterial strategies in the light of the recently reported structure of ribosome-bound RF1.
Collapse
Affiliation(s)
- Elizabeth Diago-Navarro
- Department of Molecular Microbiology, Centro de Investigaciones Biológicas CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | | | | | | | | |
Collapse
|
45
|
United we stand: combining structural methods. Curr Opin Struct Biol 2008; 18:617-22. [DOI: 10.1016/j.sbi.2008.07.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Accepted: 07/29/2008] [Indexed: 01/20/2023]
|
46
|
McDevitt CA, Shintre CA, Grossmann JG, Pollock NL, Prince SM, Callaghan R, Ford RC. Structural insights into P-glycoprotein (ABCB1) by small angle X-ray scattering and electron crystallography. FEBS Lett 2008; 582:2950-6. [PMID: 18657537 DOI: 10.1016/j.febslet.2008.07.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Accepted: 07/14/2008] [Indexed: 11/29/2022]
Abstract
P-glycoprotein (ABCB1) is an ATP-binding cassette protein that is associated with the acquisition of multi-drug resistance in cancer and the failure of chemotherapy in humans. Structural insights into this protein are described using a combination of small angle X-ray scattering data and cryo-electron crystallography data. We have compared the structures with bacterial homologues, and discuss the development of homology models for P-glycoprotein based on the bacterial Sav1866 structure.
Collapse
Affiliation(s)
- Christopher A McDevitt
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | | | | | | | | | | | | |
Collapse
|
47
|
Laurberg M, Asahara H, Korostelev A, Zhu J, Trakhanov S, Noller HF. Structural basis for translation termination on the 70S ribosome. Nature 2008; 454:852-7. [PMID: 18596689 DOI: 10.1038/nature07115] [Citation(s) in RCA: 264] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Accepted: 05/23/2008] [Indexed: 11/09/2022]
Abstract
At termination of protein synthesis, type I release factors promote hydrolysis of the peptidyl-transfer RNA linkage in response to recognition of a stop codon. Here we describe the crystal structure of the Thermus thermophilus 70S ribosome in complex with the release factor RF1, tRNA and a messenger RNA containing a UAA stop codon, at 3.2 A resolution. The stop codon is recognized in a pocket formed by conserved elements of RF1, including its PxT recognition motif, and 16S ribosomal RNA. The codon and the 30S subunit A site undergo an induced fit that results in stabilization of a conformation of RF1 that promotes its interaction with the peptidyl transferase centre. Unexpectedly, the main-chain amide group of Gln 230 in the universally conserved GGQ motif of the factor is positioned to contribute directly to peptidyl-tRNA hydrolysis.
Collapse
Affiliation(s)
- Martin Laurberg
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | | | | | | | | | | |
Collapse
|
48
|
Petry S, Weixlbaumer A, Ramakrishnan V. The termination of translation. Curr Opin Struct Biol 2008; 18:70-7. [PMID: 18206363 DOI: 10.1016/j.sbi.2007.11.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2007] [Revised: 11/21/2007] [Accepted: 11/26/2007] [Indexed: 11/29/2022]
Abstract
Recent results from cryoelectron microscopy, crystallography, and biochemical experiments have shed considerable light on the process by which protein synthesis is terminated when a stop codon is reached. However, a detailed understanding of the underlying mechanisms will require higher-resolution structures of the various states involved.
Collapse
Affiliation(s)
- Sabine Petry
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | | | | |
Collapse
|
49
|
Fdez E, Jowitt TA, Wang MC, Rajebhosale M, Foster K, Bella J, Baldock C, Woodman PG, Hilfiker S. A role for soluble N-ethylmaleimide-sensitive factor attachment protein receptor complex dimerization during neurosecretion. Mol Biol Cell 2008; 19:3379-89. [PMID: 18508917 DOI: 10.1091/mbc.e08-01-0010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The interactions underlying the cooperativity of soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complexes during neurotransmission are not known. Here, we provide a molecular characterization of a dimer formed between the cytoplasmic portions of neuronal SNARE complexes. Dimerization generates a two-winged structure in which the C termini of cytosolic SNARE complexes are in apposition, and it involves residues from the vesicle-associated SNARE synaptobrevin 2 that lie close to the cytosol-membrane interface within the full-length protein. Mutation of these residues reduces stability of dimers formed between SNARE complexes, without affecting the stability of each individual SNARE complex. These mutations also cause a corresponding decrease in the ability of botulinum toxin-resistant synaptobrevin 2 to rescue regulated exocytosis in toxin-treated neuroendocrine cells. Moreover, such synaptobrevin 2 mutants give rise to a dominant-negative inhibition of exocytosis. These data are consistent with an important role for SNARE complex dimers in neurosecretion.
Collapse
Affiliation(s)
- Elena Fdez
- Institute of Parasitology and Biomedicine López-Neyra, Consejo Superior de Investigaciones Cientificas, 18100 Granada, Spain
| | | | | | | | | | | | | | | | | |
Collapse
|
50
|
X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Q Rev Biophys 2008; 40:191-285. [PMID: 18078545 DOI: 10.1017/s0033583507004635] [Citation(s) in RCA: 844] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Crystallography supplies unparalleled detail on structural information critical for mechanistic analyses; however, it is restricted to describing low energy conformations of macromolecules within crystal lattices. Small angle X-ray scattering (SAXS) offers complementary information about macromolecular folding, unfolding, aggregation, extended conformations, flexibly linked domains, shape, conformation, and assembly state in solution, albeit at the lower resolution range of about 50 A to 10 A resolution, but without the size limitations inherent in NMR and electron microscopy studies. Together these techniques can allow multi-scale modeling to create complete and accurate images of macromolecules for modeling allosteric mechanisms, supramolecular complexes, and dynamic molecular machines acting in diverse processes ranging from eukaryotic DNA replication, recombination and repair to microbial membrane secretion and assembly systems. This review addresses both theoretical and practical concepts, concerns and considerations for using these techniques in conjunction with computational methods to productively combine solution scattering data with high-resolution structures. Detailed aspects of SAXS experimental results are considered with a focus on data interpretation tools suitable to model protein and nucleic acid macromolecular structures, including membrane protein, RNA, DNA, and protein-nucleic acid complexes. The methods discussed provide the basis to examine molecular interactions in solution and to study macromolecular flexibility and conformational changes that have become increasingly relevant for accurate understanding, simulation, and prediction of mechanisms in structural cell biology and nanotechnology.
Collapse
|