251
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Kim H, Hsin J, Liu Y, Selvin PR, Schulten K. Formation of salt bridges mediates internal dimerization of myosin VI medial tail domain. Structure 2011; 18:1443-9. [PMID: 21070943 DOI: 10.1016/j.str.2010.09.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Revised: 08/18/2010] [Accepted: 09/01/2010] [Indexed: 01/02/2023]
Abstract
The unconventional motor protein, myosin VI, is known to dimerize upon cargo binding to its C-terminal end. It has been shown that one of its tail domains, called the medial tail domain, is a dimerization region. The domain contains an unusual pattern of alternating charged residues and a few hydrophobic residues. To reveal the unknown dimerization mechanism of the medial tail domain, we employed molecular dynamics and single-molecule experimental techniques. Both techniques suggest that the formation of electrostatic-based interhelical salt bridges between oppositely charged residues is a key dimerization factor. For the dimerization to occur, the two identical helices within the dimer do not bind in a symmetric fashion, but rather with an offset of about one helical repeat. Calculations of the dimer-dissociation energy find the contribution of hydrophobic residues to the dimerization process to be minor; they also find that the asymmetric homodimer state is energetically favorable over a state of separate helices.
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Affiliation(s)
- Hyeongjun Kim
- Department of Physics and Center of the Physics of Living Cells, University of Illinois, Urbana, IL 61801, USA
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252
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Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1. Proc Natl Acad Sci U S A 2011; 108:3918-23. [PMID: 21368145 DOI: 10.1073/pnas.1017425108] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mitochondria have their own translational machineries for the synthesis of thirteen polypeptide chains that are components of the complexes that participate in the process of oxidative phosphorylation (or ATP generation). Translation initiation in mammalian mitochondria requires two initiation factors, IF2(mt) and IF3(mt), instead of the three that are present in eubacteria. The mammalian IF2(mt) possesses a unique 37 amino acid insertion domain, which is known to be important for the formation of the translation initiation complex. We have obtained a three-dimensional cryoelectron microscopic map of the mammalian IF2(mt) in complex with initiator fMet-tRNA(iMet) and the eubacterial ribosome. We find that the 37 amino acid insertion domain interacts with the same binding site on the ribosome that would be occupied by the eubacterial initiation factor IF1, which is absent in mitochondria. Our finding suggests that the insertion domain of IF2(mt) mimics the function of eubacterial IF1, by blocking the ribosomal aminoacyl-tRNA binding site (A site) at the initiation step.
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253
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Baker ML, Abeysinghe SS, Schuh S, Coleman RA, Abrams A, Marsh MP, Hryc CF, Ruths T, Chiu W, Ju T. Modeling protein structure at near atomic resolutions with Gorgon. J Struct Biol 2011; 174:360-73. [PMID: 21296162 DOI: 10.1016/j.jsb.2011.01.015] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 01/27/2011] [Accepted: 01/31/2011] [Indexed: 11/29/2022]
Abstract
Electron cryo-microscopy (cryo-EM) has played an increasingly important role in elucidating the structure and function of macromolecular assemblies in near native solution conditions. Typically, however, only non-atomic resolution reconstructions have been obtained for these large complexes, necessitating computational tools for integrating and extracting structural details. With recent advances in cryo-EM, maps at near-atomic resolutions have been achieved for several macromolecular assemblies from which models have been manually constructed. In this work, we describe a new interactive modeling toolkit called Gorgon targeted at intermediate to near-atomic resolution density maps (10-3.5 Å), particularly from cryo-EM. Gorgon's de novo modeling procedure couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques to generate initial protein backbone models. Beyond model building, Gorgon is an extensible interactive visualization platform with a variety of computational tools for annotating a wide variety of 3D volumes. Examples from cryo-EM maps of Rotavirus and Rice Dwarf Virus are used to demonstrate its applicability to modeling protein structure.
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Affiliation(s)
- Matthew L Baker
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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254
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Abstract
Three-dimensional (3D) cryoelectron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and macromolecular complexes. EMDataBank.org, a joint effort of the Protein Databank in Europe (PDBe), the Research Collaboratory for Structural Bioinformatics (RCSB), and the National Center for Macromolecular Imaging (NCMI), is a "one-stop shop" resource for global deposition and retrieval of cryo-EM map, model, and associated metadata. The resource unifies public access to the two major EM Structural Data archives: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data of macromolecules and macromolecular complexes by the wider scientific community.
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Affiliation(s)
- Catherine L Lawson
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, USA
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255
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Weis F, Bron P, Giudice E, Rolland JP, Thomas D, Felden B, Gillet R. tmRNA-SmpB: a journey to the centre of the bacterial ribosome. EMBO J 2010; 29:3810-8. [PMID: 20953161 DOI: 10.1038/emboj.2010.252] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Accepted: 09/21/2010] [Indexed: 11/09/2022] Open
Abstract
Ribosomes mediate protein synthesis by decoding the information carried by messenger RNAs (mRNAs) and catalysing peptide bond formation between amino acids. When bacterial ribosomes stall on incomplete messages, the trans-translation quality control mechanism is activated by the transfer-messenger RNA bound to small protein B (tmRNA-SmpB ribonucleoprotein complex). Trans-translation liberates the stalled ribosomes and triggers degradation of the incomplete proteins. Here, we present the cryo-electron microscopy structures of tmRNA-SmpB accommodated or translocated into stalled ribosomes. Two atomic models for each state are proposed. This study reveals how tmRNA-SmpB crosses the ribosome and how, as the problematic mRNA is ejected, the tmRNA resume codon is placed onto the ribosomal decoding site by new contacts between SmpB and the nucleotides upstream of the tag-encoding sequence. This provides a structural basis for the transit of the large tmRNA-SmpB complex through the ribosome and for the means by which the tmRNA internal frame is set for translation to resume.
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Affiliation(s)
- Félix Weis
- Université de Rennes, UMR CNRS Equipe Structure et Dynamique des Macromolécules, Rennes, France
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256
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Trabuco LG, Schreiner E, Gumbart J, Hsin J, Villa E, Schulten K. Applications of the molecular dynamics flexible fitting method. J Struct Biol 2010; 173:420-7. [PMID: 20932910 DOI: 10.1016/j.jsb.2010.09.024] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2010] [Revised: 09/19/2010] [Accepted: 09/28/2010] [Indexed: 12/12/2022]
Abstract
In recent years, cryo-electron microscopy (cryo-EM) has established itself as a key method in structural biology, permitting the structural characterization of large biomolecular complexes in various functional states. The data obtained through single-particle cryo-EM has recently seen a leap in resolution thanks to landmark advances in experimental and computational techniques, resulting in sub-nanometer resolution structures being obtained routinely. The remaining gap between these data and revealing the mechanisms of molecular function can be closed through hybrid modeling tools that incorporate known atomic structures into the cryo-EM data. One such tool, molecular dynamics flexible fitting (MDFF), uses molecular dynamics simulations to combine structures from X-ray crystallography with cryo-EM density maps to derive atomic models of large biomolecular complexes. The structures furnished by MDFF can be used subsequently in computational investigations aimed at revealing the dynamics of the complexes under study. In the present work, recent applications of MDFF are presented, including the interpretation of cryo-EM data of the ribosome at different stages of translation and the structure of a membrane-curvature-inducing photosynthetic complex.
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Affiliation(s)
- Leonardo G Trabuco
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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257
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Lawson CL, Baker ML, Best C, Bi C, Dougherty M, Feng P, van Ginkel G, Devkota B, Lagerstedt I, Ludtke SJ, Newman RH, Oldfield TJ, Rees I, Sahni G, Sala R, Velankar S, Warren J, Westbrook JD, Henrick K, Kleywegt GJ, Berman HM, Chiu W. EMDataBank.org: unified data resource for CryoEM. Nucleic Acids Res 2010; 39:D456-64. [PMID: 20935055 PMCID: PMC3013769 DOI: 10.1093/nar/gkq880] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Cryo-electron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and macromolecular complexes. EMDataBank.org, a joint effort of the Protein Data Bank in Europe (PDBe), the Research Collaboratory for Structural Bioinformatics (RCSB) and the National Center for Macromolecular Imaging (NCMI), is a global ‘one-stop shop’ resource for deposition and retrieval of cryoEM maps, models and associated metadata. The resource unifies public access to the two major archives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data of macromolecules and macromolecular complexes by the wider scientific community.
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Affiliation(s)
- Catherine L Lawson
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA.
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258
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Kim SJ. The use of artificial structure as an initial reference model for projection-matching three dimensional reconstruction: visualization of macromolecular structure using cryo-electron microscopy. J Anal Sci Technol 2010. [DOI: 10.5355/jast.2010.159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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259
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Trabuco LG, Harrison CB, Schreiner E, Schulten K. Recognition of the regulatory nascent chain TnaC by the ribosome. Structure 2010; 18:627-37. [PMID: 20462496 DOI: 10.1016/j.str.2010.02.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 02/03/2010] [Accepted: 02/06/2010] [Indexed: 10/19/2022]
Abstract
Regulatory nascent chains interact with the ribosomal exit tunnel and modulate their own translation. To characterize nascent chain recognition by the ribosome at the atomic level, extensive molecular dynamics simulations of TnaC, the leader peptide of the tryptophanase operon, inside the exit tunnel were performed for an aggregate time of 2.1 mus. The simulations, complemented by quantum chemistry calculations, suggest that the critical TnaC residue W12 is recognized by the ribosome via a cation-pi interaction, whereas TnaC's D16 forms salt bridges with ribosomal proteins. The simulations also show that TnaC-mediated translational arrest does not involve a swinging of ribosomal protein L22, as previously proposed. Furthermore, bioinformatic analyses and simulations suggest nascent chain elements that may prevent translational arrest in various organisms. Altogether, the current study unveils atomic-detail interactions that explain the role of elements of TnaC and the ribosome essential for translational arrest.
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Affiliation(s)
- Leonardo G Trabuco
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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260
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Stone JE, Hardy DJ, Ufimtsev IS, Schulten K. GPU-accelerated molecular modeling coming of age. J Mol Graph Model 2010; 29:116-25. [PMID: 20675161 PMCID: PMC2934899 DOI: 10.1016/j.jmgm.2010.06.010] [Citation(s) in RCA: 210] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Revised: 06/24/2010] [Accepted: 06/30/2010] [Indexed: 12/19/2022]
Abstract
Graphics processing units (GPUs) have traditionally been used in molecular modeling solely for visualization of molecular structures and animation of trajectories resulting from molecular dynamics simulations. Modern GPUs have evolved into fully programmable, massively parallel co-processors that can now be exploited to accelerate many scientific computations, typically providing about one order of magnitude speedup over CPU code and in special cases providing speedups of two orders of magnitude. This paper surveys the development of molecular modeling algorithms that leverage GPU computing, the advances already made and remaining issues to be resolved, and the continuing evolution of GPU technology that promises to become even more useful to molecular modeling. Hardware acceleration with commodity GPUs is expected to benefit the overall computational biology community by bringing teraflops performance to desktop workstations and in some cases potentially changing what were formerly batch-mode computational jobs into interactive tasks.
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Affiliation(s)
- John E. Stone
- Beckman Institute, University of Illinois at Urbana-Champaign, 405N. Mathews Ave., Urbana, IL, 61801
| | - David J. Hardy
- Beckman Institute, University of Illinois at Urbana-Champaign, 405N. Mathews Ave., Urbana, IL, 61801
| | - Ivan S. Ufimtsev
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, CA 94305
| | - Klaus Schulten
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W. Green, Urbana, IL, 61801
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261
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Affiliation(s)
- Cameron Mura
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, United States of America.
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262
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The role of L1 stalk-tRNA interaction in the ribosome elongation cycle. J Mol Biol 2010; 402:741-60. [PMID: 20691699 DOI: 10.1016/j.jmb.2010.07.056] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Revised: 07/23/2010] [Accepted: 07/27/2010] [Indexed: 01/08/2023]
Abstract
The ribosomal L1 stalk is a mobile structure implicated in directing tRNA movement during translocation through the ribosome. This article investigates three aspects of L1 stalk-tRNA interaction. First, by combining data from cryo electron microscopy, X-ray crystallography, and molecular dynamics simulations through the molecular dynamics flexible fitting method, we obtained atomic models of different tRNAs occupying the hybrid P/E state interacting with the L1 stalk. These models confirm the assignment of fluorescence resonance energy transfer states from previous single-molecule investigations of L1 stalk dynamics. Second, the models reconcile how initiator tRNA(fMet) interacts less strongly with the L1 stalk compared to elongator tRNA(Phe), as seen in previous single-molecule experiments. Third, results from a simulation of the entire ribosome in which the L1 stalk is moved from a half-closed conformation to its open conformation are found to support the hypothesis that L1 stalk opening is involved in tRNA release from the ribosome.
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263
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Hsin J, Strümpfer J, Sener M, Qian P, Hunter CN, Schulten K. Energy Transfer Dynamics in an RC-LH1-PufX Tubular Photosynthetic Membrane. NEW JOURNAL OF PHYSICS 2010; 12:085005. [PMID: 21152381 PMCID: PMC2997751 DOI: 10.1088/1367-2630/12/8/085005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Light absorption and the subsequent transfer of excitation energy are the first two steps of the photosynthetic process, carried out by protein-bound pigments, mainly bacteriochlorophylls (BChls), in photosynthetic bacteria. BChls are anchored in light-harvesting (LH) complexes, such as light-harvesting complex I (LH1), which directly associates with the reaction center (RC), forming the RC-LH1 core complex. In Rhodobacter sphaeroides, RC-LH1 core complexes contain an additional protein, PufX, and assemble into dimeric RC-LH1-PufX core complexes. In the absence of light-harvesting complexes II, the former complexes can aggregate into a helically ordered tubular photosynthetic membrane. We examined the excitation transfer dynamics in a single RC-LH1-PufX core complex dimer using the hierarchical equations of motion for dissipative quantum dynamics that accurately, yet computationally costly, treat the coupling between BChls and their protein environment. A widely employed description, generalized Förster theory, was also used to calculate the transfer rates of the same excitonic system in order to verify the accuracy of this computationally cheap method. Additionally, in light of the structural uncertainties in the Rhodobacter sphaeroides RC-LH1-PufX core complex, geometrical alterations were introduced in the BChl organization. It is shown that the energy transfer dynamics is not affected by the considered changes in the BChl organization, and that generalized Förster theory provides accurate transfer rates. An all-atom model for a tubular photosynthetic membrane is then constructed on the basis of electron microscopy data, and the overall energy transfer properties of this membrane are computed.
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Affiliation(s)
- Jen Hsin
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Johan Strümpfer
- Center for Biophysics and Computational Biology and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Melih Sener
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Pu Qian
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - C. Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Klaus Schulten
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
- Center for Biophysics and Computational Biology and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
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264
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Hsin J, Chandler DE, Gumbart J, Harrison CB, Şener M, Strumpfer J, Schulten K. Self-assembly of photosynthetic membranes. Chemphyschem 2010; 11:1154-9. [PMID: 20183845 PMCID: PMC3086839 DOI: 10.1002/cphc.200900911] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Indexed: 11/08/2022]
Abstract
Bacterial photosynthetic membranes, also known as chromatophores, are tightly packed with integral membrane proteins that work together to carry out photosynthesis. Chromatophores display a wide range of cellular morphologies; spherical, tubular, and lamellar chromatophores have all been observed in different bacterial species, or with different protein constituents. Through recent computational modeling and simulation, it has been demonstrated that the light-harvesting complexes abundant in chromatophores induce local membrane curvature via multiple mechanisms. These protein complexes assemble to generate a global curvature and sculpt the chromatophores into various cellular-scale architectures.
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Affiliation(s)
- Jen Hsin
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, USA
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Danielle E. Chandler
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, USA
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
| | - James Gumbart
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
| | | | - Melih Şener
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Johan Strumpfer
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Klaus Schulten
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, USA
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, USA
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265
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Gumbart J, Trabuco LG, Schreiner E, Villa E, Schulten K. Regulation of the protein-conducting channel by a bound ribosome. Structure 2010; 17:1453-64. [PMID: 19913480 DOI: 10.1016/j.str.2009.09.010] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Revised: 09/13/2009] [Accepted: 09/15/2009] [Indexed: 01/01/2023]
Abstract
During protein synthesis, it is often necessary for the ribosome to form a complex with a membrane-bound channel, the SecY/Sec61 complex, in order to translocate nascent proteins across a cellular membrane. Structural data on the ribosome-channel complex are currently limited to low-resolution cryo-electron microscopy maps, including one showing a bacterial ribosome bound to a monomeric SecY complex. Using that map along with available atomic-level models of the ribosome and SecY, we have determined, through molecular dynamics flexible fitting (MDFF), an atomic-resolution model of the ribosome-channel complex. We characterized computationally the sites of ribosome-SecY interaction within the complex and determined the effect of ribosome binding on the SecY channel. We also constructed a model of a ribosome in complex with a SecY dimer by adding a second copy of SecY to the MDFF-derived model. The study involved 2.7-million-atom simulations over altogether nearly 50 ns.
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Affiliation(s)
- James Gumbart
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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266
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Abstract
Today, electron cryomicroscopy (cryo-EM) can routinely achieve subnanometer resolutions of complex macromolecular assemblies. From a density map, one can extract key structural and functional information using a variety of computational analysis tools. At subnanometer resolution, these tools make it possible to isolate individual subunits, identify secondary structures, and accurately fit atomic models. With several cryo-EM studies achieving resolutions beyond 5Å, computational modeling and feature recognition tools have been employed to construct backbone and atomic models of the protein components directly from a density map. In this chapter, we describe several common classes of computational tools that can be used to analyze and model subnanometer resolution reconstructions from cryo-EM. A general protocol for analyzing subnanometer resolution density maps is presented along with a full description of steps used in analyzing the 4.3Å resolution structure of Mm-cpn.
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Affiliation(s)
- Matthew L Baker
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
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267
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Walter NG. The blessing and curse of RNA dynamics: past, present, and future. Methods 2009; 49:85-6. [PMID: 19782935 DOI: 10.1016/j.ymeth.2009.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 09/01/2009] [Indexed: 11/15/2022] Open
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