Path of nascent polypeptide in exit tunnel revealed by molecular dynamics simulation of ribosome.

No abstract is available for this paper.

• Publication year

  2008

• Venue

  Biophysical Journal

• Publication date

  2008-12-15

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1529/biophysj.108.134890PMID 18936244PMCID PMC2599861
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements.

  2014cited by this paper
• A structural understanding of the dynamic ribosome machine

  2008influential reference
• High performance computing in biology: multimillion atom simulations of nanoscale systems.

  2007cited by this paper
• Spontaneous Formation of KCl Aggregates in Biomolecular Simulations: A Force Field Issue?

  2007cited by this paper
• Mapping the electrostatic potential within the ribosomal exit tunnel.

  2007cited by this paper
• Analysis of the Function of a Large-scale Supra-biomolecule System by Molecular Dynamics Simulation System, SCUBA (Simulation Codes for hUge Biomolecular Assembly)

  2007cited by this paper
• The ribosomal stalk binds to translation factors IF2, EF-Tu, EF-G and RF3 via a conserved region of the L12 C-terminal domain.

  2007cited by this paper
• The geometry of the ribosomal polypeptide exit tunnel.

  2006cited by this paper
• Structure of the 70S Ribosome Complexed with mRNA and tRNA

  2006cited by this paper
• Energy landscape of the ribosomal decoding center.

  2006cited by this paper
• Structures of the Bacterial Ribosome at 3.5 Å Resolution

  2005cited by this paper
• Translational Operator of mRNA on the Ribosome: How Repressor Proteins Exclude Ribosome Binding

  2005cited by this paper
• Simulating movement of tRNA into the ribosome during decoding.

  2005cited by this paper
• Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance.

  2005cited by this paper
• Exploring global motions and correlations in the ribosome.

  2005cited by this paper
• Features of ribosome-peptidyl-tRNA interactions essential for tryptophan induction of tna operon expression.

  2005cited by this paper
• UCSF Chimera—A visualization system for exploratory research and analysis

  2004cited by this paper
• Atomic model of the Thermus thermophilus 70S ribosome developed in silico.

  2004cited by this paper
• Global ribosome motions revealed with elastic network model.

  2004cited by this paper
• The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit.

  2004cited by this paper
• The mechanism of action of macrolides, lincosamides and streptogramin B reveals the nascent peptide exit path in the ribosome.

  2003cited by this paper
• Structural insight into the role of the ribosomal tunnel in cellular regulation

  2003influential reference
• Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit.

  2003cited by this paper
• Locking and unlocking of ribosomal motions.

  2003cited by this paper
• Structures of deacylated tRNA mimics bound to the E site of the large ribosomal subunit.

  2003cited by this paper
• Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy

  2003cited by this paper
• The chemistry of protein synthesis and voyage through the ribosomal tunnel.

  2003cited by this paper
• Structural basis of the ribosomal machinery for peptide bond formation, translocation, and nascent chain progression.

  2003cited by this paper
• L23 protein functions as a chaperone docking site on the ribosome

  2002cited by this paper
• Regulatory nascent peptides in the ribosomal tunnel.

  2002cited by this paper
• All-atom homology model of the Escherichia coli 30S ribosomal subunit

  2002cited by this paper
• Instruction of Translating Ribosome by Nascent Peptide

  2002cited by this paper
• The ribosomal exit tunnel functions as a discriminating gate.

  2002cited by this paper
• Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50.

  2002cited by this paper
• Crystal Structure of the Ribosome at 5.5 Å Resolution

  2001cited by this paper
• The polypeptide tunnel system in the ribosome and its gating in erythromycin resistance mutants of L4 and L22.

  2001cited by this paper
• Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria

  2001cited by this paper
• High resolution structure of the large ribosomal subunit from a mesophilic eubacterium.

  2001cited by this paper
• Recognition of Cognate Transfer RNA by the 30S Ribosomal Subunit

  2001cited by this paper
• Steered molecular dynamics and mechanical functions of proteins.

  2001cited by this paper
• Efficient multiple time step method for use with Ewald and particle mesh Ewald for large biomolecular systems

  2001cited by this paper
• A single adenosine with a neutral pKa in the ribosomal peptidyl transferase center.

  2000cited by this paper
• The structural basis of ribosome activity in peptide bond synthesis.

  2000cited by this paper
• Collective protein dynamics in relation to function.

  2000cited by this paper
• The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 A resolution.

  2000cited by this paper
• A ratchet-like inter-subunit reorganization of the ribosome during translocation

  2000cited by this paper
• The complete atomic structure of the large ribosomal subunit at 2.4 A resolution.

  2000cited by this paper
• A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat.

  1999cited by this paper
• Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme

  1998cited by this paper
• Explicit reversible integrators for extended systems dynamics

  1996cited by this paper
• AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules

  1995cited by this paper
• Essential dynamics of proteins

  1993cited by this paper
• Large-amplitude nonlinear motions in proteins.

  1992cited by this paper
• Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations

  1991cited by this paper
• The effects of solvent on the conformation and the collective motions of protein: normal mode analysis and molecular dynamics simulations of melittin in water and in vacuum

  1991cited by this paper
• Comparison of simple potential functions for simulating liquid water

  1983cited by this paper
• Regulation of Biosynthesis of Ribosomes

  1974cited by this paper
• Description of Thermus thermophilus (Yoshida and Oshima) comb. nov., a Nonsporulating Thermophilic Bacterium from a Japanese Thermal Spa

  1974cited by this paper
• Computer Simulation Using Particles

  1966cited by this paper

• Sensitivity of peptide conformational dynamics in carbon nanotubes to directional mechanical forces.

  2024cites this paper
• The Identity of the Constriction Region of the Ribosomal Exit Tunnel Is Important to Maintain Gene Expression in Escherichia coli

  2022cites this paper
• Free energy landscape of H2A-H2B displacement from nucleosome.

  2022cites this paper
• Torsional stress can regulate the unwrapping of two outer half superhelical turns of nucleosomal DNA

  2021cites this paper
• A ribosomal protein variant that confers macrolide resistance differentially regulates acid resistance, catabolism, and biofilm formation related genes in Escherichia coli

  2021cites this paper
• The outward shift of clarithromycin binding to the ribosome in mutant Helicobacter pylori strains

  2020cites this paper
• Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR.

  2019cites this paper
• Free energy profile for unwrapping outer superhelical turn of CENP-A nucleosome

  2019cites this paper
• Protein Interaction with Charged Macromolecules: From Model Polymers to Unfolded Proteins and Post-Translational Modifications

  2019cites this paper
• Differences in the path to exit the ribosome across the three domains of life

  2018cites this paper
• Species Exit tunnelRibosome structure Geometric Features Archaea Eukarya

  2018cites this paper
• RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

  2018cites this paper
• Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA

  2018cites this paper
• H4 Tails Potentially Produce the Diversity in the Orientation of Two Nucleosomes.

  2017cites this paper
• Investigation of ribosomes using molecular dynamics simulation methods

  2016cites this paper
• Mechanism for verification of mismatched and homoduplex DNAs by nucleotides‐bound MutS analyzed by molecular dynamics simulations

  2016cites this paper
• Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions.

  2015cites this paper
• Essential function of the N‐termini tails of the proteasome for the gating mechanism revealed by molecular dynamics simulations

  2014cites this paper
• Free-Energy Landscape of Reverse tRNA Translocation through the Ribosome Analyzed by Electron Microscopy Density Maps and Molecular Dynamics Simulations

  2014cites this paper
• Functional implications of ribosomal RNA methylation in response to environmental stress

  2014cites this paper
• Single-molecule nanometry for biological physics

  2013cites this paper
• Molecular Dynamics Simulations of the Ribosome

  2012cites this paper
• Protein synthesis factors (RF1, RF2, RF3, RRF, and tmRNA) and peptidyl-tRNA hydrolase rescue stalled ribosomes at sense codons.

  2012cites this paper
• Computational studies of molecular machines: the ribosome.

  2012cites this paper
• 9.5 Dynamics of Very Large Systems: The Ribosome

  2012cites this paper
• Key intermolecular interactions in the E. coli 70S ribosome revealed by coarse-grained analysis.

  2011cites this paper
• Dissecting DNA-histone interactions in the nucleosome by molecular dynamics simulations of DNA unwrapping.

  2011cites this paper
• Molecular Dynamics Simulation System for Structural Analysis of Biomolecules by High Performance Computing

  2011cites this paper
• Recognition of the regulatory nascent chain TnaC by the ribosome.

  2010cites this paper
• Transient tertiary structure formation within the ribosome exit port.

  2010cites this paper
• Branch migration of Holliday junction in RuvA tetramer complex studied by umbrella sampling simulation using a path‐search algorithm

  2010cites this paper
• From nucleosomes to chromatin fibers: molecular dynamics and Monte Carlo simulations of nucleosome organization and interactions

  2010cites this paper
• A novel back-door pathway for glutamine release from GlnBP revealed by steered molecular dynamics simulation

  2009cites this paper
• Global conformational changes of ribosome observed by normal mode fitting for 3D Cryo-EM structures.

  2009cites this paper
• Regulation of the protein-conducting channel by a bound ribosome.

  2009influential citation
• Simulating activity of the bacterial ribosome

  2009cites this paper