Hyper-swivel head domain motions are required for complete mRNA-tRNA translocation and ribosome resetting

Specific length and structure rather than high thermodynamic stability enable regulatory mRNA stem-loops to pause translation

(2022) Chen Bao et al.   Nature Communications

Structural basis of early translocation events on the ribosome

(2021) Emily J. Rundlet et al.   NATURE

Time-resolved cryo-EM visualizes ribosomal translocation with EF-G and GTP

(2021) Christine E. Carbone et al.   Nature Communications

Integrative/Hybrid Modeling Approaches for Studying Biomolecules

(2020) Ashutosh Srivastava et al.   JOURNAL OF MOLECULAR BIOLOGY

Elongation Factor-Tu switch I is a gate for aminoacyl-tRNA selection

(2020) Dylan Girodat et al.   JOURNAL OF MOLECULAR BIOLOGY

Elongation factor-Tu can repetitively engage aminoacyl-tRNA within the ribosome during the proofreading stage of tRNA selection

(2020) Justin C. Morse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers

(2020) Zhichao Miao et al.   RNA

Loss of m1acp3Ψ Ribosomal RNA Modification Is a Major Feature of Cancer

(2020) Artem Babaian et al.   Cell Reports

Structural and functional conservation of the programmed −1 ribosomal frameshift signal of SARS coronavirus 2 (SARS-CoV-2)

(2020) Jamie A. Kelly et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mutations in Domain IV of Elongation Factor EF-G Confer -1 Frameshifting

(2020) Dustin NIblett et al.   RNA

Pairs of amino acids at the P- and A-sites of the ribosome predictably and causally modulate translation-elongation rates

(2020) Nabeel Ahmed et al.   JOURNAL OF MOLECULAR BIOLOGY

Free energy calculations of RNA interactions

(2019) Christoffer Lind et al.   METHODS

Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR

(2019) Karissa Y Sanbonmatsu   CURRENT OPINION IN STRUCTURAL BIOLOGY

Converting GTP hydrolysis into motion: versatile translational elongation factor G

(2019) Marina V. Rodnina et al.   BIOLOGICAL CHEMISTRY

Active role of elongation factor G in maintaining the mRNA reading frame during translation

(2019) Bee-Zen Peng et al.   Science Advances

Molecular simulations of the ribosome and associated translation factors

(2018) Lars V Bock et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The structure of an elongation factor G-ribosome complex captured in the absence of inhibitors

(2018) Kevin Macé et al.   NUCLEIC ACIDS RESEARCH

EF-Tu and EF-G are activated by allosteric effects

(2018) Dibyendu Mondal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alternative Mode of E-Site tRNA Binding in the Presence of a Downstream mRNA Stem Loop at the Entrance Channel

(2018) Yan Zhang et al.   STRUCTURE

Structures of translationally inactive mammalian ribosomes

(2018) Alan Brown et al.   eLife

The Intersubunit Bridge B1b of the Bacterial Ribosome Facilitates Initiation of Protein Synthesis and Maintenance of Translational Fidelity

(2017) Silva Lilleorg et al.   JOURNAL OF MOLECULAR BIOLOGY

The ribosome moves: RNA mechanics and translocation

(2017) Harry F Noller et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Tuning RNA folding and function through rational design of junction topology

(2017) May Daher et al.   NUCLEIC ACIDS RESEARCH

Miscoding-induced stalling of substrate translocation on the bacterial ribosome

(2017) Jose L. Alejo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

(2017) Zhichao Miao et al.   RNA

Recurring RNA structural motifs underlie the mechanics of L1 stalk movement

(2017) Srividya Mohan et al.   Nature Communications

The ribosome moves: RNA mechanics and translocation

(2017) Harry F Noller et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Ribosome rearrangements at the onset of translational bypassing

(2017) Xabier Agirrezabala et al.   Science Advances

Bulky Lesion Bypass Requires Dpo4 Binding in Distinct Conformations

(2017) Pramodha S. Liyanage et al.   Scientific Reports

Scanning of 16S Ribosomal RNA for Peptide Nucleic Acid Targets

(2016) Anna Górska et al.   JOURNAL OF PHYSICAL CHEMISTRY B

EF4 disengages the peptidyl-tRNA CCA end and facilitates back-translocation on the 70S ribosome

(2016) Dejiu Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Multiperspective smFRET reveals rate-determining late intermediates of ribosomal translocation

(2016) Michael R Wasserman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Choreography of molecular movements during ribosome progression along mRNA

(2016) Riccardo Belardinelli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition

(2016) Matthieu G. Gagnon et al.   NUCLEIC ACIDS RESEARCH

Structure of the mammalian antimicrobial peptide Bac7(1–16) bound within the exit tunnel of a bacterial ribosome

(2016) A. Carolin Seefeldt et al.   NUCLEIC ACIDS RESEARCH

Translocation as continuous movement through the ribosome

(2016) Riccardo Belardinelli et al.   RNA Biology

Steric interactions lead to collective tilting motion in the ribosome during mRNA–tRNA translocation

(2016) Kien Nguyen et al.   Nature Communications

EF4 disengages the peptidyl-tRNA CCA end and facilitates back-translocation on the 70S ribosome

(2016) Dejiu Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Multiperspective smFRET reveals rate-determining late intermediates of ribosomal translocation

(2016) Michael R Wasserman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Choreography of molecular movements during ribosome progression along mRNA

(2016) Riccardo Belardinelli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

SMOG 2: A Versatile Software Package for Generating Structure-Based Models

(2016) Jeffrey K. Noel et al.   PLoS Computational Biology

Structural Snapshots of Actively Translating Human Ribosomes

(2015) Elmar Behrmann et al.   CELL

Conformational Changes of Elongation Factor G on the Ribosome during tRNA Translocation

(2015) Jinzhong Lin et al.   CELL

Structure of the human 80S ribosome

(2015) Heena Khatter et al.   NATURE

Structure of the E. coli ribosome–EF-Tu complex at

(2015) Niels Fischer et al.   NATURE

Chemically related 4,5-linked aminoglycoside antibiotics drive subunit rotation in opposite directions

(2015) Michael R. Wasserman et al.   Nature Communications

Fluctuations between multiple EF-G-induced chimeric tRNA states during translocation on the ribosome

(2015) Sarah Adio et al.   Nature Communications

Mechanisms of ribosome stalling by SecM at multiple elongation steps

(2015) Jun Zhang et al.   eLife

Activation of GTP hydrolysis in mRNA-tRNA translocation by elongation factor G

(2015) W. Li et al.   Science Advances

Synchronous tRNA movements during translocation on the ribosome are orchestrated by elongation factor G and GTP hydrolysis

(2014) Wolf Holtkamp et al.   BIOESSAYS

Structure of the Mammalian Ribosome-Sec61 Complex to 3.4 Å Resolution

(2014) Rebecca M. Voorhees et al.   CELL

Regulation of the Mammalian Elongation Cycle by Subunit Rolling: A Eukaryotic-Specific Ribosome Rearrangement

(2014) Tatyana V. Budkevich et al.   CELL

Molecular mechanics of 30S subunit head rotation

(2014) Srividya Mohan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How the ribosome hands the A-site tRNA to the P site during EF-G-catalyzed translocation

(2014) J. Zhou et al.   SCIENCE

Structures of Yeast 80S Ribosome-tRNA Complexes in the Rotated and Nonrotated Conformations

(2014) Egor Svidritskiy et al.   STRUCTURE

The Antibiotics Dityromycin and GE82832 Bind Protein S12 and Block EF-G-Catalyzed Translocation

(2014) David Bulkley et al.   Cell Reports

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Ribosome-targeting antibiotics and mechanisms of bacterial resistance

(2013) Daniel N. Wilson   NATURE REVIEWS MICROBIOLOGY

Energy barriers and driving forces in tRNA translocation through the ribosome

(2013) Lars V Bock et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structure of EF-G–ribosome complex in a pretranslocation state

(2013) Yun Chen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Crystal Structure of 70S Ribosome with Both Cognate tRNAs in the E and P Sites Representing an Authentic Elongation Complex

(2013) Shu Feng et al.   PLoS One

Visualization of two transfer RNAs trapped in transit during elongation factor G-mediated translocation

(2013) D. J. F. Ramrath et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of the ribosome with elongation factor G trapped in the pretranslocation state

(2013) A. F. Brilot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crystal Structures of EF-G-Ribosome Complexes Trapped in Intermediate States of Translocation

(2013) J. Zhou et al.   SCIENCE

Control of Ribosomal Subunit Rotation by Elongation Factor G

(2013) A. Pulk et al.   SCIENCE

Elongation Factor G Bound to the Ribosome in an Intermediate State of Translocation

(2013) D. S. Tourigny et al.   SCIENCE

Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome

(2013) Paul C. Whitford et al.   PLoS Computational Biology

Unraveling the dynamics of ribosome translocation

(2012) Jin Chen et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

GPU/CPU Algorithm for Generalized Born/Solvent-Accessible Surface Area Implicit Solvent Calculations

(2012) David E. Tanner et al.   Journal of Chemical Theory and Computation

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

The Shadow Map: A General Contact Definition for Capturing the Dynamics of Biomolecular Folding and Function

(2012) Jeffrey K. Noel et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The complex of tmRNA–SmpB and EF-G on translocating ribosomes

(2012) David J. F. Ramrath et al.   NATURE

Structure and mechanical properties of the ribosomal L1 stalk three-way junction

(2012) Kamila Réblová et al.   NUCLEIC ACIDS RESEARCH

Impact of methylations of m2G966/m5C967 in 16S rRNA on bacterial fitness and translation initiation

(2012) Dmitry E. Burakovsky et al.   NUCLEIC ACIDS RESEARCH

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

(2012) Marcus D Hanwell et al.   Journal of Cheminformatics

Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation

(2011) J. Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structures of the Bacterial Ribosome in Classical and Hybrid States of tRNA Binding

(2011) J. A. Dunkle et al.   SCIENCE

Role of the Initiation Factors in mRNA Start Site Selection and fMet-tRNA Recruitment by Bacterial Ribosomes

(2010) Claudio O. Gualerzi et al.   ISRAEL JOURNAL OF CHEMISTRY

Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy

(2010) Niels Fischer et al.   NATURE

Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites

(2010) Andreas H. Ratje et al.   NATURE

Structural aspects of messenger RNA reading frame maintenance by the ribosome

(2010) Lasse B Jenner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

SMOG@ctbp: simplified deployment of structure-based models in GROMACS

(2010) Jeffrey K. Noel et al.   NUCLEIC ACIDS RESEARCH

Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways

(2010) P. C. Whitford et al.   RNA

The A–Z of bacterial translation inhibitors

(2009) Daniel N. Wilson   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

The Ribosome as a Conveying Thermal Ratchet Machine

(2009) Alexander S. Spirin   JOURNAL OF BIOLOGICAL CHEMISTRY

Contribution of ribosomal residues to P-site tRNA binding

(2009) Shinichiro Shoji et al.   NUCLEIC ACIDS RESEARCH

Following movement of the L1 stalk between three functional states in single ribosomes

(2009) Peter V. Cornish et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Structure of the Ribosome with Elongation Factor G Trapped in the Posttranslocational State

(2009) Y.-G. Gao et al.   SCIENCE

Navigating the ribosome's metastable energy landscape

(2009) James B. Munro et al.   TRENDS IN BIOCHEMICAL SCIENCES

Coupling of Ribosomal L1 Stalk and tRNA Dynamics during Translation Elongation

(2008) Jingyi Fei et al.   MOLECULAR CELL

Spontaneous Intersubunit Rotation in Single Ribosomes

(2008) Peter V. Cornish et al.   MOLECULAR CELL

Crystal structure of a translation termination complex formed with release factor RF2

(2008) A. Korostelev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields

(2008) Paul C. Whitford et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A role for the 30S subunit E site in maintenance of the translational reading frame

(2008) A. Devaraj et al.   RNA