The molecular choreography of protein synthesis: translational control, regulation, and pathways

doi:10.1017/S0033583516000056

Bypassing of stems versus linear base-by-base inspection of mammalian mRNAs during ribosomal scanning

The ATP-dependent interaction of eukaryotic initiation factors with mRNA

Reconstitution of yeast translation initiation

Kinetic analysis of late steps of eukaryotic translation initiation

Modified nucleosides and bizarre 5′-termini in mouse myeloma mRNA

Formation of circular polyribosomes on eukaryotic mRNA without cap-structure and poly(A)-tail: a cryo electron tomography study

Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu

Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome

A mechanistic overview of translation initiation in eukaryotes

Following the intersubunit conformation of the ribosome during translation in real time

Molecular crowding enhanced ATPase activity of the RNA helicase eIF4A correlates with compaction of its quaternary structure and association with eIF4G

Translation initiation in eukaryotes: versatility of the scanning model

Pi release from eIF2, not GTP hydrolysis, is the step controlled by start-site selection during eukaryotic translation initiation

Development and characterization of a reconstituted yeast translation initiation system

In vitro reconstitution of eukaryotic translation reveals cooperativity between release factors eRF1 and eRF3

Purification and characterization of protein synthesis initiation factor eIF-4E from the yeast Saccharomyces cerevisiae

mRNA cap-binding protein: cloning of the gene encoding protein synthesis initiation factor eIF-4E from Saccharomyces cerevisiae

A mammalian translation initiation factor can substitute for its yeast homologue in vivo

The Saccharomyces cerevisiae translation initiation factor Tif3 and its mammalian homologue, eIF-4B, have RNA annealing activity

Translation factors promote the formation of two states of the closed-loop mRNP

Domain and nucleotide dependence of the interaction between Saccharomyces cerevisiae translation elongation factors 3 and 1A

Functional interactions between yeast translation eukaryotic elongation factor (eEF) 1A and eEF3

Structure of eEF3 and the mechanism of transfer RNA release from the E-site

The DEAD-box helicase eIF4A: paradigm or the odd one out?

eIF4B and eIF4 G jointly stimulate eIF4A ATPase and unwinding activities by modulation of the eIF4A conformational cycle

The roles of initiation factor 2 and guanosine triphosphate in initiation of protein synthesis

Differential effects of nucleotide analogs on scanning-dependent initiation and elongation of mammalian mRNA translation in vitro

Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles

Specialized yeast ribosomes: a customized tool for selective mRNA translation

Two structurally atypical HEAT domains in the C-terminal portion of human eIF4G support binding to eIF4A and Mnk1

The mechanism of action of protein synthesis initiation factors from rabbit reticulocytes

RNA-binding activity of translation initiation factor eIF4G1 from Saccharomyces cerevisiae

Dynamics and processivity of 40S ribosome scanning on mRNA in yeast

Translation initiation factors eIF3 and HCR1 control translation termination and stop codon read-through in yeast cells

Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome

tRNA selection and kinetic proofreading in translation

tRNA dynamics on the ribosome during translation

Translation in Saccharomyces cerevisiae: initiation factor 4A-dependent cell-free system

Energy barriers and driving forces in tRNA translocation through the ribosome

Peptide chain elongation rate and ribosomal activity in Saccharomyces cerevisiae as a function of the growth rate

The three-dimensional organization of polyribosomes in intact human cells

The native 3D organization of bacterial polysomes

Structure and dynamics of the mammalian ribosomal pretranslocation complex

Regulation of the mammalian elongation cycle by subunit rolling: a eukaryotic-specific ribosome rearrangement

Revisiting the structures of several antibiotics bound to the bacterial ribosome

Programmed -1 frameshifting by kinetic partitioning during impeded translocation

Changed in translation: mRNA recoding by -1 programmed ribosomal frameshifting

A spectroscopic study of the binding of m7GTP and m7GpppG to human protein synthesis initiation factor 4E

Crystal structure of yeast initiation factor 4A, a DEAD-box RNA helicase

Differential cleavage of eIF4GI and eIF4GII in mammalian cells. Effects on translation

eIF4A3 is a novel component of the exon junction complex

Femtosecond X-ray protein nanocrystallography

Single-molecule fluorescence measurements of ribosomal translocation dynamics

Allosteric vs. spontaneous exit-site (E-site) tRNA dissociation early in protein synthesis

Dynamics of translation by single ribosomes through mRNA secondary structures

Coupling of mRNA structure rearrangement to ribosome movement during bypassing of non-coding regions

High-throughput platform for real-time monitoring of biological processes by multicolor single-molecule fluorescence

Dynamic pathways of -1 translational frameshifting

Coordinated conformational and compositional dynamics drive ribosome translocation

Unraveling the dynamics of ribosome translocation

Nonfluorescent quenchers to correlate single-molecule conformational and compositional dynamics

DEAD-box proteins can completely separate an RNA duplex using a single ATP

eIF4G, eIFiso4G, and eIF4B bind the poly(A)-binding protein through overlapping sites within the RNA recognition motif domains

N-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics

Requirement of the DEAD-Box protein ded1p for messenger RNA translation

Functional overlap between eIF4G isoforms in Saccharomyces cerevisiae

Ultrahigh-resolution optical trap with single-fluorophore sensitivity

Identification of the hypusine-containing protein hy+ as translation initiation factor eIF-4D

Spontaneous intersubunit rotation in single ribosomes

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

The p20 and Ded1 proteins have antagonistic roles in eIF4E-dependent translation in Saccharomyces cerevisiae

Differential effects of aromatic and charged residue substitutions in the RNA binding domains of the yeast poly(A)-binding protein

Widespread occurrence of N6-methyladenosine in bacterial mRNA

The elongation, termination, and recycling phases of translation in eukaryotes

The hypusine-containing translation factor eIF5A

Roles of individual domains in the function of DHX29, an essential factor required for translation of structured mammalian mRNAs

EF-P is essential for rapid synthesis of proteins containing consecutive proline residues

Entropic contribution of elongation factor P to proline positioning at the catalytic center of the Ribosome

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

The hybrid state of tRNA binding is an authentic translation elongation intermediate

Site-specific labeling of the ribosome for single-molecule spectroscopy

Ribosome structure and dynamics during translocation and termination

Structures of the bacterial ribosome in classical and hybrid states of tRNA binding

Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action

Molecular-crowding effects on single-molecule RNA folding/unfolding thermodynamics and kinetics

Mistranslation in E. coli

Initiation factor 2 crystal structure reveals a different domain organization from eukaryotic initiation factor 5B and mechanism among translational GTPases

Three tRNA binding sites in rabbit liver ribosomes and role of the intrinsic ATPase in 80S ribosomes from higher eukaryotes

Conformational selection of translation initiation factor 3 signals proper substrate selection

Observation of intersubunit movement of the ribosome in solution using FRET

mRNA translocation occurs during the second step of ribosomal intersubunit rotation

Molecular architecture of the 40SeIF1eIF3 translation initiation complex

Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation

Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation

Transfer RNA-mediated regulation of ribosome dynamics during protein synthesis

Functional dynamics within the human ribosome regulate the rate of active protein synthesis

Molecular architecture of a eukaryotic translational initiation complex

Initiation of translation by cricket paralysis virus IRES requires its translocation in the ribosome

A nuclear translation-like factor eIF4AIII is recruited to the mRNA during splicing and functions in nonsense-mediated decay

An in vivo control map for the eukaryotic mRNA translation machinery

Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy

Structure of the E. coli ribosome-EF-Tu complex at <3 A resolution by Cs-corrected cryo-EM

mRNA-programmed translation pauses in the targeting of E. coli membrane proteins

A ratchet-like inter-subunit reorganization of the ribosome during translocation

The process of mRNA-tRNA translocation

Structure and dynamics of a processive Brownian motor: the translating ribosome

Quantitative studies of mRNA recruitment to the eukaryotic ribosome

Release factor RF3 in E.coli accelerates the dissociation of release factors RF1 and RF2 from the ribosome in a GTP-dependent manner

Eukaryotic polypeptide chain release factor eRF3 is an eRF1- and ribosome-dependent guanosine triphosphatase

High accuracy FIONA-AFM hybrid imaging

A blocked structure at the 5′ terminus of mRNA from cytoplasmic polyhedrosis virus

Reovirus messenger RNA contains a methylated, blocked 5′-terminal structure: m-7G(5′)ppp(5′)G-MpCp-

Ribosome structure. Crystal structure of elongation factor 4 bound to a clockwise ratcheted ribosome

A cellular response linking eIF4AI activity to eIF4AII transcription

RF3 induces ribosomal conformational changes responsible for dissociation of class I release factors

The structure of the ribosome with elongation factor G trapped in the posttranslocational state

RNA BIOCHEMISTRY. Factor-dependent processivity in human eIF4A DEAD-box helicase

The translational repressor 4E-BP called to order by eIF4E: new structural insights by SAXS

TIF4631 and TIF4632: two yeast genes encoding the high-molecular-weight subunits of the cap-binding protein complex (eukaryotic initiation factor 4F) contain an RNA recognition motif-like sequence and carry out an essential function

Identification and characterization of cap-binding proteins from yeast

Reactivation of stalled polyribosomes in synaptic plasticity

A novel functional human eukaryotic translation initiation factor 4G

A dynamic DNA-repair complex observed by correlative single-molecule nanomanipulation and fluorescence

Multiple portions of poly(A)-binding protein stimulate translation in vivo

Characterization of eukaryotic initiation factor 4A, a protein involved in ATP-dependent binding of globin mRNA

New initiation factor activity required for globin mRNA translation

Recognition of eIF4G by rotavirus NSP3 reveals a basis for mRNA circularization

Kinetic determinants of high-fidelity tRNA discrimination on the ribosome

Ribosome loading onto the mRNA cap is driven by conformational coupling between eIF4G and eIF4E

Rotation of the head of the 30S ribosomal subunit during mRNA translocation

eIF5A promotes translation of polyproline motifs

Repression of cap-dependent translation by 4E-binding protein 1: competition with p220 for binding to eukaryotic initiation factor-4E

Crystal structure of elongation factor P from Thermus thermophilus HB8

eIF4B, eIF4G and RNA regulate eIF4A activity in translation initiation by modulating the eIF4A conformational cycle

Structure of the mammalian ribosomal 43S preinitiation complex bound to the scanning factor DHX29

The yeast eukaryotic initiation factor 4G (eIF4G) HEAT domain interacts with eIF1 and eIF5 and is involved in stringent AUG selection

Eukaryotic translation initiation factor (eIF) 5A stimulates protein synthesis in Saccharomyces cerevisiae

Coupling of open reading frames by translational bypassing

One protein from two open reading frames: mechanism of a 50 nt translational bypass

Factors that influence selection of coding resumption sites in translational bypassing: minimal conventional peptidyl-tRNA:mRNA pairing can suffice

The role of mammalian initiation factor eIF-4D and its hypusine modification in translation

The Cap-binding protein eIF4E promotes folding of a functional domain of yeast translation initiation factor eIF4G1

eIF4G stimulates the activity of the DEAD box protein eIF4A by a conformational guidance mechanism

The DEAD-box protein Ded1 modulates translation by the formation and resolution of an eIF4F-mRNA complex

Translational regulation of GCN4 and the general amino acid control of yeast

eIF3: a versatile scaffold for translation initiation complexes

Molecular mechanism of scanning and start codon selection in eukaryotes

The mechanism of eukaryotic translation initiation: new insights and challenges

Functional analysis of individual binding activities of the scaffold protein eIF4G

The role of ribosome recycling factor in dissociation of 70S ribosomes into subunits

Cofactor requirements for nuclear export of Rev response element (RRE)- and constitutive transport element (CTE)-containing retroviral RNAs. An unexpected role for actin

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

Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity

Intersubunit movement is required for ribosomal translocation

A persistent untranslated sequence within bacteriophage T4 DNA topoisomerase gene 60

Structural changes enable start codon recognition by the eukaryotic translation initiation complex

A newly identified N-terminal amino acid sequence of human eIF4G binds poly(A)-binding protein and functions in poly(A)-dependent translation

Human eukaryotic translation initiation factor 4G (eIF4G) possesses two separate and independent binding sites for eIF4A

Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling

Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes

Arrest peptides: cis-acting modulators of translation

The stretch of C-terminal acidic amino acids of translational release factor eRF1 is a primary binding site for eRF3 of fission yeast

Conserved motifs in prokaryotic and eukaryotic polypeptide release factors: tRNA-protein mimicry hypothesis

Signals for ribosomal frameshifting in the Rous sarcoma virus gag-pol region

Characterization of ribosomal frameshifting in HIV-1 gag-pol expression

The current status of vertebrate cellular mRNA IRESs

The mechanism of eukaryotic translation initiation and principles of its regulation

Termination and post-termination events in eukaryotic translation

Tandem affinity purification revealed the hypusine-dependent binding of eukaryotic initiation factor 5A to the translating 80S ribosomal complex

Structural aspects of messenger RNA reading frame maintenance by the ribosome

The kinetics of ribosomal peptidyl transfer revisited

Sequence-dependent elongation dynamics on macrolide-bound ribosomes

Genetic code translation displays a linear trade-off between efficiency and accuracy of tRNA selection

The mRNA closed-loop model: the function of PABP and PABP-interacting proteins in mRNA translation

Mammalian poly(A)-binding protein is a eukaryotic translation initiation factor, which acts via multiple mechanisms

Effect of initiation factor eIF-5A depletion on protein synthesis and proliferation of Saccharomyces cerevisiae

The general mode of translation inhibition by macrolide antibiotics

Functional characterization of the role of the N-terminal domain of the c/Nip1 subunit of eukaryotic initiation factor 3 (eIF3) in AUG recognition

A mechanism of translational repression by competition of Paip2 with eIF4G for poly(A) binding protein (PABP) binding

Novel roles for classical factors at the interface between translation termination and initiation

Intrinsic RNA binding by the eukaryotic initiation factor 4F depends on a minimal RNA length but not on the m7G cap

Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA

Purification and properties of rabbit reticulocyte protein synthesis initiation factors M2Balpha and M2Bbeta

Structural integrity of the PCI domain of eIF3a/TIF32 is required for mRNA recruitment to the 43S pre-initiation complexes

Identification of a ribosomal ATPase in Escherichia coli cells

Functional interactions of an Escherichia coli ribosomal ATPase

Fluctuations of transfer RNAs between classical and hybrid states

A frameshifting stimulatory stem loop destabilizes the hybrid state and impedes ribosomal translocation

Different modes of interaction by TIAR and HuR with target RNA and DNA

Cryo-electron microscopy of ribosomal complexes in cotranslational folding, targeting, and translocation

Taura syndrome virus IRES initiates translation by binding its tRNA–mRNA-like structural element in the ribosomal decoding center

Binding of eukaryotic initiation factor 3 to ribosomal 40S subunits and its role in ribosomal dissociation and anti-association

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

RF3:GTP promotes rapid dissociation of the class 1 termination factor

Pushing the limits of the scanning mechanism for initiation of translation

eIF5B employs a novel domain release mechanism to catalyze ribosomal subunit joining

Structural insight into the recognition of amino-acylated initiator tRNA by eIF5B in the 80S initiation complex

Mapping of functional domains in eukaryotic protein synthesis initiation factor 4 G (eIF4G) with picornaviral proteases. Implications for cap-dependent and cap-independent translational initiation

Massive programmed translational jumping in mitochondria

Simultaneous, coincident optical trapping and single-molecule fluorescence

Structural basis for translation termination on the 70S ribosome

Isolation and characterization of factors from wheat germ that exhibit eukaryotic initiation factor 4B activity and overcome 7-methylguanosine 5′-triphosphate inhibition of polypeptide synthesis

A ribosome-specialized translation initiation pathway is required for cap-dependent translation of vesicular stomatitis virus mRNAs

Translation initiation factor eIF4G-1 binds to eIF3 through the eIF3e subunit

Zero-mode waveguides for single-molecule analysis at high concentrations

The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria

Cleavage of translation initiation factor 4AI (eIF4AI) but not eIF4AII by foot-and-mouth disease virus 3C protease: identification of the eIF4AI cleavage site

Nanopore detachment kinetics of poly(A) binding proteins from RNA molecules reveals the critical role of C-terminus interactions

From unwinding to clamping - the DEAD box RNA helicase family

Interaction strengths between the ribosome and tRNA at various steps of translocation

ATP hydrolysis is required for DEAD-box protein recycling but not for duplex unwinding

Direct measurement of the mechanical work during translocation by the ribosome

Translation initiation factor eIF3b contains a nine-bladed beta-propeller and interacts with the 40S ribosomal subunit

The initiation of mammalian protein synthesis and mRNA scanning mechanism

The DEAD box protein eIF4A. 1. A minimal kinetic and thermodynamic framework reveals coupled binding of RNA and nucleotide

The DEAD box protein eIF4A. 2. A cycle of nucleotide and RNA-dependent conformational changes

Cryo-electron tomography: the challenge of doing structural biology in situ

Communication between eukaryotic translation initiation factors 5 and 1A within the ribosomal pre-initiation complex plays a role in start site selection

A conformational change in the eukaryotic translation preinitiation complex and release of eIF1 signal recognition of the start codon

Communication between eukaryotic translation initiation factors 1 and 1A on the yeast small ribosomal subunit

Exploring the structural dynamics of the translational machinery using single-molecule fluorescence resonance energy transfer

The translation initiation factor eIF-4E binds to a common motif shared by the translation factor eIF-4 gamma and the translational repressors 4E-binding proteins

Structural basis for RNA-duplex recognition and unwinding by the DEAD-box helicase Mss116p

Genome-wide analyses and functional classification of proline repeat-rich proteins: potential role of eIF5A in eukaryotic evolution

Deciphering the rules by which dynamics of mRNA secondary structure affect translation efficiency in Saccharomyces cerevisiae

Purification and properties of the heterogeneous subunits of elongation factor EF-1 from Guerin epithelioma cells

Cocrystal structure of the messenger RNA 5′ cap-binding protein (eIF4E) bound to 7-methyl-GDP

Cap-dependent translation initiation in eukaryotes is regulated by a molecular mimic of eIF4G

Topology and regulation of the human eIF4A/4G/4H helicase complex in translation initiation

Translation initiation: structures, mechanisms and evolution

Maintaining the ribosomal reading frame: the influence of the E site during translational regulation of release factor 2

Unwinding single RNA molecules using helicases involved in eukaryotic translation initiation

GTP hydrolysis by IF2 guides progression of the ribosome into elongation

Irreversible chemical steps control intersubunit dynamics during translation

Structured mRNAs regulate translation initiation by binding to the platform of the ribosome

Initiation factor 2, tRNA, and 50S subunits cooperatively stabilize mRNAs on the ribosome during initiation

The translation factor eIF5A and human cancer

Structure of translation factor eIF4E bound to m7GDP and interaction with 4E-binding protein

Posttranscriptional control of gene expression in yeast

One core, two shells: bacterial and eukaryotic ribosomes

eIF4F: a retrospective

Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons

Real-time assembly landscape of bacterial 30S translation initiation complex

Kinetic control of translation initiation in bacteria

Ribosome collisions and translation efficiency: optimization by codon usage and mRNA destabilization

The 5′−7-methylguanosine cap on eukaryotic mRNAs serves both to stimulate canonical translation initiation and to block an alternative pathway

New tools provide new insights in NMR studies of protein dynamics

Small-molecule inhibition of the interaction between the translation initiation factors eIF4E and eIF4G

Leaderless mRNAs in bacteria: surprises in ribosomal recruitment and translational control

The tmRNA system for translational surveillance and ribosome rescue

Eukaryotic translation initiation factor 4E (eIF4E) binding site and the middle one-third of eIF4GI constitute the core domain for cap-dependent translation, and the C-terminal one-third functions as a modulatory region

Cryo-EM of ribosomal 80S complexes with termination factors reveals the translocated cricket paralysis virus IRES

Identification of two distinct hybrid state intermediates on the ribosome

A fast dynamic mode of the EF-G-bound ribosome

Navigating the ribosome's metastable energy landscape

Correlated conformational events in EF-G and the ribosome regulate translocation

The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes

Emerging understanding of translation termination

A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting

Coordinated movements of eukaryotic translation initiation factors eIF1, eIF1A, and eIF5 trigger phosphate release from eIF2 in response to start codon recognition by the ribosomal preinitiation complex

Eukaryotic translation initiation factors 4 G and 4A from Saccharomyces cerevisiae interact physically and functionally

The RNA recognition motif of yeast translation initiation factor Tif3/eIF4B is required but not sufficient for RNA strand-exchange and translational activity

Biophysical studies of eIF4E cap-binding protein: recognition of mRNA 5′ cap structure and synthetic fragments of eIF4G and 4E-BP1 proteins

The allosteric three-site model for the ribosomal elongation cycle: features and future

Molecular biology. Internal mRNA methylation finally finds functions

Kinetic amplification of enzyme discrimination

N6-methyl-adenosine (m6A) in RNA: an old modification with a novel epigenetic function

Real-time observation of signal recognition particle binding to actively translating ribosomes

Signal recognition particle-ribosome binding is sensitive to nascent chain length

Programmed translational bypassing elements in mitochondria: structure, mobility, and evolutionary origin

Dynamic recognition of the mRNA cap by Saccharomyces cerevisiae eIF4E

Structural basis for the enhancement of eIF4A helicase activity by eIF4G

Recognition of cognate transfer RNA by the 30S ribosomal subunit

Inhibition of translational initiation in Saccharomyces cerevisiae by secondary structure: the roles of the stability and position of stem-loops in the mRNA leader

The yeast poly(A)-binding protein Pab1p stimulates in vitro poly(A)-dependent and cap-dependent translation by distinct mechanisms

Duplex unwinding and ATPase activities of the DEAD-box helicase eIF4A are coupled by eIF4G and eIF4B

Chemical exchange in biomacromolecules: past, present, and future

DEAD-box helicase proteins disrupt RNA tertiary structure through helix capture

Structure of the eukaryotic translation initiation factor eIF4E in complex with 4EGI-1 reveals an allosteric mechanism for dissociating eIF4G

Complete kinetic mechanism of elongation factor Tu-dependent binding of aminoacyl-tRNA to the A site of the E. coli ribosome

Multiple elements in the eIF4G1 N-terminus promote assembly of eIF4G1•PABP mRNPs in vivo

Yeast eukaryotic initiation factor 4B (eIF4B) enhances complex assembly between eIF4A and eIF4G in vivo

Functional significance of eIF5A and its hypusine modification in eukaryotes

HuD RNA recognition motifs play distinct roles in the formation of a stable complex with AU-rich RNA

Errors and alternatives in reading the universal genetic code

The helicase protein DHX29 promotes translation initiation, cell proliferation, and tumorigenesis

mRNA helicases: the tacticians of translational control

The eukaryotic translation initiation factors eIF1 and eIF1A induce an open conformation of the 40S ribosome

Elongation factor 4 (EF4/LepA) accelerates protein synthesis at increased Mg2+ concentrations

Distinct XPPX sequence motifs induce ribosome stalling, which is rescued by the translation elongation factor EF-P

Targeting the eIF4F translation initiation complex: a critical nexus for cancer development

In vitro and in vivo single-molecule fluorescence imaging of ribosome-catalyzed protein synthesis

Timing of GTP binding and hydrolysis by translation termination factor RF3

Sequence of steps in ribosome recycling as defined by kinetic analysis

Eukaryotic ribosomes require initiation factors 1 and 1A to locate initiation codons

The joining of ribosomal subunits in eukaryotes requires eIF5B

Further in vitro exploration fails to support the “allosteric three-site model”

Single-molecule analysis of translational dynamics

Recycling of eukaryotic posttermination ribosomal complexes

Ribosomal position and contacts of mRNA in eukaryotic translation initiation complexes

The role of ABCE1 in eukaryotic posttermination ribosomal recycling

Translation initiation on mammalian mRNAs with structured 5′UTRs requires DExH-box protein DHX29

Expression of translation initiation factor 4A from yeast and mouse in Saccharomyces cerevisiae

Context specific misreading of phenylalanine codons

Repressor binding to a dorsal regulatory site traps human eIF4E in a high cap-affinity state

Cooperative modulation by eIF4G of eIF4E-binding to the mRNA 5′ cap in yeast involves a site partially shared by p20

Control of ribosomal subunit rotation by elongation factor G

Structured mRNA induces the ribosome into a hyper-rotated state

The ribosome uses two active mechanisms to unwind messenger RNA during translation

Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1

Specific domains in yeast translation initiation factor eIF4G strongly bias RNA unwinding activity of the eIF4F complex toward duplexes with 5′-overhangs

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

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

Insights into domain-domain motions in proteins and RNA from solution NMR

ATP-dependent unwinding of messenger RNA structure by eukaryotic initiation factors

Ribosomes cannot interact simultaneously with elongation factors EF Tu and EF G

Regulation of cap-dependent translation by eIF4E inhibitory proteins

Further biochemical and kinetic characterization of human eukaryotic initiation factor 4H

Purification and characterization of a new eukaryotic protein translation factor. Eukaryotic initiation factor 4H

Quality control of mRNA decoding on the bacterial ribosome

The ribosome as a versatile catalyst: reactions at the peptidyl transferase center

Hydrolysis of GTP by elongation factor G drives tRNA movement on the ribosome

ATPase strongly bound to higher eukaryotic ribosomes

Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms

Ribosome fidelity: tRNA discrimination, proofreading and induced fit

Further characterization of the helicase activity of eIF4A. Substrate specificity

Modulation of the helicase activity of eIF4A by eIF4B, eIF4H, and eIF4F

Biochemical and kinetic characterization of the RNA helicase activity of eukaryotic initiation factor 4A

X-ray structures of the universal translation initiation factor IF2/eIF5B: conformational changes on GDP and GTP binding

Structure and thermodynamics of N6-methyladenosine in RNA: a spring-loaded base modification

Quantifying elongation rhythm during full-length protein synthesis

eIF5A and EF-P: two unique translation factors are now traveling the same road

A practical guide to single-molecule FRET

Bidirectional RNA helicase activity of eucaryotic translation initiation factors 4A and 4F

Interactions between eIF4AI and its accessory factors eIF4B and eIF4H

Regulatory elements in eIF1A control the fidelity of start codon selection by modulating tRNA(i)(Met) binding to the ribosome

Hypusine-containing protein eIF5A promotes translation elongation

Advances in the determination of nucleic acid conformational ensembles

High-efficiency translational bypassing of non-coding nucleotides specified by mRNA structure and nascent peptide

Ribosomal protein L1 from Escherichia coli. Its role in the binding of tRNA to the ribosome and in elongation factor g-dependent GTP hydrolysis

Takeover of host ribosomes by divergent IRES elements

Correlative microscopy: bridging the gap between fluorescence light microscopy and cryo-electron tomography

An elongation factor G-induced ribosome rearrangement precedes tRNA–mRNA translocation

Phosphorylation of eukaryotic initiation factor 4E markedly reduces its affinity for capped mRNA

What recent ribosome structures have revealed about the mechanism of translation

The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA

Initiation of mammalian protein synthesis. I. Purification and characterization of seven initiation factors

Crystal structure of the yeast eIF4A–eIF4G complex: an RNA-helicase controlled by protein–protein interactions

Structural insight into nascent polypeptide chain-mediated translational stalling

Molecular mechanism of the dual activity of 4EGI-1: dissociating eIF4G from eIF4E but stabilizing the binding of unphosphorylated 4E-BP1

Structure of the 70S ribosome complexed with mRNA and tRNA

The DEAD-box helicase Ded1 from yeast is an mRNP cap-associated protein that shuttles between the cytoplasm and nucleus

Rate-limiting steps in yeast protein translation

The Ded1/DDX3 subfamily of DEAD-box RNA helicases

Capping of eucaryotic mRNAs

Activated GTPase movement on an RNA scaffold drives co-translational protein targeting

Hypusine, a new amino acid occurring in bovine brain. Isolation and structural determination

Critical roles of RNA helicase DDX3 and its interactions with eIF4E/PABP1 in stress granule assembly and stress response

Kinetic analysis reveals the ordered coupling of translation termination and ribosome recycling in yeast

Structural insights into the allosteric effects of 4EBP1 on the eukaryotic translation initiation factor eIF4E

Sequential eukaryotic translation initiation factor 5 (eIF5) binding to the charged disordered segments of eIF4G and eIF2β stabilizes the 48S preinitiation complex and promotes its shift to the initiation mode

A comprehensive, quantitative, and genome-wide model of translation

Reinitiation and other unconventional posttermination events during eukaryotic translation

Stopped-flow kinetic analysis of eIF4E and phosphorylated eIF4E binding to cap analogs and capped oligoribonucleotides: evidence for a one-step binding mechanism

Kinetic mechanism for assembly of the m7GpppG.eIF4E.eIF4G complex

Human eukaryotic initiation factor 2 (eIF2)–GTP–Met-tRNAi ternary complex and eIF3 stabilize the 43 S preinitiation complex

eIF4E, the mRNA cap-binding protein: from basic discovery to translational research

A polypeptide in eukaryotic initiation factors that crosslinks specifically to the 5′-terminal cap in mRNA

The crystal structure of human eukaryotic release factor eRF1 – mechanism of stop codon recognition and peptidyl-tRNA hydrolysis

DEAD-box protein DDX3 associates with eIF4F to promote translation of selected mRNAs

A model of the functioning ribosome: locking and unlocking of the ribosome subparticles

How does a scanning ribosomal particle move along the 5′-untranslated region of eukaryotic mRNA? Brownian Ratchet model

Large-scale movement of elongation factor G and extensive conformational change of the ribosome during translocation

Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling

The eukaryotic initiation factor eIF4H facilitates loop-binding, repetitive RNA unwinding by the eIF4A DEAD-box helicase

Single-molecule kinetics of the eukaryotic initiation factor 4AI upon RNA unwinding

Structures of yeast 80S ribosome-tRNA complexes in the rotated and nonrotated conformations

The requirement for eukaryotic initiation factor 4A (elF4A) in translation is in direct proportion to the degree of mRNA 5′ secondary structure

Local control of a disorder–order transition in 4E-BP1 underpins regulation of translation via eIF4E

mRNA helicase activity of the ribosome

Advanced solid-state NMR approaches for structure determination of membrane proteins and amyloid fibrils

The current understanding of Ded1p/DDX3 homologs from yeast to human

Association of the yeast poly(A) tail binding protein with translation initiation factor eIF-4G

Cryo-EM structure of the mammalian eukaryotic release factor eRF1–eRF3-associated termination complex

Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation

The mechanism of action of eukaryotic initiation factor 4C in protein synthesis

Mode of action of protein synthesis initiation factor eIF-1 from rabbit reticulocytes

Frameshifting dynamics

Secondary structure of bacteriophage T4 gene 60 mRNA: implications for translational bypassing

Structural basis for mRNA Cap-Binding regulation of eukaryotic initiation factor 4E by 4E-binding protein, studied by spectroscopic, X-ray crystal structural, and molecular dynamics simulation methods

Crystal structures of 7-methylguanosine 5′-triphosphate (m(7)GTP)- and P(1)-7-methylguanosine-P(3)-adenosine-5′,5′-triphosphate (m(7)GpppA)-bound human full-length eukaryotic initiation factor 4E: biological importance of the C-terminal flexible region

Crystal structure of human eIF5A1: insight into functional similarity of human eIF5A1 and eIF5A2

Cap and cap-binding proteins in the control of gene expression

Super-accuracy and super-resolution getting around the diffraction limit

Elongation factor G bound to the ribosome in an intermediate state of translocation

Recognition of the regulatory nascent chain TnaC by the ribosome

The elongation factor 3 unique in higher fungi and essential for protein biosynthesis is an E site factor

The dynamics of SecM-induced translational stalling

Heterogeneous pathways and timing of factor departure during translation initiation

The impact of aminoglycosides on the dynamics of translation elongation

Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance

Translation elongation factor EF-P alleviates ribosome stalling at polyproline stretches

Real-time tRNA transit on single translating ribosomes at codon resolution

Peptide bond formation destabilizes Shine-Dalgarno interaction on the ribosome

Single-molecule imaging of full protein synthesis by immobilized ribosomes

‘Ribozoomin’–translation initiation from the perspective of the ribosome-bound eukaryotic initiation factors (eIFs)

RNA helicase DDX3: at the crossroad of viral replication and antiviral immunity

Locking and unlocking of ribosomal motions

Unidirectional constant rate motion of the ribosomal scanning particle during eukaryotic translation initiation

Molecular mechanism of drug-dependent ribosome stalling

Inhibition of translational initiation in the yeast Saccharomyces cerevisiae as a function of the stability and position of hairpin structures in the mRNA leader

Selective translation of leaderless mRNAs by specialized ribosomes generated by MazF in Escherichia coli

Bacterial polypeptide release factor RF2 is structurally distinct from eukaryotic eRF1

Human eukaryotic initiation factor 4 G (eIF4G) protein binds to eIF3c, -d, and -e to promote mRNA recruitment to the ribosome

Cap-free structure of eIF4E suggests a basis for conformational regulation by its ligands

Stabilization of eukaryotic initiation factor 4E binding to the mRNA 5′-cap by domains of eIF4G

Folding transitions during assembly of the eukaryotic mRNA cap-binding complex

Interaction of eIF4 G with poly(A)-binding protein stimulates translation and is critical for Xenopus oocyte maturation

Yeast eIF4B binds to the head of the 40S ribosomal subunit and promotes mRNA recruitment through its N-terminal and internal repeat domains

Global ribosome motions revealed with elastic network model

A nascent peptide is required for ribosomal bypass of the coding gap in bacteriophage T4 gene 60

The crystal structure of the eukaryotic 40S ribosomal subunit in complex with eIF1 and eIF1A

Insights into translational termination from the structure of RF2 bound to the ribosome

Circularization of mRNA by eukaryotic translation initiation factors

Following translation by single ribosomes one codon at a time

Translational bypassing without peptidyl-tRNA anticodon scanning of coding gap mRNA

The structure and function of the eukaryotic ribosome

Structure of the 30S ribosomal subunit

Nascent peptides that block protein synthesis in bacteria

Specialized ribosomes: a new frontier in gene regulation and organismal biology

Molecular architecture of the ribosome-bound Hepatitis C virus internal ribosomal entry site RNA

Structure of the mammalian 80S initiation complex with initiation factor 5B on HCV-IRES RNA

Requirement of RNA binding of mammalian eukaryotic translation initiation factor 4GI (eIF4GI) for efficient interaction of eIF4E with the mRNA cap

Codon-by-codon modulation of translational speed and accuracy via mRNA folding

DEAD-box proteins unwind duplexes by local strand separation

The DEAD-box protein Ded1 unwinds RNA duplexes by a mode distinct from translocating helicases

Noninvasive measurement of the mechanical force generated by motor protein EF-G during ribosome translocation

Myosin V walks hand-over-hand: single fluorophore imaging with 1·5-nm localization

Polypeptide-chain-elongation rate in Escherichia coli B/r as a function of growth rate

Position of eukaryotic translation initiation factor eIF1A on the 40S ribosomal subunit mapped by directed hydroxyl radical probing

Crystal structure of the ribosome at 5·5 A resolution

The path of messenger RNA through the ribosome

Fidelity at the molecular level: lessons from protein synthesis

eIF5A binds to translational machinery components and affects translation in yeast

A posttermination ribosomal complex is the guanine nucleotide exchange factor for peptide release factor RF3

Peptidyl-tRNA regulates the GTPase activity of translation factors

Release of peptide promoted by the GGQ motif of class 1 release factors regulates the GTPase activity of RF3

Flipping of the ribosomal A-site adenines provides a basis for tRNA selection

Conformational changes in the P site and mRNA entry channel evoked by AUG recognition in yeast translation preinitiation complexes

Structures of the ribosome in intermediate states of ratcheting

Identification and characterization of functionally critical, conserved motifs in the internal repeats and N-terminal domain of yeast translation initiation factor 4B (yeIF4B)

Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation

Termination of translation in eukaryotes is governed by two interacting polypeptide chain release factors, eRF1 and eRF3

A single amino acid substitution in yeast eIF-5A results in mRNA stabilization

Get 20M+ Full-Text Papers For Less Than $1.50/day. Start a 7-Day Trial for You or Your Team.

Learn More →

The molecular choreography of protein synthesis: translational control, regulation, and pathways

The molecular choreography of protein synthesis: translational control, regulation, and pathways

Get 20M+ Full-Text Papers For Less Than $1.50/day. Start a 7-Day Trial for You or Your Team.

Learn More →

The molecular choreography of protein synthesis: translational control, regulation, and pathways

The molecular choreography of protein synthesis: translational control, regulation, and pathways

References

Abstract

Journal

Recommended Articles

References

Our policy towards the use of cookies