scholarly journals A structural ensemble of a ribosome–nascent chain complex during cotranslational protein folding

2016 ◽  
Vol 23 (4) ◽  
pp. 278-285 ◽  
Author(s):  
Lisa D Cabrita ◽  
Anaïs M E Cassaignau ◽  
Hélène M M Launay ◽  
Christopher A Waudby ◽  
Tomasz Wlodarski ◽  
...  
Keyword(s):  
Protein Folding ◽  
Chain Complex ◽  
Nascent Chain ◽  
Structural Ensemble

scholarly journals Chaperoning ribosome assembly

2010 ◽  
Vol 189 (1) ◽  
pp. 11-12 ◽  
Author(s):  
Katrin Karbstein
Keyword(s):  
Protein Folding ◽  
Ribosome Assembly ◽  
Cell Biol ◽  
Nascent Chain ◽  
Cellular Compartments

Chaperones help proteins fold in all cellular compartments, and many associate directly with ribosomes, capturing nascent chains to assist their folding and prevent aggregation. In this issue, new data from Koplin et al. (2010. J. Cell Biol. doi: 10.1083/jcb.200910074) and Albanèse et al. (2010. J. Cell Biol. doi: 10.1083/jcb.201001054) suggest that in addition to promoting protein folding, the chaperones ribosome-associated complex (RAC), nascent chain–associated complex (NAC), and Jjj1 also help in the assembly of ribosomes.

scholarly journals Early encounters of a nascent membrane protein

2005 ◽  
Vol 170 (1) ◽  
pp. 27-35 ◽  
Author(s):  
Edith N.G. Houben ◽  
Raz Zarivach ◽  
Bauke Oudega ◽  
Joen Luirink
Keyword(s):  
Membrane Protein ◽  
Ribosomal Proteins ◽  
Transmembrane Domain ◽  
Signal Recognition Particle ◽  
Chain Complex ◽  
Signal Recognition ◽  
Inner Membrane ◽  
Ribosomal Tunnel ◽  
Nascent Chain ◽  
Inner Membrane Protein

An unbiased photo–cross-linking approach was used to probe the “molecular path” of a growing nascent Escherichia coli inner membrane protein (IMP) from the peptidyl transferase center to the surface of the ribosome. The nascent chain was initially in proximity to the ribosomal proteins L4 and L22 and subsequently contacted L23, which is indicative of progression through the ribosome via the main ribosomal tunnel. The signal recognition particle (SRP) started to interact with the nascent IMP and to target the ribosome–nascent chain complex to the Sec–YidC complex in the inner membrane when maximally half of the transmembrane domain (TM) was exposed from the ribosomal exit. The combined data suggest a flexible tunnel that may accommodate partially folded nascent proteins and parts of the SRP and SecY. Intraribosomal contacts of the nascent chain were not influenced by the presence of a functional TM in the ribosome.

scholarly journals Ribosome binding induces repositioning of the signal recognition particle receptor on the translocon

2015 ◽  
Vol 211 (1) ◽  
pp. 91-104 ◽  
Author(s):  
Patrick Kuhn ◽  
Albena Draycheva ◽  
Andreas Vogt ◽  
Narcis-Adrian Petriman ◽  
Lukas Sturm ◽  
...  
Keyword(s):  
Protein Targeting ◽  
Signal Recognition Particle ◽  
Resonance Energy Transfer ◽  
Chain Complex ◽  
Resonance Energy ◽  
Endoplasmic Reticulum Membrane ◽  
Signal Recognition ◽  
Ribosomal Tunnel ◽  
Nascent Chain

Cotranslational protein targeting delivers proteins to the bacterial cytoplasmic membrane or to the eukaryotic endoplasmic reticulum membrane. The signal recognition particle (SRP) binds to signal sequences emerging from the ribosomal tunnel and targets the ribosome-nascent-chain complex (RNC) to the SRP receptor, termed FtsY in bacteria. FtsY interacts with the fifth cytosolic loop of SecY in the SecYEG translocon, but the functional role of the interaction is unclear. By using photo-cross-linking and fluorescence resonance energy transfer measurements, we show that FtsY–SecY complex formation is guanosine triphosphate independent but requires a phospholipid environment. Binding of an SRP–RNC complex exposing a hydrophobic transmembrane segment induces a rearrangement of the SecY–FtsY complex, which allows the subsequent contact between SecY and ribosomal protein uL23. These results suggest that direct RNC transfer to the translocon is guided by the interaction between SRP and translocon-bound FtsY in a quaternary targeting complex.

scholarly journals Emerging role of long noncoding RNA-encoded micropeptides in cancer

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Mujie Ye ◽  
Jingjing Zhang ◽  
Meng Wei ◽  
Baihui Liu ◽  
Kuiran Dong
Keyword(s):  
Noncoding Rna ◽  
Cancer Metabolism ◽  
Chain Complex ◽  
Ribosome Profiling ◽  
Open Reading Frames ◽  
Clinical Value ◽  
Anti Cancer ◽  
Nascent Chain ◽  
Reading Frames

Abstract Increasing evidence has indicated that long noncoding RNAs (lncRNAs) play various important roles in the development of cancers. The widespread applications of ribosome profiling and ribosome nascent chain complex sequencing revealed that some short open reading frames of lncRNAs have micropeptide-coding potential. The resulting micropeptides have been shown to participate in N6-methyladenosine modification, tumor angiogenesis, cancer metabolism, and signal transduction. This review summarizes current information regarding the reported roles of lncRNA-encoded micropeptides in cancer, and explores the potential clinical value of these micropeptides in the development of anti-cancer drugs and prognostic tumor biomarkers.

scholarly journals The ribosome and its role in protein folding: looking through a magnifying glass

2017 ◽  
Vol 73 (6) ◽  
pp. 509-521 ◽  
Author(s):  
Abid Javed ◽  
John Christodoulou ◽  
Lisa D. Cabrita ◽  
Elena V. Orlova
Keyword(s):  
Protein Folding ◽  
Structural Biology ◽  
Polypeptide Chain ◽  
Structure And Function ◽  
Cellular Activity ◽  
Cryo Electron Microscopy ◽  
Nascent Chain ◽  
Exit Tunnel ◽  
Dynamics Simulations ◽  
And Function

Protein folding, a process that underpins cellular activity, begins co-translationally on the ribosome. During translation, a newly synthesized polypeptide chain enters the ribosomal exit tunnel and actively interacts with the ribosome elements – the r-proteins and rRNA that line the tunnel – prior to emerging into the cellular milieu. While understanding of the structure and function of the ribosome has advanced significantly, little is known about the process of folding of the emerging nascent chain (NC). Advances in cryo-electron microscopy are enabling visualization of NCs within the exit tunnel, allowing early glimpses of the interplay between the NC and the ribosome. Once it has emerged from the exit tunnel into the cytosol, the NC (still attached to its parent ribosome) can acquire a range of conformations, which can be characterized by NMR spectroscopy. Using experimental restraints within molecular-dynamics simulations, the ensemble of NC structures can be described. In order to delineate the process of co-translational protein folding, a hybrid structural biology approach is foreseeable, potentially offering a complete atomic description of protein folding as it occurs on the ribosome.

scholarly journals Insights Into Translatomics in the Nervous System

2020 ◽  
Vol 11 ◽  
Author(s):  
Shuxia Zhang ◽  
Yeru Chen ◽  
Yongjie Wang ◽  
Piao Zhang ◽  
Gang Chen ◽  
...  
Keyword(s):  
Nervous System ◽  
Fragile X ◽  
Neurological Diseases ◽  
Chain Complex ◽  
Proteomic Profiling ◽  
Translation Process ◽  
Protein Levels ◽  
Proteomics Approach ◽  
Nascent Chain ◽  
Translational Process

Most neurological disorders are caused by abnormal gene translation. Generally, dysregulation of elements involved in the translational process disrupts homeostasis in neurons and neuroglia. Better understanding of how the gene translation process occurs requires detailed analysis of transcriptomic and proteomic profile data. However, a lack of strictly direct correlations between mRNA and protein levels limits translational investigation by combining transcriptomic and proteomic profiling. The much better correlation between proteins and translated mRNAs than total mRNAs in abundance and insufficiently sensitive proteomics approach promote the requirement of advances in translatomics technology. Translatomics which capture and sequence the mRNAs associated with ribosomes has been effective in identifying translational changes by genetics or projections, ribosome stalling, local translation, and transcript isoforms in the nervous system. Here, we place emphasis on the main three translatomics methods currently used to profile mRNAs attached to ribosome-nascent chain complex (RNC-mRNA). Their prominent applications in neurological diseases including glioma, neuropathic pain, depression, fragile X syndrome (FXS), neurodegenerative disorders are outlined. The content reviewed here expands our understanding on the contributions of aberrant translation to neurological disease development.

scholarly journals Optimal design of adaptively sampled NMR experiments for measurement of methyl group dynamics with application to a ribosome-nascent chain complex

2020 ◽  
Author(s):  
Christopher A. Waudby ◽  
Charles Burridge ◽  
John Christodoulou
Keyword(s):  
Optimal Design ◽  
Group Dynamics ◽  
Adaptive Sampling ◽  
Design Theory ◽  
Pulse Sequence ◽  
Chemical Exchange ◽  
Rotational Diffusion ◽  
Chain Complex ◽  
Chain Complexes ◽  
Nascent Chain

AbstractNMR measurements of cross-correlated nuclear spin relaxation provide powerful probes of polypeptide dynamics and rotational diffusion, free from contributions due to chemical exchange or interactions with external spins. Here, we report on the development of a sensitivity-optimized pulse sequence for the measurement of cross-correlated relaxation in methyl spin systems by analysis of the differential relaxation of transitions within the 13C multiplet. We describe the application of optimal design theory to implement a real-time ‘on-the-fly’ adaptive sampling scheme that maximizes the accuracy of the measured rate constants. The increase in sensitivity obtained using this approach enables, for the first time, quantitative measurements of rotational diffusion within folded states of translationally-arrested ribosome–nascent chain complexes of the FLN5 filamin domain, and can be used to place strong limits on interactions between the domain and the ribosome surface.

scholarly journals Nascent Chain Biology: Translation Dynamics and Cotranslational Protein Folding

2019 ◽  
Vol 59 (3) ◽  
pp. 137-140
Author(s):  
Hideki TAGUCHI ◽  
Yuhei CHADANI ◽  
Tatsuya NIWA
Keyword(s):  
Protein Folding ◽  
Nascent Chain
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