scholarly journals Studying the Nascent Peptide Chain in the Ribosomal Exit Tunnel

2018 ◽  
Vol 114 (3) ◽  
pp. 595a
Author(s):  
Nadin Haase ◽  
Wolf Holtkamp ◽  
Reinhard Lipowsky ◽  
Marina Rodnina ◽  
Sophia Rudorf
2011 ◽  
Vol 286 (17) ◽  
pp. 14903-14912 ◽  
Author(s):  
Noriyuki Onoue ◽  
Yui Yamashita ◽  
Nobuhiro Nagao ◽  
Derek B. Goto ◽  
Hitoshi Onouchi ◽  
...  

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Marija Liutkute ◽  
Manisankar Maiti ◽  
Ekaterina Samatova ◽  
Jörg Enderlein ◽  
Marina V Rodnina

Nascent polypeptides begin to fold in the constrained space of the ribosomal peptide exit tunnel. Here we use force-profile analysis (FPA) and photo-induced energy-transfer fluorescence correlation spectroscopy (PET-FCS) to show how a small α-helical domain, the N-terminal domain of HemK, folds cotranslationally. Compaction starts vectorially as soon as the first α-helical segments are synthesized. As nascent chain grows, emerging helical segments dock onto each other and continue to rearrange at the vicinity of the ribosome. Inside or in the proximity of the ribosome, the nascent peptide undergoes structural fluctuations on the µs time scale. The fluctuations slow down as the domain moves away from the ribosome. Mutations that destabilize the packing of the domain’s hydrophobic core have little effect on folding within the exit tunnel, but abolish the final domain stabilization. The results show the power of FPA and PET-FCS in solving the trajectory of cotranslational protein folding and in characterizing the dynamic properties of folding intermediates.


2020 ◽  
Author(s):  
Marija Liutkute ◽  
Manisankar Maiti ◽  
Ekaterina Samatova ◽  
Jörg Enderlein ◽  
Marina V. Rodnina

ABSTRACTNascent polypeptides begin to fold in the constrained space of the ribosomal peptide exit tunnel. Here we use force profile analysis (FPA) and photo-induced energy-transfer fluorescence correlation spectroscopy (PET-FCS) to show how a small α-helical domain, the N-terminal domain of HemK, folds cotranslationally. Compaction starts vectorially as soon as the first α-helical segments are synthesized. As nascent chain grows, emerging helical segments dock onto each other and continue to rearrange at the vicinity of the ribosome. Inside or in the proximity of the ribosome, the nascent peptide undergoes structural fluctuations on the μs time scale. The fluctuations slow down as the domain moves away from the ribosome. Folding mutations have little effect on folding within the exit tunnel, but abolish the final domain stabilization. The results show the power of FPA and PET-FCS in solving the trajectory of cotranslational protein folding and in characterizing the dynamic properties of folding intermediates.


2015 ◽  
Vol 23 (16) ◽  
pp. 5198-5209 ◽  
Author(s):  
Arren Z. Washington ◽  
Subhasish Tapadar ◽  
Alex George ◽  
Adegboyega K. Oyelere
Keyword(s):  

2014 ◽  
pp. 87-97
Author(s):  
Thomas Bornemann ◽  
Wolf Holtkamp ◽  
Wolfgang Wintermeyer
Keyword(s):  

2019 ◽  
Vol 48 (4) ◽  
pp. 1985-1999 ◽  
Author(s):  
Seidai Takamatsu ◽  
Yubun Ohashi ◽  
Noriyuki Onoue ◽  
Yoko Tajima ◽  
Tomoya Imamichi ◽  
...  

Abstract A number of regulatory nascent peptides have been shown to regulate gene expression by causing programmed ribosome stalling during translation. Nascent peptide emerges from the ribosome through the exit tunnel, and one-third of the way along which β-loop structures of ribosomal proteins uL4 and uL22 protrude into the tunnel to form the constriction region. Structural studies have shown interactions between nascent peptides and the exit tunnel components including the constriction region. In eukaryotes, however, there is a lack of genetic studies for the involvement of the constriction region in ribosome stalling. Here, we established transgenic Arabidopsis lines that carry mutations in the β-loop structure of uL4. Translation analyses using a cell-free translation system derived from the transgenic Arabidopsis carrying the mutant ribosome showed that the uL4 mutations reduced the ribosome stalling of four eukaryotic stalling systems, including those for which stalled structures have been solved. Our data, which showed differential effects of the uL4 mutations depending on the stalling systems, explained the spatial allocations of the nascent peptides at the constriction that were deduced by structural studies. Conversely, our data may predict allocation of the nascent peptide at the constriction of stalling systems for which structural studies are not done.


2013 ◽  
Vol 42 (2) ◽  
pp. 1245-1256 ◽  
Author(s):  
A. K. Martinez ◽  
E. Gordon ◽  
A. Sengupta ◽  
N. Shirole ◽  
D. Klepacki ◽  
...  

2017 ◽  
Vol 429 (12) ◽  
pp. 1873-1888 ◽  
Author(s):  
Pengse Po ◽  
Erin Delaney ◽  
Howard Gamper ◽  
D. Miklos Szantai-Kis ◽  
Lee Speight ◽  
...  

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Haruka Tsutsumi ◽  
Tomohiro Kuroda ◽  
Hiroyuki Kimura ◽  
Yuki Goto ◽  
Hiroaki Suga

AbstractAzoles are five-membered heterocycles often found in the backbones of peptidic natural products and synthetic peptidomimetics. Here, we report a method of ribosomal synthesis of azole-containing peptides involving specific ribosomal incorporation of a bromovinylglycine derivative into the nascent peptide chain and its chemoselective conversion to a unique azole structure. The chemoselective conversion was achieved by posttranslational dehydrobromination of the bromovinyl group and isomerization in aqueous media under fairly mild conditions. This method enables us to install exotic azole groups, oxazole and thiazole, at designated positions in the peptide chain with both linear and macrocyclic scaffolds and thereby expand the repertoire of building blocks in the mRNA-templated synthesis of designer peptides.


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