Consecutive Ribosomal Incorporation of α-Aminoxy/α-Hydrazino Acids with l/d-Configurations into Nascent Peptide Chains

2021 ◽  
Author(s):  
Takayuki Katoh ◽  
Hiroaki Suga
Keyword(s):  
Nascent Peptide

LATTICE SIMULATION OF NASCENT PEPTIDE FOLDING

2004 ◽  
Vol 18 (15) ◽  
pp. 2195-2202 ◽  
Author(s):  
JIAFENG ZHUO ◽  
LINSEN ZHANG ◽  
CHANGJUN CHEN ◽  
YI HE ◽  
YI XIAO
Keyword(s):  
Lattice Model ◽  
Peptide Folding ◽  
Synthesis Process ◽  
Lattice Simulation ◽  
Native State ◽  
Second Stage ◽  
Nascent Peptide ◽  
Two Stages

The nascent peptide folding in vivo is different from the denatured peptide refolding in vitro and can be divided into two stages. In the first stage, the peptide is folding as it is being synthesized until the whole peptide chain is synthesized. The final conformation formed in this stage is called as nascent state. In the second stage, the protein folds beginning with the nascent state formed in the first stage into the native state. We use a lattice model to simulate these two stages and investigate the folding time of the nascent peptide comparing with that of the denatured peptide refolding. Our results show that the synthesis process may affect the folding time of the nascent peptide. This may be helpful to understand why the former folds faster than the latter.

scholarly journals Trigger Factor Binding to Ribosomes with Nascent Peptide Chains of Varying Lengths and Sequences

2006 ◽  
Vol 281 (38) ◽  
pp. 28033-28038 ◽  
Author(s):  
Amanda Raine ◽  
Martin Lovmar ◽  
Jarl Wikberg ◽  
Måns Ehrenberg
Keyword(s):  
Trigger Factor ◽  
Factor Binding ◽  
Nascent Peptide

scholarly journals Gradual compaction of the nascent peptide during cotranslational folding on the ribosome

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Marija Liutkute ◽  
Manisankar Maiti ◽  
Ekaterina Samatova ◽  
Jörg Enderlein ◽  
Marina V Rodnina
Keyword(s):  
Profile Analysis ◽  
Dynamic Properties ◽  
Correlation Spectroscopy ◽  
Hydrophobic Core ◽  
Fluorescence Correlation ◽  
Nascent Peptide ◽  
Nascent Chain ◽  
Force Profile ◽  
Exit Tunnel ◽  
Domain Stabilization

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.

scholarly journals Gradual Compaction of the Nascent Peptide During Cotranslational Folding on the Ribosome

2020 ◽  
Author(s):  
Marija Liutkute ◽  
Manisankar Maiti ◽  
Ekaterina Samatova ◽  
Jörg Enderlein ◽  
Marina V. Rodnina
Keyword(s):  
Profile Analysis ◽  
Dynamic Properties ◽  
Correlation Spectroscopy ◽  
Fluorescence Correlation ◽  
Cotranslational Folding ◽  
Nascent Peptide ◽  
Nascent Chain ◽  
Force Profile ◽  
Exit Tunnel ◽  
Domain Stabilization

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.

scholarly journals Exploiting translational stalling peptides in an effort to extend azithromycin interaction within the prokaryotic ribosome nascent peptide exit tunnel

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

Nascent Peptide-Induced Signaling from the Exit Tunnel to the Outside of the Ribosome

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

Translation Elongation Arrest Induced by S-Adenosyl-l-Methionine-Sensing Nascent Peptide in Plants

2014 ◽  
pp. 187-201
Author(s):  
Yui Yamashita ◽  
Noriyuki Onoue ◽  
Katsunori Murota ◽  
Hitoshi Onouchi ◽  
Satoshi Naito
Keyword(s):  
Translation Elongation ◽  
Nascent Peptide

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
Keyword(s):  
Peptide Chain ◽  
Nascent Peptide ◽  
Exit Tunnel

Structure of the C-terminal end of the nascent peptide influences translation termination.

1996 ◽  
Vol 15 (7) ◽  
pp. 1696-1704 ◽  
Author(s):  
A. Björnsson ◽  
S. Mottagui-Tabar ◽  
L. A. Isaksson
Keyword(s):  
Translation Termination ◽  
Nascent Peptide
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