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

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 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.

The VES KM: a pathway for protein folding in vivo

2020 ◽  
Vol 92 (1) ◽  
pp. 179-191
Author(s):  
Leonor Cruzeiro
Keyword(s):  
Amino Acids ◽  
Protein Folding ◽  
Protein Structures ◽  
Kinetic Mechanism ◽  
Thermal Bath ◽  
Charged Amino Acids ◽  
Nascent Chain ◽  
Dynamics Simulations ◽  
Positively Charged

AbstractWhile according to the thermodynamic hypothesis, protein folding reproducibility is ensured by the assumption that the native state corresponds to the minimum of the free energy in normal cellular conditions, here, the VES kinetic mechanism for folding in vivo is described according to which the nascent chain of all proteins is helical and the first and structure defining step in the folding pathway is the bending of that initial helix around a particular amino acid site. Molecular dynamics simulations are presented which indicate both the viability of this mechanism for folding and its limitations in the presence of a Markovian thermal bath. An analysis of a set of protein structures formed only of helices and loops suggests that bending sites are correlated with regions bounded, on the N-side, by positively charged amino acids like Lysine and Histidine and on the C-side by negatively charged amino acids like Aspartic acid.

scholarly journals Statistical Evidence for a Helical Nascent Chain

Biomolecules ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 357
Author(s):  
Leonor Cruzeiro ◽  
Andrew C. Gill ◽  
J. Chris Eilbeck
Keyword(s):  
Amino Acids ◽  
Protein Folding ◽  
Amino Acid ◽  
Secondary Structures ◽  
Initial Structure ◽  
The Novel ◽  
Nascent Chain ◽  
Equilibrium Process ◽  
Β Sheets ◽  
Α Helix

We investigate the hypothesis that protein folding is a kinetic, non-equilibrium process, in which the structure of the nascent chain is crucial. We compare actual amino acid frequencies in loops, α-helices and β-sheets with the frequencies that would arise in the absence of any amino acid bias for those secondary structures. The novel analysis suggests that while specific amino acids exist to drive the formation of loops and sheets, none stand out as drivers for α-helices. This favours the idea that the α-helix is the initial structure of most proteins before the folding process begins.

scholarly journals Co-Translational Protein Folding and Sorting in Chloroplasts

Plants ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 214 ◽  
Author(s):  
Fabian Ries ◽  
Claudia Herkt ◽  
Felix Willmund
Keyword(s):  
Protein Folding ◽  
Protein Synthesis ◽  
Carbon Fixation ◽  
Current Knowledge ◽  
Protein Coding ◽  
Light Reaction ◽  
Fast Kinetics ◽  
Final Maturation ◽  
Nascent Chain ◽  
Early Processing

Cells depend on the continuous renewal of their proteome composition during the cell cycle and in order to replace aberrant proteins or to react to changing environmental conditions. In higher eukaryotes, protein synthesis is achieved by up to five million ribosomes per cell. With the fast kinetics of translation, the large number of newly made proteins generates a substantial burden for protein homeostasis and requires a highly orchestrated cascade of factors promoting folding, sorting and final maturation. Several of the involved factors directly bind to translating ribosomes for the early processing of emerging nascent polypeptides and the translocation of ribosome nascent chain complexes to target membranes. In plant cells, protein synthesis also occurs in chloroplasts serving the expression of a relatively small set of 60–100 protein-coding genes. However, most of these proteins, together with nucleus-derived subunits, form central complexes majorly involved in the essential processes of photosynthetic light reaction, carbon fixation, metabolism and gene expression. Biogenesis of these heterogenic complexes adds an additional level of complexity for protein biogenesis. In this review, we summarize the current knowledge about co-translationally binding factors in chloroplasts and discuss their role in protein folding and ribosome translocation to thylakoid membranes.

scholarly journals Signal Sequences Encode Information for Protein Folding in the Endoplasmic Reticulum

2020 ◽  
Author(s):  
Sha Sun ◽  
Xia Li ◽  
Malaiyalam Mariappan
Keyword(s):  
Endoplasmic Reticulum ◽  
Protein Folding ◽  
Protein Translocation ◽  
Signal Sequence ◽  
Signal Sequences ◽  
Sequence Dependent ◽  
Proteomic Approach ◽  
Multiple Protein ◽  
Nascent Chain ◽  
In Cells

SummaryRoughly one-third of newly synthesized proteins enter into the endoplasmic reticulum (ER) via the Sec61 translocon. It is unclear how nascent chains bind correct chaperones and properly fold upon entering the ER lumen. We find that signal sequences harbor information to recruit specific chaperones for protein folding in the ER. Using a substrate-trapping proteomic approach, we identify that marginally hydrophobic signal sequences are transiently clogged at the Sec61 translocon, which recruits BiP chaperone through Sec63 to bind onto nascent chains. Surprisingly, this privileged BiP binding not only releases clogged nascent chains into the ER lumen but also prevent inappropriate interactions and promotes folding and maturation. Signal sequence swapping bypasses BiP-dependent unclogging and translocation, but the translocated nascent chain is terminally misfolded after binding the wrong chaperone in the ER lumen. Thus, signal sequence-dependent chaperone recruitment explains why signal sequences are paradoxically diverse and use multiple protein translocation pathways in cells.

scholarly journals Effects of protein size, thermodynamic stability, and net charge on cotranslational folding on the ribosome

2018 ◽  
Author(s):  
José Arcadio Farías-Rico ◽  
Frida Ruud Selin ◽  
Ioanna Myronidi ◽  
Marie Frühauf ◽  
Gunnar von Heijne
Keyword(s):  
Protein Folding ◽  
Thermodynamic Stability ◽  
Protein Size ◽  
Ribosomal Protein S6 ◽  
Complex Process ◽  
Cotranslational Folding ◽  
Nascent Chain ◽  
Comprehensive Picture ◽  
Pulse Proteolysis ◽  
Net Charges

AbstractDuring the last five decades, studies of protein folding in dilute buffer solutions have produced a rich picture of this complex process. In the cell, however, proteins can start to fold while still attached to the ribosome (cotranslational folding) and it is not yet clear how the ribosome affects the folding of protein domains of different sizes, thermodynamic stabilities, and net charges. Here, by using arrest peptides as force sensors and on-ribosome pulse proteolysis, we provide a comprehensive picture of how the distance from the peptidyl transferase center in the ribosome at which proteins fold correlates with protein size. Moreover, an analysis of a large collection of mutants of theE. coliribosomal protein S6 shows that the force exerted on the nascent chain by protein folding varies linearly with the thermodynamic stability of the folded state, and that the ribosome environment disfavors folding of domains of high net-negative charge.

scholarly journals The Driving Force for Co-translational Protein Folding is Weaker In the Ribosome Vestibule due to Greater Water Ordering

2021 ◽  
Author(s):  
Quyen V Vu ◽  
Yang Jiang ◽  
Mai Suan Li ◽  
Edward O'Brien
Keyword(s):  
Protein Folding ◽  
Driving Force ◽  
Nascent Chain ◽  
Tertiary Folding ◽  
Exit Tunnel

Interactions between the ribosome and nascent chain can destabilize folded domains in the ribosome exit tunnel’s vestibule, the last 3 nm of the exit tunnel where tertiary folding can occur....

scholarly journals On the Effect of the Ribosome and Trigger Factor on Nascent Chain Protein Folding

2011 ◽  
Vol 100 (3) ◽  
pp. 17a
Author(s):  
Edward P. O'Brien ◽  
John Christodoulou ◽  
Christopher Dobson ◽  
Michele Vendruscolo
Keyword(s):  
Protein Folding ◽  
Trigger Factor ◽  
Nascent Chain

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
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