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.

3. Proteins

2021 ◽  
pp. 34-51
Author(s):  
Mark Lorch
Keyword(s):  
Amino Acids ◽  
Protein Folding ◽  
Protein Structure ◽  
Protein Structures ◽  
Structure And Function ◽  
Vast Array ◽  
A Cell ◽  
Cellular Machinery ◽  
And Function ◽  
The Relationship

This chapter examines proteins, the dominant proportion of cellular machinery, and the relationship between protein structure and function. The multitude of biological processes needed to keep cells functioning are managed in the organism or cell by a massive cohort of proteins, together known as the proteome. The twenty amino acids that make up the bulk of proteins produce the vast array of protein structures. However, amino acids alone do not provide quite enough chemical variety to complete all of the biochemical activity of a cell, so the chapter also explores post-translation modifications. It finishes by looking as some dynamic aspects of proteins, including enzyme kinetics and the protein folding problem.

A urea channel from Bacillus cereus reveals a novel hexameric structure

2012 ◽  
Vol 445 (2) ◽  
pp. 157-166 ◽  
Author(s):  
Gerard H. M. Huysmans ◽  
Nathan Chan ◽  
Jocelyn M. Baldwin ◽  
Vincent L. G. Postis ◽  
Svetomir B. Tzokov ◽  
...  
Keyword(s):  
Bacillus Cereus ◽  
Structure And Function ◽  
Size Exclusion ◽  
Fluorescent Labelling ◽  
Transmembrane Helices ◽  
Cryo Electron Microscopy ◽  
C Terminus ◽  
Exclusion Chromatography ◽  
Urea Channel ◽  
And Function

Urea is exploited as a nitrogen source by bacteria, and its breakdown products, ammonia and bicarbonate, are employed to counteract stomach acidity in pathogens such as Helicobacter pylori. Uptake in the latter is mediated by UreI, a UAC (urea amide channel) family member. In the present paper, we describe the structure and function of UACBc, a homologue from Bacillus cereus. The purified channel was found to be permeable not only to urea, but also to other small amides. CD and IR spectroscopy revealed a structure comprising mainly α-helices, oriented approximately perpendicular to the membrane. Consistent with this finding, site-directed fluorescent labelling indicated the presence of seven TM (transmembrane) helices, with a cytoplasmic C-terminus. In detergent, UACBc exists largely as a hexamer, as demonstrated by both cross-linking and size-exclusion chromatography. A 9 Å (1 Å=0.1 nm) resolution projection map obtained by cryo-electron microscopy of two-dimensional crystals shows that the six protomers are arranged in a planar hexameric ring. Each exhibits six density features attributable to TM helices, surrounding a putative central channel, while an additional helix is peripherally located. Bioinformatic analyses allowed individual TM regions to be tentatively assigned to the density features, with the resultant model enabling identification of residues likely to contribute to channel function.

scholarly journals The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Renuka Kudva ◽  
Pengfei Tian ◽  
Fátima Pardo-Avila ◽  
Marta Carroni ◽  
Robert B Best ◽  
...  
Keyword(s):  
Protein Folding ◽  
Protein Domain ◽  
Coarse Grained ◽  
E Coli ◽  
Folded Structure ◽  
Bacterial Ribosome ◽  
Folded Proteins ◽  
Exit Tunnel ◽  
Ribosome Exit Tunnel ◽  
Dynamics Simulations

The E. coli ribosome exit tunnel can accommodate small folded proteins, while larger ones fold outside. It remains unclear, however, to what extent the geometry of the tunnel influences protein folding. Here, using E. coli ribosomes with deletions in loops in proteins uL23 and uL24 that protrude into the tunnel, we investigate how tunnel geometry determines where proteins of different sizes fold. We find that a 29-residue zinc-finger domain normally folding close to the uL23 loop folds deeper in the tunnel in uL23 Δloop ribosomes, while two ~ 100 residue proteins normally folding close to the uL24 loop near the tunnel exit port fold at deeper locations in uL24 Δloop ribosomes, in good agreement with results obtained by coarse-grained molecular dynamics simulations. This supports the idea that cotranslational folding commences once a protein domain reaches a location in the exit tunnel where there is sufficient space to house the folded structure.

Native Mass Spectrometry: Recent Progress and Remaining Challenges

2022 ◽  
Vol 51 (1) ◽  
Author(s):  
Kelly R. Karch ◽  
Dalton T. Snyder ◽  
Sophie R. Harvey ◽  
Vicki H. Wysocki
Keyword(s):  
Mass Spectrometry ◽  
Gas Phase ◽  
Structural Biology ◽  
Recent Progress ◽  
Native Mass Spectrometry ◽  
Structure And Function ◽  
Annual Review ◽  
Publication Date ◽  
Analysis Software ◽  
And Function

Native mass spectrometry (nMS) has emerged as an important tool in studying the structure and function of macromolecules and their complexes in the gas phase. In this review, we cover recent advances in nMS and related techniques including sample preparation, instrumentation, activation methods, and data analysis software. These advances have enabled nMS-based techniques to address a variety of challenging questions in structural biology. The second half of this review highlights recent applications of these technologies and surveys the classes of complexes that can be studied with nMS. Complementarity of nMS to existing structural biology techniques and current challenges in nMS are also addressed. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Abstract 291: MANF, a Structurally Unique ER Stress-inducible Protein, Restores ER-protein Folding in ER Stressed Cardiac Myocytes and in the Ischemic Heart

2016 ◽  
Vol 119 (suppl_1) ◽  
Author(s):  
Adrian Arrieta ◽  
Winston T Stauffer ◽  
Amber N Pentoney ◽  
Erik A Blackwood ◽  
Shirin Doroudgar ◽  
...  
Keyword(s):  
Protein Folding ◽  
Stress Response ◽  
Er Stress ◽  
Structure And Function ◽  
Ischemic Heart ◽  
Misfolded Proteins ◽  
Er Stress Response ◽  
Er Chaperone ◽  
And Function

The sarco/endoplasmic reticulum (SR/ER) of cardiomyocytes is a critical site of protein synthesis and folding, as most secreted and membrane proteins including receptors, growth factors, ion channels, and calcium-handling proteins are made at this location. Myocardial ischemia induces ER stress, during which toxic, misfolded proteins accumulate in the SR/ER and contribute to cardiomyocyte death. The branch of the ER stress response mediated by the transcription factor, ATF6, induces ER chaperones that restore SR/ER protein folding. We found that ATF6 also induces mesencephalic astrocyte-derived neurotrophic factor (MANF), a novel, ubiquitously expressed, ER-luminal protein of unknown function. MANF is structurally unique, thus its function cannot be inferred by structural analogy to known proteins. Since it is ATF6-inducible, and resides in the ER lumen, we hypothesized that MANF is an ER chaperone required for optimal viability of cardiac myocytes during ER stresses, including ischemia. The characteristics of MANF gene induction by ER stress, and the effects of MANF knockdown on the ER stress response and cell viability were determined in cultured neonatal rat ventricular myocytes (NRVM). The ability of recombinant MANF to restore structure and function to model misfolded proteins was also examined. Finally, the effects of MANF loss-of-function in the ischemic heart, in vivo , were determined by generating a transgenic mouse model that expresses a cardiomyocyte-specific MANF-targeted microRNA. MANF induction and functional characteristics phenocopied those of a well-studied ER chaperone, glucose-regulated protein 78 (Grp78). Like Grp78, MANF was induced by ER stress in an ATF6-dependent manner. Like knockdown of Grp78, knockdown of MANF in NRVM increased myocyte death in response to ER stress. Like recombinant Grp78, recombinant MANF exhibited a robust ability to restore structure and function to model misfolded proteins, in vitro. Finally, MANF knockdown in the heart, in vivo , increased damage in a mouse model of myocardial infarction. These results suggest that MANF is an SR/ER-resident chaperone required for restoration of SR/ER protein folding during the adaptive ER stress response, and decreasing tissue damage in the ischemic heart.

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