scholarly journals An intrinsically disordered nascent protein interacts with specific regions of the ribosomal surface near the exit tunnel

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Valeria Guzman-Luna ◽  
Andrew M. Fuchs ◽  
Anna J. Allen ◽  
Alexios Staikos ◽  
Silvia Cavagnero
Keyword(s):  
Ribosomal Proteins ◽  
Ribosomal Subunit ◽  
Intrinsically Disordered Protein ◽  
Protein Chain ◽  
Net Charge ◽  
Weakly Interact ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Exit Tunnel

AbstractThe influence of the ribosome on nascent chains is poorly understood, especially in the case of proteins devoid of signal or arrest sequences. Here, we provide explicit evidence for the interaction of specific ribosomal proteins with ribosome-bound nascent chains (RNCs). We target RNCs pertaining to the intrinsically disordered protein PIR and a number of mutants bearing a variable net charge. All the constructs analyzed in this work lack N-terminal signal sequences. By a combination chemical crosslinking and Western-blotting, we find that all RNCs interact with ribosomal protein L23 and that longer nascent chains also weakly interact with L29. The interacting proteins are spatially clustered on a specific region of the large ribosomal subunit, close to the exit tunnel. Based on chain-length-dependence and mutational studies, we find that the interactions with L23 persist despite drastic variations in RNC sequence. Importantly, we also find that the interactions are highly Mg+2-concentration-dependent. This work is significant because it unravels a novel role of the ribosome, which is shown to engage with the nascent protein chain even in the absence of signal or arrest sequences.

scholarly journals The Ambivalent Role of Proline Residues in an Intrinsically Disordered Protein: From Disorder Promoters to Compaction Facilitators

2020 ◽  
Vol 432 (9) ◽  
pp. 3093-3111 ◽  
Author(s):  
Borja Mateos ◽  
Clara Conrad-Billroth ◽  
Marco Schiavina ◽  
Andreas Beier ◽  
Georg Kontaxis ◽  
...  
Keyword(s):  
Intrinsically Disordered Protein ◽  
Intrinsically Disordered ◽  
Disordered Protein

scholarly journals Characterization of AMBN I and II Isoforms and Study of Their Ca2+-Binding Properties

2020 ◽  
Vol 21 (23) ◽  
pp. 9293
Author(s):  
Veronika Vetyskova ◽  
Monika Zouharova ◽  
Lucie Bednarova ◽  
Ondřej Vaněk ◽  
Petra Sázelová ◽  
...  
Keyword(s):  
Intrinsically Disordered Protein ◽  
Significant Feature ◽  
Amino Acid Residues ◽  
Binding Properties ◽  
Specific Sequence ◽  
Intrinsically Disordered ◽  
Disordered Protein

Ameloblastin (Ambn) as an intrinsically disordered protein (IDP) stands for an important role in the formation of enamel—the hardest biomineralized tissue commonly formed in vertebrates. The human ameloblastin (AMBN) is expressed in two isoforms: full-length isoform I (AMBN ISO I) and isoform II (AMBN ISO II), which is about 15 amino acid residues shorter than AMBN ISO I. The significant feature of AMBN—its oligomerization ability—is enabled due to a specific sequence encoded by exon 5 present at the N-terminal part in both known isoforms. In this study, we characterized AMBN ISO I and AMBN ISO II by biochemical and biophysical methods to determine their common features and differences. We confirmed that both AMBN ISO I and AMBN ISO II form oligomers in in vitro conditions. Due to an important role of AMBN in biomineralization, we further addressed the calcium (Ca2+)-binding properties of AMBN ISO I and ISO II. The binding properties of AMBN to Ca2+ may explain the role of AMBN in biomineralization and more generally in Ca2+ homeostasis processes.

scholarly journals Rapid Identification of Secondary Structure and Binding Site Residues in an Intrinsically Disordered Protein Segment

2021 ◽  
Vol 12 ◽  
Author(s):  
Soumyanetra Chandra ◽  
Gopinath Chattopadhyay ◽  
Raghavan Varadarajan
Keyword(s):  
Intrinsically Disordered Protein ◽  
Rapid Identification ◽  
Relative Reduction ◽  
Toxin Binding ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Yeast Surface ◽  
Binding Residues ◽  
Endoribonuclease Activity

Mycobacterium tuberculosis harbours nine toxin-antitoxin (TA) systems of the MazEF family. MazEF TA modules are of immense importance due to the perceived role of the MazF toxin in M. tuberculosis persistence and disease. The MazE antitoxin has a disordered C-terminal domain that binds the toxin, MazF and neutralizes its endoribonuclease activity. However, the structure of most MazEF TA complexes remains unsolved till date, obscuring structural and functional information about the antitoxins. We present a facile method to identify toxin binding residues on the disordered antitoxin. Charged residue scanning mutagenesis was used to screen a yeast surface displayed MazE6 antitoxin library against its purified cognate partner, the MazF6 toxin. Binding residues were deciphered by probing the relative reduction in binding to the ligand by flow cytometry. We have used this to identify putative antitoxin interface residues and local structure attained by the antitoxin upon interaction in the MazEF6 TA system and the same methodology is readily applicable to other intrinsically disordered protein regions.

Self-Assembling Micelles Based on an Intrinsically Disordered Protein Domain

2018 ◽  
Author(s):  
Sarah Klass ◽  
Matthew J. Smith ◽  
Tahoe Fiala ◽  
Jessica Lee ◽  
Anthony Omole ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Fusion Proteins ◽  
Organic Molecules ◽  
Intrinsically Disordered Protein ◽  
Protein Domain ◽  
Enzymatic Cleavage ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Self Assembling ◽  
Protein Tag

Herein, we describe a new series of fusion proteins that have been developed to self-assemble spontaneously into stable micelles that are 27 nm in diameter after enzymatic cleavage of a solubilizing protein tag. The sequences of the proteins are based on a human intrinsically disordered protein, which has been appended with a hydrophobic segment. The micelles were found to form across a broad range of pH, ionic strength, and temperature conditions, with critical micelle concentration (CMC) values below 1 µM being observed in some cases. The reported micelles were found to solubilize hydrophobic metal complexes and organic molecules, suggesting their potential suitability for catalysis and drug delivery applications.

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