@article {2018|2129,
	title = {Probing the quality control mechanism of the  twin-arginine translocase with folding variants of a -designed heme protein.},
	journal = {J Biol Chem},
	volume = {293},
	year = {2018},
	month = {2018 05 04},
	pages = {6672-6681},
	abstract = {<p>Protein transport across the cytoplasmic membrane of bacterial cells is mediated by either the general secretion (Sec) system or the twin-arginine translocase (Tat). The Tat machinery exports folded and cofactor-containing proteins from the cytoplasm to the periplasm by using the transmembrane proton motive force as a source of energy. The Tat apparatus apparently senses the folded state of its protein substrates, a quality-control mechanism that prevents premature export of nascent unfolded or misfolded polypeptides, but its mechanistic basis has not yet been determined. Here, we investigated the innate ability of the model Tat system to recognize and translocate -designed protein substrates with experimentally determined differences in the extent of folding. Water-soluble, four-helix bundle maquette proteins were engineered to bind two, one, or no heme cofactors, resulting in a concomitant reduction in the extent of their folding, assessed with temperature-dependent CD spectroscopy and one-dimensional H NMR spectroscopy. Fusion of the archetypal N-terminal Tat signal peptide of the trimethylamine--oxide (TMAO) reductase (TorA) to the N terminus of the protein maquettes was sufficient for the Tat system to recognize them as substrates. The clear correlation between the level of Tat-dependent export and the degree of heme -induced folding of the maquette protein suggested that the membrane-bound Tat machinery can sense the extent of folding and conformational flexibility of its substrates. We propose that these artificial proteins are ideal substrates for future investigations of the Tat system\&$\#$39;s quality-control mechanism.</p>
},
	keywords = {Amino Acid Sequence, Bacterial Proteins, Circular Dichroism, Escherichia coli, Escherichia coli Proteins, Heme-Binding Proteins, Hemeproteins, Membrane Transport Proteins, Methylamines, Models, Molecular, Oxidoreductases, N-Demethylating, Periplasm, Protein Folding, Protein Sorting Signals, Protein Stability, Protein Transport, Proton Magnetic Resonance Spectroscopy, Substrate Specificity, Temperature},
	issn = {1083-351X},
	doi = {10.1074/jbc.RA117.000880},
	author = {Sutherland, George A and Grayson, Katie J and Adams, Nathan B P and Mermans, Daphne M J and Jones, Alexander S and Robertson, Angus J and Auman, Dirk B and Brindley, Amanda A and Sterpone, Fabio and Tuffery, Pierre and Philippe Derreumaux and Dutton, P Leslie and Robinson, Colin and Hitchcock, Andrew and Hunter, C Neil}
}
@article {2016|1733,
	title = {PEP-FOLD3: faster denovo structure prediction for linear peptides in solution and in complex},
	journal = {Nucleic Acids Res.},
	volume = {44},
	number = {W1},
	year = {2016},
	pages = {W449-W454},
	abstract = {Structure determination of linear peptides of 5-50 amino acids in aqueous solution and interacting with proteins is a key aspect in structural biology. PEP-FOLD3 is a novel computational framework, that allows both (i) de novo free or biased prediction for linear peptides between 5 and 50 amino acids, and (ii) the generation of native-like conformations of peptides interacting with a protein when the interaction site is known in advance. PEP-FOLD3 is fast, and usually returns solutions in a few minutes. Testing PEP-FOLD3 on 56 peptides in aqueous solution led to experimental-like conformations for 80\% of the targets. Using a benchmark of 61 peptide-protein targets starting from the unbound form of the protein receptor, PEP-FOLD3 was able to generate peptide poses deviating on average by 3.3 angstrom from the experimental conformation and return a native-like pose in the first 10 clusters for 52\% of the targets. PEP-FOLD3 is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD3.},
	issn = {0305-1048},
	doi = {10.1093/nar/gkw329},
	author = {Lamiable, Alexis and Thevenet, Pierre and Rey, Julien and Vavrusa, Marek and Philippe Derreumaux and Pierre Tuffery}
}
@article {2012|1944,
	title = {PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides},
	journal = {Nucleic Acids Res.},
	volume = {40},
	number = {W1},
	year = {2012},
	month = {jul},
	pages = {W288-W293},
	doi = {10.1093/nar/gks419},
	author = {Thevenet, Pierre and Shen, Yimin and Maupetit, Julien and Guyon, Frederic and Philippe Derreumaux and Pierre Tuffery}
}
@article {2009|1734,
	title = {PEP-FOLD: an online resource for de novo peptide structure prediction},
	journal = {Nucleic Acids Res.},
	volume = {37},
	year = {2009},
	month = {jul},
	pages = {W498-W503},
	doi = {10.1093/nar/gkp323},
	author = {Maupetit, Julien and Philippe Derreumaux and Pierre Tuffery}
}
@article {2009|1942,
	title = {PEP-FOLD: an online resource for de novo peptide structure prediction.},
	journal = {Nucleic Acids Res.},
	volume = {37},
	number = {Web Server issue},
	year = {2009},
	month = {jul},
	pages = {W498{\textendash}W503},
	keywords = {Algorithms, Internet, Models, Molecular, Peptides, Protein, Protein Conformation, Reproducibility of Results, Sequence Analysis, Software, User-Computer Interface},
	doi = {10.1093/nar/gkp323},
	author = {Julien Maupetit and Philippe Derreumaux and Pierre Tuffery}
}
