@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 {2017|2039,
	title = {A Computational Methodology to Overcome the Challenges Associated With the Search for Specific Enzyme Targets to Develop Drugs Against.},
	journal = {Bioinform Biol Insights},
	volume = {11},
	year = {2017},
	month = {2017},
	pages = {1177932217712471},
	abstract = {<p>We present an approach for detecting enzymes that are specific ofcompared withand provide targets that may assist research in drug development. This approach is based on traditional techniques of sequence homology comparison by similarity search and Markov modeling; it integrates the characterization of enzymatic functionality, secondary and tertiary protein structures, protein domain architecture, and metabolic environment. From 67 enzymes represented by 42 enzymatic activities classified by AnEnPi (Analogous Enzymes Pipeline) as specific forcompared with, only 40 (23 Enzyme Commission [EC] numbers) could actually be considered as strictly specific ofand 27 enzymes (19 EC numbers) were disregarded for having ambiguous homologies or analogies with. Among the 40 strictly specific enzymes, we identified sterol 24-C-methyltransferase, pyruvate phosphate dikinase, trypanothione synthetase, and RNA-editing ligase as 4 essential enzymes forthat may serve as targets for drug development.</p>
},
	issn = {1177-9322},
	doi = {10.1177/1177932217712471},
	author = {Catharina, Larissa and Lima, Carlyle Ribeiro and Franca, Alexander and Guimar{\~a}es, Ana Carolina Ramos and Alves-Ferreira, Marcelo and Tuffery, Pierre and Philippe Derreumaux and Carels, Nicolas}
}
@article {2016|1711,
	title = {In silico structural characterization of protein targets for drug development against Trypanosoma cruzi},
	journal = {J. Mol. Model.},
	volume = {22},
	number = {10},
	year = {2016},
	month = {oct},
	abstract = {Trypanosoma cruzi is the protozoan pathogen responsible for Chagas disease, which is a major public health problem in tropical and subtropical regions of developing countries and particularly in Brazil. Despite many studies, there is no efficient treatment against Chagas disease, and the search for new therapeutic targets specific to T. cruzi is critical for drug development. Here, we have revisited 41 protein sequences proposed by the analogous enzyme pipeline, and found that it is possible to provide structures for T. cruzi sequences with clear homologs or analogs in H. sapiens and likely associated with trypanothione reductase, cysteine synthase, and ATPase functions, and structures for sequences specific to T. cruzi and absent in H. sapiens associated with 2,4-dienoyl-CoA reductase, and leishmanolysin activities. The implications of our structures refined by atomistic molecular dynamics (monomer or dimer states) in their in vitro environments (aqueous solution or membrane bilayers) are discussed for drug development and suggest that all protein targets, except cysteine synthase, merit further investigation.},
	issn = {1610-2940},
	doi = {10.1007/s00894-016-3115-9},
	author = {Lima, Carlyle Ribeiro and Carels, Nicolas and Ramos Guimaraes, Ana Carolina and Pierre Tuffery and Philippe Derreumaux}
}
@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 {2014|1893,
	title = {Improved PEP-FOLD Approach for Peptide and Miniprotein Structure Prediction},
	journal = {J. Chem. Theory Comput.},
	volume = {10},
	number = {10},
	year = {2014},
	month = {oct},
	pages = {4745{\textendash}4758},
	doi = {10.1021/ct500592m},
	author = {Shen, Yimin and Maupetit, Julien and Philippe Derreumaux and Pierre Tuffery}
}
@article {2014|1798,
	title = {The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems},
	journal = {Chem. Soc. Rev.},
	volume = {43},
	number = {13},
	year = {2014},
	pages = {4871{\textendash}4893},
	doi = {10.1039/c4cs00048j},
	author = {F. Sterpone and S. Melchionna and Pierre Tuffery and S. Pasquali and N. Mousseau and T. Cragnolini and Y Chebaro and J.-F. St-Pierre and M. Kalimeri and A. Barducci and Y. Laurin and A. Tek and Marc Baaden and Phuong Hoang Nguyen and Philippe Derreumaux}
}
@article {2012|1911,
	title = {Delivering the native structures of peptides from computer simulations and predicted NMR proton chemical shifts},
	journal = {J. Pept. Sci.},
	volume = {18},
	number = {1},
	year = {2012},
	month = {sep},
	pages = {S38},
	author = {Thevenet, P. and Shen, Y. and Maupetit, J. and Guyon, F. and Padilla, A. and Philippe Derreumaux and Pierre Tuffery}
}
@article {2012|1932,
	title = {Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches},
	journal = {Journal of the Royal Society Interface},
	volume = {9},
	number = {66},
	year = {2012},
	month = {jan},
	pages = {20{\textendash}33},
	doi = {10.1098/rsif.2011.0584},
	author = {Pierre Tuffery and Philippe Derreumaux}
}
@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 {2010|1901,
	title = {A Fast Method for Large-Scale De Novo Peptide and Miniprotein Structure Prediction},
	journal = {J. Comput. Chem.},
	volume = {31},
	number = {4},
	year = {2010},
	month = {mar},
	pages = {726{\textendash}738},
	doi = {10.1002/jcc.21365},
	author = {Maupetit, Julien and Philippe Derreumaux and Pierre Tuffery}
}
@article {2009|1436,
	title = {A fast method for large-scale De Novo peptide and miniprotein structure prediction.},
	journal = {J. Comput. Chem.},
	year = {2009},
	month = {jun},
	doi = {10.1002/jcc.21365},
	author = {Julien Maupetit 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}
}
@article {2007|1985,
	title = {A coarse-grained protein force field for folding and structure prediction},
	journal = {Proteins: Struct., Funct., Bioinf.},
	volume = {69},
	number = {2},
	year = {2007},
	month = {nov},
	pages = {394{\textendash}408},
	doi = {10.1002/prot.21505},
	author = {Maupetit, Julien and Pierre Tuffery and Philippe Derreumaux}
}
@article {2005|1979,
	title = {Dependency between consecutive local conformations helps assemble protein structures from secondary structures using Go potential and greedy algorithm},
	journal = {Proteins: Struct., Funct., Bioinf.},
	volume = {61},
	number = {4},
	year = {2005},
	month = {dec},
	pages = {732{\textendash}740},
	doi = {10.1002/prot.20698},
	author = {Pierre Tuffery and Philippe Derreumaux}
}
@article {2005|1900,
	title = {Improved greedy algorithm for protein structure reconstruction},
	journal = {J. Comput. Chem.},
	volume = {26},
	number = {5},
	year = {2005},
	month = {apr},
	pages = {506{\textendash}513},
	doi = {10.1002/jcc.20181},
	author = {Pierre Tuffery and Guyon, F and Philippe Derreumaux}
}
