title: Retro operation on the Trp-cage miniprotein sequence produces an unstructured molecule capable of folding similar to the original only upon 2,2,2-trifluoroethanol addition.
abstract: Amino acid sequence and environment are the most important factors determining the structure, stability and dynamics of proteins. To evaluate their roles in the process of folding, we studied a retroversion of the well-described Trp-cage miniprotein in water and 2,2,2-trifluoroethanol (TFE) solution. We show, by circular dichroism spectroscopy and nuclear magnetic resonance (NMR) measurement, that the molecule has no stable structure under conditions in which the Trp-cage is folded. A detectable stable structure of the retro Trp-cage, with the architecture similar to that of the original Trp-cage, is established only upon addition of TFE to 30% of the total solvent volume. The retro Trp-cage structure shows a completely different pattern of stabilizing contacts between amino acid residues, involving the guanidinium group of arginine and the aromatic group of tryptophan. The commonly used online prediction methods for protein and peptide structures Robetta and PEP-FOLD failed to predict that the retro Trp-cage is unstructured under default prediction conditions. On the other hand, both methods provided structures with a fold similar to those of the experimentally determined NMR structure in water/TFE but with different contacts between amino acids.
authors.affiliation: Academy of Sciences of the Czech Republic, Center for Biomolecules and Complex Molecular Systems, Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 16610 Prague 6, Czech Republic.
authors.forename: Jiří
authors.initials: J
authors.lastname: Vymětal
authors.affiliation: National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic CEITEC, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
authors.forename: Sreenivas Reddy
authors.initials: SR
authors.lastname: Bathula
authors.affiliation: Institute of Biotechnology, Academy of Sciences of the Czech Republic, Videnska 1043, 142 20 Prague 4, Czech Republic.
authors.forename: Jiří
authors.initials: J
authors.lastname: Cerný
authors.affiliation: Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.
authors.forename: Radka
authors.initials: R
authors.lastname: Chaloupková
authors.affiliation: National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic CEITEC, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
authors.forename: Lukáš
authors.initials: L
authors.lastname: Zídek
authors.affiliation: National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic CEITEC, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
authors.forename: Vladimír
authors.initials: V
authors.lastname: Sklenář
authors.affiliation: Academy of Sciences of the Czech Republic, Center for Biomolecules and Complex Molecular Systems, Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 16610 Prague 6, Czech Republic jiri.vondrasek@uochb.cas.cz.
authors.forename: Jiří
authors.initials: J
authors.lastname: Vondrášek
mesh_terms: D000595:Amino Acid Sequence; D001120:Arginine / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D010455:Peptides / Q000138:chemical synthesis / Q000737:chemistry*; D017510:Protein Folding; D055550:Protein Stability; D017433:Protein Structure, Secondary; D055672:Static Electricity; D013816:Thermodynamics; D014270:Trifluoroethanol / Q000737:chemistry*; D014364:Tryptophan / Q000737:chemistry*; D014867:Water / Q000737:chemistry
chemical_list: D010455:Peptides; C508725:Trp-cage peptide; D014867:Water; D014270:Trifluoroethanol; D014364:Tryptophan; D001120:Arginine
keywords: CD spectroscopy; NMR methods; molecular dynamics; protein folding; protein-structure prediction