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Statements

Subject Item
n2:RIV%2F61388963%3A_____%2F14%3A00438291%21RIV15-GA0-61388963
rdf:type
n13:Vysledek skos:Concept
dcterms:description
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. 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.
dcterms: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 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
skos:prefLabel
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 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
skos:notation
RIV/61388963:_____/14:00438291!RIV15-GA0-61388963
n3:aktivita
n10:I n10:P
n3:aktivity
I, P(GA203/08/0114), P(LH11020)
n3:cisloPeriodika
12
n3:dodaniDat
n12:2015
n3:domaciTvurceVysledku
n11:1136933 n11:7358946
n3:druhVysledku
n16:J
n3:duvernostUdaju
n7:S
n3:entitaPredkladatele
n14:predkladatel
n3:idSjednocenehoVysledku
42564
n3:idVysledku
RIV/61388963:_____/14:00438291
n3:jazykVysledku
n17:eng
n3:klicovaSlova
protein folding; protein-structure prediction; molecular dynamics; NMR methods; CD spectroscopy
n3:klicoveSlovo
n5:protein%20folding n5:protein-structure%20prediction n5:CD%20spectroscopy n5:molecular%20dynamics n5:NMR%20methods
n3:kodStatuVydavatele
GB - Spojené království Velké Británie a Severního Irska
n3:kontrolniKodProRIV
[ADD5949489FA]
n3:nazevZdroje
Protein Engineering Design and Selection
n3:obor
n18:CE
n3:pocetDomacichTvurcuVysledku
2
n3:pocetTvurcuVysledku
7
n3:projekt
n8:LH11020 n8:GA203%2F08%2F0114
n3:rokUplatneniVysledku
n12:2014
n3:svazekPeriodika
27
n3:tvurceVysledku
Vymětal, Jiří Žídek, L. Sklenář, V. Černý, Jiří Chaloupková, R. Vondrášek, Jiří Bathula, S. R.
n3:wos
000345837300001
s:issn
1741-0126
s:numberOfPages
10
n4:doi
10.1093/protein/gzu046