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

J 2014

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

VYMETAL, Jiří, Sreenivas Reddy BATHULA, Jiří ČERNÝ, Radka CHALOUPKOVÁ, Lukáš ŽÍDEK et. al.

Základní údaje

Originální název

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

Autoři

VYMETAL, Jiří (203 Česká republika), Sreenivas Reddy BATHULA (356 Indie, domácí), Jiří ČERNÝ (203 Česká republika), Radka CHALOUPKOVÁ (203 Česká republika, domácí), Lukáš ŽÍDEK (203 Česká republika, garant, domácí), Vladimír SKLENÁŘ (203 Česká republika, domácí) a Jiří VONDRÁŠEK (203 Česká republika)

Vydání

PROTEIN ENGINEERING DESIGN & SELECTION, OXFORD, OXFORD UNIV PRESS, 2014, 1741-0126

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 2.537

Kód RIV

RIV/00216224:14740/14:00074482

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1093/protein/gzu046

UT WoS

000345837300001

Klíčová slova anglicky

protein folding; protein-structure prediction; molecular dynamics; NMR methods; CD spectroscopy

Štítky

kontrola MP, MP, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 3. 4. 2015 07:03, prof. Mgr. Lukáš Žídek, Ph.D.

Anotace

V originále

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.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

GA203/08/0114, projekt VaV

Název: Specifické iontové efekty pro proteiny v roztocích a podobné biologicky relevantní systémy.

Investor: Grantová agentura ČR, Specifické iontové efekty pro proteiny v roztocích a podobné biologicky relevantní systémy

LO1214, projekt VaV

Název: Centrum pro výzkum toxických látek v prostředí (Akronym: RECETOX)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Centrum pro výzkum toxických látek v prostředí

Citovat

VYMETAL, Jiří, Sreenivas Reddy BATHULA, Jiří ČERNÝ, Radka CHALOUPKOVÁ, Lukáš ŽÍDEK, Vladimír SKLENÁŘ a Jiří VONDRÁŠEK. 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. PROTEIN ENGINEERING DESIGN & SELECTION. OXFORD: OXFORD UNIV PRESS, 2014, roč. 27, č. 12, s. 463-472. ISSN 1741-0126. Dostupné z: https://dx.doi.org/10.1093/protein/gzu046.

@article{1231793,
   author = {Vymetal, Jiří and Bathula, Sreenivas Reddy and Černý, Jiří and Chaloupková, Radka and Žídek, Lukáš and Sklenář, Vladimír and Vondrášek, Jiří},
   article_location = {OXFORD},
   article_number = {12},
   doi = {http://dx.doi.org/10.1093/protein/gzu046},
   keywords = {protein folding; protein-structure prediction; molecular dynamics; NMR methods; CD spectroscopy},
   language = {eng},
   issn = {1741-0126},
   journal = {PROTEIN ENGINEERING DESIGN & SELECTION},
   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},
   url = {http://peds.oxfordjournals.org/content/27/12/463.full.pdf+html},
   volume = {27},
   year = {2014}
}

TY  - JOUR
ID  - 1231793
AU  - Vymetal, Jiří - Bathula, Sreenivas Reddy - Černý, Jiří - Chaloupková, Radka - Žídek, Lukáš - Sklenář, Vladimír - Vondrášek, Jiří
PY  - 2014
TI  - 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
JF  - PROTEIN ENGINEERING DESIGN & SELECTION
VL  - 27
IS  - 12
SP  - 463-472
EP  - 463-472
PB  - OXFORD UNIV PRESS
SN  - 17410126
KW  - protein folding
KW  - protein-structure prediction
KW  - molecular dynamics
KW  - NMR methods
KW  - CD spectroscopy
UR  - http://peds.oxfordjournals.org/content/27/12/463.full.pdf+html
L2  - http://peds.oxfordjournals.org/content/27/12/463.full.pdf+html
N2  - 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.
ER  -

VYMETAL, Jiří, Sreenivas Reddy BATHULA, Jiří ČERNÝ, Radka CHALOUPKOVÁ, Lukáš ŽÍDEK, Vladimír SKLENÁŘ a Jiří VONDRÁŠEK. 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. \textit{PROTEIN ENGINEERING DESIGN \&{}amp; SELECTION}. OXFORD: OXFORD UNIV PRESS, 2014, roč.~27, č.~12, s.~463-472. ISSN~1741-0126. Dostupné z: https://dx.doi.org/10.1093/protein/gzu046.

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