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.

Basic information

Original name

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

Authors

VYMETAL, Jiří (203 Czech Republic), Sreenivas Reddy BATHULA (356 India, belonging to the institution), Jiří ČERNÝ (203 Czech Republic), Radka CHALOUPKOVÁ (203 Czech Republic, belonging to the institution), Lukáš ŽÍDEK (203 Czech Republic, guarantor, belonging to the institution), Vladimír SKLENÁŘ (203 Czech Republic, belonging to the institution) and Jiří VONDRÁŠEK (203 Czech Republic)

Edition

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

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 2.537

RIV identification code

RIV/00216224:14740/14:00074482

Organization unit

Central European Institute of Technology

DOI

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

UT WoS

000345837300001

Keywords in English

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

Abstract

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.

Links

ED1.1.00/02.0068, research and development project

Name: CEITEC - central european institute of technology

GA203/08/0114, research and development project

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

Investor: Czech Science Foundation, Specific ion effects for proteins in solutions and related biologically relevant systems

LO1214, research and development project

Name: Centrum pro výzkum toxických látek v prostředí (Acronym: RECETOX)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

VYMETAL, Jiří, Sreenivas Reddy BATHULA, Jiří ČERNÝ, Radka CHALOUPKOVÁ, Lukáš ŽÍDEK, Vladimír SKLENÁŘ and 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, vol. 27, No 12, p. 463-472. ISSN 1741-0126. Available from: 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 and 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, vol.~27, No~12, p.~463-472. ISSN~1741-0126. Available from: https://dx.doi.org/10.1093/protein/gzu046.

Detailed Information on Publication Record