Exploration of Protein Unfolding by Modelling Calorimetry Data
from Reheating

J 2017

Exploration of Protein Unfolding by Modelling Calorimetry Data from Reheating

MAZURENKO, Stanislav, Antonín KUNKA, Koen BEERENS, Christopher M. JOHNSON, Jiří DAMBORSKÝ et. al.

Basic information

Original name

Exploration of Protein Unfolding by Modelling Calorimetry Data from Reheating

Authors

MAZURENKO, Stanislav (643 Russian Federation, belonging to the institution), Antonín KUNKA (203 Czech Republic, belonging to the institution), Koen BEERENS (56 Belgium, belonging to the institution), Christopher M. JOHNSON (826 United Kingdom of Great Britain and Northern Ireland), Jiří DAMBORSKÝ (203 Czech Republic, guarantor, belonging to the institution) and Zbyněk PROKOP (203 Czech Republic, belonging to the institution)

Edition

Scientific Reports, London, NATURE PUBLISHING GROUP, 2017, 2045-2322

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10700 1.7 Other natural 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: 4.122

RIV identification code

RIV/00216224:14310/17:00095387

Organization unit

Faculty of Science

DOI

http://dx.doi.org/10.1038/s41598-017-16360-y

UT WoS

000416137700009

Keywords in English

DIFFERENTIAL SCANNING CALORIMETRY; THERMAL-DENATURATION; THEORETICAL-ANALYSIS; AGGREGATION; STABILITY; LYSOZYME; STABILIZATION; SPECTROSCOPY; TRANSITIONS; PROFILES

Abstract

V originále

Studies of protein unfolding mechanisms are critical for understanding protein functions inside cells, de novo protein design as well as defining the role of protein misfolding in neurodegenerative disorders. Calorimetry has proven indispensable in this regard for recording full energetic profiles of protein unfolding and permitting data fitting based on unfolding pathway models. While both kinetic and thermodynamic protein stability are analysed by varying scan rates and reheating, the latter is rarely used in curve-fitting, leading to a significant loss of information from experiments. To extract this information, we propose fitting both first and second scans simultaneously. Four most common single-peak transition models are considered: (i) fully reversible, (ii) fully irreversible, (iii) partially reversible transitions, and (iv) general three-state models. The method is validated using calorimetry data for chicken egg lysozyme, mutated Protein A, three wild-types of haloalkane dehalogenases, and a mutant stabilized by protein engineering. We show that modelling of reheating increases the precision of determination of unfolding mechanisms, free energies, temperatures, and heat capacity differences. Moreover, this modelling indicates whether alternative refolding pathways might occur upon cooling. The Matlab-based data fitting software tool and its user guide are provided as a supplement.

Links

ED2.1.00/19.0382, research and development project

Name: CETOCOEN UPgrade

EE2.3.30.0037, research and development project

Name: Zaměstnáním nejlepších mladých vědců k rozvoji mezinárodní spolupráce

GA16-07965S, research and development project

Name: Řízená evoluce dynamických elementů v enzymech s využitím mikrofluidních čipů

Investor: Czech Science Foundation

LM2015051, research and development project

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

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

LM2015055, research and development project

Name: Centrum pro systémovou biologii (Acronym: C4SYS)

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

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

MAZURENKO, Stanislav, Antonín KUNKA, Koen BEERENS, Christopher M. JOHNSON, Jiří DAMBORSKÝ and Zbyněk PROKOP. Exploration of Protein Unfolding by Modelling Calorimetry Data from Reheating. Scientific Reports. London: NATURE PUBLISHING GROUP, 2017, vol. 7, November, p. nestránkováno, 14 pp. ISSN 2045-2322. Available from: https://dx.doi.org/10.1038/s41598-017-16360-y.

@article{1403068,
   author = {Mazurenko, Stanislav and Kunka, Antonín and Beerens, Koen and Johnson, Christopher M. and Damborský, Jiří and Prokop, Zbyněk},
   article_location = {London},
   article_number = {November},
   doi = {http://dx.doi.org/10.1038/s41598-017-16360-y},
   keywords = {DIFFERENTIAL SCANNING CALORIMETRY; THERMAL-DENATURATION; THEORETICAL-ANALYSIS; AGGREGATION; STABILITY; LYSOZYME; STABILIZATION; SPECTROSCOPY; TRANSITIONS; PROFILES},
   language = {eng},
   issn = {2045-2322},
   journal = {Scientific Reports},
   title = {Exploration of Protein Unfolding by Modelling Calorimetry Data from Reheating},
   url = {https://loschmidt.chemi.muni.cz/peg/publications/exploration-of-protein-unfolding-by-modelling-calorimetry-data-from-reheating/},
   volume = {7},
   year = {2017}
}

TY  - JOUR
ID  - 1403068
AU  - Mazurenko, Stanislav - Kunka, Antonín - Beerens, Koen - Johnson, Christopher M. - Damborský, Jiří - Prokop, Zbyněk
PY  - 2017
TI  - Exploration of Protein Unfolding by Modelling Calorimetry Data from Reheating
JF  - Scientific Reports
VL  - 7
IS  - November
SP  - nestránkováno
EP  - nestránkováno
PB  - NATURE PUBLISHING GROUP
SN  - 20452322
KW  - DIFFERENTIAL SCANNING CALORIMETRY
KW  - THERMAL-DENATURATION
KW  - THEORETICAL-ANALYSIS
KW  - AGGREGATION
KW  - STABILITY
KW  - LYSOZYME
KW  - STABILIZATION
KW  - SPECTROSCOPY
KW  - TRANSITIONS
KW  - PROFILES
UR  - https://loschmidt.chemi.muni.cz/peg/publications/exploration-of-protein-unfolding-by-modelling-calorimetry-data-from-reheating/
N2  - Studies of protein unfolding mechanisms are critical for understanding protein functions inside cells, de novo protein design as well as defining the role of protein misfolding in neurodegenerative disorders. Calorimetry has proven indispensable in this regard for recording full energetic profiles of protein unfolding and permitting data fitting based on unfolding pathway models. While both kinetic and thermodynamic protein stability are analysed by varying scan rates and reheating, the latter is rarely used in curve-fitting, leading to a significant loss of information from experiments. To extract this information, we propose fitting both first and second scans simultaneously. Four most common single-peak transition models are considered: (i) fully reversible, (ii) fully irreversible, (iii) partially reversible transitions, and (iv) general three-state models. The method is validated using calorimetry data for chicken egg lysozyme, mutated Protein A, three wild-types of haloalkane dehalogenases, and a mutant stabilized by protein engineering. We show that modelling of reheating increases the precision of determination of unfolding mechanisms, free energies, temperatures, and heat capacity differences. Moreover, this modelling indicates whether alternative refolding pathways might occur upon cooling. The Matlab-based data fitting software tool and its user guide are provided as a supplement.
ER  -

MAZURENKO, Stanislav, Antonín KUNKA, Koen BEERENS, Christopher M. JOHNSON, Jiří DAMBORSKÝ and Zbyněk PROKOP. Exploration of Protein Unfolding by Modelling Calorimetry Data from Reheating. \textit{Scientific Reports}. London: NATURE PUBLISHING GROUP, 2017, vol.~7, November, p.~nestránkováno, 14 pp. ISSN~2045-2322. Available from: https://dx.doi.org/10.1038/s41598-017-16360-y.

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