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.

Základní údaje

Originální název

Exploration of Protein Unfolding by Modelling Calorimetry Data from Reheating

Autoři

MAZURENKO, Stanislav (643 Rusko, domácí), Antonín KUNKA (203 Česká republika, domácí), Koen BEERENS (56 Belgie, domácí), Christopher M. JOHNSON (826 Velká Británie a Severní Irsko), Jiří DAMBORSKÝ (203 Česká republika, garant, domácí) a Zbyněk PROKOP (203 Česká republika, domácí)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10700 1.7 Other natural sciences

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 4.122

Kód RIV

RIV/00216224:14310/17:00095387

Organizační jednotka

Přírodovědecká fakulta

DOI

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

UT WoS

000416137700009

Klíčová slova anglicky

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

Štítky

NZ, rivok

Změněno: 3. 4. 2018 15:36, Ing. Nicole Zrilić

Anotace

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.

Návaznosti

ED2.1.00/19.0382, projekt VaV

Název: CETOCOEN UPgrade

EE2.3.30.0037, projekt VaV

Název: Zaměstnáním nejlepších mladých vědců k rozvoji mezinárodní spolupráce

GA16-07965S, projekt VaV

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

Investor: Grantová agentura ČR, Řízená evoluce dynamických elementů v enzymech s využitím mikrofluidních čipů

LM2015051, projekt VaV

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

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Výzkumná infrastruktura RECETOX

LM2015055, projekt VaV

Název: Centrum pro systémovou biologii (Akronym: C4SYS)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, The national infrastructure C4SYS - Centre for Systems Biology

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

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

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