Study of Protein Conformational Dynamics Using
Hydrogen/Deuterium Exchange Mass Spectrometry

C 2023

Study of Protein Conformational Dynamics Using Hydrogen/Deuterium Exchange Mass Spectrometry

UHRIK, Lukas, Tomas HENEK, Joan PLANAS IGLESIAS, Josef KUCERA, Jiří DAMBORSKÝ et. al.

Základní údaje

Originální název

Study of Protein Conformational Dynamics Using Hydrogen/Deuterium Exchange Mass Spectrometry

Autoři

UHRIK, Lukas, Tomas HENEK, Joan PLANAS IGLESIAS (724 Španělsko, domácí), Josef KUCERA, Jiří DAMBORSKÝ (203 Česká republika, domácí), Martin MAREK (203 Česká republika, domácí) a Lenka HERNYCHOVA

Vydání

New York, Advanced Methods in Structural Biology, od s. 293-318, 26 s. 1. 2023

Nakladatel

Springer Nature

Další údaje

Jazyk

angličtina

Typ výsledku

Kapitola resp. kapitoly v odborné knize

Obor

30403 Technologies involving identifying the functioning of DNA, proteins and enzymes and how they influence the onset of disease and maintenance of well-being

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Forma vydání

tištěná verze "print"

Odkazy

URL

Kód RIV

RIV/00216224:14310/23:00133541

Organizační jednotka

Přírodovědecká fakulta

ISBN

978-1-0716-3146-1

DOI

http://dx.doi.org/10.1007/978-1-0716-3147-8_18

Klíčová slova anglicky

Ancestral luciferase; Hydrogen/deuterium exchange; LoopGrafter; Mass spectrometry; Protein dynamics; Protein engineering

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 15. 2. 2024 14:48, Mgr. Marie Šípková, DiS.

Anotace

V originále

Intrinsic protein dynamics contribute to their biological functions. Rational engineering of protein dynamics is extremely challenging with only a handful of successful examples. Hydrogen/deuterium exchange coupled to mass spectrometry (HDX-MS) represents a powerful technique for quantitative analysis of protein dynamics. Here we provide a detailed description of the preparation of protein samples, collection of high-quality data, and their in-depth analysis using various computational tools. We illustrate the application of HDX-MS for the study of protein dynamics in the rational engineering of flexible loops in the reconstructed ancestor of haloalkane dehalogenase and Renilla luciferase. These experiments provided unique and valuable data rigorously describing the modification of protein dynamics upon grafting of the loop-helix element. Tips and tricks are provided to stimulate the wider use of HDX-MS to study and engineer protein dynamics.

Návaznosti

GA22-09853S, projekt VaV

Název: Analýza vzniku nových proteinových funkcí v rámci rodiny halogenalkan dehalogenas

Investor: Grantová agentura ČR, Analýza vzniku nových proteinových funkcí v rámci rodiny halogenalkan dehalogenas

LX22NPO5102, projekt VaV

Název: Národní ústav pro výzkum rakoviny (Akronym: NÚVR)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Národní ústav pro výzkum rakoviny, 5.1 EXCELES

Citovat

UHRIK, Lukas, Tomas HENEK, Joan PLANAS IGLESIAS, Josef KUCERA, Jiří DAMBORSKÝ, Martin MAREK a Lenka HERNYCHOVA. Study of Protein Conformational Dynamics Using Hydrogen/Deuterium Exchange Mass Spectrometry. In Ângela Sousa, Luis Passarinha. Advanced Methods in Structural Biology. New York: Springer Nature, 2023, s. 293-318. 1. ISBN 978-1-0716-3146-1. Dostupné z: https://dx.doi.org/10.1007/978-1-0716-3147-8_18.

@inbook{2374292,
   author = {Uhrik, Lukas and Henek, Tomas and Planas Iglesias, Joan and Kucera, Josef and Damborský, Jiří and Marek, Martin and Hernychova, Lenka},
   address = {New York},
   booktitle = {Advanced Methods in Structural Biology},
   doi = {http://dx.doi.org/10.1007/978-1-0716-3147-8_18},
   editor = {Ângela Sousa, Luis Passarinha},
   keywords = {Ancestral luciferase; Hydrogen/deuterium exchange; LoopGrafter; Mass spectrometry; Protein dynamics; Protein engineering},
   howpublished = {tištěná verze "print"},
   language = {eng},
   location = {New York},
   isbn = {978-1-0716-3146-1},
   pages = {293-318},
   publisher = {Springer Nature},
   title = {Study of Protein Conformational Dynamics Using Hydrogen/Deuterium Exchange Mass Spectrometry},
   url = {https://link.springer.com/protocol/10.1007/978-1-0716-3147-8_18},
   year = {2023}
}

TY  - CHAP
ID  - 2374292
AU  - Uhrik, Lukas - Henek, Tomas - Planas Iglesias, Joan - Kucera, Josef - Damborský, Jiří - Marek, Martin - Hernychova, Lenka
PY  - 2023
TI  - Study of Protein Conformational Dynamics Using Hydrogen/Deuterium Exchange Mass Spectrometry
VL  - 1.
PB  - Springer Nature
CY  - New York
SN  - 9781071631461
KW  - Ancestral luciferase
KW  - Hydrogen/deuterium exchange
KW  - LoopGrafter
KW  - Mass spectrometry
KW  - Protein dynamics
KW  - Protein engineering
UR  - https://link.springer.com/protocol/10.1007/978-1-0716-3147-8_18
N2  - Intrinsic protein dynamics contribute to their biological functions. Rational engineering of protein dynamics is extremely challenging with only a handful of successful examples. Hydrogen/deuterium exchange coupled to mass spectrometry (HDX-MS) represents a powerful technique for quantitative analysis of protein dynamics. Here we provide a detailed description of the preparation of protein samples, collection of high-quality data, and their in-depth analysis using various computational tools. We illustrate the application of HDX-MS for the study of protein dynamics in the rational engineering of flexible loops in the reconstructed ancestor of haloalkane dehalogenase and Renilla luciferase. These experiments provided unique and valuable data rigorously describing the modification of protein dynamics upon grafting of the loop-helix element. Tips and tricks are provided to stimulate the wider use of HDX-MS to study and engineer protein dynamics.
ER  -

UHRIK, Lukas, Tomas HENEK, Joan PLANAS IGLESIAS, Josef KUCERA, Jiří DAMBORSKÝ, Martin MAREK a Lenka HERNYCHOVA. Study of Protein Conformational Dynamics Using Hydrogen/Deuterium Exchange Mass Spectrometry. In \^Angela Sousa, Luis Passarinha. \textit{Advanced Methods in Structural Biology}. New York: Springer Nature, 2023, s.~293-318. 1. ISBN~978-1-0716-3146-1. Dostupné z: https://dx.doi.org/10.1007/978-1-0716-3147-8\_{}18.

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