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.

Basic information

Original name

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

Authors

UHRIK, Lukas, Tomas HENEK, Joan PLANAS IGLESIAS (724 Spain, belonging to the institution), Josef KUCERA, Jiří DAMBORSKÝ (203 Czech Republic, belonging to the institution), Martin MAREK (203 Czech Republic, belonging to the institution) and Lenka HERNYCHOVA

Edition

New York, Advanced Methods in Structural Biology, p. 293-318, 26 pp. 1. 2023

Publisher

Springer Nature

Other information

Language

English

Type of outcome

Kapitola resp. kapitoly v odborné knize

Field of Study

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

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

printed version "print"

References:

URL

RIV identification code

RIV/00216224:14310/23:00133541

Organization unit

Faculty of Science

ISBN

978-1-0716-3146-1

DOI

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

Keywords in English

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

Abstract

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.

Links

GA22-09853S, research and development project

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

Investor: Czech Science Foundation

LX22NPO5102, research and development project

Name: Národní ústav pro výzkum rakoviny (Acronym: NÚVR)

Investor: Ministry of Education, Youth and Sports of the CR, National institute for cancer research, 5.1 EXCELES

Citovat

UHRIK, Lukas, Tomas HENEK, Joan PLANAS IGLESIAS, Josef KUCERA, Jiří DAMBORSKÝ, Martin MAREK and 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, p. 293-318. 1. ISBN 978-1-0716-3146-1. Available from: 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 and 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, p.~293-318. 1. ISBN~978-1-0716-3146-1. Available from: https://dx.doi.org/10.1007/978-1-0716-3147-8\_{}18.

Detailed Information on Publication Record