Detailed insight into dynamics of intrinsically disordered
proteins using high-resolution relaxometry

k 2023

Detailed insight into dynamics of intrinsically disordered proteins using high-resolution relaxometry

ZAPLETAL, Vojtěch, Nicola SALVI, Andrea FLAMM, Zuzana JASEŇÁKOVÁ, Dennis KURZBACH et. al.

Basic information

Original name

Detailed insight into dynamics of intrinsically disordered proteins using high-resolution relaxometry

Authors

ZAPLETAL, Vojtěch, Nicola SALVI, Andrea FLAMM, Zuzana JASEŇÁKOVÁ, Dennis KURZBACH, Mateos BORJA, Milan ZACHRDLA, Petr PADRTA, Subhash NARASIMHAN, Thorsten MARQUARDSEN, Jean-Max TYBURN, Jozef HRITZ, Robert KONRAT, Lukáš ŽÍDEK, Martin BLACKLEDGE, Fabien FERRAGE and Pavel KADEŘÁVEK

Edition

2023

Other information

Language

English

Type of outcome

Prezentace na konferencích

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

Slovakia

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Organization unit

Central European Institute of Technology

Keywords in English

NMR; protein dynamics

Abstract

V originále

Dynamics are known to be very important for proteins allowing them to fulfill their function in the living organisms as was documented by multiple examples of globular proteins. The dynamics and conformational plasticity appear to be even more critical for intrinsically disordered proteins (IDPs), allowing them to adopt various conformations, to bind multiple ligand targets, and to play their typical roles in signaling pathways and regulations of cellular molecular machinery. Nuclear magnetic resonance (NMR) was recognized to be a unique experimental method capable of providing a detailed description of dynamics of biomolecules with atomic resolution at various timescales. The internal dynamics in the range of picoseconds and nanoseconds is most typical for IDPs and can be studied by analysing NMR relaxation rates. However, such studies are usually limited by the number of magnetic fields at which the relaxation rates can be collected. Especially the relaxation rates at low magnetic fields (below 9.4 T) are often not accessible for biomolecules because a higher magnetic field is required to reach a sufficient resolution and sensitivity necessary for studies of biomolecules including IDPs. Unfortunately, the data at low magnetic fields holds a majority of information about motions slower than a few nanoseconds related to important segmental motions of IDPs. High-resolution relaxometry was suggested to overcome this problem. The sample is transferred very rapidly between positions of the stray field with different magnetic fields and the high-field magnetic center, granting a possibility to detect at high magnetic fields necessary for high resolution and sensitivity, and to record relaxation rates at a low magnetic field within a single NMR experiment. Here, we present two case studies where such an approach has been successfully applied to IDPs. First, the delta subunit of RNA polymerase from Bacillus subtilis represents a challenging system of a protein containing both structured and disordered domain. Its disordered domain contains a highly repetitive sequence which makes the analysis very challenging, yet the analysis provides a detailed insight into its dynamics. Second, we studied the internal dynamics of osteopontin and we described the effects of heparin binding to osteopontin on its internal motions.

Links

EF18_070/0009846, research and development project

Name: MSCAfellow2@MUNI

GJ18-04197Y, research and development project

Name: Charakterizace flexibilních oblastí RNA polymerázy Bacillus subtilis

Investor: Czech Science Foundation

LM2018127, research and development project

Name: Česká infrastruktura pro integrativní strukturní biologii (Acronym: CIISB)

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

Citovat

@proceedings{2386900,
   author = {Zapletal, Vojtěch and Salvi, Nicola and Flamm, Andrea and Jaseňáková, Zuzana and Kurzbach, Dennis and Borja, Mateos and Zachrdla, Milan and Padrta, Petr and Narasimhan, Subhash and Marquardsen, Thorsten and Tyburn, JeanandMax and Hritz, Jozef and Konrat, Robert and Žídek, Lukáš and Blackledge, Martin and Ferrage, Fabien and Kadeřávek, Pavel},
   keywords = {NMR; protein dynamics},
   language = {eng},
   title = {Detailed insight into dynamics of intrinsically disordered proteins using high-resolution relaxometry},
   url = {https://ml4ngp.eu/conference-bratislava/},
   year = {2023}
}

TY  - CONF
ID  - 2386900
AU  - Zapletal, Vojtěch - Salvi, Nicola - Flamm, Andrea - Jaseňáková, Zuzana - Kurzbach, Dennis - Borja, Mateos - Zachrdla, Milan - Padrta, Petr - Narasimhan, Subhash - Marquardsen, Thorsten - Tyburn, Jean-Max - Hritz, Jozef - Konrat, Robert - Žídek, Lukáš - Blackledge, Martin - Ferrage, Fabien - Kadeřávek, Pavel
PY  - 2023
TI  - Detailed insight into dynamics of intrinsically disordered proteins using high-resolution relaxometry
KW  - NMR
KW  - protein dynamics
UR  - https://ml4ngp.eu/conference-bratislava/
N2  - Dynamics are known to be very important for proteins allowing them to fulfill their function in the living organisms as was documented by multiple examples of globular proteins. The dynamics and conformational plasticity appear to be even more critical for intrinsically disordered proteins (IDPs), allowing them to adopt various conformations, to bind multiple ligand targets, and to play their typical roles in signaling pathways and regulations of cellular molecular machinery. Nuclear magnetic resonance (NMR) was recognized to be a unique experimental method capable of providing a detailed description of dynamics of biomolecules with atomic resolution at various timescales. The internal dynamics in the range of picoseconds and nanoseconds is most typical for IDPs and can be studied by analysing NMR relaxation rates. However, such studies are usually limited by the number of magnetic fields at which the relaxation rates can be collected. Especially the relaxation rates at low magnetic fields (below 9.4 T) are often not accessible for biomolecules because a higher magnetic field is required to reach a sufficient resolution and sensitivity necessary for studies of biomolecules including IDPs. Unfortunately, the data at low magnetic fields holds a majority of information about motions slower than a few nanoseconds related to important segmental motions of IDPs. High-resolution relaxometry was suggested to overcome this problem. The sample is transferred very rapidly between positions of the stray field with different magnetic fields and the high-field magnetic center, granting a possibility to detect at high magnetic fields necessary for high resolution and sensitivity, and to record relaxation rates at a low magnetic field within a single NMR experiment. Here, we present two case studies where such an approach has been successfully applied to IDPs. First, the delta subunit of RNA polymerase from Bacillus subtilis represents a challenging system of a protein containing both structured and disordered domain. Its disordered domain contains a highly repetitive sequence which makes the analysis very challenging, yet the analysis provides a detailed insight into its dynamics. Second, we studied the internal dynamics of osteopontin and we described the effects of heparin binding to osteopontin on its internal motions.
ER  -

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