Employment of 5D non-uniform sampling NMR assignment strategy
to assign disordered protein regions with repetitive motifs

a 2023

Employment of 5D non-uniform sampling NMR assignment strategy to assign disordered protein regions with repetitive motifs

HOFROVÁ, Alena, Karin RAVASZOVÁ, Radek CRHA, Adela FEJFAROVÁ, Pavel SRB et. al.

Basic information

Original name

Employment of 5D non-uniform sampling NMR assignment strategy to assign disordered protein regions with repetitive motifs

Authors

HOFROVÁ, Alena, Karin RAVASZOVÁ, Radek CRHA, Adela FEJFAROVÁ, Pavel SRB, Jiri BRYNDA, Pavlína MALOY ŘEZÁČOVÁ and Jozef HRITZ

Edition

EUROMAR conference, 2023

Other information

Language

English

Type of outcome

Konferenční abstrakt

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Organization unit

Faculty of Science

Keywords (in Czech)

karbonická anhydráza IX, NMR, NUS, 5D

Keywords in English

carbonic anhydrase IX, NMR, NUS, 5D

Abstract

V originále

Nuclear Magnetic resonance (NMR) is often the method of choice when characterizing intrinsically disordered regions (IDRs). However, when using standard triple resonance assignment experiments the successful IDR assignment often becomes unfeasible, as IDRs frequently contain repetitive motifs and numerous prolines resulting in strong signal overlaps in spectra. In order to overcome these challenges in assigning IDRs, 13C-detected 5D non-uniformly sampled (NUS) experiments which were developed in cooperation with our research group and successfully utilized in the past. The 5D NUS experiments CACONCACO and HC(CC-TOCSY)CACON were complementarily used for both the backbone and aliphatic side-chain assignment of 2N4R human variant of Tau protein (441 residues) which is linked with neurodegenerative diseases. Over 99% of Tau residues were successfully assigned when employing the 5D NUS experiments. The assignment efficiency is noteworthy as the 2N4R Tau variant contains 18 aa stretches of the motifs VXSK to PGGG and a proline-rich domain. The assignment provided information about secondary structure propensities and proline-conformation analysis. The obtained assignment will be used to determine amino acids essential for interaction with binding partners e.g., 14-3-3 proteins. Moreover, this approach was recently employed for the IDR (residues 38-137) of the extracellular surface variant of carbonic anhydrase IX (CA IXsv, residues 38-391) which is associated with aggressive tumor growth and metastasis. As CA IX´s activity is increased with the presence of IDR and lower extracellular pH typical for solid tumors, the obtained assignment will be subsequently utilized to investigate the influence of various pH conditions on its local structure features and involvement in the activity of CA IX.

Links

MUNI/C/0003/2022, interní kód MU

Name: Charakteristika dynamické struktury a interakcí PG domény karbonát anhydrázy IX s ohledem na inhibici

Investor: Masaryk University, Excellent diploma thesis

Citovat

HOFROVÁ, Alena, Karin RAVASZOVÁ, Radek CRHA, Adela FEJFAROVÁ, Pavel SRB, Jiri BRYNDA, Pavlína MALOY ŘEZÁČOVÁ and Jozef HRITZ. Employment of 5D non-uniform sampling NMR assignment strategy to assign disordered protein regions with repetitive motifs. In EUROMAR conference. 2023.

@proceedings{2301850,
   author = {Hofrová, Alena and Ravaszová, Karin and Crha, Radek and Fejfarová, Adela and Srb, Pavel and Brynda, Jiri and Maloy Řezáčová, Pavlína and Hritz, Jozef},
   booktitle = {EUROMAR conference},
   keywords = {carbonic anhydrase IX, NMR, NUS, 5D},
   language = {eng},
   title = {Employment of 5D non-uniform sampling NMR assignment strategy to assign disordered protein regions with repetitive motifs},
   url = {https://euromar2023.org/wp-content/uploads/2023/07/PA-Book-v3.pdf},
   year = {2023}
}

TY  - CONF
ID  - 2301850
AU  - Hofrová, Alena - Ravaszová, Karin - Crha, Radek - Fejfarová, Adela - Srb, Pavel - Brynda, Jiri - Maloy Řezáčová, Pavlína - Hritz, Jozef
PY  - 2023
TI  - Employment of 5D non-uniform sampling NMR assignment strategy to assign disordered protein regions with repetitive motifs
KW  - carbonic anhydrase IX, NMR, NUS, 5D
UR  - https://euromar2023.org/wp-content/uploads/2023/07/PA-Book-v3.pdf
N2  - Nuclear Magnetic resonance (NMR) is often the method of choice when characterizing intrinsically disordered regions (IDRs). However, when using standard triple resonance assignment experiments the successful IDR assignment often becomes unfeasible, as IDRs frequently contain repetitive motifs and numerous prolines resulting in strong signal overlaps in spectra. In order to overcome these challenges in assigning IDRs, 13C-detected 5D non-uniformly sampled (NUS) experiments which were developed in cooperation with our research group and successfully utilized in the past. The 5D NUS experiments CACONCACO and HC(CC-TOCSY)CACON were complementarily used for both the backbone and aliphatic side-chain assignment of 2N4R human variant of Tau protein (441 residues) which is linked with neurodegenerative diseases. Over 99% of Tau residues were successfully assigned when employing the 5D NUS experiments. The assignment efficiency is noteworthy as the 2N4R Tau variant contains 18 aa stretches of the motifs VXSK to PGGG and a proline-rich domain. The assignment provided information about secondary structure propensities and proline-conformation analysis. The obtained assignment will be used to determine amino acids essential for interaction with binding partners e.g., 14-3-3 proteins. Moreover, this approach was recently employed for the IDR (residues 38-137) of the extracellular surface variant of carbonic anhydrase IX (CA IXsv, residues 38-391) which is associated with aggressive tumor growth and metastasis. As CA IX´s activity is increased with the presence of IDR and lower extracellular pH typical for solid tumors, the obtained assignment will be subsequently utilized to investigate the influence of various pH conditions on its local structure features and involvement in the activity of CA IX.
ER  -

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