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, 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.

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

• Original language: English
• Type of outcome: Conference abstract
• Country of publisher: United Kingdom of Great Britain and Northern Ireland
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Organization unit: Faculty of Science
• Keywords (in Czech): karbonická anhydráza IX, NMR, NUS, 5D
• Keywords in English: carbonic anhydrase IX, NMR, NUS, 5D
• Tags: International impact

Abstract

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