Convergent views on disordered protein dynamics from NMR and computational approaches

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Publikace nespadá pod Pedagogickou fakultu, ale pod Středoevropský technologický institut. Oficiální stránka publikace je na webu muni.cz.
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SALVI Nicola ZAPLETAL Vojtěch JASEŇÁKOVÁ Zuzana ZACHRDLA Milan PADRTA Petr NARASIMHAN Subhash MARQUARDSEN Thorsten TYBURN Jean-Max ŽÍDEK Lukáš BLACKLEDGE Martin FERRAGE Fabien KADEŘÁVEK Pavel

Rok publikování 2022
Druh Článek v odborném periodiku
Časopis / Zdroj BIOPHYSICAL JOURNAL
Fakulta / Pracoviště MU

Středoevropský technologický institut

Citace
www https://linkinghub.elsevier.com/retrieve/pii/S0006-3495(22)00766-4
Doi http://dx.doi.org/10.1016/j.bpj.2022.09.016
Klíčová slova NMR; protein dynamics
Popis Intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs) is a class of biologically important proteins exhibiting specific biophysical characteristics. They lack a hydrophobic core, and their conformational behavior is strongly influenced by electrostatic interactions. IDPs and IDRs are highly dynamic, and a characterization of the motions of IDPs and IDRs is essential for their physically correct description. NMR together with molecular dynamics simulations are the methods best suited to such a task because they provide information about dynamics of proteins with atomistic resolution. Here, we present a study of motions of a disordered C-terminal domain of the delta subunit of RNA polymerase from Bacillus subtilis. Positively and negatively charged residues in the studied domain form transient electrostatic contacts critical for the biological function. Our study is focused on investigation of ps-ns dynamics of backbone of the delta subunit based on analysis of amide 15N NMR relaxation data and molecular dynamics simulations. In order to extend an informational content of NMR data to lower frequencies, which are more sensitive to slower motions, we combined standard (high-field) NMR relaxation experiments with high-resolution relaxometry. Altogether, we collected data reporting the relaxation at 12 different magnetic fields, resulting in an unprecedented data set. Our results document that the analysis of such data provides a consistent description of dynamics and confirms the validity of so far used protocols of the analysis of dynamics of IDPs also for a partially folded protein. In addition, the potential to access detailed description of motions at the timescale of tens of ns with the help of relaxometry data is discussed. Interestingly, in our case, it appears to be mostly relevant for a region involved in the formation of temporary contacts within the disordered region, which was previously proven to be biologically important.
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