N-terminal domain of polypyrimidine-tract binding protein is a dynamic folding platform for adaptive RNA recognition

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F24%3A00598827" target="_blank" >RIV/68081707:_____/24:00598827 - isvavai.cz</a>

Výsledek na webu

<a href="https://academic.oup.com/nar/article/52/17/10683/7740593" target="_blank" >https://academic.oup.com/nar/article/52/17/10683/7740593</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/nar/gkae713" target="_blank" >10.1093/nar/gkae713</a>

Jazyk výsledku

angličtina

Název v původním jazyce

N-terminal domain of polypyrimidine-tract binding protein is a dynamic folding platform for adaptive RNA recognition

Popis výsledku v původním jazyce

The N-terminal RNA recognition motif domain (RRM1) of polypyrimidine tract binding protein (PTB) forms an additional C-terminal helix alpha 3, which docks to one edge of the beta-sheet upon binding to a stem-loop RNA containing a UCUUU pentaloop. Importantly, alpha 3 does not contact the RNA. The alpha 3 helix therefore represents an allosteric means to regulate the conformation of adjacent domains in PTB upon binding structured RNAs. Here we investigate the process of dynamic adaptation by stem-loop RNA and RRM1 using NMR and MD in order to obtain mechanistic insights on how this allostery is achieved. Relaxation data and NMR structure determination of the free protein show that alpha 3 is partially ordered and interacts with the domain transiently. Stem-loop RNA binding quenches fast time scale dynamics and alpha 3 becomes ordered, however microsecond dynamics at the protein-RNA interface is observed. MD shows how RRM1 binding to the stem-loop RNA is coupled to the stabilization of the C-terminal helix and helps to transduce differences in RNA loop sequence into changes in alpha 3 length and order. IRES assays of full length PTB and a mutant with altered dynamics in the alpha 3 region show that this dynamic allostery influences PTB function in cultured HEK293T cells.

Název v anglickém jazyce

N-terminal domain of polypyrimidine-tract binding protein is a dynamic folding platform for adaptive RNA recognition

Popis výsledku anglicky

The N-terminal RNA recognition motif domain (RRM1) of polypyrimidine tract binding protein (PTB) forms an additional C-terminal helix alpha 3, which docks to one edge of the beta-sheet upon binding to a stem-loop RNA containing a UCUUU pentaloop. Importantly, alpha 3 does not contact the RNA. The alpha 3 helix therefore represents an allosteric means to regulate the conformation of adjacent domains in PTB upon binding structured RNAs. Here we investigate the process of dynamic adaptation by stem-loop RNA and RRM1 using NMR and MD in order to obtain mechanistic insights on how this allostery is achieved. Relaxation data and NMR structure determination of the free protein show that alpha 3 is partially ordered and interacts with the domain transiently. Stem-loop RNA binding quenches fast time scale dynamics and alpha 3 becomes ordered, however microsecond dynamics at the protein-RNA interface is observed. MD shows how RRM1 binding to the stem-loop RNA is coupled to the stabilization of the C-terminal helix and helps to transduce differences in RNA loop sequence into changes in alpha 3 length and order. IRES assays of full length PTB and a mutant with altered dynamics in the alpha 3 region show that this dynamic allostery influences PTB function in cultured HEK293T cells.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10608 - Biochemistry and molecular biology

Projekt

<a href="/cs/project/GA23-05639S" target="_blank" >GA23-05639S: Molekulové simulace RNA: od statických struktur k molekulárním souborům</a><br>

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2024

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Nucleic Acids Research

ISSN

0305-1048

e-ISSN

1362-4962

Svazek periodika

52

Číslo periodika v rámci svazku

17

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

22

Strana od-do

10683-10704

Kód UT WoS článku

001297149500001

EID výsledku v databázi Scopus

2-s2.0-85204819720