Intrinsically disordered regions may lower the hydration free energy in proteins: A case study of nudix hydrolase in the bacterium Deinococcus radiodurans

Publikation: Beitrag in FachzeitschriftForschungsartikelBeigetragenBegutachtung

Beitragende

  • Omar Awile - , Mediterranean Institute for Life Sciences, Swiss Institute of Bioinformatics (SIB), ETH Zurich (Autor:in)
  • Anita Krisko - , Universität Paris Descartes 5 (Autor:in)
  • Ivo F. Sbalzarini - , Mediterranean Institute for Life Sciences, Swiss Institute of Bioinformatics (SIB), ETH Zurich (Autor:in)
  • Bojan Zagrovic - , Mediterranean Institute for Life Sciences, University of Split, Universität Wien (Autor:in)

Abstract

The proteome of the radiation- and desiccation-resistant bacterium D. radiodurans features a group of proteins that contain significant intrinsically disordered regions that are not present in non-extremophile homologues. Interestingly, this group includes a number of housekeeping and repair proteins such as DNA polymerase III, nudix hydrolase and rotamase. Here, we focus on a member of the nudix hydrolase family from D. radiodurans possessing low-complexity N- and C-terminal tails, which exhibit sequence signatures of intrinsic disorder and have unknown function. The enzyme catalyzes the hydrolysis of oxidatively damaged and mutagenic nucleotides, and it is thought to play an important role in D. radiodurans during the recovery phase after exposure to ionizing radiation or desiccation. We use molecular dynamics simulations to study the dynamics of the protein, and study its hydration free energy using the GB/SA formalism. We show that the presence of disordered tails significantly decreases the hydration free energy of the whole protein. We hypothesize that the tails increase the chances of the protein to be located in the remaining water patches in the desiccated cell, where it is protected from the desiccation effects and can function normally. We extrapolate this to other intrinsically disordered regions in proteins, and propose a novel function for them: intrinsically disordered regions increase the "surface-properties" of the folded domains they are attached to, making them on the whole more hydrophilic and potentially influencing, in this way, their localization and cellular activity.

Details

OriginalspracheEnglisch
Aufsatznummere1000854
Seiten (von - bis)12
Seitenumfang1
FachzeitschriftPLOS computational biology
Jahrgang6
Ausgabenummer7
PublikationsstatusVeröffentlicht - Juli 2010
Peer-Review-StatusJa
Extern publiziertJa

Externe IDs

PubMed 20657662
ORCID /0000-0003-4414-4340/work/159608319