Molecular dynamics simulations of the MntR protein from the bacterium Halalkalibacterium halodurans

Abstract

Ioni prijelaznih metala neizostavna su komponenta brojnih staničnih procesa živih organizama. Ipak, prevelika stanična koncentracija metalnih iona može biti toksična za stanicu pa su neophodni osjetljivi mehanizmi regulacije njihove stanične koncentracije. Protein MntR je transkripcijski faktor koji sudjeluje u mehanizmu regulacije stanične koncentracije manganovih(II) iona u bakteriji Halalkalibacterium halodurans. U otopini je prisutan kao homodimer koji se vezanjem dva manganova(II) iona aktivira za vezanje na DNA te sprječava transkripciju gena za unos manganovih(II) iona. Simulacijama molekulske dinamike (MD) istražene su razlike u strukturnim i dinamičkim svojstvima proteina MntR u apo (bez vezanih manganovih(II) iona) i holo (s vezanim manganovim(II) ionima) obliku. Analizom MD simulacija identificirane su konformacijske odlike koje holo strukturi olakšavaju vezanje u dva susjedna velika utora molekule DNA. Pronađene su nekovalentne interakcije koje potencijalno imaju važnu ulogu u molekulskom mehanizmu koji dovodi do povećanja afiniteta MntR proteina prema DNA uslijed vezanja manganovih(II) iona. Rezultati simulacija upućuju da prisustvo manganovih(II) iona u veznom mjestu proteina dovodi do zamijene vodikove veze Arg72 i Asp111 s kation–π interakcijom između Arg72 i Trp107 što se reflektira na savijanje α4 – zavojnice i udaljenost između DNA vezujućih domena. Računalni rezultati uspoređeni su s literaturno dostupnim eksperimentalnim podacima. Ključne riječi: homeostaza mangana, alosterička aktivacija, nekovalentna interakcija, vodikova veza, kation-π interakcijaTransition metal ions are an indispensable component of numerous cellular processes of living organisms. However, excessive cellular concentration of metal ions can be toxic to the cell, so sensitive mechanisms of regulation of their cellular concentration are necessary. The MntR protein is a transcription factor that participates in the mechanism of regulation of the cellular concentration of manganese(II) ions in the bacterium Halalkalibacterium halodurans. In the solution, it is present as a homodimer which, by binding two manganese(II) ions, is activated to bind to DNA and prevents the transcription of genes for the intake of manganese(II) ions. Molecular dynamics (MD) simulations were used to investigate the differences in the structural and dynamic properties of the MntR protein in the apoprotein (without bound manganese(II) ions) and holoprotein (with bound manganese(II) ions) form. The analysis of MD simulations identified conformational features that facilitate the binding of the holoprotein in two adjacent large grooves of the DNA molecule. Noncovalent interactions were found that potentially play an important role in the molecular mechanism that leads to an increase in the affinity of the MntR protein to DNA due to the binding of manganese(II) ions. The simulation results suggest that the presence of manganese(II) ions in the binding site of the protein leads to the replacement of the hydrogen bond between Arg72 and Asp111 with a cation–π interaction between Arg72 and Trp107, which is reflected in the bending of the α4 helix and the distance between the DNA binding domains. The computational results were compared with experimental data available in the literatur