Molecular dynamics comparison of E. coli WrbA apoprotein and holoprotein

0437116 - ÚVGZ 2015 RIV CZ eng J - Journal Article
Řeha, David - Balasubramanian, H. - Sinha, Dhiraj - Kukačka, Zdeněk - McSally, J. - Ettrichová, Olga - Novák, Petr - Carey, J. - Ettrich, Rüdiger
Molecular dynamics comparison of E. coli WrbA apoprotein and holoprotein.
Journal of Molecular Modeling. Roč. 20, č. 9 (2014), s. 2400. ISSN 1610-2940. E-ISSN 0948-5023
R&D Projects: GA ČR GAP207/10/1934
Institutional support: RVO:67179843 ; RVO:61388971
Keywords : global motions * force field parametrization * binding site volume * electrostatic potential surface * NAD(P)H:quinone oxidoreductase
Subject RIV: EH - Ecology, Behaviour
Impact factor: 1.736, year: 2014

WrbA is a novel multimeric flavodoxin-like protein of unknown function. A recent high-resolution X-ray crystal structure of E. coli WrbA holoprotein revealed a methionine sulfoxide residue with full occupancy in the FMN-binding site, a finding that was confirmed by mass spectrometry. In an effort to evaluate whether methionine sulfoxide may have a role in WrbA function, the present analyses were undertaken using molecular dynamics simulations in combination with further mass spectrometry of the protein. Methionine sulfoxide formation upon reconstitution of purified apoWrbA with oxidized FMN is fast as judged by kinetic mass spectrometry, being complete in similar to 5 h and resulting in complete conversion at the active-site methionine with minor extents of conversion at heterogeneous second sites. Analysis of methionine oxidation states during purification of holoWrbA from bacterial cells reveals that methionine is not oxidized prior to reconstitution, indicating that methionine sulfoxide is unlikely to be relevant to the function of WrbA in vivo. Although the simulation results, the first reported for WrbA, led to no hypotheses about the role of methionine sulfoxide that could be tested experimentally, they elucidated the origins of the two major differences between apo- and holoWrbA crystal structures, an alteration of inter-subunit distance and a rotational shift within the tetrameric assembly.
Permanent Link: http://hdl.handle.net/11104/0240703