Molecular dynamics comparison of E. coli WrbA apoprotein and holoprotein
Jazyk angličtina Země Německo Médium print-electronic
Typ dokumentu srovnávací studie, časopisecké články, práce podpořená grantem
- MeSH
- apoproteiny chemie izolace a purifikace metabolismus MeSH
- flavinmononukleotid chemie metabolismus MeSH
- hmotnostní spektrometrie s elektrosprejovou ionizací MeSH
- kinetika MeSH
- konformace proteinů MeSH
- methionin analogy a deriváty chemie metabolismus MeSH
- oxidace-redukce MeSH
- proteiny z Escherichia coli chemie izolace a purifikace metabolismus MeSH
- represorové proteiny chemie izolace a purifikace metabolismus MeSH
- simulace molekulární dynamiky * MeSH
- stabilita proteinů MeSH
- vazba proteinů MeSH
- vazebná místa MeSH
- vztahy mezi strukturou a aktivitou MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
- Názvy látek
- apoproteiny MeSH
- flavinmononukleotid MeSH
- methionin MeSH
- methionine sulfoxide MeSH Prohlížeč
- proteiny z Escherichia coli MeSH
- represorové proteiny MeSH
- WrbA protein, E coli MeSH Prohlížeč
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 ∼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.
Zobrazit více v PubMed
Biochemistry. 2007 Jan 16;46(2):543-53 PubMed
Chembiochem. 2013 May 10;14(7):890-7 PubMed
J Mol Model. 2014 Jul;20(7):2334 PubMed
Proteins. 2002 May 15;47(3):393-402 PubMed
Proteins. 2006 Nov 15;65(3):712-25 PubMed
PLoS One. 2012;7(8):e43902 PubMed
J Mol Model. 2014 Jul;20(7):2330 PubMed
Proc Natl Acad Sci U S A. 1995 Sep 12;92(19):8846-50 PubMed
J Bacteriol. 2006 May;188(10):3498-506 PubMed
Proc Natl Acad Sci U S A. 1993 Jun 15;90(12):5796-800 PubMed
J Comput Chem. 2005 Dec;26(16):1701-18 PubMed
Proteins. 1996 Dec;26(4):363-76 PubMed
Bioinformatics. 2013 Apr 1;29(7):845-54 PubMed
Acta Crystallogr D Biol Crystallogr. 2013 Sep;69(Pt 9):1748-57 PubMed
Protein Sci. 1994 Dec;3(12):2185-93 PubMed
J Biol Chem. 1998 Aug 14;273(33):20960-6 PubMed
Biochim Biophys Acta. 2009 Sep;1794(9):1288-98 PubMed
Langmuir. 2006 Feb 28;22(5):2378-83 PubMed
Protein Sci. 2007 Oct;16(10):2301-5 PubMed
PLoS Comput Biol. 2010 Jun 03;6(6):e1000801 PubMed
Methods Enzymol. 2011;492:151-88 PubMed
