title: A PM6 study of Rhodopseudomonas Acidophila light harvesting center II B800 bacteriochlorophylls in representative protein environment.
abstract: Bacterial light-harvesting II (LH-II) centers contain two types of Bacteriochlorophylls (Bchl). One is named B800 and found as a single molecule within one monomer of the complex while the other named B850 is found as a dimer. Their names indicate their peak of UV absorbance around red spectrum. Both types of molecules are attached to the protein chain via ligation of their central Magnesium atom to an either Histidine or Deoxymethionine amino acid. They are also coordinated by peripheral hydrogen bonds that they accept with their carboxyl side group. Both the ligation and the hydrogen bonding are thought to have an effect on electronic structure of the Bchl hence its UV absorbance and energy transfer rate. Experiments and theoretic studies performed on this subject support the above idea. This theoretical molecular modeling study case aims to mimic the experimental mutations performed on certain amino acids in silico and study its effects on the electronic structure of Bchl. By comparison with experimental results it was observed that the likely place for the nearby Arginine is not below the plane of the Bchl as in the X-ray crystallographic structure but above the plane defined by the four nitrogen atoms and their rings. It was also seen that the coordination of the acetyl group is very sensitive to changes in ligation of the Bchl molecule.
authors.affiliation: Department of Physics, Faculty of Arts&Sciences, Boğaziçi University, İstanbul, Turkey. sina.tureli@boun.edu.tr
authors.forename: Sina
authors.initials: S
authors.lastname: Türeli
authors.forename: Tereza
authors.initials: T
authors.lastname: Varnalı
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry*; D001429:Bacteriochlorophylls / Q000737:chemistry; D056831:Coordination Complexes / Q000737:chemistry; D006860:Hydrogen Bonding; D045342:Light-Harvesting Protein Complexes / Q000737:chemistry*; D008274:Magnesium / Q000737:chemistry; D008958:Models, Molecular; D008968:Molecular Conformation; D011485:Protein Binding; D011487:Protein Conformation; D012044:Regression Analysis; D012241:Rhodopseudomonas; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D001429:Bacteriochlorophylls; D056831:Coordination Complexes; D045342:Light-Harvesting Protein Complexes; D008274:Magnesium
references.citation: Biochem J. 1994 May 1;299 ( Pt 3):695-700
references.pmid: 8192657
references.citation: J Mol Biol. 2003 Mar 7;326(5):1523-38
references.pmid: 12595263
references.citation: J Bacteriol. 1999 Jul;181(13):3869-79
references.pmid: 10383951
references.citation: Biophys J. 2003 Apr;84(4):2483-91
references.pmid: 12668456
references.citation: J Gen Physiol. 1932 Nov 20;16(2):191-205
references.pmid: 19872698
references.citation: J Comput Chem. 2004 Jan 15;25(1):123-38
references.pmid: 14635000
references.citation: Proc Natl Acad Sci U S A. 2006 Dec 19;103(51):19243-8
references.pmid: 17159147
references.citation: Proc Natl Acad Sci U S A. 1998 May 26;95(11):5935-41
references.pmid: 9600895
references.citation: Proc Natl Acad Sci U S A. 1994 Jul 19;91(15):7124-8
references.pmid: 8041757