title: Profile hidden Markov models for analyzing similarities and dissimilarities in the bacterial reaction center and photosystem II.
abstract: The bacterial photosynthetic reaction center is the evolutionary ancestor of the Photosystem II reaction center. These proteins share the same fold and perform the same biological function. Nevertheless, the details of their molecular reaction mechanism differ. It is of significant biological and biochemical interest to determine which functional characteristics are conserved at the level of the protein sequences. Since the level of sequence identity between the bacterial photosynthetic reaction center and Photosystem II is low, a progressive multiple-sequence alignment leads to errors in identifying the conserved residues. In such a situation, profile hidden Markov models (pHMM) can be used to obtain reliable multiple-sequence alignments. We therefore constructed the pHMM with the help of a sequence alignment based on a structural superposition of both proteins. To validate the multiple-sequence alignments obtained with the pHMM, the conservation of residues with known functional importance was examined. Having confirmed the correctness of the multiple-sequence alignments, we analyzed the conservation of residues involved in hydrogen bonding and redox potential tuning of the cofactors. Our analysis reveals similarities and dissimilarities between the bacterial photosynthetic reaction center and Photosystem II at the protein sequence level, hinting at different charge separation and charge transfer mechanisms. The conservation analysis that we perform in this paper can be considered as a model for analyzing the conservation in proteins with a low level of sequence identity.
authors.affiliation: Structural Biology/Bioinformatics, University of Bayreuth, Universitatsstrasse 30, BGI, 95447 Bayreuth, Germany.
authors.forename: Eva-Maria
authors.initials: EM
authors.lastname: Krammer
authors.forename: Pierre
authors.initials: P
authors.lastname: Sebban
authors.forename: G Matthias
authors.initials: GM
authors.lastname: Ullmann
mesh_terms: D000595:Amino Acid Sequence; D001429:Bacteriochlorophylls / Q000737:chemistry; D001665:Binding Sites; D003067:Coenzymes; D017124:Conserved Sequence; D004579:Electron Transport; D006860:Hydrogen Bonding; D008390:Markov Chains; D008958:Models, Molecular; D008969:Molecular Sequence Data; D045332:Photosystem II Protein Complex / Q000737:chemistry*; D010860:Pigments, Biological / Q000737:chemistry; D021122:Protein Subunits / Q000737:chemistry; D012242:Rhodobacter sphaeroides / Q000737:chemistry*; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein
chemical_list: D001429:Bacteriochlorophylls; D003067:Coenzymes; D045332:Photosystem II Protein Complex; D010860:Pigments, Biological; D021122:Protein Subunits