Proton-transfer pathways in photosynthetic reaction centers analyzed by profile hidden markov models and network calculations.

In the bacterial reaction center (bRC) of Rhodobacter sphaeroides, the key residues of proton transfer to the secondary quinone (Q(B)) are known. Also, several possible proton entry points and proton-transfer pathways have been proposed. However, the mechanism of the proton transfer to Q(B) remains unclear. The proton transfer to Q(B) in the bRC of Blastochloris viridis is less explored. To analyze whether the bRCs of different species use the same key residues for proton transfer to Q(B), we determined the conservation of these residues. We performed a multiple-sequence alignment based on profile hidden Markov models. Residues involved in proton transfer but not located at the protein surface are conserved or are only exchanged to functionally similar amino acids, whereas potential proton entry points are not conserved to the same extent. The analysis of the hydrogen-bond network of the bRC from R. sphaeroides and that from B. viridis showed that a large network connects Q(B) with the cytoplasmic region in both bRCs. For both species, all non-surface key residues are part of the network. However, not all proton entry points proposed for the bRC of R. sphaeroides are included in the network in the bRC of B. viridis. From our analysis, we could identify possible proton entry points. These proton entry points differ between the two bRCs. Together, the results of the conservation analysis and the hydrogen-bond network analysis make it likely that the proton transfer to Q(B) is not mediated by distinct pathways but by a large hydrogen-bond network.

Profile hidden Markov models for analyzing similarities and dissimilarities in the bacterial reaction center and photosystem II.

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.