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Statistical Coupling Analysis of the Photosystem II D1 Protein
Janan Zhu1; Nicholas Polizzi2;
Statistical coupling analysis can be applied to alignments of related
proteins to examine “sectors” in the sequences that are evolving
independently of each other. Our application of this technique to the
D1 protein of photosystem II identified 4 significant sectors and we
assigned different functions to each of the based on their location
within the protein. The resulting sectors appear to be clustered around
the cofactors of the protein that are involved in the photosynthetic
electron transport pathway. These results suggest that the cofactor
binding sites in the D1 protein have evolved independently to some
degree, a fact that may contribute to further biochemical and structural
of Mathematics, Duke University; 2Department of Chemistry, Duke University
D1 Protein Cofactors in the Electron Transfer Pathway
Sector Definition
Positions in the eigenmodes with a weight greater than 0.09 were
considered to be part of the corresponding sectors. Some of the sectors
obtained from the raw eigenmodes contained large regions of overlap with
other sectors and were merged to simplify functional description.
Tyrosine Z
Chlorophyll pair
The photosystem II D1 protein is vital to the photosynthetic electron
transport pathway as it houses the reaction center chlorophylls in
addition to the cofactors that channel the excited electrons to other
proteins in the membrane. Studies of protein conservation promote a
better understanding of how the protein facilitates the transfer of
electrons between cofactors.
Figure depicting the merging process for three sectors. The unified sector
consisted of the union of the pairwise intersections of the sectors.
The flow of electrons between the cofactors is shown in green.
Plastoquinone B is the final electron acceptor and dissociates from the
protein into the thylakoid membrane.
A set of 152 representative sequences was generated using a BLAST
search for sequences similar to that of the T. vulcanus photosystem II D1
protein (length 344 AA). These sequences were then aligned and the
alignments were weighted by the Kullback-Leibler relative entropy, a
measure of the degree of conservation at a particular position. These
weighted pairwise alignments were used to create the 344 x 344 positional
correlation matrix, which indicated the degree of correlated evolution
between each pair of positions.
The number of sectors was determined from empirical observation of their
3D mapping onto the T. vulcanus structure. A defining characteristic of a
sector aside from statistical independence is physical connectivity in space
(Halabi et al. 2009). Eigenmodes with higher eigenvalues accounts for a
greater degree of the variance in the correlation matrix. Therefore, the
eigenmodes were considered in order of descending eigenvalues until they
yielded sectors with disparate amino acids of low descriptive value. This
method resulted in four sectors being defined.
Overview of the sectors in the D1
The photosystem II complex, with the D1 protein highlighted
A graphical representation of the positional correlation matrix
Spectral decomposition of the positional correlation matrix was used to
identify statistically independent groups of amino acids (sectors). The
eigenvectors (also called eigenmodes) used to represent the matrix
contain weights for the significance of the position within the sector.
Binding the water oxidizing complex
and its substrates. This sector
contains several histidines which are
directly bonded to the complex. There
are also amino acids that are
hydrogen bonded to the water
molecules shown in green.
Description of Sectors
Method: Eigenvalue Decomposition of Positional Correlations
Source: Biochemistry Mathews,Van Holde, Ahern 3E
Lowering energetic barrier for
electron transfer from tyrosine Z
(orange) to chlorophyll special pair
(red). Electrons from tyrosine Z
replenish excited electrons that leave
the reaction center. The amino acids
in this sector contain many aromatic
rings, which bridge the gap between
the tyrosine and the special pair.
His198 in this sector is coordinated to
the chlorophyll and is directly linked
to its electron density.
Proposed function
Facilitating proton-coupled electron transfer
to plastoquinone B. The amino acids in this
sector are colored by element, with green
representing carbon. They appear to be
largely hydrophobic, which stabilizes the
binding of the aliphatic tail of the quinone.
Several amino acids known to be involved
in proton donation are also present in this
sector, including Ser246 and Tyr264.
Structural linkage to antenna
pigments. The hydrophobic amino
acids in this sector are located in
close proximity to chain I (yellow) of
photosystem II, which is known to
stabilize the pigment-containing light
harvesting complex. This sector thus
holds these antenna pigments within
short distance of the reaction center.
Summary and Discussion
The application of statistical coupling analysis to the photosystem II D1
protein yielded independent sectors that appear to have biological
relevance. The sectors are clustered around the different cofactors of the
photosynthetic electron transport pathway. We conclude that the different
steps in electron transport appear to be facilitated by evolutionarily
independent parts of the protein. This has important implications, as the
overall proton-coupled electron transfer is believed to be a concerted
reaction, yet separate sectors were found for each step. It remains to be
shown if this is true for electron transfer proteins in general and this study
has demonstrated the viability of statistical coupling analysis for this
N. Halabi, O. Rivoire, S. Leibler, R. Ranganathan. Cell, 138: 774-786, 2009