Ahmet Selim Vakkasoglu
Functions of Photosynthetic Reaction Center and
Structural Changes in QB Site
Introduction:
In photosynthesis, the important issue is the trapping of light energy. In most
plants and photosynthetic bacteria chlorophyll is the photoreceptor molecule.
Chlorophylls are polyenes that means they have alternating double and single bonds. This
property makes them photoreceptors. They have absorption bands at visible region. This
is the best region to absorb the sunlight that comes to the earth’s surface. Adsorbed light
excites an electron and if this electron cannot find a suitable acceptor, then it relaxes back
and emits heat. So this excited electron is given to an acceptor and a couple of positive
and negative charges are produced. This process is called photoinduced charge
separation. This process occurs in reaction center.
Reaction center is a membrane protein which contains three subunits, L, M, and
H. It has four kinds of cofactors; four bacteriochlorophylls, two bacteriopheophytins, two
quinones and one non heme high spin Fe2+. (FIG1) L and M subunits are the structural
and functional ones. They are positioned mostly in the transmembrane region of the
protein. Each have five membrane spanning helices where H subunit has only one. H
subunit lies on the cyoplasmic side of the membrane.
Bacterichlorophylls (Bchl) are similar to chlorophylls with minor differences
which shift absorption wavelength to near infrared. Bacteriopheophytin (BPh) has two
protons instead of the magnesium ion at bacteriochlorophyll`s center.
Figure 1: Bacteriochlorophyll (on the left) and bacteropheophytin (on the right)
Function:
Chemical reaction starts with the absorption of light by the Bchl-b dimer. This
dimer is also called special pair due to its fundamental role in photosynthesis. Special
pair is located near to the periplasmic side of the membrane. It absorbs at 960nm so it is
often referred as P960. Absorption results in ejection of an electron. This electron is
transferred to the BPh in the L subunit. This electron transfer occurs in less than 10psec.
At this point positively charged P960+ and negatively charged BPh- can recombine,
which conversion of the adsorbed light energy into heat. Three factors can be listed to
answer the question “why do not recombination of the charges occur?”. Firstly, there is
another acceptor, (QA), the tightly bound quinone. It is positioned at less than 10A away
from BPh-. Secondly, the reduced heme in cytochrome is less than 10A away from the
Bchl dimer. It`s known that electron transfer strongly depends on the distance. So these
two factors seem to be challenging. The third one is the rate of the electron transfer
reaction from BPh- to P960+. The rate of this reaction is slower than the reverse reaction.
Thus, electron proceeds to QA from BPh-.
After the electron reaches to QA, it proceeds to QB, loosely bound quinone.
Repetition of this electron transfer beginning with the absorption of a photon results in
the reduction of QB from Q, quinone, to QH2, quinole. These protons are taken from the
cytoplasm and cause the development of a proton gradient across the cell membrane.
In this report, the function-structure relationship of loosely bound quinone, QB, in
charge neutral (DQAQB) and charge separated (D+QAQB-) states will be discussed. (where
D is the primary donor, dimer). In addition to this, the possible pathways of proton uptake
from cytosol will be shown. In the rest of the report QB binding site will be discussed,
because the other cofactors like, Bchl, BPh are structurally more conserved during the
electron transfer.
The electron transfer rate from primary ubiquinone QA- to secondary ubiquinone
QB is increased when the RCs are frozen under illumination which means the charge
separated state D+QAQB-, when compared to RCs frozen in dark. In Figure 2, the QB
binding pocket is shown, both in dark and light structures. There are two binding
structures in the dark state, QB1 and QB2. The light structure is very similar to the QB2 one.
Ubiquinone is positioned in the binding pocket with O1 of QB, 6.72A away from the
nitrogen of the His L190. The other carbonyl oxygen of the quinone, O4, form a H-bond
Figure 2: O1 to His 190 distance is 6.72A. O4 to Ile 224 backbone distance is 3.14A
with amide backbone of Ile L224. The ubiquinone ring lies parallel to Phe L216 (Figure
3). This residue is conserved and contributes to the binding affinity of the ubiquinone.
Actually there are several published papers (Ermler et. al., Chang et al., Arnoux et al.,
Allen et al.) claiming different positions for QB binding pocket. These discrepancies can
be due to the electrons created by the X-ray irradiation during data collection. These
electrons can reduce the ubiquinone in the QB binding pocket.
The structure of the charge separated (light) state is similar to the dark one. Here,
carbonyl oxygen, O4, of the ubiquinone makes a H-bond to His L190. (Figure 4) O1
carbonyl oxygen makes another H-bond to the backbone amide nitrogen of Ile L224. In
Figure 3: Phe L216 lies parallel to quinone ring.
addition to these two H-bonds, O1 can have two other H-bonds to Ser L223 and to the
backbone of L225, where the distances to O1 are 3.21A and 3.27A, respectively.
The most important difference between light and dark structures of the
ubiquinone is the movement of the center of ubiquinone by 4.5A toward the cytoplasmic
region.. Because of the proton uptake is done in the light state (D+QAQB-), this movement
enables quinone to come to closer to the cytoplasmic side and take the protons easier.
Another change in the structure is the twist of the isoprene tail by 180o.
It is known that electron transfer is achieved in the samples of RCs frozen under
illumination where it is not observed in the samples of RCs which are frozen in the dark.
Up to this point two positions of the QB binding pocket is told. One is the structure that
the electron at QA- cannot be transferred to QB, that is, transfer is inhibited. The other
Figure 4: Bond distances beginning from the upper left 2.96A, 3.21A, 3.17A, 2.81A.
enables the electron transfer. In dark, QB1 is thermodynamically favored. Electron
transfer pathway is cut in this structure, because the 4.5A moved position of the quinone
unables it to have H-bond to His L190. The way electrons followfrom QA- to QB includes
His L190. So in QB1 electron cannot jump to quinone where in QB2 it can. So movement
of ubiquinone from QB1 to QB2 is a necessary step for the electron transfer from QA-QB to
QAQB-.
From the previous experiments it is known that the rate limiting step is not the
electron transfer (Graige et al.) These experiments are done by changing the kind of
ubiquinone in the QA site. Thus, the rate limiting step is the conversion step between
these two states, QB1 and QB2. So energy barrier between these states becomes very
important.
Conversion of the ubiquinone (Q) to ubiquinol (QH2) requires 2 electrons. So a
second electron is transferred in the same way and reduces the ubiquinone. The formed
ubiquinol leaves RC, goes to quinol pool in the membrane. So the protons taken from
cytoplasm form a proton gradient. At this point, the way that the protons follow from
cytoplasm to the quinone binding site is important. Normally it is accepted that the
protons follow proton donor and accepter groups. These groups can be the side chains of
aminoacids and the water molecules. Although several aminoacids that are used in proton
uptake are known by site directed mutagenesis, the positions of the water molecules are
not well known. They require higher resolution.
Two possible proton pathways are indicated in Figure 5 as P1 and P2. Pathway
P1 lies along ~23A from QB binding pocket to the cytoplasmic side. This pathway is
perpendicular to the membrane surface. It includes Ser L223, Thr L226, Glu L212, Asp
L210, Lys H130, Glu H122, Glu M236, His H68 and Arg H70 (Figure 6). The second
pathway, P2, follows the interface between H and M subunits parallel to the membrane
surface. In this pathway, Ser L223, Glu L212, Asp L 213, Glu H173, Asn M44, Ser M8,
Gln H174 and Gln M11 exist (Figure 7). End of this pathway is at the negative charged
membrane where proton concentration is higher than bulk water.
Figure 5: Proton pathways P1 and P2 beginning from QB binding site.
Next and the final step is the release of the quinol and replacement by ubiquinone.
For this replacement the binding affinities of three species QBH2, QB- and QB are
important. Firstly binding affinity of the QB- should be higher than others. Because
release of this chemically reactive ubisemiquinone would be detrimental. It has to be kept
due to its functionality. Binding affinity of QB is expected to be higher than the QBH2 for
the replacement. Experiments showed that this is true (Wraight et al.). So the binding
affinities are in the decreasing order of QB- > QB > QBH2. These results are in accordance
with the structures shown here. As it is told above, QB- has 3 H-bonds by both carbonyl
oxygens, where the QB has only one carbonyl oxygen having H-bond. In the case of the
ubiquinol, both carbonyl oxygens are protonated, resulting in weaker binding.
Figure 6: P1 proton pathway goes perpendicular to the membrane surface.
Figure 7: P2 proton pathway lies on the interface of H and M subunits.
Reference:
1)
M. H. B. Stowell, T. M. McPhillips, D.C. Rees, S. M. Soltis, E.
Abresch, G. Feher, Science, 276, 1997, p812.
2)
E. Takahashi, C. A. Wraight, Biochim. Biophys. Acta, 1020, 1990,107
3)
M.S. Graige, G. Feher, M. Y. Okamura, Biophys J. 70, 1996, Abstr 10
4)
“ Structure and Function of the Reaction Center From
Rhodopseudomonas Sphareoides” G. Feher, M. Y. Okamura.
5)
Biochemistry, J. Berg, J. Tymoczko, L. Stryer, 5th edt. Freeman, 2001
6)
“The Photosynthetic Reaction Center”, J. Deisenhofer, J. R. Norris, Vol
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