Ó Springer 2005
Photosynthesis Research (2005) 85: 33–50
Review
Structural and functional organization of the peripheral light-harvesting
system in Photosystem I
Alexander N. Melkozernov* & Robert E. Blankenship
Department of Chemistry and Biochemistry and Center for the Study of Early Events in Photosynthesis,
Tempe, AZ 85287-1604, USA; * Author for correspondence (e-mail: [email protected]; fax:
+1-480-965-2747)
Received 1 August 2004; accepted in revised form 19 November 2004
Key words: chlorophyll, excitation energy transfer, green algae, higher plants, homology modeling,
peripheral light-harvesting antenna, photosynthesis, Photosystem I core antenna, red pigments, threedimensional structure
Abstract
This review centers on the structural and functional organization of the light-harvesting system in the
peripheral antenna of Photosystem I (LHC I) and its energy coupling to the Photosystem I (PS I) core
antenna network in view of recently available structural models of the eukaryotic Photosystem I–LHC I
complex, eukaryotic LHC II complexes and the cyanobacterial Photosystem I core. A structural model
based on the 3D homology of Lhca4 with LHC II is used for analysis of the principles of pigment
arrangement in the LHC I peripheral antenna, for prediction of the protein ligands for the pigments that
are unique for LHC I and for estimates of the excitonic coupling in strongly interacting pigment dimers.
The presence of chlorophyll clusters with strong pigment–pigment interactions is a structural feature of PS
I, resulting in the characteristic red-shifted fluorescence. Analysis of the interactions between the PS I core
antenna and the peripheral antenna leads to the suggestion that the specific function of the red pigments is
likely to be determined by their localization with respect to the reaction center. In the PS I core antenna, the
Chl clusters with a different magnitude of low energy shift contribute to better spectral overlap of Chls in
the reaction center and the Chls of the antenna network, concentrate the excitation around the reaction
center and participate in downhill enhancement of energy transfer from LHC II to the PS I core. Chlorophyll clusters forming terminal emitters in LHC I are likely to be involved in photoprotection against
excess energy.
Abbreviations: 3D – three-dimensional; Chl – chlorophyll; LHC I – light-harvesting complex I; LHC I-730
– subpopulation of LHC I; Lhca1 and Lhca4 – subunits of the LHC I-730 heterodimer; PS I – Photosystem
I; P700 – primary electron donor in Photosystem I
Introduction
Photosystem I (PS I) is an important part of the
photosynthetic machinery that catalyzes transmembrane electron transfer via plastocyanin/ferredoxin oxido-reductase activity and produces
NADPH for CO2 assimilation (Blankenship 2002).
In PS I, redox active chlorophylls of the reaction
center sensitize solar energy conversion, while the
integral core and the peripheral light-harvesting
antennas supply the reaction centers with the
excitation energy via efficient transfer in the Chl
antenna network (Melkozernov and Blankenship
in press). PS I complexes from cyanobacteria,
green algae and higher plants possess a red-shifted
chlorophyll fluorescence, which is widely used as a
34
PS I fingerprint in functional studies of the
complex. In green algae and higher plants, the red
shift is thought to be associated with the formation
of pigment dimers or clusters in both the PS I core
and the LHC I peripheral antenna (Gobets and
van Grondelle 2001; Melkozernov 2001).
The search for the molecular mechanisms of the
prominent red spectral shift has been a driving
force in functional and structural studies of PS I
and LHC I. The low energy absorbing pigments in
the PS I core localize the excitation; and the
involvement of these pigments into a well connected network of excitation energy transfer
makes these pigments a transient excitation trap
on the picosecond time scale, followed by efficient
excitation energy trapping by the reaction center
(Trissl 1993; Melkozernov 2001; Gobets and van
Grondelle 2001; Sener et al. 2002; Byrdin et al.
2002; Yang et al. 2003). At low temperatures, the
low energy pigments in the PS I core become deep
excitation traps, eventually releasing the localized
energy in the form of significantly red shifted fluorescence (van Grondelle et al. 1994). In contrast,
the red pigments in the peripheral LHC I antenna
efficiently localize the excitation even at physiological temperatures, giving rise to a red shifted
emission in the region from 690 to 730 nm
depending on the type of the Lhca proteins associated with LHC I (Tjus et al. 1995; Schmid et al.
1997; Croce et al. 2002).
Advances in structural biology have revealed
the atomic structure of the PS I core from cyanobacteria (Jordan et al. 2001; Fromme et al.
2001), a structural model of the PS I–LHC I from
pea (Ben-Shem et al. 2003) and important structural features of the association of the LHC I
peripheral antenna to the PS I core (Boekema
et al. 2001; Germano et al. 2002; Kargul et al.
2003). A recent breakthrough in understanding of
structural details of the abundant LHC II protein
from peripheral antenna of PS II (Liu et al. 2004)
has opened up an opportunity for comparison of
LHC I and LHC II and deciphering the structural
causes of the striking spectral differences of these
proteins. In the absence of a detailed atomic
structure of LHC I, homology modeling can provide tools for prediction of these structural features (Melkozernov and Blankenship 2003).
This review discusses the principles of structure–functional organization of light-harvesting in
the PS I–LHC I supercomplex from eukaryotes.
The discussion is largely motivated by the search
for the structural implications of the functional
features of the PS I–LHC I complexes discovered
by recent excitation energy studies of LHC I
monomers, LHC I dimers and PS I–LHC I supercomplexes.
Structural homology of LHC I and LHC II
The LHC I polypeptides of the peripheral antenna
associated with PS I in algae and higher plants
belong to a group of three-helical integral membrane chlorophyll–carotenoid proteins containing
Chl a/b, Chl a/c and Chl a binding proteins of
photosynthetic eukaryotes (Durnford et al. 1999;
Green 2003; Gantt et al. 2003). These proteins are
part of the large superfamily of chlorophyll-binding proteins that share similarity with early light
induced proteins (ELIPs) of green algae and higher
plants (Heddad and Adamska 2002), the high-light
induced proteins (hlips) in cyanobacteria, the PsbS
subunit of PS II and one- or two-helix stress-expressed proteins of higher plants (Montané and
Kloppstech 2000; Heddad and Adamska 2002;
Jansson et al. 2000).
Figure 1 illustrates an alignment of sequences
of four representative LHC I proteins from higher
plants and the LHC II protein from spinach, for
which the crystal structure with resolution of
2.72 Å has been recently determined (Liu et al.
2004). Secondary structure prediction methods
based on multiple sequence alignment (Melkozernov and Blankenship 2003) predict, with a good
level of confidence for LHC I proteins, four
regions with a helical structure corresponding to
three transmembrane helices (boxes 1, 2 and 3 in
Figure 1) and the fourth lumenal helix at the
C-terminus (box 4). The fifth helix (box 5) identified in the LHC II crystal structure in the lumenal
loop between helices I and II is pseudo-symmetry
related to helix IV at C-terminus (box 4). A symmetrical arrangement of the protein fold in the Chl
a/b binding proteins is thought to originate from a
duplication of the ancestor gene coding for transmembrane helix I during evolution (Green 2003).
Helices I and III exhibit conserved amino acid
motifs in the evolutionarily distant light-harvesting pigment binding proteins (Green and Kühlbrandt 1995; Durnford et al. 1999; Green 2003;
Garczarek et al. 2003). A conserved amino acid
35
Figure 1. Alignment of representative primary sequences of the LHC I proteins and the LHC II protein from spinach (1RWT), for
which the crystal structure has been defined (Liu et al. 2004). Boxes 1–4, helical regions of the sequence with largely conserved protein
fold; box 5, sequence region corresponding to the fifth helix detected in LHC II; boxes 6 and 7, carotenoid retaining motifs. Multiple
alignments were performed using T-Coffee (Notredame et al. 2000). Modified from Melkozernov and Blankenship (2003).
pattern at the N-end of the protein sequence of
helices I and III (see boxes 6 and 7 in Figure 1)
forms carotenoid-retaining motifs. The centrally
located lutein molecules in the structure of LHC II
are retained by the hydrophobic interactions
between the end-groups of luteins and the aromatic residues of the conserved carotenoid binding
regions in the loops (Green and Kühlbrandt 1995;
Liu et al. 2004).
Significant differences among the primary
sequences of LHCs are observed in the region of the
N-termini, the middle part of the alignments corresponding to transmembrane helix II and the
lumenal and stromal interhelical loop regions.
Results of the multiple alignments in the middle
most diversified region depend on the number of
sequences used in the alignment and the algorithms
and parameters of the analysis. Despite variation in
the sequences of helix II, a general amino acid motif
in LHC I includes conserved potential pigmentbinding sites separated by seven predominantly
hydrophobic residues in green algae and higher
plants, and eight residues in Chl a/c binding and Chl
a binding red algae (Tan et al. 1997; Melkozernov
and Blankenship 2003). In contrast to LHC II, the
primary sequences in the LHC I proteins are characterized by deletions in the lumenal loop between
helices I and II, and inserts in the stromal loop
anchored by helices II and III (Figure 1).
Homology based 3D model of Lhca4
Comparative protein structure modeling is an
accurate structure prediction method utilizing
primary sequence analysis, motif searching and
protein fold recognition (Marti-Renom et al.
2000; Kopp et al. 2003). The homology-based 3D
structure of Lhca4 is used in this review for prediction of the structural features of LHC I proteins that are important for understanding of
structure–functional organization of the peripheral light-harvesting in the PS I–LHC I complex.
Three-dimensional structures of the proteins
within a family are more conserved than their
primary sequences (Lesk and Chotia 1980; Chotia
and Lesk 1986). The largely unchanged orientation of the protein helices in LHC I and LHC II
(Figure 2) supports this general concept. The
conservation of the protein fold in LHC I and
LHC II was used recently for the three-dimensional reconstruction of the Lhca4 protein from
higher plants based on the primary sequence of
the protein and the structure of LHC II (Melkozernov and Blankenship 2003). The model presented in Figure 3 visualizes a 3D fold of the
Lhca4 protein built by a computer fit of the protein sequence of Lhca4 to the 3D structure of the
LHC II template.
While the protein fold in the homology model
of Lhca4 is similar to that in the structural template (LHC II; see Figure 2), the pigments in the
model are fixed to the atomic coordinates of the
tetrapyrrole macrocycles determined in the crystal
structure of the LHC I protein assigned to Lhca4
(Ben-Shem et al. 2003; pdb code 1QZV). The
structure of pigments in LHC I can be reconstructed from analogous pigments in LHC II from
spinach by minimal translations and rotations of
their atomic coordinates determined by the recent
36
Figure 2. Overlap of the a-carbon backbone traces of the Chl a/b binding light-harvesting complexes: LHC II from spinach (red), LHC
II from pea (blue) and Lhca4 from the PS I–LHC I from pea (yellow). Atomic coordinates are taken from Protein Data Bank for LHC
II from spinach (file 1RWT; Liu et al. 2004) and PS I–LHC I from pea (1QZV; Ben-Shem et al. 2003). Coordinates of a-carbon atoms
of LHC II from pea are courtesy of W. Kühlbrandt (Kühlbrandt et al. 1994).
X-ray crystallography study with 2.72 Å resolution (Liu et al. 2004).
The LHC II crystal structure identified molecular ligands to 14 Chl molecules including 8 Chl a
molecules and 6 Chl b molecules. Pigments in LHC
II are arranged in two layers, lumenal and stromal.
Figure 4 compares layers of pigments in LHC II
and Lhca4. For the sake of comparison, the
majority of the pigments in LHC II and Lhca4 are
labeled according to the nomenclature proposed
by Kühlbrandt et al. for the 3.4 Å resolution
crystal structure of LHC II from pea (Kühlbrandt
et al. 1994). The original labeling of the pigments
in the structures of LHC II (Liu et al. 2004) and
LHC I, particularly in Lhca4 (Ben-Shem et al.
2003), is provided in Table 1. In both structures,
pseudo-symmetry in the arrangement of the protein fold determines the symmetry-related positions of the bound pigments.
In the stromal layer of LHC II (Figure 4a),
helices I and III bind two pairs of symmetry-related Chl a (a1–a4 and a2–a5), while in the lumenal layer (Figure 4b) there is only one pair of Chl a
counterparts (a3 and a6). In both layers, each
symmetry-related molecule of Chl a is accompanied by a pigment (Chl a or Chl b) located
peripherally at a short distance. Each Chl a
molecule bound to helices I and III form a dimer
with its immediate neighbor. The pseudo-symmetry in the lumenal layer is disrupted by two Chl b
molecules, a7 and b605, located between helices I
and II. Each pigment in the group of symmetryrelated Chl a molecules (a1–a6) approaches a
carotenoid molecule at a short distance (3–4 Å in
the LHC II crystal structure), which form a Chl–
carotenoid contact, enabling either quenching of
Chl a triplet states by carotenoids that prevent
formation of toxic singlet oxygen (Kühlbrandt
et al. 1994) or direct energy transfer from Chl a to
the carotenoid molecule (Ma et al. 2003).
Comparison of the layers of pigments in LHC
II and Lhca4 in Figure 4 shows that the majority
of pigments in LHC I retain the positions of the
pigments found in the crystal structure of LHC II
although the orientation of the planes of the tetrapyrrole rings in several pigments is changed
relative to those in LHC II (Ben-Shem et al. 2003).
One-to-one correspondence can be found between
almost all pigments of LHC II and the pigments of
LHC I with the exception of the LHC II-specific
Chl b-605 and LHC I-specific linker 1 and linker 2
(Table 1).
Three pigments in the LHC I structure can be
related to Chl b-601 in LHC II. A Chl molecule
37
Figure 3. Model of three-dimensional structure of the Lhca4 polypeptide based on secondary structure prediction, and structural
homologies of LHC I and LHC II. (a) Top view. (b) Side view. N and C label the N- and C-termini, respectively. I–IV, helices. Quality
check of the model using Procheck (Laskowski et al. 1993) indicates that more than 91% of the residues are in most favored regions of
the Ramachandran plot. Molecular graphics rendered using modeled atomic coordinates of Lhca4 and Web Lab Viewer from
Molecular Simulations. Modified from Melkozernov and Blankenship (2003).
labeled as linker 3 in Lhca2 (Chl 21033)
(Figure 4c) occupies a location similar to that in
the LHC II monomer suggesting that this pigment
is a Chl b molecule bound by the N-terminus of the
Lhca4 protein. Similarly, Chl molecules labeled as
linker 3 in Lhca4 (Chl 41033) and linker 3 in Lhca3
(Chl 31033) represent the Chl b molecule bound to
the N-terminus of the neighboring Lhca1 and
Lhca2, respectively. The Chls identified as linker 1
in Lhca1 (Chl 11031), Lhca2 (Chl 21031), Lhca3
(Chl 31031), and Lhca4 (Chl 41031) are unique for
LHC I. Modeling of the helix I in each subunit
suggests that this pigment is also bound by the
N-termini of the subunits in close proximity to Chl
a a4.
3D modeling of helix II in LHC I and LHC II
based on primary sequences of the proteins,
(Melkozernov and Blankenship 2003) predicted
that the outer surface of helix II is very diverse in
terms of electrostatic and hydrophobic interactions. Figure 5 compares the modeled 3D structures of Lhca1, Lhca2, Lhca3 and Lhca4. In higher
plant LHCs, seven amino acid residues between
the potential protein ligands to chlorophylls b6
and b5 in the second helix are always hydrophobic
with the exception of the presence of a 100%
conserved histidine residue in Lhca4 (Figures 5a
and 6a). Location of the strong Chl ligand in
Lhca4 between protein ligands to chlorophylls b6
and b5 suggests binding of the putative molecule
of Chl close to Chl b5 (Melkozernov and Blankenship 2003). Two rotamer conformations of the
histidine residue predict strong excitonic interactions of the bound pigment with Chl b5, which
38
Figure 4. Comparison of the stromal (upper panel) and lumenal (lower panel) layers of pigments in the LHC II (a, b) and Lhca4 (c, d).
Molecular graphics rendered using Web Lab Viewer from Molecular Simulations, and atomic coordinates of the Chls and luteins from
the crystal structure of spinach LHC II (pdb code 1RWT, Liu et al. 2004) and homology 3D model of Lhca4 (Melkozernov and
Blankenship 2003) built on the basis of LHC I protein assigned to Lhca4 in the crystal structure of PS I–LHC I from pea (pdb code
1QZV; Ben-Shem et al. 2003). For the sake of comparison majority of pigments are labeled according to Kühlbrandt et al. (1994).
Pigments unique for the structures are labeled according to original models (see Table 1). Phytyl groups of the pigments are removed
for clarity.
might be the case in vitro, or liganding of linker 2
Chl in vivo (as shown in Figure 5a). Figure 6
illustrates a sequence alignment of the region of
helix II in LHC I proteins from different species of
higher plants. The comparison shows that Lhca1
and Lhca3 also possess a histidine residue in the
helix II, however, the residue is located in a different place compared to that in Lhca4 (Figures 5b
and c). In Lhca3 this residue also might be a ligand
to linker 2, which is displaced, compared to linker
2 in Lhca4. A His residue in Lhca1 is not conserved (Figure 6b). Since helix II of Lhca1 was
shown to be involved in a tight protein–protein
interaction with one of the helices of PsaG of the
PS I (Ben-Shem et al. 2003), the His residue in this
protein might not be important for pigment
binding.
Comparison of the 3D structures of LHC II
and LHC I demonstrates that the pigment layouts
in both proteins are largely similar. Only two
pigments, Linkers 1 in all Lhca proteins and
Linkers 2 in Lhca3 and Lhca4, are unique for
LHC I. 3D homology modeling of LHC I proteins
allows us to predict possible ligands to Linkers 2 in
Lhca3 and Lhca4.
Excitonic interactions in Lhca4 and the problem
of the terminal emitter
The general structural feature of the pigment
layout in both LHC II and the LHC I proteins is
that each symmetry-related Chl a molecule
(a1–a6) bound to helices I and III is involved in
interaction with a closely located pigment,
resulting in formation of strongly interacting
dimers (Figure 4). Despite this similarity, orientations of the tetrapyrrole planes in some pigments in Lhca4 (e.g. a3, a5, b3, a6, a7) are
significantly changed. Moreover, shorter centerto-center distances in dimers in Lhca4 and the
presence of extra pigments could result in stronger excitonic interactions than in LHC II. The
latter could explain a difference between LHC I
and LHC II associated with the presence in LHC
I of pigments with significantly red shifted
39
Table 1. Labeling and identification of pigments in stromal and
lumenal layers of LHCII and Lhca4
Pigments
in LHCII
Identity
(Chl a or Chl b)
a1 (610)
a2 (612)
a4 (602)
a5 (603)
b1 (608)
b 601
a
a
a
a
b
b
b2 (611)
b5 (609)
a
b
a3 (613)
a6 (604)
b3 (614)
b6 (606)
a7 (607)
b 605
a
a
a
b
b
b
Pigments in
Lhca4
Stromal layer
a1 (41011)
a2 (41012)
a4 (41014)
a5 (41015)
b1 (41021)
linker 3 (21033)
from Lhca2a
b2 (41022)
b5 (41025)
linker 1 (41031)b
linker 2 (41032)c
linker 3 (41032)d
Lumenal layer
a3 (41013)
a6 (41016)
b3 (41023)
b6 (41026)
a7 (41017)
–
Suggested
identity
a
a
a
a
b
b
a
b or a
b or a
b or a
b
a
a
a
b
b
Pigments are labeled according to Kühlbrandt et al. (1994).
Numbers in parenthesis correspond to original pigment
nomenclature (pdb code 1RWT for LHC II and 1QZV for
Lhca4 in the PS I–LHC I crystal structure). See Figure 4 for
details.
a
Being analogous to Chl b 601 in LHC II, the pigment is likely
to be bound to Lhca4 (see Figure 4).
b
This Chl is a close neighbor to a4 in all Lhca proteins.
c
Unique for Lhca4 and Lhca3.
d
Being analogous to Chl b 601 in LHC II, the pigment is likely
to be bound to a neighboring Lhca1.
absorption (red pigments) and a prominent
Stokes shift of the fluorescence.
In LHC II, Chl a homodimer a2–b2 exhibits
the strongest excitonic interaction with a coupling
strength of 145 or 119 cm)1 depending on calculation method (see V121 and V122 for LHC II in
Table 2), which could satisfactorily explain a red
shift in site energy for the terminal emitter at
680 nm (Rogl and Kühlbrandt 1999; Remelli et al.
1999; van Amerongen and van Grondelle 2001;
Schubert et al. 2002; Liu et al. 2004). The terminal
emitter is located on the surface of the LHC II
trimer and acts as an excitation energy donor
either to the surface of the PS II core antenna
(Yakushevska et al. 2001; Barber 2003) or to the
surface of the PS I core antenna after docking to
the PsaH subunit (Haldrup et al. 2001; Scheller
et al. 2001; Jensen et al. 2003).
In the LHC I protein from higher plants, the
presence of the red pigments determines a significant red spectral shift of the steady-state fluorescence maximum in the region from 702 to 730 nm
depending on the type of the Lhca protein (Schmid
et al. 1997, 2002; Ganeteg et al. 2001; Croce et al.
2002; Morosinotto et al. 2002; Casteletti et al.
2003). Despite a different degree of the red spectral
shift in all Lhca proteins, biochemical and mutational studies suggest that the low energy absorption in the 690–710 nm region originates in the
pigment cluster, a5–b5–b6 located between transmembrane helices I and II (Rupprecht et al. 2001;
Morosinotto et al. 2002, 2003a; Schmid et al.
2002; Casteletti et al. 2003).
The homology-based model of Lhca4
(Figure 3) predicts the orientation of the vectors of
the Qy transition dipole moments in Chls, which
permits estimation of the coupling strengths in the
Chl dimers. Table 2 compares the coupling
strengths (V12) in excitonically interacting Chls in
LHC II and Lhca4. V121 represents the coupling
strength calculated using the point-dipole
approximation approach applied earlier for LHC
II (van Amerongen and van Grondelle 2001; van
Amerongen et al. 2000; Schmidt et al. 2001; Liu
et al. 2004; see Equation (A.1) in Appendix A). V122
is calculated according to Equation (A.1) but
accounted for the complex dependence of the
chlorophyll dipole strength on the in situ refractive
index and coulombic interactions (Knox and van
Amerongen 2002; Knox 2003; Knox and Spring
2003). Earlier reports claim that the point-dipole
approximation approach satisfactorily predicts the
site energy of the terminal emitter in LHC II (van
Amerongen and van Grondelle 2001; Schubert
et al. 2002; Liu et al. 2004). Surprisingly, application of similar approaches to LHC I proteins fails
to explain the significant shift in absorption of the
red pigments in LHC I, thus demonstrating that
the approaches based only on the mutual geometry
of the interacting Chls do not work in LHC I. The
reader should be aware that the values of the
coupling strengths for Lhca4 in Table 2 are not
likely to reflect the real interactions. The taking
into account of additional specific molecular
details is needed (see below).
Table 2, however, allows the conclusion that
changes in mutual geometry and interpigment
40
Figure 5. Comparison of 3D structural models of the second transmembrane helix in Lhca4 (a), Lhca1 (b), Lhca3 (c) and Lhca2 (d).
Structures are obtained by 3D fitting of the primary sequences of this region in Lhca proteins from tomato. In all Lhca proteins the
helix binds three pigments, b1, b5 and b6. In Lhca4 and Lhca3, the conserved His residues might serve as ligands to linker 2 pigments.
Scale and orientation are similar for the models. Modified from Melkozernov and Blankenship (2003).
distances in Lhca4 result in a changed redistribution of the coupling strengths among dimers. In
contrast to LHC II, where the strongest dimers are
a2–b2, a6–b6 and a5–b5, calculations of the excitonic coupling strengths in Lhca4 show that the
strongest coupling is predicted for Chl a homodimer a4-linker 1 (V121 value of 153 cm)1, see
Table 2), Chl a–b heterodimer a1–b1 (140 cm)1),
and Chl a–b heterodimer a5–b5 (83 cm)1).
Pigment–protein interaction is one of the factors that affect the site energy of the pigments.
Influence of the protein environment on the spectral properties of LHC I proteins was demonstrated recently by Morosinotto et al. (2003a) who
showed that exchange of an asparagine residue
that binds a5 in Lhca4 by a histidine, resulted in a
blue shift of the low temperature fluorescence
peak. In silico mutation of this pigment binding
site in the 3D homology model of Lhca4 predicts
that substitution of Asn for a bulky His residue
could move Chl a-a5 out of close interaction with
Chl b or Chl a b5, which could trigger the spectral
changes.
Additional factors that might be responsible for
the red absorption shifts of the Chls include conformational changes in the planarity of the Chl
macrocycle caused by neighboring protein residues
(Gudowska-Nowak et al. 1990; Fajer 2000; Cogdell et al. 2002) as well as the influence of specific
charged amino acid residues on the site-energy of
low energy absorbing pigments (Damjanovic et al.
2002a). Higher resolution structural data of LHC I
is needed to take these structural factors into
account.
The 2.72 Å resolution crystal structure of
spinach LHC II illustrates remarkable structural
connections among the pigments bound in the
interface between helices I and II (Liu et al. 2004).
Water molecules are involved in direct liganding of
Chls a6, b6, a7 and b1. A histidine residue binding
41
Figure 6. Sequence alignment of the region of the helix II in
Lhca4 (a), Lhca1 (b) and Lhca3 (c) from different species. Conserved pigment-binding sites and potential Chl ligands are shown
in bold. Accession number of the sequences: Lhca4 from pea
(Q9SQL2), tomato (S14305), pine (Q07489), Chlamydomonas
reinhardtii (AW676138 and BE761374); Lhca1 from tomato
(P12360), Arabidopsis thaliana (Q01667), barley (Q36717), pine
(Q02069), Chlamydomonas reinhardtii (AAD03734); Lhca3 from
pea (Q32904), Arabidopsis (Q43381), pine (Q02071).
Chl a-a5 also donates an H-bond to the side group
of the neighboring Chl b-b5. It is likely that in
LHC I proteins where the orientations of a5, a6
and a7 are significantly changed, the pattern of
hydrogen bonding might be disturbed. It should be
noted that a specific hydrogen bonding in Chl
a–water aggregates produces a significant red shift
in absorption of Chl a (from 670 nm in monomers
to 750 nm in aggregates) (Scherz et al. 1991).
Results of a recent hole-burning study of the
PS I–LHC I from higher plants (Ihalainen et al.
2003) indicate unusual spectroscopic properties of
the Chl molecules comprising a terminal emitter in
LHC I. Comparison of the Huang–Rhys factors
of the lowest Chl (BChl) energy states in various
light-harvesting antennas (Table 3), demonstrates
that the LHC I antenna from higher plants possesses the strongest electron–phonon coupling of
all the photosynthetic antenna systems. An
increased Huang–Rhys factor reflects a suppression of the zero-phonon line and a dominance of
the phonon wing in the optical transition due to
low frequency intramolecular vibrations of Chls
and the vibrations induced by interaction with the
environment (van Amerongen et al. 2000; Reinot
et al. 2001). Such a spectral behavior is consistent
with the formation of Chl dimers with strong
pigment–pigment interactions with an admixture
of charge transfer state (Hayes et al. 2000;
Zazubovich et al. 2002; Ihalainen et al. 2000,
2003). Self-trapping of this state in a protein
environment of the interface between helices I and
II containing water and charged protein residues
in LHC I could promote a spread of the charge
through the pigment cluster and formation of a
polaron state, a common cause of the red spectral
shift (Polivka et al. 2000; Damjanovic et al.
2002b).
This energy-localizing region is a possible site
for energy loss in LHC I. In LHC I dimers in
vitro, an energy redistribution that occurs on the
time scale of tens of picoseconds was ascribed to
intersubunit energy transfer (Melkozernov et al.
1998; Gobets et al. 2001a). Gobets et al. (2001a)
noted that the characteristics of this energy
transfer are indicative of the excitation energy
loss in the spectral range of absorption and fluorescence of the red pigments in LHC I. The
mechanisms of the loss are not clear for LHC I.
Among the possible causes of the loss the authors
suggested, are the presence of superradiance of
the excitonically-coupled pigments (Monshouwer
et al. 1997), quenching of the excitation by a
nearby amino acid residue (Peterman et al. 1998)
and a strong interaction of the Chl Qy state with
the S1 state of carotenoids (van Amerongen and
van Grondelle 2001; Polivka et al. 2002). An
indirect indication of energy losses in LHC I
proteins is a decreased fluorescence yield of LHC
I proteins compared to that of LHC II proteins,
possibly resulting from a constitutive dissipative
conformation of LHC I proteins (Morosinotto
et al. 2002). Changes in the protein conformation
might be induced by binding of carotenoids with
distinct molecular structures (Polivka et al. 2002).
Structural aspects of energy coupling of the
peripheral antenna to the PS I core
Energy entry paths from LHC I to the PS I core
antenna
Time-resolved spectroscopic studies of LHC I
complexes in vitro confirmed that elementary
energy transfer processes in the chlorophyll a/bbinding LHC I are as effective and fast as those in
the Ch l a binding PS I core antenna (reviewed in
42
Table 2. Comparison of the coupling strengths in strongly interacting Chl dimers in LHC II (Liu et al. 2004) and Lhca4 (homology
based 3D model)
LHCII
a
Lhca4
Interacting Chls
Chl
Chl
Chl
Chl
Chl
Chl
Chl
a
a
a
a
b
a
a
a2–Chl
a6–Chl
a5–Chl
a1–Chl
a7–Chl
a3–Chl
a4–Chl
a
b
b
b
b
a
b
b2
b6
b5
b1
b6
b3
601
Rc–c
(Å)
c
9.76
8.05
9.74
11.57
9.46
9.30
12.79
cos b
d
1
V12
e
)1
)0.79
0.80
)0.88
)0.54
0.88
0.21
)0.69
2
V12
f
b
Interacting Chls
)1
(cm )
(cm )
144.9
123.4
106.7
68.9
63.6
)62.5
54.1
118.9
103.6
89.7
57.9
54.0
)51.3
45.5
Chl a a2–Chl a b2
Chl a a6–Chl b b6
Chl a a5–Chl b b5
Chl a a1–Chl b b1
Chl b a7–Chl b b6
Chl a a3–Chl a b3
Chl a a4–Chl b linker 3 from
Lhca2
Chl a a4–Chl a linker 1
Chl a linker 1–Chl b linker 3 from
Lhca2
linker 2–linker 3
Rc–c
Å
c
cos b
d
1
V12
e
)1
2
V12
f
(cm )
(cm)1)
9.8
8.0
8.0
8.6
10.2
7.9
13.2
)0.65
0.32
)0.98
)0.45
0.39
0.64
)0.67
74.6
28.3
83.3
140.3
35.9
46.0
30.4
61.2
23.8
70.0
117.9
30.5
37.7
25.5
8.2
12.6
0.98
0.61
152.7
57.9
125.4
48.7
11.4
)0.72
57.0
47.9
See Figure 4 and Table 1 for pigment’s labeling.
a
Coordinates of the pigment’s atoms taken from the crystal structure of LHC II from spinach (pdb file 1RWT; Liu et al. 2004).
b
Atom coordinates from the homology based 3D model of Lhca4.
c
Distance between centers of the molecules in Å.
d
Cosine of the angle between two transition dipoles running through atoms NB and ND of the pyrrole ring.
e
V121 , coupling strength (cm)1) calculated as in van Amerongen and van Grondelle (2001).
f
V122 , coupling strength calculated based on in situ Chl dipole strengths (Knox and Spring 2003, see Appendix A).
Table 3. Comparison of electron–phonon coupling properties of the lowest energy states of chlorophylls (bacteriochlorophylls) in
various photosynthetic light-harvesting antennas
Light-harvesting antenna
BChl a light-harvesting protein
(Fenna–Matthew–Olson protein)
from green sulphur bacteria
Chl a containing CP47 from PS II
Chl a containing CP43 from PS II
Chl a/b binding CP29 from higher plants
Chl a/b binding LHC II from higher plants
BChl a binding LH1 from purple bacteria
BChl a binding LH2 from purple bacteria
Peridinin–Chl a protein (PCP) from dinoflagellates
Chl a containing PS I core from cyanobacteria
Chl a/b binding LHC I from higher plants
Huang–Rhys
factora
Reference
0.25
0.2
0.4
0.5
0.8
0.85
1.05
1
2.0
2.9
Matsuzaki et al. (2000)
Chang et al. (1994)
Jankowiak et al. (2000)
Pieper et al. (2000)
Pieper et al. (1999)
Timpmann et al. (2004)
Timpmann et al. (2004)
Kleima et al. (2000)
Hayes et al. (2000)
Ihalainen et al. (2003)
a
Huang–Rhys factor reflects the strength of electron–phonon coupling of the electronic transition indicating an average number of
phonons excited at the transition.
Gobets and van Grondelle 2001; Melkozernov
2001) and in the Chl a/b binding LHC II antenna
(reviewed in van Amerongen and van Grondelle
2001; van Amerongen and Dekker 2003). In LHC I
monomers, interpigment distances within the
lumenal and stromal layers in the range of 8–17 Å
(Figure 3) could enable relatively fast Chl b to Chl
a and Chl a to Chl a energy transfer in the range of
0.2–0.7 ps, while energy redistribution among the
Chls of different layers followed by localization of
the excitation on the terminal emitter occurs within
2–8 ps.
43
Despite largely similar pigment layouts in
LHC II and LHC I monomers, the terminal
emitters in these complexes are different. In evolution, natural selection of the structural changes
in LHC I were driven by adjustments of the
pigment orientations relative to the PS I core
antenna, resulting in a location of the terminal
emitter in LHC I in the interface between helices
I and II in proximity to Chls on the periphery of
the PS I core antenna. The structural changes
also involved binding of extra pigments, including
linkers in LHC I monomers and gap pigments in
the cleft between the PS I core and the LHC I
that structurally connect the terminal emitters
and the PS I core antenna network (Figures 7
and 8). The gap pigments appear to provide
independent functional pathways for energy
transfer from terminal emitters in LHC I monomers to the PS I core antenna network, thus
demonstrating the functional significance of the
monomeric light-harvesting complexes in the
eukaryotic peripheral antenna.
Figure 7 illustrates pigment arrangements in
the Lhca4 monomer with the linker pigments of
its neighbors (Lhca2 and Lhca1) and the gap
pigments coupled to the interface between the
Lhca4 and the PS I core. This region appears to
be important for energy coupling between the
LHC I and the PS I core, since 7 out of 10 gap
pigments are located here. These pigments are
oriented as a chain of Chls with center-to-center
distances in the range of 11–12 Å. Short interplanar distances in this chain (5 Å) would
predict that the location of the phytyl group
between the interacting Chl macrocycles is
unlikely due to possible steric hindrance. Since
the relative positions of ND and NB nitrogen
atoms in the Chl macrocycle, through which the
Qy transition vector runs, and the C-173 carboxylic group which is esterified with the phytyl
residue are fixed, the model suggests the orientation of the Qy vectors in this group of Chls.
The gap pigments in Figure 7 are modeled as
Chl a molecules. The rates of the Förster energy
transfer calculated for pairs of pigments in
Lhca4 including linkers and the gap pigments
predict a subpicosecond connectivity of the pigments in Lhca4 and the gap pigments (A.N.
Melkozernov and R.E. Blankenship, unpublished). A sum of energy transfer rates in the
pathway including a chain of gap pigments
(gap7, gap6, gap4, gap2, gap 3) and Chl a 11235
(B35 in the cyanobacterial PS I) in the PS I core
antenna corresponds to a transfer time of 2 ps
(Figure 7). Similar independent pathways of the
fast energy transfer include linker 1 of Lhca1,
gap1 and Chl a 11220 (B20) and a6, b6, b7 and
Chl 11233 (B33). These chains of pigments
enabling pairwise subpicosecond hopping of the
excitation most likely represent the energy
Figure 7. Top view of pigments in the interface between Lhca4 and the PS I core. Color code: orange, two molecules of carotenoids
(luteins); blue, Chls in the stromal layer of Lhca4; light green, lumenal Chls in Lhca4; light blue, linkers including linker 1 from Lhca1
and linker 3 from Lhca2; red, gap Chls; dark green, Chls of the PS I core antenna. The pigments are modeled based on atomic
coordinates of the tetrapyrrole rings of Chls in the PS I–LHC I crystal structure (pdb code 1QZV; Ben-Shem et al. 2003) and the
atomic coordinates of the PS I core antenna pigments from cyanobacteria (pdb code 1JBO; Jordan et al. 2001). See text for discussion.
44
Figure 8. Pigment arrangement of the light-harvesting antenna network in the PS I–LHC I supercomplex from higher plants based on
the crystal structure with 4.4 Å resolution (Ben-Shem et al. 2003). Color code: light green, PS I core antenna Chls; red, pigment in
clusters with strong interpigment interactions; dark green; Chls in the peripheral LHC I antenna; magenta; gap pigments. Encircled are
clusters of pigments in the LHCI peripheral antenna (terminal emitters a5–b5, clusters A–D) and in the PS I core antenna network
(clusters I–VIII). Cluster I, A38, A39 and A40 (linker); cluster II, A31, A32, B06, B07, B38, B37 and B39 (linker); cluster III, B31, B32,
B33; cluster IV, B24, B25, B26; cluster V, B22, B34; cluster VI, A33, A34, A24, A35; cluster VII, A26, A27; cluster VIII, A12, A14.
Pigments are labeled according to nomenclature of the PSI core Chls by Jordan et al. (2001). Assignment of the clusters to the longest
wavelength absorbing red pigments in the PSI core antenna is not conclusive (see Byrdin et al. 2002; Damjanovic et al. 2002a; Sener
et al. 2002; Yang et al. 2003).
transfer pathways that allow for the excitation
escape from LHC I monomers to the PS I core
antenna network. The scenario predicts that
picosecond delivery of the excitation to the surface of PS I would compete with the process of
excitation equilibration and localization of the
excitation in the terminal emitter, which also
occur on the picosecond time scale (Melkozernov
et al. 2000; Gobets et al. 2001a).
The crystal structure of the PS I–LHC I (BenShem et al. 2003) demonstrates that the LHC I
peripheral antenna is attached to the PS I core as a
belt of four evenly spaced Lhca monomers. The
distances between LHC I monomers indicate relatively weak intersubunit interactions. Recent
low-resolution electron microscopy studies of the
PS I–LHC I supercomplexes from green algae
C. reinhardtii (Germano et al. 2002; Kargul et al.
2003) reported on the presence of additional Lhca
polypeptides interacting independently with the PS
I core. Overall, this suggests that the Lhca
monomers might be independent suppliers of
energy to the PS I core since the excitation equil-
ibration between the LHC I subunits is slow (see
below).
Structural causes for the slow energy transfer
phases in PS I–LHC I
Energy transfer studies of the PS I–LHC I supercomplexes from higher plants (Ihalainen et al.
2002) and the green alga Chlamydomonas
reinhardtii (Melkozernov et al. 2004) reported a
slow 80–120 ps equilibration phase in the excitation dynamics of the PS I–LHC I, in addition to the
photochemical trapping in the PS I core antenna.
In higher plant PS I supercomplexes with an
increased number of the low energy pigments in the
peripheral antenna, the slow phase was associated
with the uphill energy transfer processes from the
red pigments in Lhca1–Lhca4 heterodimer to the
PS I core antenna, while in the PS I–LHC I from
Chlamydomonas, the slow equilibration phase
involves predominantly bulk LHC I antenna Chls,
which are isoenergetic with the bulk PS I core
antenna. The latter suggests that the slow energy
45
transfer processes are not limited only to the uphill
energy transfer from the red pigments in LHC I to
the PS I core, but also have structural origins.
Analysis of the structure provides several possible explanations for the slow excitation energy
equilibration in the PS I–LHC I supercomplexes
from higher plants and green algae. Presence of the
Chls assigned in the crystal structure of PS I–LHC
I from pea to linkers between the LHC I monomers predicts that the excitation energy transfer
between subunits in the LHC I belt is in the range
of several picoseconds. However, excitation
equilibration between the monomers in LHC I
dimers in vitro takes tens of picoseconds (Melkozernov et al. 1998; Gobets et al. 2001a). Intersubunit energy redistribution in the LHC II trimers in
vitro was found to occur on a similar time scale
(van Amerongen and van Grondelle 2001). Since
in each LHC I monomer the excitation localizes on
a terminal emitter cluster a5–b5, the slow intersubunit energy equilibration might be explained by
a large distance (40 Å) between a5–b5 of the
energy donor and a5–b5 of the energy acceptor, at
least between Lhca1 and Lhca4. Another structural feature that might interfere with the rate of
intersubunit energy transfer is localization of the
Chl b molecules in the intersubunit interface
observed in the crystal structure of LHC II (Liu
et al. 2004). The function of Chl b as linkers (e.g.
pigment analogous to Chl b-601 in all LHC I
monomers) suggests an energetically unfavorable
uphill energy transfer from Chl a spectral forms of
one subunit to a bridging Chl b in the intersubunit
interface.
A slow energy redistribution process such as
that observed in the LHC I dimers in vitro could be
kinetically unfavorable in the LHC I monomers
that are structurally coupled to the PS I core, since
each Lhca protein seems to have a faster energy
transfer pathway to the PS I core antenna network
via gap pigments. On the basis of distances
between pigments in these pathways, the fastest
energy transfer would be expected for the Lhca1–
Lhca4 interface while the slowest should be
observed for the Lhca2 interface.
Energy loss in the terminal emitter associated
most probably with the structural peculiarities of
the interface between helix I and helix II could
decrease the efficiency of excitation energy transfer
from the peripheral antenna to the PS I core
(Gobets et al. 2001a).
Biological functions of the red pigments in the
PS I–LHC I supercomplex
Pigment clusters in the PS I antenna network ensure
better spectral overlap of P700 and the
light-harvesting antenna
Structural coupling of the LHC I antenna to the
PS I core increases the light-harvesting capacity of
the PS I supercomplex. In the PS I core antenna,
the relative positions of Chls are optimized for
efficient delivery of the excitations to the reaction
center (Byrdin et al. 2002). A dense packing of the
pigments in the PS I core enhances connectivity of
the antenna via random subpicosecond hopping of
the excitations in the network. Energy equilibration between the pools of pigments occurs on the
picosecond time scale and involves the longestwavelength absorbing (red) pigments.
Overlap of the structures of the cyanobacterial
PS I core (Jordan et al. 2001) and the PS I–LHC I
from pea (Ben-Shem et al. 2003) shows that the
overwhelming majority of the pigments in the PS I
core antenna retain similar orientations and positions in both structures. The changes are minimal
and they affect several pigments on the periphery
of the core antenna network (Ben-Shem et al.
2003). This suggests that the orientation of the
major pools of the red pigments might be preserved in the PS I core antenna from eukaryotes
(at least in the PS I core from pea) as compared to
that from cyanobacteria. One of the structural
changes that could affect the pool of the red pigments in the eukaryotic PS I core includes a
change in a position of Chl B33 (labeled according
to Jordan et al. 2001), which is a part of the
peripherally located Chl trimer (see cluster III in
Figure 8). In the cyanobacterial PS I core this
trimer, B33–B32–B31, is assigned to the longest
wavelength absorbing Chls (Jordan et al. 2001;
Byrdin et al. 2002). The other clusters of red pigments suggested in recent structure-based modeling studies (Byrdin et al. 2002; Damjanovic et al.
2002a; Sener et al. 2002; Yang et al; 2003; see
Figure 8) are not changed in the PS I core antenna
from pea (Ben-Shem et al. 2003). Unfortunately,
the modeling studies did not arrive at a consensus
on the identification of all red absorbing Chls in
the PS I core from Synechococcus elongatus.
However, a general agreement might be reached
on two symmetry related dimers, A32–B07 and
46
A38–A39, which are located in the lumenal part of
the PsaA–PsaB interface close to the linkers B39
and A40, respectively (see clusters I and II in
Figure 8). Additional clusters of the pigments
proposed by the modeling studies represent
potential candidates for the pigments that promote
a low energy shift of different magnitude contributing to the spectral heterogeneity in the 670–
710 nm region. Excitonic interactions in these
clusters favor further broadening of the absorption
spectra and better overlap with the absorption
spectrum of the primary donor P700 in the reaction center, which leads to efficient energy trapping. Pigment clusters in the PS I core antenna
ensure a spectral overlap with the terminal emitters
in the LHC I that would favor a thermally assisted
uphill energy transfer (Jennings et al. 2003).
The number of red pigments in PS I is speciesdependent (Gobets et al. 2001b; Gobets and van
Grondelle 2001; Melkozernov 2001; Reinot et al.
2001). Formation of additional red absorbing species is induced by structural oligomerization of the
PS I core complexes. In cyanobacteria, trimerization of the PS I core complexes results in strong
interactions of the Chl cluster adjacent to the
peripheral PsaL subunit (see cluster II in Figure 8)
promoting further red spectral shifts (Karapetyan
et al. 1999). Structural association of the peripheral
LHC I antenna with the PS I core in green algae and
higher plants was suggested to induce low energy
spectral shifts of the PS I–LHC I emission (Knoetzel
et al. 1998; Kargul et al. 2003). Since the interface
between the LHC I and the PS I core is filled with
additional gap pigments, interactions of those Chls
with the Chls of the peripheral antenna or core
antenna could induce red spectral shifts. However,
distances among the majority of pigments in the PS
I–LHC I cleft are beyond the range allowing for
strong excitonic interactions. The only exception is
the interaction of the Chl gap 5 with the Chl a 11228
(or B28) (see Figure 7). This pair of pigments has a
center-to-center distance of 7.4 Å. Mutual geometry of the pigments predicts an excitonic coupling of
195 cm)1 (see Appendix A). Again as with the
excitonic interactions in the Lhca4, this is not sufficient to explain a significant red shift in absorption
unless the interacting pigments have unusual protein environment inducing additional low energy
shifts.
The red pigments in the Lhca proteins (Schmid
et al. 1997, 2002; Croce et al. 2002; Ganeteg et al.
2001; Casteletti et al. 2003; Melkozernov and
Blankenship 2003) associated with the terminal
emitters form the third separate pool of the low
energy absorbing Chls in the PS I–LHC I supercomplex in addition to the red pigments in the PS I
core and interaction-induced pigment clusters.
Concentrating the excitation around the reaction
center
A decade ago Trissl (1993) predicted that red
pigments in the PS I core antenna extend the
absorption cross-section of the PS I in the region
above 700 nm and focus the excitation to the
reaction center. Positioning of two symmetry-related clusters of red pigments in proximity to
linking Chls (clusters I and II in Figure 8) agrees
with these functions of the red pigments in the PS I
core. The fact that clusters of the red pigments in
the PS I core antenna are structurally well connected with the other Chls in the network makes
these pigment transient excitation traps on the
picosecond time scale followed by efficient excitation energy trapping by the reaction center (Trissl
1993; Melkozernov 2001; Gobets and van Grondelle 2001).
Downhill enhancement of the energy transfer from
LHC II to PS I
The functioning of the PsaL-adjacent cluster of
pigments in the PS I core antenna (cluster II in
Figure 8) as a transient trap in the PS I–LHC I
might be considered as a biological adaptation that
enhances the downhill energy transfer from the
attached LHC II to the PS I core antenna. Two
groups of pigments, lumenal cluster A31–A32–
B06–B07 and stromal cluster B37–B38 including
linker B39, are both energetically accessible from a
chain of pigments bound to PsaL and PsaH in the
PS I–LHC I supercomplex. This chain includes
pigments H01, L01, L02 and L03 (Figure 8). The
interpigment distances of 12–13 Å in the chain
could determine a subpicosecond energy transfer
pathway to the cluster of red pigments. Docking of
the LHC II to the PS I core at the PsaH docking site
in State 1–State 2 regulatory transitions (Lunde
et al. 2000; Wollman 2001) could induce a downhill
energy transfer from the LHC II trimers (fluorescence at 680 nm) to the low energy-absorbing
cluster of pigments in the PS I core antenna (cluster
II in Figure 8). During evolution, the structural
changes of the eukaryotic PS I that enhance the
47
efficiency of this energy transfer pathway involved
changes in orientation of one of the pigments bound
to PsaL (CL11501 or L01 in Figure 8), which is in
close proximity to a pigment bound to the eukaryotic-specific PsaH subunit (H01 in Figure 8).
Photoprotection against excess excitation energy
Figure 8 visualizes the functional connections of
the terminal emitters in LHC I monomers (clusters
A–D) with the clusters of red pigments or potential
candidates for this role. Terminal emitters in LHC
I slow down the energy delivery from the peripheral antenna to the PS I core due to possible energy
losses in the interface between helices I and II.
However, the excitations from bulk LHC I pigments have a chance to escape localization in the
physiological deep trap via a competitive fast
energy transfer pathway to the PS I core through
gap pigments (at least in the Lhca1–Lhca4 interface; see Figure 7). The extent of energy loss in the
peripheral antenna and thus the extent of the
competition of these energy transfer pathways
might be regulated through non-light-harvesting
carotenoids in LHC I (Morosinotto et al. 2003b)
or any other processes that result in functional
uncoupling of the LHC I monomers from the
peripheral antenna (Moseley et al. 2002; Desquilbet et al. 2003; Doan et al. 2003). Energy loss in
the pigment clusters of LHC I might be considered
as a photoprotective mechanism against excess
light.
where V12 is a coupling strength (in cm)1); l1 and
l2 are transition dipole moments of the chlorophylls (in Debyes); n, refractive index, R12, distance (in nanometers) between centers of the Chl
molecules, K,$orientation
factor defined as
$
~
l1 ~
l2 3ð~
l1 R 12 Þð~
l2 R 12 Þ through normalized
vectors of the transition dipole moments and
normalized distance vector. Recently, Knox and
coworkers (Knox 2003; Knox and Spring 2003;
Knox and van Amerongen 2002) commented on
the complex nature of the dependence of the
chlorophyll dipole strengths on the refractive
index. On one hand, dependence of the dipole
strengths of Chl a and Chl b on the in situ
refractive index that account for the influence of
Lorentz or cavity field parameters is determined by
the following empirical equations (Knox and
Spring 2003):
DChla ðnÞ ¼ 20:2 þ 23:6ðn 1Þ;
ðA:2Þ
DChlb ðnÞ ¼ 9:8 þ 27:7ðn 1Þ;
ðA:3Þ
where DChla and DChlb are dipole strengths (in
Debye2) of Chl a and Chl b, respectively, calculated for n ¼ 1.5 (refractive index of the in situ
protein environment). On the other hand, the 1/n2
factor in Equation (A.1) takes account of dependence of the chlorophyll dipole strengths on coulombic interactions. Table 2 compares the
coupling strengths of the strongly interacting pigments in LHC II and LHC I calculated using these
approaches (see V121 and V122 for LHC II and LHC
I, respectively).
Acknowledgements
This work was supported by an NRI/CSREES/
USDA Grant 2003-35318-13665 to ANM, and an
NSF Grant MCB 0091250 to REB. This is publication #598 of the Center for the Study of Early
Events in Photosynthesis at ASU.
Appendix A
Using the point-dipole approximation, the excitonic coupling in a dimer of chlorophyll molecules
can be calculated according to the following
equation (van Amerongen and van Grondelle
2001; van Amerongen et al. 2000):
V12 ¼
5:042 l1 l2
K;
n2 R312
ðA:1Þ
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