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R J Cogdell

Publications and source records attributed to R J Cogdell.

At least 19 recordsLinked to original sources
PubMed2004

Conjugation length dependence of internal conversion in carotenoids: role of the intermediate state.

We report on a sub-20-fs transient absorption study of the S2(1(1)B(+)(u))-->S1(2(1)A(-)(g)) internal conversion in a series of carotenoids with a number of conjugated double bonds (N) ranging from 5 to 15. For the longer carotenoids (N>or=9), the measurements reveal the existence of an additional intermediate excited state lying between the optically allowed S2 state and the lower-lying forbidden S1 state. This state enables us to explain the nonmonotonic dependence of the S2-->S1 conversion rate on N and is expected to play an important role in photosynthetic light harvesting.

Carotenoids↗
PubMed2004

The electron conduction of photosynthetic protein complexes embedded in a membrane.

The conductivity of two photosynthetic protein-pigment complexes, a light harvesting 2 complex and a reaction center, was measured with an atomic force microscope capable of performing electrical measurements. Current-voltage measurements were performed on complexes embedded in their natural environment. Embedding the complexes in lipid bilayers made it possible to discuss the different conduction behaviors of the two complexes in light of their atomic structure.

Bacterial Proteins↗
PubMed2003

Detergent structure in crystals of the integral membrane light-harvesting complex LH2 from Rhodopseudomonas acidophila strain 10050.

Integral membrane proteins are solubilized by their incorporation into a detergent micelle. The detergent micelle has a critical influence on the formation of a three-dimensional crystal lattice. The bulk detergent phase is not seen in X-ray crystal structures of integral membrane proteins, due to its disordered character. Here, we describe the detergent structure present in crystals of the peripheral light-harvesting complex of the purple bacteria Rhodopseudomonas acidophila strain 10050 at a maximal resolution of 12A as determined by neutron crystallography. The LH2 molecule has a toroidal shape and spans the membrane completely in vivo. A volume of 16% of the unit cell could be ascribed to detergent tails, localized on both the inner and outer hydrophobic surfaces of the molecule. The detergent tail volumes were found to be associated with individual LH2 molecules and had no direct role in the formation of the crystalline lattice.

Crystallization↗
PubMed2002

Photosynthetic light harvesting by carotenoids: detection of an intermediate excited state.

We present the first direct evidence of the presence of an intermediate singlet excited state (Sx) mediating the internal conversion from S2 to S1 in carotenoids. The S2 to Sx transition is extremely fast and is completed within approximately 50 femtoseconds. These results require a reassessment of the energy transfer pathways from carotenoids to chlorophylls in the primary step of photosynthesis.

Carotenoids↗
PubMed2001

The crystallographic structure of the B800-820 LH3 light-harvesting complex from the purple bacteria Rhodopseudomonas acidophila strain 7050.

The B800-820, or LH3, complex is a spectroscopic variant of the B800-850 LH2 peripheral light-harvesting complex. LH3 is synthesized by some species and strains of purple bacteria when growing under what are generally classed as "stressed" conditions, such as low intensity illumination and/or low temperature (<30 degrees C). The apoproteins in these complexes modify the absorption properties of the chromophores to ensure that the photosynthetic process is highly efficient. The crystal structure of the B800-820 light-harvesting complex, an integral membrane pigment-protein complex, from the purple bacteria Rhodopseudomonas (Rps.) acidophila strain 7050 has been determined to a resolution of 3.0 A by molecular replacement. The overall structure of the LH3 complex is analogous to that of the LH2 complex from Rps. acidophila strain 10050. LH3 has a nonameric quaternary structure where two concentric cylinders of alpha-helices enclose the pigment molecules bacteriochlorophyll a and carotenoid. The observed spectroscopic differences between LH2 and LH3 can be attributed to differences in the primary structure of the apoproteins. There are changes in hydrogen bonding patterns between the coupled Bchla molecules and the protein that have an effect on the conformation of the C3-acetyl groups of the B820 molecules. The structure of LH3 shows the important role that the protein plays in modulating the characteristics of the light-harvesting system and indicates the mechanisms by which the absorption properties of the complex are altered to produce a more efficient light-harvesting component.

Bacterial Proteins↗
PubMed2001

Probing the binding sites of exchanged chlorophyll a in LH2 by Raman and site-selection fluorescence spectroscopies.

In this work we have selectively released the 800 nm absorbing bacteriochlorophyll a molecules of the LH2 protein from the photosynthetic bacterium Rhodopseudomonas acidophila, strain 10050, and replaced them with chlorophyll a (Chla). A combination of low-temperature electronic absorption, resonance Raman and site-selection fluorescence spectroscopies revealed that the Chla pigments are indeed bound in the B800 binding site; this is the first work that formally proves that such non-native chlorins can be inserted correctly into LH2.

Bacterial Proteins↗
PubMed2001

An unusual pathway of excitation energy deactivation in carotenoids: singlet-to-triplet conversion on an ultrafast timescale in a photosynthetic antenna.

Carotenoids are important biomolecules that are ubiquitous in nature and find widespread application in medicine. In photosynthesis, they have a large role in light harvesting (LH) and photoprotection. They exert their LH function by donating their excited singlet state to nearby (bacterio)chlorophyll molecules. In photosynthetic bacteria, the efficiency of this energy transfer process can be as low as 30%. Here, we present evidence that an unusual pathway of excited state relaxation in carotenoids underlies this poor LH function, by which carotenoid triplet states are generated directly from carotenoid singlet states. This pathway, operative on a femtosecond and picosecond timescale, involves an intermediate state, which we identify as a new, hitherto uncharacterized carotenoid singlet excited state. In LH complex-bound carotenoids, this state is the precursor on the reaction pathway to the triplet state, whereas in extracted carotenoids in solution, this state returns to the singlet ground state without forming any triplets. We discuss the possible identity of this excited state and argue that fission of the singlet state into a pair of triplet states on individual carotenoid molecules constitutes the mechanism by which the triplets are generated. This is, to our knowledge, the first ever direct observation of a singlet-to-triplet conversion process on an ultrafast timescale in a photosynthetic antenna.

Carotenoids↗
PubMed2001

Efficient energy transfer from the carotenoid S(2) state in a photosynthetic light-harvesting complex.

Previously, the spatial arrangement of the carotenoid and bacteriochlorophyll molecules in the peripheral light-harvesting (LH2) complex from Rhodopseudomonas acidophila strain 10050 has been determined at high resolution. Here, we have time resolved the energy transfer steps that occur between the carotenoid's initial excited state and the lowest energy group of bacteriochlorophyll molecules in LH2. These kinetic data, together with the existing structural information, lay the foundation for understanding the detailed mechanisms of energy transfer involved in this fundamental, early reaction in photosynthesis. Remarkably, energy transfer from the rhodopin glucoside S(2) state, which has an intrinsic lifetime of approximately 120 fs, is by far the dominant pathway, with only a minor contribution from the longer-lived S(1) state.

Bacteriochlorophylls↗
PubMed2001

Carotenoids and bacterial photosynthesis: The story so far...

This concise review describes the current status of research into how carotenoids function in bacterial photosynthesis. This is illustrated by reference to very recent studies on both the photoprotective and antenna functions of carotenoids. The major remaining open questions on the detailed molecular mechanisms involved in these reactions are highlighted.

Journal Article↗
PubMed2001

Photophysical characterization of natural cis-carotenoids.

By means of steady-state fluorescence spectroscopy we explore the photophysics of two lowest lying singlet excited states in two natural 15-cis-carotenoids, namely phytoene and phytofluene, possessing three and five conjugated double bonds (N), respectively. The results are interpreted in relation to the photophysics of all-transcarotenoids with varying N. The fluorescence of phytofluene is more Stokes-shifted relative to that of phytoene, and is ascribed to the forbidden S1-->S0 transition, with its first excited singlet state (S1) lying 3340 cm-1 below the dipole allowed second excited singlet state (S2), at 77 K. For phytoene the S2 and S1 potential surfaces are closer in energy, probably giving rise to the mixed S2 and S1 fluorescence characteristics. The origin of phytoene fluorescence is discussed and is suggested to be due to the S1-->S0 transition; with the S1 state located 1100 cm-1 below S2 at 77 K. The dependence of the fluorescence quantum yield on temperature and viscosity shows that large amplitude molecular motions are involved in the radiationless relaxation process of phytoene. The transition dipole moment of absorption and emission are parallel in phytoene and nonparallel in phytofluene.

Algorithms↗
PubMed2000

Ubiquinone binding, ubiquinone exclusion, and detailed cofactor conformation in a mutant bacterial reaction center.

The X-ray crystal structure of a Rhodobacter sphaeroides reaction center with the mutation Ala M260 to Trp (AM260W) has been determined. Diffraction data were collected that were 97.6% complete between 30.0 and 2.1 A resolution. The electron density maps confirm the conclusions of a previous spectroscopic study, that the Q(A) ubiquinone is absent from the AM260W reaction center (Ridge, J. P., van Brederode, M. E., Goodwin, M. G., van Grondelle, R., and Jones, M. R. (1999) Photosynthesis Res. 59, 9-26). Exclusion of the Q(A) ubiquinone caused by the AM260W mutation is accompanied by a change in the packing of amino acids in the vicinity of the Q(A) site that form part of a loop that connects the DE and E helices of the M subunit. This repacking minimizes the volume of the cavity that results from the exclusion of the Q(A) ubiquinone, and further space is taken up by a feature in the electron density maps that has been modeled as a chloride ion. An unexpected finding is that the occupancy of the Q(B) site by ubiquinone appears to be high in the AM260W crystals, and as a result the position of the Q(B) ubiquinone is well-defined. The high quality of the electron density maps also reveals more precise information on the detailed conformation of the reaction center carotenoid, and we discuss the possibility of a bonding interaction between the methoxy group of the carotenoid and residue Trp M75. The conformation of the 2-acetyl carbonyl group in each of the reaction center bacteriochlorins is also discussed.

Alanine↗
PubMed2000

An examination of how structural changes can affect the rate of electron transfer in a mutated bacterial photoreaction centre.

A series of reaction centres bearing mutations at the (Phe) M197 position were constructed in the photosynthetic bacterium Rhodobacter sphaeroides. This residue is adjacent to the pair of bacteriochlorophyll molecules (P(L) and P(M)) that is the primary donor of electrons (P) in photosynthetic light-energy transduction. All of the mutations affected the optical and electrochemical properties of the P bacteriochlorophylls. A mutant reaction centre with the change Phe M197 to Arg (FM197R) was crystallized, and a structural model constructed at 2.3 A (1 A=0.1 nm) resolution. The mutation resulted in a change in the structure of the protein at the interface region between the P bacteriochlorophylls and the monomeric bacteriochlorophyll that is the first electron acceptor (B(L)). The new Arg residue at the M197 position undergoes a significant reorientation, creating a cavity at the interface region between P and B(L). The acetyl carbonyl substituent group of the P(M) bacteriochlorophyll undergoes an out-of-plane rotation, which decreases the edge-to-edge distance between the macrocycles of P(M) and B(L). In addition, two new buried water molecules partially filled the cavity that is created by the reorientation of the Arg residue. These waters are in a suitable position to connect the macrocycles of P and B(L) via three hydrogen bonds. Transient absorption measurements show that, despite an inferred decrease in the driving force for primary electron transfer in the FM197R reaction centre, there is little effect on the overall rate of the primary reaction in the bulk of the reaction-centre population. Examination of the X-ray crystal structure reveals a number of small changes in the structure of the reaction centre in the interface region between the P and B(L) bacteriochlorophylls that could account for this faster-than-predicted rate of primary electron transfer.

Crystallography, X-Ray↗
PubMed2000

How carotenoids protect bacterial photosynthesis.

The essential function of carotenoids in photosynthesis is to act as photoprotective agents, preventing chlorophylls and bacteriochlorophylls from sensitizing harmful photodestructive reactions in the presence of oxygen. Based upon recent structural studies on reaction centres and antenna complexes from purple photosynthetic bacteria, the detailed organization of the carotenoids is described. Then with specific reference to bacterial antenna complexes the details of the photoprotective role, triplet triplet energy transfer, are presented.

Carotenoids↗
PubMed2000

Structural consequences of the replacement of glycine M203 with aspartic acid in the reaction center from Rhodobacter sphaeroides.

Reaction centers with the double mutation Phe M197 to Arg and Gly M203 to Asp (FM197R/GM203D) have been crystallized from an antenna-deficient strain of Rhodobacter sphaeroides, and the structure has been determined at 2.7 A resolution. Unlike in reaction centers with a single FM197R mutation, the Arg M197 residue in the FM197R/GM203D reaction center adopts a position similar to that of the native Phe residue in the wild-type reaction center. Asp M203 is packed in such a way that the gamma-carboxy group interacts with the backbone carbonyl of Arg M197. The Asp M203 residue takes up part of the volume that is occupied in the wild-type reaction center by a water molecule. This water has been proposed to form a hydrogen bond interaction with the 9-keto carbonyl group of the active branch accessory bacteriochlorophyll, particularly when the primary donor bacteriochlorophylls are oxidized. The GM203D mutation therefore appears to remove the possibility of this hydrogen bond interaction by exclusion of this water molecule, as well as altering the local dielectric environment of the 9-keto carbonyl group. We examine whether the observed structural changes can provide new or alternative explanations for the absorbance and electron-transfer properties of reaction centers with the FM197R and GM203D mutations.

Amino Acid Substitution↗
PubMed2000

X-ray crystal structure of the YM210W mutant reaction centre from Rhodobacter sphaeroides.

The X-ray crystal structure of a reaction centre from Rhodobacter sphaeroides with a mutation of tyrosine M210 to tryptophan (YM210W) has been determined to a resolution of 2.5 A. Structural conservation is very good throughout the body of the protein, with the tryptophan side chain adopting a position in the mutant complex closely resembling that of the tyrosine in the wild-type complex. The spectroscopic properties of the YM210W reaction centre are discussed with reference to the structural data, with particular focus on evidence that the introduction of the bulkier tryptophan in place of the native tyrosine may cause a small tilt of the macrocycle of the B(L) monomeric bacteriochlorophyll.

Light-Harvesting Protein Complexes↗
PubMed2000

B800-->B850 energy transfer mechanism in bacterial LH2 complexes investigated by B800 pigment exchange.

Femtosecond transient absorption measurements were performed on native and a series of reconstituted LH2 complexes from Rhodopseudomonas acidophila 10050 at room temperature. The reconstituted complexes contain chemically modified tetrapyrrole pigments in place of the native bacteriochlorophyll a-B800 molecules. The spectral characteristics of the modified pigments vary significantly, such that within the B800 binding sites the B800 Q(y) absorption maximum can be shifted incrementally from 800 to 670 nm. As the spectral overlap between the B800 and B850 Q(y) bands decreases, the rate of energy transfer (as determined by the time-dependent bleaching of the B850 absorption band) also decreases; the measured time constants range from 0.9 ps (bacteriochlorophyll a in the B800 sites, Q(y) absorption maximum at 800 nm) to 8.3 ps (chlorophyll a in the B800 sites, Q(y) absorption maximum at 670 nm). This correlation between energy transfer rate and spectral blue-shift of the B800 absorption band is in qualitative agreement with the trend predicted from Förster spectral overlap calculations, although the experimentally determined rates are approximately 5 times faster than those predicted by simulations. This discrepancy is attributed to an underestimation of the electronic coupling between the B800 and B850 molecules.

Bacterial Proteins↗