Beam-size effects in radiation damage in insulin and thaumatin crystals

Cryocooled insulin and thaumatin crystals were irradiated in a series of alternating data collections and high-dose-rate exposures using either a vertically focused or vertically defocused beam. The main result is that the radiation damage is limited to the exposed region, which can be explained by the short range of the photoelectrons and the Auger electron cascade produced by light elements. Consequently, the unexposed angular range provides significantly improved data quality and electron density compared with previously exposed angular wedges of the crystal when a vertically focused beam is used, while no differences are observed between a fresh wedge and an exposed region for the vertically defocused beam. On the other hand, the focused beam provides higher I/sigma(I) ratios at high resolution than homogeneous sample illumination but also causes more rapid sample deterioration.

Phasing in the presence of radiation damage

In the accurate estimation of small signals, redundancy of observations is often seen as an essential tool for the experimenter. This is particularly true during macromolecular structure determination by single-wavelength anomalous dispersion (SAD), where the exploitable signal can be less than a few percent. At the most intense undulator synchrotron beamlines, the effect of radiation damage can be such that all usable signal is obscured. Here the magnitude of this effect in experiments performed at the Se K-edge is quantified. Six successive data sets were collected on the same crystal, interspersed with two exposures to the X-ray beam during which data were not collected. It is shown that the very first data set has excellent phasing statistics, whereas these statistics degrade for the later data sets. Merging several data sets into one, highly redundant, data set only gave moderate improvements as a result of the presence of radiation damage. Part of the damage could be corrected for using a linear interpolation scheme. Interpolation of the data to a low-dose as well as to a high-dose data set allowed us to combine the SAD method with the radiation-damage induced phasing (RIP) technique, which further improved the experimental phases, especially after density modification. Some recommendations are given on how to mitigate the effect of radiation damage during structure determination.

Two-wavelength MAD phasing and radiation damage: a case study

Radiation damage affects MAD experiments in two ways: (i) increased absorption by the crystal at the wavelengths of interest for the experiment results in faster crystal deterioration; (ii) lack of isomorphism induced by radiation damage causes problems when scaling and merging data at different wavelengths and can prevent accurate measurement of anomalous and dispersive differences. In an attempt to overcome these problems in the case of radiation-sensitive crystals of vinculin, two-wavelength MAD data were collected at the Se absorption-edge inflection and at high-energy remote wavelengths. Although this strategy resulted in a lower total absorbed dose compared with a standard three-wavelength experiment using the peak wavelength, an increase in the unit-cell volume and other effects attributable to radiation damage were still observed. In an effort to extract the maximum information available from the data, different data-processing and scaling procedures were compared. Scaling approaches involving local scaling of unmerged reflections were consistently successful and most ordered Se sites could be located. Subsequent use of these sites for phasing resulted in an interpretable electron density map. This case demonstrates the feasibility of two-wavelength MAD in the presence of moderate radiation damage using conventional data collection strategies and widely available standard software.

Towards an understanding of radiation damage in cryocooled macromolecular crystals

Interest in radiation damage is growing rapidly owing to the surge in macromolecular crystallography experiments carried out at modern brilliant synchrotron macromolecular crystallography beamlines. Work on the characterization of radiation damage in cryocooled protein crystals is starting to have some impact on our understanding of the problem and of how damage might be affecting both the process of structure solution and the actual structure obtained. A brief review of the most recent developments is given together with an assessment of the remaining problems. Although progress is being made, the understanding of radiation damage is far from complete. Methods for recognizing the damage and treating the data are being made available but they are still at an early stage of development.

On the influence of the incident photon energy on the radiation damage in crystalline biological samples

Two series of complete and highly redundant data sets were collected at wavelengths of 1.00 and 2.00 Angstroms on a cadmium derivative of porcine pancreatic elastase (PPE). Radiation damage to the sample was evaluated qualitatively by inspecting consecutive difference electron density maps during the course of the experiment. The nature of the radiation damage was found to be identical at both wavelengths and was localized primarily at the four disulfide bridges of PPE, the cadmium site and the two methionine residues. For a quantitative examination of the radiation damage, the decrease in the peak height of the cadmium ion in various electron density maps was exploited. Again, no significant difference in radiation damage between the two wavelengths was observed. This can be rationalized by considering the wavelength dependencies of the number of diffracted photons versus the number of absorbed photons and the energy deposited in the crystal by the latter.

Radiolysis of proteins in the solid state: an approach by EPR and product analysis

Radio-induced modifications in proteins have been studied using several techniques. Electron paramagnetic resonance (EPR) was used to characterize free radicals, and analysis methods (high-performance liquid chromatography, capillary electrophoresis) were employed to visualize final degraded forms. Whereas EPR indicates that perthiyl radicals are formed, analysis does not detect any compound in which such bonds would be broken. Since EPR signals decay with time, it is concluded that rearrangements occur at subsequent steps, in which the solvent used during the analysis might play a role.

Will reduced radiation damage occur with very small crystals?

The primary event which occurs when an X-ray photon of energy less than 30 keV is absorbed in a protein crystal (or other organic material) is the production of a photoelectron with a similar energy to that of the absorbed photon. The electron then scatters inelastically off the surrounding material losing energy in the process. This reduction in energy takes place over track lengths of a few microm for 20 keV electrons. The vector distances between the initial and final positions of the photoelectrons are less than the track lengths owing to the non-linear tracks followed by the electrons. For crystals with smaller dimensions than the vector distances, a significant proportion of the energy could leave the crystal with the high-energy electrons. This could provide an advantage in terms of reduced radiation damage. In order to estimate the possible benefits, calculations of the electron tracks are given, initially using the continuous slowing-down approximation. A Monte Carlo approach is then used to provide more accurate values of the vector distance travelled by electrons inside a protein crystal. The calculations indicate that significant reductions in radiation damage could occur for crystals of a few microm in size. The benefits would be greater when operating at higher energies. In addition, a scheme for realising the possible benefits in a practical situation is described. This could then form the basis of trial experiments.

Parameters affecting the X-ray dose absorbed by macromolecular crystals

The lifetime of a macromolecular crystal in an X-ray beam is assumed to be limited by the absorbed dose. This dose, expressed in Gray (Gy = J kg(-1)), is a function of a number of parameters: the absorption coefficients of the constituent atoms of the crystal, the number of molecules per asymmetric unit, the beam energy, flux, size and profile, the crystal size, and the total irradiation time. The effects of these variables on the predicted absorbed dose, calculated using the program RADDOSE, are discussed and are illustrated with reference to the irradiation of a selenomethionine protein crystal of unknown structure. The results of RADDOSE can and will in the future be used to inform the data collection procedure as it sets a theoretical upper limit on the total exposure time at a certain X-ray source. However, as illustrated with an example for which the experimental data are compared with prediction, the actual lifetime of a crystal could become shorter in those cases where specific damage breaks down crucial crystal contacts.

Supercooled liquid-like solvent in trypsin crystals: implications for crystal annealing and temperature-controlled X-ray radiation damage studies

The study of temperature-dependent physical changes in flash-cooled macromolecular crystals is pertinent to cryocrystallography and related issues such as crystal annealing, X-ray radiation damage and kinetic crystallography. In this context, the unit-cell volume of flash-cooled trigonal and orthorhombic trypsin crystals has been monitored upon warming from 100 to 200 K and subsequent re-cooling to 100 K. Crystals of both forms were obtained under the same crystallization conditions, yet they differ in solvent content and channel size. An abrupt non-reversible unit-cell volume decrease is observed at 185 K in orthorhombic and at 195 K in trigonal crystals as the temperature is increased; this result is consistent with ultra-viscous solvent leaving the crystals. Concomitant appearance of ice rings in the diffraction patterns suggests that the transported solvent forms crystalline ice. These results demonstrate that solvent in flash-cooled protein crystals is liquid-like near its crystallization temperature, as has been proposed, yet controversially discussed, for the case of pure water. The use of mineral oil prevents the unit-cell volume decrease in trigonal but not in orthorhombic crystals. The observation of liquid-like solvent has implications in the development of annealing protocols and points a way to the rational design of temperature-controlled crystallographic studies that aim either at studying specific radiation damage or at trapping enzymatic intermediate states.

A mechanism of nonphotochemical energy dissipation, independent from PsbS, revealed by a conformational change in the antenna protein CP26

The regulation of light harvesting in higher plant photosynthesis, defined as stress-dependent modulation of the ratio of energy transfer to the reaction centers versus heat dissipation, was studied by means of carotenoid biosynthesis mutants and recombinant light harvesting complexes (LHCs) with modified chromophore binding. The npq2 mutant of Arabidopsis thaliana, blocked in the biosynthesis of violaxanthin and thus accumulating zeaxanthin, was shown to have a lower fluorescence yield of chlorophyll in vivo and, correspondingly, a higher level of energy dissipation, with respect to the wild-type strain and npq1 mutant, the latter of which is incapable of zeaxanthin accumulation. Experiments on purified thylakoid membranes from all three mutants showed that the major source of the difference between the npq2 and wild-type preparations was a change in pigment to protein interactions, which can explain the lower chlorophyll fluorescence yield in the npq2 samples. Analysis of the xanthophyll binding LHC proteins showed that the Lhcb5 photosystem II subunit (also called CP26) undergoes a change in its pI upon binding of zeaxanthin. The same effect was observed in wild-type CP26 upon treatment that leads to the accumulation of zeaxanthin in the membrane and was interpreted as the consequence of a conformational change. This hypothesis was confirmed by the analysis of two recombinant proteins obtained by overexpression of the Lhcb5 apoprotein in Escherichia coli and reconstitution in vitro with either violaxanthin or zeaxanthin. The V and Z containing pigment-protein complexes obtained by this procedure showed different pIs and high and low fluorescence yields, respectively. These results confirm that LHC proteins exist in multiple conformations, an idea suggested by previous spectroscopic measurements (Moya et al., 2001), and imply that the switch between the different LHC protein conformations is activated by the binding of zeaxanthin to the allosteric site L2. The results suggest that the quenching process induced by the accumulation of zeaxanthin contributes to qI, a component of NPQ whose origin was previously poorly understood.

Time-resolved detection of sensory rhodopsin II-transducer interaction

The dynamics of protein conformational change of Natronobacterium pharaonis sensory rhodopsin II (NpSRII) and of NpSRII fused to cognate transducer (NpHtrII) truncated at 159 amino acid sequence from the N-terminus (NpSRII-DeltaNpHtrII) are investigated in solution phase at room temperature by the laser flash photolysis and the transient grating methods in real time. The diffusion coefficients of both species indicate that the NpSRII-DeltaNpHtrII exists in the dimeric form in 0.6% dodecyl-beta-maltopyranoside (DM) solution. Rate constants of the reaction processes in the photocycles determined by the transient absorption and grating methods agree quite well. Significant differences were found in the volume change and the molecular energy between NpSRII and NpSRII-DeltaNpHtrII samples. The enthalpy of the second intermediate (L) of NpSRII-DeltaNpHtrII is more stabilized compared with that of NpSRII. This stabilization indicates the influence of the transducer to the NpSRII structure in the early intermediate species by the complex formation. Relatively large molecular volume expansion and contraction were observed in the last two steps for NpSRII. Additional volume expansion and contraction were induced by the presence of DeltaNpHtrII. This volume change, which should reflect the conformational change induced by the transducer protein, suggested that this is the signal transduction process of the NpSRII-DeltaNpHtrII.

Charge-transfer Zn-porphyrin derivatives with very large two-photon absorption cross sections at 1.3–1.5 μm fundamental wavelengths

A series of charge-transfer Zn-porphyrin derivatives with large two-photon absorption cross sections at 1.3-1.5 microm fundamental wavelengths are designed using time-dependent hybrid density functional theory. The fluorescence of these chromospheres is expected to be in the region of 700-900 nm. These unique features make them suitable for a variety of biophotonic and telecommunication applications.

Acid sphingomyelinase is indispensable for UV light-induced Bax conformational change at the mitochondrial membrane

Ultraviolet light-induced apoptosis can be caused by DNA damage but also involves immediate-early cell death cascades characteristic of death receptor signaling. Here we show that the UV light-induced apoptotic signaling pathway is unique, targeting Bax activation at the mitochondrial membrane independent of caspase-8 or cathepsin D activity. Cells deficient in acid sphingomyelinase (ASMase) do not show UV light-induced Bax activation, cytochrome c release, or apoptosis. In ASMase-deficient cells, the apoptotic UV light response is restored by stable or transient expression of human ASMase. Bax conformational change in ASMase(-/-) cells is also caused by synthetic C(16)-ceramide acting on intact cells or isolated mitochondria. The results suggest that UV light-triggered ASMase activation is essentially required for Bax conformational change leading to mitochondrial release of pro-apoptotic factors like cytochrome c and Smac.

Intensity-dependent effects of microwave electromagnetic fields on acetylcholinesterase activity and protein conformation in frog skeletal muscles

BACKGROUND

This study was conducted to investigate the effects of continuous microwaves (2.45 GHz) of different field intensity on acetylcholinesterase activity and protein conformation in muscle fractions from frog skeletal muscles.

MATERIALS/METHODS

[corrected] Acetylcholinesterase activity in samples from muscle homogenate fractions exposed for 30 min to microwaves of low (10 mW/cm2) or high (20 mW/cm2) intensity at almost constant temperature (1.8 degrees - 2.0 degrees C) was measured by spectrophotometry for three consecutive days after irradiation and compared with the activity in a sham-exposed fraction. Infrared spectroscopy (between 1400 cm(-1)-1800 cm(-1) was performed on the lyophilised fractions using Bruker IFS 113 v.

RESULTS

A significant decrease in enzyme activity on the day of exposure (by 8.4% and 13.6% at high and low field intensity, respectively) was observed. Forty-eight hours later the decrease in enzyme activity in samples exposed to both high- and low-intensity microwaves was less than that in sham-exposed samples. Infrared spectroscopy data showed the Amide I band to be negligibly affected and the absorption maximum in the Amide II band to be significantly shifted from 1540 cm-' (shamexposed) to 1559 cm(1) (exposed) after irradiation.

CONCLUSIONS

Exposure to microwaves results in non-thermal, intensity-dependent, prolonged modification of acetylcholinesterase activity in frog skeletal muscles traced up to 48 hrs after exposure. Infrared spectroscopy data argue for induced conformational changes in the secondary structure of muscle proteins: increased content of beta-structures, random coils, and amorphous structures, which were more expressed at low field intensity.

Evidence of electroconformational changes in membrane proteins: field-induced reductions in intra membrane nonlinear charge movement currents

Experimental results are presented to show that a pulsed, intensive membrane potential can reduce intra membrane, nonlinear charge movement currents, which are the voltage-sensors in the voltage-dependent membrane proteins and in the excitation-contraction coupling of skeletal muscle fibers. The results indicate a possible mechanism involved in electrical injury: dysfunctions of the voltage-dependent membrane proteins caused by electroconformational damages in their voltage-sensors.

Specific Radiation Damage Illustrates Light-Induced Structural Changes in the Photosynthetic Reaction Center

The photosynthetic reaction center of the purple non-sulfur bacterium Blastochloris viridis was frozen in the presence and absence of illumination. Differences in the resulting datasets are monitored using the difference Fourier method. Radiation damage is localized to those parts of the protein that are significant for electron transfer, and show changes that are sensitive to oxidation and protonation state.

Origins of Helix−Coil Switching in a Light-Sensitive Peptide

Intramolecular cross-linking of peptides by the light-sensitive compound diiodoacetamideazobenzene has been shown to permit reversible photocontrol of the helix-coil transition. Cross-linking between Cys residues spaced at i and i + 7 positions with the trans form of the linker was found to produce a decreased helix content compared to that of the non-cross-linked peptide. Photoisomerization to the cis form of the linker led to substantially higher helix content than in the non-cross-linked peptide. Detailed conformational analysis of the system leads to the conclusion that photocontrol of helix content does not involve specific interactions between the linker and the peptide. Instead, the change in peptide helix content caused by photoisomerization can be predicted by comparing the length ranges of the cis and trans forms of the linker with the expected distance distribution of the Cys attachment points in the intrinsic conformational ensemble of the peptide. The analysis presented here should help to guide the use of these and related linkers for the conformational control of a variety of peptide and protein systems.

Protein thermal aggregation involves distinct regions: sequential events in the heat-induced unfolding and aggregation of hemoglobin

Protein thermal aggregation plays a crucial role in protein science and engineering. Despite its biological importance, little is known about the mechanism and pathway(s) involved in the formation of aggregates. In this report, the sequential events occurring during thermal unfolding and aggregation process of hemoglobin were studied by two-dimensional infrared correlation spectroscopy. Analysis of the infrared spectra recorded at different temperatures suggested that hemoglobin denatured by a two-stage thermal transition. At the initial structural perturbation stage (30-44 degrees C), the fast red shift of the band from alpha-helix indicated that the native helical structures became more and more solvent-exposed as temperature increased. At the thermal unfolding stage (44-54 degrees C), the unfolding of solvent-exposed helical structures dominated the transition and was supposed to be responsible to the start of aggregation. At the thermal aggregation stage (54-70 degrees C), the transition was dominated by the formation of aggregates and the further unfolding of the buried structures. A close inspection of the sequential events occurring at different stages suggested that protein thermal aggregation involves distinct regions.

Glutamic acid residues of bacteriorhodopsin at the extracellular surface as determinants for conformation and dynamics as revealed by site-directed solid-state 13C NMR

We recorded (13)C NMR spectra of [3-(13)C]Ala- and [1-(13)C]Val-labeled bacteriorhodopsin (bR) and a variety of its mutants, E9Q, E74Q, E194Q/E204Q (2Glu), E9Q/E194Q/E204Q (3Glu), and E9Q/E74Q/E194Q/E204Q (4Glu), to clarify contributions of the extracellular (EC) Glu residues to the conformation and dynamics of bR. Replacement of Glu-9 or Glu-74 and Glu-194/204 at the EC surface by glutamine(s) induced significant conformational changes in the cytoplasmic (CP) surface structure. These changes occurred in the C-terminal alpha-helix and loops, and also those of the EC surface, as viewed from (13)C NMR spectra of [3-(13)C]Ala- and [1-(13)C]Val-labeled proteins. Additional conformational changes in the transmembrane alpha-helices were induced as modified retinal-protein interactions for multiple mutants involving the E194Q/E204Q pair. Significant dynamic changes were induced for the triple or quadruple mutants, as shown by broadened (13)C NMR peaks of [1-(13)C]Val-labeled proteins. These changes were due to acquired global fluctuation motions of the order of 10(-4)-10(-5) s as a result of disorganized trimeric form. In such mutants (13)C NMR signals from Val residues of [1-(13)C]Val-labeled triple and quadruple mutants near the CP and EC surfaces (including 8.7-A depth from the surface) were substantially suppressed, as shown by comparative (13)C NMR studies with and without 40 micro M Mn(2+) ion. We conclude that these Glu residues at the EC surface play an important role in maintaining the native secondary structure of bR in the purple membrane.

Dependence of Tyrosine Oxidation in Highly Oxidizing Bacterial Reaction Centers on pH and Free-Energy Difference

The pH and temperature dependences of tyrosine oxidation were measured in reaction centers from mutants of Rhodobacter sphaeroides containing a tyrosine residue near a highly oxidizing bacteriochlorophyll dimer. Under continuous illumination, a rapid increase in the absorption change at 420 nm was observed because of the formation of a charge-separated state involving the oxidized dimer and reduced primary quinone, followed by a slow absorption decrease attributed to tyrosine oxidation. Both the amplitude and rate of the slow absorption change showed a pH dependency, indicating that, at low pH, the rate of tyrosine oxidation is limited by the transfer of the phenolic proton to a nearby base. Below 17 degrees C, the rate of the slow absorption change had a strong exponential dependence on the temperature, indicating a high activation energy. At higher pH and temperature, the overall rate of tyrosyl formation appears to be limited by a proposed conformational change in the reaction center that is also observed in reaction centers that do not undergo tyrosine oxidation. The yield of tyrosyl formation measured using electron paramagnetic resonance spectroscopy decreased significantly at 4 degrees C compared to 20 degrees C and was lower at both temperatures in mutants expected to have a slightly smaller driving force for tyrosyl formation.

FTIR difference spectroscopy in combination with isotope labeling for identification of the carbonyl modes of P700 and P700+ in photosystem I

Room temperature, light induced (P700(+)-P700) Fourier transform infrared (FTIR) difference spectra have been obtained using photosystem I (PS I) particles from Synechocystis sp. PCC 6803 that are unlabeled, uniformly (2)H labeled, and uniformly (15)N labeled. Spectra were also obtained for PS I particles that had been extensively washed and incubated in D(2)O. Previously, we have found that extensive washing and incubation of PS I samples in D(2)O does not alter the (P700(+)-P700) FTIR difference spectrum, even with approximately 50% proton exchange. This indicates that the P700 binding site is inaccessible to solvent water. Upon uniform (2)H labeling of PS I, however, the (P700(+)-P700) FTIR difference spectra are considerably altered. From spectra obtained using PS I particles grown in D(2)O and H(2)O, a ((1)H-(2)H) isotope edited double difference spectrum was constructed, and it is shown that all difference bands associated with ester/keto carbonyl modes of the chlorophylls of P700 and P700(+) downshift 4-5/1-3 cm(-1) upon (2)H labeling, respectively. It is also shown that the ester and keto carbonyl modes of the chlorophylls of P700 need not be heterogeneously distributed in frequency. Finally, we find no evidence for the presence of a cysteine mode in our difference spectra. The spectrum obtained using (2)H labeled PS I particles indicates that a negative difference band at 1698 cm(-1) is associated with at least two species. The observed (15)N and (2)H induced band shifts strongly support the idea that the two species are the 13(1) keto carbonyl modes of both chlorophylls of P700. We also show that a negative difference band at approximately 1639 cm(-1) is somewhat modified in intensity, but unaltered in frequency, upon (2)H labeling. This indicates that this band is not associated with a strongly hydrogen bonded keto carbonyl mode of one of the chlorophylls of P700.

Selective dissociation of non-covalent bonds in biological molecules by laser spray

The laser spray developed in our laboratory was applied to the analysis of bovine serum albumin (BSA), double-stranded DNA (dsDNA) and a protein-DNA complex. The tip of a stainless-steel capillary was irradiated with a 10.6 micro m infrared laser by increasing the laser power from 0 W (electrospray) to 1.4 W. The laser beam was focused to about 0.3 mm at the tip of the stainless-steel capillary. When BSA aqueous solution was irradiated by the laser, highly charged monomer ions were newly observed in addition to the multiply charged ions of non-denatured monomer, dimer and trimer moieties. This indicates that BSA suffers from denaturation on irradiation with an infrared laser in solution. A 1.4 W laser power is not sufficient to cause the complete denaturation of BSA under the present experimental conditions. Whereas dsDNA was found to dissociate almost completely to single-stranded DNA constituents on laser irradiation with a power of 1.2 W, no fragmentation of DNA molecules was observed. For a protein-DNA complex, i.e. a complex of c-Myb DNA binding domain and dsDNA, dissociation of the complex to the component moieties was observed. These findings indicate that the laser spray can selectively dissociate non-covalent complexes into subunits without causing dissociation of the covalent bonds of the subunits. The laser spray will be a versatile method for the investigation of the structures and stabilities of biomolecules including non-covalent complexes.

QM/MM study of energy storage and molecular rearrangements due to the primary event in vision

The energy storage and the molecular rearrangements due to the primary photochemical event in rhodopsin are investigated by using quantum mechanics/molecular mechanics hybrid methods in conjunction with high-resolution structural data of bovine visual rhodopsin. The analysis of the reactant and product molecular structures reveals the energy storage mechanism as determined by the detailed molecular rearrangements of the retinyl chromophore, including rotation of the (C11-C12) dihedral angle from -11 degrees in the 11-cis isomer to -161 degrees in the all-trans product, where the preferential sense of rotation is determined by the steric interactions between Ala-117 and the polyene chain at the C13 position, torsion of the polyene chain due to steric constraints in the binding pocket, and stretching of the salt bridge between the protonated Schiff base and the Glu-113 counterion by reorientation of the polarized bonds that localize the net positive charge at the Schiff-base linkage. The energy storage, computed at the ONIOM electronic-embedding approach (B3LYP/6-31G*:AMBER) level of theory and the S0-->S1 electronic-excitation energies for the dark and product states, obtained at the ONIOM electronic-embedding approach (TD-B3LYP/6-31G*//B3LYP/6-31G*:AMBER) level of theory, are in very good agreement with experimental data. These results are particularly relevant to the development of a first-principles understanding of the structure-function relations in prototypical G-protein-coupled receptors.

Observation of the energy-level structure of the low-light adapted B800 LH4 complex by single-molecule spectroscopy

Low-light adapted B800 light-harvesting complex 4 (LH4) from Rhodopseudomonas palustris is a complex in which the arrangement of the bacteriochloropyll a pigments is very different from the well-known B800-850 LH2 complex. For bulk samples, the main spectroscopic feature in the near-infrared is the occurrence of a single absorption band at 802 nm. Single-molecule spectroscopy can resolve the narrow bands that are associated with the exciton states of the individual complexes. The low temperature (1.2 K) fluorescence excitation spectra of individual LH4 complexes are very heterogeneous and display unique features. It is shown that an exciton model can adequately reproduce the polarization behavior of the complex, the experimental distributions of the number of observed peaks per complex, and the widths of the absorption bands. The results indicate that the excited states are mainly localized on one or a few subunits of the complex and provide further evidence supporting the recently proposed structure model.

Circular dichroism of carotenoids in bacterial light-harvesting complexes: experiments and modeling

In this work we investigate the origin and characteristics of the circular dichroism (CD) spectrum of rhodopin glucoside and lycopene in the light-harvesting 2 complex of Rhodopseudomonas acidophila and Rhodospirillum molischianum, respectively. We successfully model their absorption and CD spectra based on the high-resolution structures. We assume that these spectra originate from seven interacting transition dipole moments: the first corresponds to the 0-0 transition of the carotenoid, whereas the remaining six represent higher vibronic components of the S2 state. From the absorption spectra we get an estimate of the Franck-Condon factors of these transitions. Furthermore, we investigate the broadening mechanisms that lead to the final shape of the spectra and get an insight into the interaction energy between carotenoids. Finally, we examine the consequences of rotations of the carotenoid transition dipole moment and of deformations in the light-harvesting 2 complex rings. Comparison of the modeled carotenoid spectra with modeled spectra of the bacteriochlorophyll QY region leads to a refinement of the modeling procedure and an improvement of all calculated results. We therefore propose that the combined carotenoid and bacteriochlorophyll CD can be used as an accurate reflection of the overall structure of the light-harvesting complexes.