Computational study of short-range interactions in bacteriochlorophyll aggregates

Alster, Jan; Kabeláč, Martin; Tůma, Roman; Pšenčı́k, Jakub; Burda, Jaroslav V.

doi:10.1016/j.comptc.2012.07.001

Cited by 16 publications

(20 citation statements)

References 31 publications

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“…We simulated the assembly of 17 2 -farnesyl-( R or S )-[8-ethyl,12-ethyl]BChl c or d pigments, which have been considered extensively in the experimental and simulation literature. 5 , 7 , 13 , 31 The ratio between R and S components in the dimer is 1:1 in agreement with Ganapathy et al 7 …”

Section: Computational Detailssupporting

confidence: 88%

“…By performing simulations for an initially planar system, containing either BChl c or BChl d , we resolve the molecular origin of curvature and determine the distinct structural variability and global dynamic heterogeneity of the BChls within a curved assembly. Recent computational work based on molecular mechanics and density functional theory (DFT) has not been able to reveal these basic properties 13 because their phase space exploration capability is too limited. 14 As the time scale τ for structural rearrangement scales as τ ≈ ξ z , with ξ the correlation length (∼size) and z > 0 a dynamical exponent that depends on the kinetic model, the starting structure for large-scale MD simulations should be chosen with care to avoid kinetic trapping.…”

Section: Introductionmentioning

confidence: 99%

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Contrasting Modes of Self-Assembly and Hydrogen-Bonding Heterogeneity in Chlorosomes of Chlorobaculum tepidum

Buda

Groot

et al. 2018

J. Phys. Chem. C

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Chlorosome antennae form an interesting class of materials for studying the role of structural motifs and dynamics in nonadiabatic energy transfer. They perform robust and highly quantum-efficient transfer of excitonic energy while allowing for compositional variation and completely lacking the usual regulatory proteins. Here, we first cast the geometrical analysis for ideal tubular scaffolding models into a formal framework, to relate effective helical properties of the assembly structures to established characterization data for various types of chlorosomes. This analysis shows that helicity is uniquely defined for chlorosomes composed of bacteriochlorophyll (BChl) d and that three chiral angles are consistent with the nuclear magnetic resonance (NMR) and electron microscope data for BChl c, including two novel ones that are at variance with current interpretations of optical data based on perfect cylindrical symmetry. We use this information as a starting point for investigating dynamic and static heterogeneity at the molecular level by unconstrained molecular dynamics. We first identify a rotational degree of freedom, along the Mg–OH coordination bond, that alternates along the syn–anti stacks and underlies the (flexible) curvature on a larger scale. Because rotation directly relates to the formation or breaking of interstack hydrogen bonds of the O–H···O=C structural motif along the syn–anti stacks, we analyzed the relative fractions of hydrogen-bonded and the nonbonded regions, forming stripe domains in otherwise spectroscopically homogeneous curved slabs. The ratios 7:3 for BChl c and 9:1 for BChl d for the two distinct structural components agree well with the signal intensities determined by NMR. In addition, rotation with curvature-independent formation of stripe domains offers a viable explanation for the localization and dispersion of exciton states over two fractions, as observed in single chlorosome fluorescence decay studies.

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Section: Computational Detailssupporting

confidence: 88%

Section: Introductionmentioning

confidence: 99%

Contrasting Modes of Self-Assembly and Hydrogen-Bonding Heterogeneity in Chlorosomes of Chlorobaculum tepidum

Buda

Groot

et al. 2018

J. Phys. Chem. C

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“…It has been suggested that the -interaction between the planar conjugated systems of the -ring and the BChl chlorin is responsible for the close contact between the two molecules (34). Since BChl-BChl -stacking plays an important role in stabilization of the aggregate (35), it is likely that the same is true for BChl-carotenoid interactions in chlorosomes from Chlorobi species. It is reasonable to expect that -interactions are stronger in BChl c-containing C. tepidum than in BChl e-containing brown bacteria, such as C. phaeovibrioides, because the aldehyde group at C-7 of BChl e (Fig.…”

Section: Discussionmentioning

confidence: 83%

Structural and Functional Roles of Carotenoids in Chlorosomes

et al. 2013

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fChlorosomes are large light-harvesting complexes found in three phyla of anoxygenic photosynthetic bacteria. Chlorosomes are primarily composed of self-assembling pigment aggregates. In addition to the main pigment, bacteriochlorophyll c, d, or e, chlorosomes also contain variable amounts of carotenoids. Here, we use X-ray scattering and electron cryomicroscopy, complemented with absorption spectroscopy and pigment analysis, to compare the morphologies, structures, and pigment compositions of chlorosomes from Chloroflexus aurantiacus grown under two different light conditions and Chlorobaculum tepidum. High-purity chlorosomes from C. aurantiacus contain about 20% more carotenoid per bacteriochlorophyll c molecule when grown under low light than when grown under high light. This accentuates the light-harvesting function of carotenoids, in addition to their photoprotective role. The low-light chlorosomes are thicker due to the overall greater content of pigments and contain domains of lamellar aggregates. Experiments where carotenoids were selectively extracted from intact chlorosomes using hexane proved that they are located in the interlamellar space, as observed previously for species belonging to the phylum Chlorobi. A fraction of the carotenoids are localized in the baseplate, where they are bound differently and cannot be removed by hexane. In C. tepidum, carotenoids cannot be extracted by hexane even from the chlorosome interior. The chemical structure of the pigments in C. tepidum may lead to -interactions between carotenoids and bacteriochlorophylls, preventing carotenoid extraction. The results provide information about the nature of interactions between bacteriochlorophylls and carotenoids in the protein-free environment of the chlorosome interior.

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“…Supramolecular structures of BChl-c and -d self-assemblies in natural and modified chlorosomes have also been investigated by NMR spectroscopy, [18,51,[60][61][62][63][64][65][66][67][68][69][70][71] and 5a nd 10 nm tube-shaped and lamellar supramolecular nanostructures werem odeled by computational studies. [72][73][74][75][76] ChlorosomalB Chl-c,-d,-e,a nd -f molecules are magnesium complexes of 3 1 -hydroxy-13 1 -oxo-chlorins, the C13 2 atom of which lacks the methoxycarbonyl group found in the other natural Chls and BChls (Figure 1, left). The central magnesium atom as well as the peripheral 3 1 -hydroxy and 13-keto carbonyl groups are requisite for the chlorosomals elf-assembly.T he molecular organization of the chlorosomal self-assemblies is based on mainly three intermolecularinteractions, that is, coordination bonding (Mg···OH), hydrogenb onding (OÀH···O=C), and chlorin p-p stacking.…”

Section: Introductionmentioning

confidence: 99%

“…tepidum lacking methyl transferases BchQ/R and BchQ/R/U, the major pigments of which are farnesyl 8‐ethyl‐12‐methyl‐BChl‐ c and ‐ d , respectively. Supramolecular structures of BChl‐ c and ‐ d self‐assemblies in natural and modified chlorosomes have also been investigated by NMR spectroscopy, and 5 and 10 nm tube‐shaped and lamellar supramolecular nanostructures were modeled by computational studies …”

Section: Introductionmentioning

confidence: 99%

Self‐Assemblies of Zinc Bacteriochlorophyll‐d Analogues Having Amide, Ester, and Urea Groups as Substituents at 17‐Position and Observation of Lamellar Supramolecular Nanostructures

et al. 2018

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Chlorosomes are unique light-harvesting apparatuses in photosynthetic green bacteria. Single chlorosomes contain a large number of bacteriochlorophyll (BChl)-c, -d, -e, and -f molecules, which self-assemble without protein assistance. These BChl self-assemblies involving specific intermolecular interactions (Mg⋅⋅⋅O3 -H⋅⋅⋅O=C13 and π-π stacks of chlorin skeletons) in a chlorosome have been reported to be round-shaped rods (or tubes) with diameters of 5 or 10 nm, or lamellae with a layer spacing of approximately 2 nm. Herein, the self-assembly of synthetic zinc BChl-d analogues having ester, amide, and urea groups in the 17-substituent is reported. Spectroscopic analyses indicate that the zinc BChl-d analogues self-assemble in a nonpolar organic solvent in a similar manner to natural chlorosomal BChls with additional assistance by hydrogen-bonding of secondary amide (or urea) groups (CON-H⋅⋅⋅O=CNH). Microscopic analyses of the supramolecules of a zinc BChl-d analogue bearing amide and urea groups show round- or square-shaped rods with widths of about 65 nm. Cryogenic TEM shows a lamellar arrangement of the zinc chlorin with a layer spacing of 1.5 nm inside the rod. Similar thick rods are also visible in the micrographs of self-assemblies of zinc BChl-d analogues with one or two secondary amide moieties in the 17-substituent.

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Computational study of short-range interactions in bacteriochlorophyll aggregates

Cited by 16 publications

References 31 publications

Contrasting Modes of Self-Assembly and Hydrogen-Bonding Heterogeneity in Chlorosomes of Chlorobaculum tepidum

Contrasting Modes of Self-Assembly and Hydrogen-Bonding Heterogeneity in Chlorosomes of Chlorobaculum tepidum

Structural and Functional Roles of Carotenoids in Chlorosomes

Self‐Assemblies of Zinc Bacteriochlorophyll‐d Analogues Having Amide, Ester, and Urea Groups as Substituents at 17‐Position and Observation of Lamellar Supramolecular Nanostructures

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