Andrew A. Freer

Structure‐Based Calculations of the Optical Spectra of the LH2 Bacteriochlorophyll‐Protein Complex from Rhodopseudomonas acidophila

Abstract— The molecular structure of the light‐harvesting complex 2 (LH2) bacteriochlorophyll‐protein antenna complex from the purple non‐sulfur photosynthetic bacterium Rhodopseudomonas acidophila, strain 10050 provides the positions and orientations of the 27 bacteriochlorophyll (BChl) molecules in the complex. Our structure‐based model calculations of the distinctive optical properties (absorption, CD, polarization) of LH2 in the near‐infrared region use a point‐monopole approximation to represent the BChl Qy transition moment. The results of the calculations support the assignment of the ring of 18 closely coupled BChl to B850 (BChl absorbing at 850 nm) and the larger diameter, parallel ring of 9 weakly coupled BChl to B800. All of the significantly allowed transitions in the near infrared are calculated to be perpendicular to the C9 symmetry axis, in agreement with polarization studies of this membrane‐associated complex. To match the absorption maxima of the B800 and B850 components using a relative permittivity (dielectric constant) of 2.1, we assign different site energies (12 500 and 12260 cm−1, respectively) for the Qy transitions of the respective BChl in their protein binding sites. Excitonic coupling is particularly strong among the set of B850 chromophores, with pairwise interaction energies nearly 300 cm between nearest neighbors, comparable with the experimental absorption bandwidths at room temperature. These strong interactions, for the full set of 18 B850 chromophores, result in an excitonic manifold that is 1200 cm−1 wide. Some of the upper excitonic states should result in weak absorption and perhaps stronger CD features. These predictions from the calculations await experimental verification.

A model for the photosynthetic apparatus of purple bacteria

Abstract The photosynthetic apparatus of purple bacteria is composed of light-harvesting complexes and reaction centres. Recent work on the structures of light-harvesting complexes combined with existing knowledge of the structure of the reaction centre now makes it feasible, for the first time, to model the entire photosynthetic apparatus. Questions can be asked about the functional implications of such a model in the light of the most recent spectroscopic data.

The purple bacterial photosynthetic unit

Now is a very exciting time for researchers in the area of the primary reactions of purple bacterial photosynthesis. Detailed structural information is now available for not only the reaction center (Lancaster et al. 1995, in: Blankenship RE et al. (eds) Anoxygenic Photosynthetic Bacteria, pp 503–526), but also LH2 from Rhodopseudomonas acidophila (McDermott et al. 1995, Nature 374: 517–521) and LH1 from Rhodospirillum rubrum (Karrasch et al. 1995. EMBO J 14: 631–638). These structures can now be integrated to produce models of the complete photosynthetic unit (PSU) (Papiz et al., 1996, Trends Plant Sci, in press), which opens the door to a much more detailed understanding of the energy transfer events occurring within the PSU.

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.

The structural basis of light-harvesting in purple bacteria

A typical purple bacterial photosynthetic unit consists of two types of light‐harvesting complex (LH1 and LH2) together with a reaction centre. This short review presents a description of the structure of the LH2 complex from Rhodopseudomonas acidophila, which has recently been improved to a resolution of 2.0 Å [Papiz et al., J. Mol. Biol. 326 (2003) 1523–1538]. We show how this structure has helped to reveal the details of the various excitation energy transfer events in which it is involved.

Biomineral proteins from Mytilus edulis mantle tissue transcriptome.

The common blue mussel, Mytilus edulis, has a bimineralic shell composed of approximately equal proportions of the two major polymorphs of calcium carbonate: calcite and aragonite. The exquisite biological control of polymorph production is the focus of research interest in terms of understanding the details of biomineralisation and the proteins involved in the process of complex shell formation. Recent advances in ease and availability of pyrosequencing and assembly have resulted in a sharp increase in transcriptome data for invertebrate biominerals. We have applied Roche 454 pyrosequencing technology to profile the transcriptome for the mantle tissue of the bivalve M. edulis. A comparison was made between the results of several assembly programs: Roche Newbler assembler versions 2.3, 2.5.2 and 2.6 and MIRA 3.2.1 and 3.4.0. The Newbler and MIRA assemblies were subsequently merged using the CAP3 assembler to give a higher consensus in alignments and a more accurate estimate of the true size of the M. edulis transcriptome. Comparison sequence searches show that the mantle transcripts for M. edulis encode putative proteins exhibiting sequence similarities with previously characterised shell proteins of other species of Mytilus, the Bivalvia Pinctada and haliotid gastropods. Importantly, this enhanced transcriptome has detected several transcripts that encode proteins with sequence similarity with previously described shell biomineral proteins including Shematrins and lysine-rich matrix proteins (KRMPs) not previously found in Mytilus.

Screening of biomineralization using microfluidics

Biomineralization is the process where biological systems produce well-defined composite structures such as shell, teeth, and bones. Currently, there is substantial momentum to investigate the processes implicated in biomineralization and to unravel the complex roles of proteins in the control of polymorph switching. An understanding of these processes may have wide-ranging significance in health care applications and in the development of advanced materials. We have demonstrated a microfluidic approach toward these challenges. A reversibly sealed T-junction microfluidic device was fabricated to investigate the influence of extrapallial (EP) fluid proteins in polymorph control of crystal formation in mollusk shells. A range of conditions were investigated on chip, allowing fast screening of various combinations of ion, pH, and protein concentrations. The dynamic formation of crystals was monitored on chip and combined with in situ Raman to reveal the polymorph in real time. To this end, we have demonstrated the unique advantages of this integrated approach in understanding the processes involved in biomineralization and revealing information that is impossible to obtain using traditional methods.

Light-harvesting mechanisms in purple photosynthetic bacteria.

The processes by which photosynthetic bacteria capture light and transfer the energy to the reaction centre continue to be studied using an array of methodologies, both physical and biological. With the publication this year of the crystal structure of the LH2 complex from Rhodopseudomonas acidophila and the projection structure of the LH1 complex from Rhodospirillum rubrum, structural models now exist for all the components in the bacterial photosynthetic apparatus.

Sirodesmins A, B, C, and G, antiviral epipolythiopiperazine-2,5-diones of fungal origin: X-ray analysis of sirodesmin A diacetate

The isolation, structures, and absolute configurations of sirodesmins A, B, C, and G, epipolythiopiperazine-2,5-dione antibiotics produced by Sirodesmium diversum, are reported. The structure of sirodesmin A (1), an epidithiopiperazinedione, was determined by X-ray analysis of the derived diacetate (6). The structures of sirodesmins B (3), C (2), and G (7), epi-tetra-,-tri-, and -di-thiopiperazinediones, respectively, were determined by comparison of their chemical and spectroscopic properties with those of sirodesmin A. Sirodesmins B and C differ from sirodesmin A only in the size of the polysulphide bridge; sirodesmins A and G are epimers.

Control of crystal polymorph in microfluidics using molluscan 28 kDa Ca2+-binding protein

Biominerals produced by biological systems in physiologically relevant environments possess extraordinary properties that are often difficult to replicate under laboratory conditions. Understanding the mechanism that underlies the process of biomineralisation can lead to novel strategies in the development of advanced materials. Using microfluidics, we have demonstrated for the first time, that an extrapallial (EP) 28 kDa protein, located in the extrapallial compartment between mantle and shell of Mytilus edulis, can influence, at both micro- and nanoscopic levels, the morphology, structure and polymorph that is laid down in the shell ultrastructure. Crucially, this influence is predominantly dependent on the existence of an EP protein concentration gradient and its consecutive interaction with Ca²(+) ions. Novel lemon-shaped hollow vaterite structures with a clearly defined nanogranular assembly occur only where particular EP protein and Ca²(+) gradients co-exist. Computational fluid dynamics enabled the progress of the reaction to be mapped and the influence of concentration gradients across the device to be calculated. Importantly, these findings could not have been observed using conventional bulk mixing methods. Our findings not only provide direct experimental evidence of the potential influence of EP proteins in crystal formation, but also offer a new biomimetic strategy to develop functional biomaterials for applications such as encapsulation and drug delivery.