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Theory of Intelligent Design, the best explanation of Origins » Photosynthesis, Protozoans,Plants and Bacterias » Phycobilisome light-harvesting complex

Phycobilisome light-harvesting complex

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1 Phycobilisome light-harvesting complex on Sat Mar 01, 2014 3:51 pm



Phycobilisomes are protein complexes (up to 600 polypeptides) anchored to thylakoid membranes. They are made of stacks of chromophorylated proteins , the Phycobiliprotein, and their associated linker polypeptides. Each phycobilisome consists of a core made of allophycocyanin, from which several outwardly oriented rods made of stacked disks of phycocyanin and (if present) phycoerythrin(s) or phycoerythrocyanin. The spectral property of phycobiliproteins are mainly dictated by their prosthetic groups, which are linear tetrapyrroles known as phycobilins including phycocyanobilin, phycoerythrobilin, phycourobilin and phycobiliviolin. The spectral properties of a given phycobilin is influenced by its protein environment.

The colorful antennae of marine Synechococcus

Phycobilisomes are light harvesting antennae of photosystem II
in cyanobacteria, red algae and glaucophytes.

The geometrical arrangement of a phycobilisome is very elegant and results in 95% efficiency of energy transfer


Phycobilins  are light-capturing bilanes found in cyanobacteria and in the chloroplasts of red algae, glaucophytes and some cryptomonads (though not in green algae and higher plants). Most of their molecules consist of a chromophore which makes them colored. They are unique among the photosynthetic pigments in that they are bonded to certain water-soluble proteins, known as phycobiliproteins. Phycobiliproteins then pass the light energy to chlorophylls for photosynthesis.

Phycobilins are complex photoreceptor pigments – open-chain tetrapyrroles that are structurally related to mammalian bile pigments. Phytochromes are phycobilin-protein pigments involved in floral induction. There are two classes of phycobilins and they occur only in Cyanobacteria and Rhodophyta. The phycobilin component is similar to the porphyrins without a metallic atom. Water-soluble phycobilin pigments are found in the stroma of the chloroplast. In at least two groups of algae, phycobiliproteins are aggregated in a highly ordered protein complex called a phycobilisome (PBS), making these phycobilins unique among photosynthetic pigments.


Bilins, bilanes or bile pigments are biological pigments formed in many organisms as a metabolic product of certain porphyrins. Bilin (also called bilichrome) was named as a bile pigment of mammals, but can also be found in lower vertebrates, invertebrates, as well as red algae, green plants and cyanobacteria. Bilins can range in color from red, orange, yellow or brown to blue or green.

In chemical terms, bilins are linear arrangements of four pyrrole rings (tetrapyrroles). In human metabolism, bilirubin is a breakdown product of heme.

Examples of bilins are found in animals, and phycocyanobilin, the chromophore of the photosynthetic pigment phycocyanin in algae and plants. In plants, bilins also serve as the photopigments of the photoreceptor protein phytochrome. .


Phycobiliproteins are water-soluble proteins present in cyanobacteria and certain algae (rhodophytes, cryptomonads, glaucocystophytes) that capture light energy, which is then passed on to chlorophylls during photosynthesis. Phycobiliproteins are formed of a complex between proteins and covalently bound phycobilins that act as chromophores  (the light-capturing part). They are most important constituents of the phycobilisomes.

Phycobiliproteins are water soluble proteins bound to chromophores, and are found within cyanobacteria and certain types of algae.  Functioning as accessory pigments to chlorophyll, the antennae-like structures capture light energy during photosynthesis and convey it through fluorescence resonance energy transfer to specialized chlorophyll molecules within the algal photosynthetic reaction center.  Phycobiliproteins have evolved to maximize both absorption and fluorescence, while minimizing the impact of external factors such as pH or ionic composition of their environment.


A chromophore is the part of a molecule responsible for its colour.  The colour arises when a molecule absorbs certain wavelengths of visible light and transmits or reflects others. The chromophore is a region in the molecule where the energy difference between two different molecular orbitals falls within the range of the visible spectrum. Visible light that hits the chromophore can thus be absorbed by exciting an electron from its ground state into an excited state.

In biological molecules that serve to capture or detect light energy, the chromophore is the moiety that causes a conformational change of the molecule when hit by light.

In the conjugated chromophores, the electrons jump between energy levels that are extended pi orbitals, created by a series of alternating single and double bonds,

The excited (energized) molecule can pass the energy to another molecule or release it in the form of light or

Some of these are metal complex chromophores, which contain a metal in a coordination complex with ligands. Examples are chlorophyll, which is used by plants for photosynthesis.

metal complex chromophores

a metal is complexed at the center of a tetrapyrrole macrocycle ring:  magnesium complexed in a chlorin-type ring in the case of chlorophyll.


Magnesium-containing chlorins are called chlorophylls, and are the central photosensitive pigment in chloroplasts.


In molecular biology, phycoerythrin (PE), like all phycobiliproteins, is composed of a protein part covalently binding chromophores called phycobilins, and organised mostly in a hexameric structure of alpha and beta chains. In the phycoerythrin family, the phycobilins are: phycoerythrobilin, the typical phycoerythrin acceptor chromophore, and sometimes phycourobilin (marine organisms). Phycoerythrins are the phycobiliproteins that bind the highest number of phycobilins (up to six per alpha-beta subunit dimer).

Absorption peaks in the visible light spectrum are measured at 495 and 545/566 nm, depending on the chromophores bound and the considered organism. A strong emission peak exists at 575 ± 10 nm. (i.e., phycoerythrin absorbs slightly blue-green/yellowish light and emits slightly orange-yellow light.)

Phycobilisomes are attached to the cytosol (stromal) face of the thylakoid. Extending into the cytosol, the phycobilisomes consist of a cluster of phycobilin pigments including phycocyanin (blue) and phycoerythrin (red) attached by their phycobiliproteins. These particles serve as light-energy antennae for photosynthesis. Phycobilisomes preferentially funnel light energy into photosystem II for the splitting of water and generation of oxygen. While many photosynthetic eubacteria possess photosystem I to oxidize reduced molecules such as H2S, only Cyanobacteria have photosystem II. The evolution of photosystem II apparently occured in Cyanobacteria.

R-Phycoerythrin and B-Phycoerythrin are among the brightest fluorescent dyes ever identified.

Scientists stitch up photosynthetic megacomplex

The photosynthetic megacomplex from a cyanobacterium, which scientists have managed to isolate in its complete, functioning form, weighs about 6 million Daltons. It has three parts: on top is a light-harvesting antenna complex called a phycobilisome that captures and funnels the energy in sunlight to two reaction centers, Photosystem II (the complex protruding beneath the antenna) and Photosystem I (the complexes to either side Photosystem II). The megacomplex is embedded in a membrane shown as a green carpet. Credit: Haijun Liu

When sunlight strikes a photosynthesizing organism, energy flashes between proteins just beneath its surface until it is trapped as separated electric charges. Improbable as it may seem these tiny hits of energy eventually power the growth and movement of all plants and animals. They are literally the sparks of life.

The three clumps of protein—a light-harvesting antenna called a phycobilisome and photosystems I and II—look like random scrawls in illustrations but this is misleading. They are able to do their job only because they are positioned with exquisite precision.

If the distances between proteins were too great or the transfers too slow, the energy would be wasted and—ultimately—all entropy-defying assemblages like plants and animals would fall to dust.

But until now scientists weren't even sure the three complex cohered as a single sun-worshipping megacomplex. Previous attempts to isolated connected complexes failed because the weak links that held them together broke and the megacomplex fell apart.

In the Nov. 29 issue of Science scientists at Washington University in St. Louis report on a new technique that finally allows the megacomplex to be plucked out entire and examined as a functioning whole.

Like a seamstress basting together the pieces of a dress, the scientists chemically linked the proteins in the megacomplex. Stabilized by the stitches, or crosslinks, it was isolated in its complete, fully functional form and subjected to the full armamentarium of their state-of-the-art labs, including tandem mass spectrometers and ultra-fast lasers.

The work was done at PARC (Photosynthetic Antenna Research Center), an Energy Frontier Research Center funded by the Department of Energy that is focused on the scientific groundwork needed to maximize photosynthetic efficiency in living organisms and to design biohybrid or synthetic ones to drive chemical processes or generate photocurrent.

Robert Blankenship, PhD, PARC's director and the Lucille P. Markey Distinguished Professor of Arts & Sciences, said that one outcome of the work in the long term might be the ability to double or triple the efficiency of crop plants—now stuck at a woeful 1 to 3 percent. "We will need such a boost to feed the 9 or 10 billion people predicted to be alive by 2050," he said.

Wizards of the lab

The scientists worked with the model organism often used to study photosynthesis in the lab, a cyanobacterium, sometimes called a blue-green alga.

Cyanobacteria are ancient organisms, known from fossils that are 3.5 billion years old, nearly as old as the oldest known rocks, and thought to be the first organisms to release oxygen into the noxious primitive atmosphere.

All photosynthesizing organisms have light-harvesting anntenas made up of many molecules that absorb light and transfer the excitation energy to reaction centers, where it is stored as charge separation.

In free-living cyanobacteria the antenna, called a phycobilisome, consists of splayed rods made up of disks of proteins containing intensely colored bilin pigments. The antenna sits directly above one reaction center, Photosystem II, and kitty corner to the other, Photosystem I.

PARC research scientist Haijun Liu, PhD, proposed stitching together the megacomplex and then engineered a strain of cyanobacteria that has a tag on the bottom of Photosystem II.

The mutant cells were treated with reagents that stitched together the complexes, then broken open, and the tag used to pull out Photosystem II and anything attached to it.

To figure out how the proteins were interconnected, the scientists repeatedly cut or shattered the proteins, analyzing them by mass spectrometry down to the level of the individual amino acid.

The amino acid sequences derived in this way were then compared to known sequences within the megacomplex, and the location of cross links between different complexes helped establish the overall structure of the megacomplex.

"It's a very complicated data analysis routine that literally generates tens of thousands of peptides that took a team of students and postdoctoral associates overseen by Hao Zhang and Michael Gross, months to analyze," Blankenship said. Hao Zhang, PhD, is a PARC research Scientist and Michael Gross, PhD, is professor of chemistry and Director of the Mass Spectrometry Resource in Arts & Sciences.

In the meantime research scientist Dariusz Niedzwiedzki, PhD, in the PARC Ultrafast Laser Facility was exciting the phycobilisome in intact megacomplexes and tracking the energy through the complex by the faint glow of fluorescencing molecules.

Typical energy transfers within the complex take place in a picosecond (a trillionth of a second), way too fast for humans to perceive. If one picosecond were a second, a second would be 31,700 years.

"PARC is one of the only places in the world that has available this sophisticated combination of experience and advanced techniques," said Blankenship, "and to solve this problem we were brought all of our expertise to bear.

"The work provides a new level of understanding of the organization of these photosynthetic membranes and that is something that a lot of people have tried to understand for a long time," he said.

"It also introduces the methodology of the crosslinking and then the mass spectrometry analysis that could potentially be applicable to a lot of other complexes, not just photosynthetic ones," he said.

"For example, enzymes in some metabolic pathways have long been thought to form supercomplexes that channel the products of one reaction directly to the next one. This technique might finally allow channeling supercomplexes to be identified in cases where the complex is only very weakly associated," he said.

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Exciton Coherence and Energy Transport in the Light-Harvesting Dimers of Allophycocyanin

Femtosecond transient grating and photon echo spectroscopies with a sub-20 fs time resolution are applied to allophycocyanin (APC), a protein located at the base of the phycobilisome antenna of cyanobacteria. Coupling between pairs of phycocyanobilin pigments with nondegenerate energy levels gives rise to the four-level exciton electronic structure of APC. Spectroscopic signals obtained in multiple experiments (e.g., linear absorption, fluorescence, transient grating, 2D Fourier transform photon echo) are used to constrain the parameters of a Frenkel exciton Hamiltonian. Comparison between experiment and theory yields a robust microscopic understanding of the electronic and nuclear relaxation dynamics. In agreement with previous work, transient absorption anisotropy establishes that internal conversion between the exciton states of the dimer occurs with time constants of 35, 220, and 280 fs. The sub-100 fs dynamics are decomposed into three distinct relaxation processes: electronic population transfer, intramolecular vibrational energy redistribution, and the dephasing of electronic and nuclear coherences. Model calculations show that the sub-100 fs red-shift in the transient absorption signal spectrum reflects interference between stimulated emission (ESE) and excited state absorption (ESA) signal components. It is also established that the pigment fluctuations in the dimer are not well-correlated, although further experiments will be required to precisely quantify the amount of correlation. The findings of this paper suggest that the light harvesting function of APC is enhanced by nondegeneracy of the pigments comprising the dimer and strong vibronic coupling of intramolecular modes on the phycocyanobilins. We find that the exciton states are 96% localized to the individual molecular sites within a particular dimer. Localization of the transition densities, in turn, is suggested to promote significant vibronic coupling which serves to both broaden the absorption line shape and open channels for fast internal conversion. The dominant internal conversion channel is assigned to a promoting mode near 800 cm−1 involving hydrogen out-of-plane (HOOP) wagging motion similar to that observed in phytochrome and retinal. This rate enhancement ensures that all photoexcitations quickly and efficiently relax to the electronic origin of the lower energy exciton state from which energy transfer to the reaction center occurs.

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The Crystal Structure of a Novel Unmethylated Form of C-phycocyanin, a Possible Connector Between Cores and Rods in Phycobilisomes

The planes of the rings that make up the hexamers in the rods are perpendicular to both the APC core and to the membrane, so that in essence the APC hexamer disks bind the PC rods by their outer circumference. In addition to the pigment-binding pycobiliproteins, a number of linker proteins have been found associated with PB components (6, 7). It has been suggested that these linker proteins occupy positions running through the internal cavities of the disks and may play roles in complex stabilization, rod-core assembly, and in inducing the directionality of energy transfer toward Photosystem II. Light energy trapped by the most prevalent pigments (phycoerythrobilin, λmax = 560 nm; phycocyanobilin, λmax = 620 nm) traverses down through the rods to the APC pigments (λmax = 652 nm) and from these pigments to the chlorophyll pigments of the reaction center (λmax = 674–680 nm) (3, 4).

A significant number of PB protein structures have been determined over the past few years (8–25). All of these structures show a very high degree of similarity in the overall structures, the details of the pigment surroundings, the solvent interactions, and the protein residue positions in each structure, and thus have given us an excellent molecular view of the constituents of the PBs.

The PB is an antenna complex finely tuned to transfer energy to the reaction center of Photosystem II with an efficiency of over 95% (36). It performs this function with a high degree of directionality, even though there are large numbers of similar pigment molecules within each complex (3). A number of possible energy transfer pathways have been described in great detail on the basis of crystal structures and Förster energy transfer theory (10, 12, 20). The initiation point of energy transfer takes into account that each of the different phycobilin pigments has modified absorption/emission properties as a result of the unique chemical background formed by the protein matrix. In PC, the three phycocyanobilin co-factors have slightly different absorption maxima, and in combination with their relative geometric position it has been proposed that the β155 co-factor is a sensitizing type pigment (absorbing to the blue), the β84 co-factor is a fluorescing type pigment (absorbing further to the red), and the α84 co-factor is an intermediate pigment type (4).

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