Phycoerythrin

{{main|Phycobilisome}}

File:Phycobilisome structure.jpgs (like phycoerythrin) usually form rods of stacked disks in phycobilisomes.]]

Phycobiliproteins are part of huge light harvesting antennae protein complexes called phycobilisomes. In red algae they are anchored to the stromal side of thylakoid membranes of chloroplasts, whereas in cryptophytes phycobilisomes are reduced and (phycobiliprotein 545 PE545 molecules here) are densely packed inside the lumen of thylakoides. {{r|WeijDeWit06|Glazer85}}

Phycobiliproteins have many practical application to them including imperative properties like hepato-protective, anti-oxidants, anti-inflammatory and anti-aging activity of PBPs enable their use in food, cosmetics, pharmaceutical and biomedical industries. PBPs have been also noted to show beneficial effect in therapeutics of some disease like Alzheimer and cancer.{{cite journal | vauthors = Sonani RR, Rastogi RP, Patel R, Madamwar D | title = Recent advances in production, purification and applications of phycobiliproteins | journal = World Journal of Biological Chemistry | volume = 7 | issue = 1 | pages = 100–109 | date = February 2016 | pmid = 26981199 | pmc = 4768114 | doi = 10.4331/wjbc.v7.i1.100 | doi-access = free }}

Phycoerythrin is an accessory pigment to the main chlorophyll pigments responsible for photosynthesis. The light energy is captured by phycoerythrin and is then passed on to the reaction centre chlorophyll pair, most of the time via the phycobiliproteins phycocyanin and allophycocyanin.

Phycoerythrins except phycoerythrin 545 (PE545) are composed of (αβ) monomers assembled into disc-shaped (αβ)₆ hexamers or (αβ)₃ trimers with 32 or 3 symmetry and enclosing central channel. In phycobilisomes (PBS) each trimer or hexamer contains at least one linker protein located in central channel. B-phycoerythrin (B-PE) and R-phycoerythrin (R-PE) from red algae in addition to α and β chains have a third, γ subunit contributing both linker and light-harvesting functions, because it bears chromophores. {{r|Ficner93}}

File:B-phycoerythrin 3V57.png Porphyridium cruentum (PDB ID: 3V57 {{r|PDB3V57|CamaraArtigas12|RasTop}}). The asymmetric unit ({{color|green|α}}{{color|blue|β}})₂ on the left and assumed biological molecule ({{color|green|α}}{{color|blue|β}})₃. It contains {{color|#FF40FF|phycoerythrobilin}}, {{color|#FF6600|N-methyl asparagine}} and {{color|#FFD500|{{chem|SO|4|2-}}}}.]]

R-phycoerythrin is predominantly produced by red algae. The protein is made up of at least three different subunits and varies according to the species of algae that produces it. The subunit structure of the most common R-PE is (αβ)₆γ. The α subunit has two phycoerythrobilins (PEB), the β subunit has 2 or 3 PEBs and one phycourobilin (PUB), while the different gamma subunits are reported to have 3 PEB and 2 PUB (γ₁) or 1 or 2 PEB and 1 PUB (γ₂). The molecular weight of R-PE is 250,000 daltons.

Crystal structures available in the Protein Data Bank {{r|PDBwww}} contain in one (αβ)₂ or (αβγ)₂ asymmetric unit of different phycoerythrins:

File:Phycoerythrobilin2.svg of chlorophyll for example, but tetrapyrrole is linear, not closed into ring with metal ion in the middle.]]

File:Gracilaria2.JPG Gracilaria contains R-phycoerythrin.]]

File:Phycoerythrin 545 1XG0.gif cryptophyte Rhodomonas CS24 (PDB ID: 1XG0 {{r|PDB1XG0|Doust04|RasTop}}). Colors: chains – {{color|#80FF00|alpha-2}}, {{color|#00BF00|alpha-3}}, {{color|#0080FF|beta}}, {{color|#5B5BFF|beta}} (helixes, sheets are yellow), {{color|#FF40FF|phycoerythrobilin}}, {{color|#BF00BF|15,16-dihydrobiliverdin}} (15,16-DHBV), {{color|#800000|5-hydroxylysine}}, {{color|#FF6600|N-methyl asparagine}}, {{color|red|Mg²⁺}}, {{color|#FFD500|Cl⁻}}.]]

The assumed biological molecule of phycoerythrin 545 (PE545) is (αβ)₂ or rather {{nowrap|(α₃β)(α₂β)}}. The numbers 2 and 3 after the α letters in second formula are part of chain names here, not their counts. The synonym cryptophytan name of α₃ chain is α₁ chain.

The largest assembly of B-phycoerythrin (B-PE) is (αβ)₃ trimer {{r|PDB3V57|CamaraArtigas12}}. However, preparations from red algae yield also (αβ)₆ hexamer {{r|Ficner93}}. In case of R-phycoerythrin (R-PE) the largest assumed biological molecule here is (αβγ)₆, {{nowrap|(αβγ)₃(αβ)₃}} or (αβ)₆ dependently on publication, for other phycoerythrin types (αβ)₆. These γ chains from the Protein Data Bank are very small and consist only of three or six recognizable amino acids {{r|PDB1EYX|ContrerasMartel01}}, whereas described at the beginning of this section linker γ chain is large (for example 277 amino acid long 33 kDa in case of γ³³ from red algae Aglaothamnion neglectum) {{r|Apt93|Ficner93}}. This is because the electron density of the gamma-polypeptide is mostly averaged out by its threefold crystallographic symmetry and only a few amino acids can be modeled {{r|PDB1EYX|ContrerasMartel01|PDB1B8D|Ritter99}}.

For (αβγ)₆, (αβ)₆ or {{nowrap|(αβγ)₃(αβ)₃}} the values from the table should be simply multiplied by 3, (αβ)₃ contain intermediate numbers of non-protein molecules. (this non sequitur needs to be corrected)

In phycoerythrin PE545 above, one α chain (-2 or -3) binds one molecule of billin, in other examples it binds two molecules. The β chain always binds to three molecules. The small γ chain binds to none.

Two molecules of N-methyl asparagine are bound to the β chain, one 5-hydroxylysine to α (-3 or -2), one Mg²⁺ to α-3 and β, one Cl⁻ to β, 1–2 molecules of {{chem|SO|4|2−}} to α or β.

Below is sample crystal structure of R-phycoerythrin from Protein Data Bank:

File:R-phycoerythrin 1EYX 1 of 2.gif Gracilaria chilensis (PDB ID: 1EYX {{r|PDB1EYX|ContrerasMartel01|RasTop}}) - basic oligomer ({{color|green|α}}{{color|blue|β}}{{color|red|γ}})₂ (so called asymmetric unit). It contains {{color|#BF00BF|phycocyanobilin}}, {{color|#FF40FF|biliverdine IX alpha}}, {{color|#FF80FF|phycourobilin}}, {{color|#FF6600|N-methyl asparagine}}, {{color|#FFD500|SO₄²⁻}}. One fragment of γ chain is red, second one white because it is not considered as alpha helix despite identical aminoacid sequence.]]

File:R-phycoerythrin 1EYX 2 of 2.gif of R-phycoerythrin from Gracilaria chilensis ({{color|green|α}}{{color|blue|β}}{{color|red|γ}})₆ (PDB ID: 1EYX {{r|PDB1EYX|ContrerasMartel01|RasTop}})]]

File:Pycoerythrin spectra.jpg

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. (Phycoerythrin absorbs slightly blue-green/yellowish light and emits slightly orange-yellow light.)

PEB and DBV bilins in PE545 absorb in the green spectral region too, with maxima at 545 and 569 nm respectively. The fluorescence emission maximum is at 580 nm. {{r|WeijDeWit06}}

File:RPEexemComparison.png

As mentioned above, phycoerythrin can be found in a variety of algal species. As such, there can be variation in the efficiency of absorbance and emission of light required for facilitation of photosynthesis. This could be a result of the depth in the water column that a specific alga typically resides and a consequent need for greater or less efficiency of the accessory pigments.

With advances in imaging and detection technology which can avoid rapid photobleaching, protein fluorophores have become a viable and powerful tool for researchers in fields such as microscopy, microarray analysis and Western blotting. In light of this, it may be beneficial for researchers to screen these variable R-phycoerythrins to determine which one is most appropriate for their particular application. Even a small increase in fluorescent efficiency could reduce background noise and lower the rate of false-negative results.

R-Phycoerythrin (also known as PE or R-PE) is useful in the laboratory as a fluorescence-based indicator for the presence of cyanobacteria and for labeling antibodies, most often for flow cytometry. Its also used in microarray assays, ELISAs, and other applications that require high sensitivity but not photostability.{{Cite web|title=R-phycoerythrin (R-PE) - US|url=https://www.thermofisher.com/us/en/home/life-science/cell-analysis/fluorophores/r-phycoerythrin.html|access-date=2021-12-11|website=www.thermofisher.com|language=en}} Its use is limited in immunofluorescence microscopy due to its rapid photobleaching characteristics. There are also other types of phycoerythrins, such as B-phycoerythrin, which have slightly different spectral properties. B-Phycoerythrin absorbs strongly at about 545 nm (slightly yellowish green) and emits strongly at 572 nm (yellow) instead and could be better suited for some instruments. B-Phycoerythrin may also be less "sticky" than R-phycoerythrin and contributes less to background signal due to nonspecific binding in certain applications.{{citation needed|date=October 2016}} However, R-PE is much more commonly available as an antibody conjugate. Phycoerythrin (PE, λA max = 540–570 nm; λF max = 575–590 nm)

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

{{Reflist|refs=

{{cite journal |url=http://www.rcsb.org/pdb/explore/explore.do?structureId=1XG0 |title=High resolution crystal structure of phycoerythrin 545 from the marine cryptophyte rhodomonas CS24 | vauthors = Doust AB, Marai CN, Harrop SJ, Wilk KE, Curmi PM, Scholes GD |date=2004-09-16 |publisher=RCSB Protein Data Bank (PDB) |id=PDB ID: 1XG0 |doi=10.2210/pdb1xg0/pdb |access-date=11 October 2012}}

{{cite journal | vauthors = Doust AB, Marai CN, Harrop SJ, Wilk KE, Curmi PM, Scholes GD | title = Developing a structure-function model for the cryptophyte phycoerythrin 545 using ultrahigh resolution crystallography and ultrafast laser spectroscopy | journal = Journal of Molecular Biology | volume = 344 | issue = 1 | pages = 135–153 | date = November 2004 | pmid = 15504407 | doi = 10.1016/j.jmb.2004.09.044 | id = PDB ID: 1XG0 }}

{{cite journal |url=http://www.rcsb.org/pdb/explore/explore.do?structureId=1EYX |title=Crystal structure of R-phycoerythrin at 2.2 angstroms | vauthors = Contreras-Martel C, Martinez-Oyanedel J, Bunster M, Legrand P, Piras C, Vernede X, Fontecilla-Camps JC |date=2000-05-09 |publisher=RCSB Protein Data Bank (PDB) |id=PDB ID: 1EYX |doi=10.2210/pdb1eyx/pdb |access-date=11 October 2012}}

{{cite journal | vauthors = Contreras-Martel C, Martinez-Oyanedel J, Bunster M, Legrand P, Piras C, Vernede X, Fontecilla-Camps JC | title = Crystallization and 2.2 A resolution structure of R-phycoerythrin from Gracilaria chilensis: a case of perfect hemihedral twinning | journal = Acta Crystallographica. Section D, Biological Crystallography | volume = 57 | issue = Pt 1 | pages = 52–60 | date = January 2001 | pmid = 11134927 | doi = 10.1107/S0907444900015274 | s2cid = 216930 | id = PDB ID: 1EYX | doi-access = }}

{{cite journal |url=http://www.rcsb.org/pdb/explore/explore.do?structureId=3V57 |title=Crystal Structure of the B-phycoerythrin from the red algae Porphyridium cruentum at pH8 |author=Camara-Artigas, A. |date=2011-12-16 |publisher=RCSB Protein Data Bank (PDB) |id=PDB ID: 3V57 |doi=10.2210/pdb3v57/pdb |access-date=12 October 2012}}

{{cite journal | vauthors = Camara-Artigas A, Bacarizo J, Andujar-Sanchez M, Ortiz-Salmeron E, Mesa-Valle C, Cuadri C, Martin-Garcia JM, Martinez-Rodriguez S, Mazzuca-Sobczuk T, Ibañez MJ, Allen JP | display-authors = 6 | title = pH-dependent structural conformations of B-phycoerythrin from Porphyridium cruentum | journal = The FEBS Journal | volume = 279 | issue = 19 | pages = 3680–3691 | date = October 2012 | pmid = 22863205 | doi = 10.1111/j.1742-4658.2012.08730.x | s2cid = 31253970 | id = PDB ID: 3V57 }}

{{cite journal | vauthors = Ritter S, Hiller RG, Wrench PM, Welte W, Diederichs K | title = Crystal structure of a phycourobilin-containing phycoerythrin at 1.90-A resolution | journal = Journal of Structural Biology | volume = 126 | issue = 2 | pages = 86–97 | date = June 1999 | pmid = 10388620 | doi = 10.1006/jsbi.1999.4106 | url = http://nbn-resolving.de/urn:nbn:de:bsz:352-opus-40951 | id = PDB ID: 1B8D }}

{{cite journal | url = http://www.rcsb.org/pdb/explore/explore.do?structureId=1B8D |title=Crystal structure of a phycourobilin-containing phycoerythrin | vauthors = Ritter S, Hiller RG, Wrench PM, Welte W, Diederichs K |date=1999-01-29 |id=PDB ID: 1B8D |doi=10.2210/pdb1b8d/pdb }}

{{cite web |url=http://www.rcsb.org/pdb/ |title=Protein Data Bank |publisher=RCSB Protein Data Bank (PDB) |access-date=12 October 2012 |url-status=dead |archive-url=https://web.archive.org/web/20080828002005/http://www.rcsb.org./pdb |archive-date=28 August 2008 }}

Image created with [http://www.geneinfinity.org/rastop/ RasTop] (Molecular Visualization Software).

{{cite journal | vauthors = Glazer AN | title = Light harvesting by phycobilisomes | journal = Annual Review of Biophysics and Biophysical Chemistry | volume = 14 | pages = 47–77 | date = 1985 | pmid = 3924069 | doi = 10.1146/annurev.bb.14.060185.000403 }}

{{cite journal | vauthors = van der Weij-De Wit CD, Doust AB, van Stokkum IH, Dekker JP, Wilk KE, Curmi PM, Scholes GD, van Grondelle R | display-authors = 6 | title = How energy funnels from the phycoerythrin antenna complex to photosystem I and photosystem II in cryptophyte Rhodomonas CS24 cells | journal = The Journal of Physical Chemistry B | volume = 110 | issue = 49 | pages = 25066–25073 | date = December 2006 | pmid = 17149931 | doi = 10.1021/jp061546w | url = http://www.nat.vu.nl/en/Images/06-19_tcm69-87480.pdf | url-status = dead | archive-url = https://web.archive.org/web/20131030102747/http://www.nat.vu.nl/en/Images/06-19_tcm69-87480.pdf | archive-date = 30 October 2013 }}

{{cite journal | vauthors = Apt KE, Hoffman NE, Grossman AR | title = The gamma subunit of R-phycoerythrin and its possible mode of transport into the plastid of red algae | journal = The Journal of Biological Chemistry | volume = 268 | issue = 22 | pages = 16208–16215 | date = August 1993 | pmid = 8344905 | doi = 10.1016/S0021-9258(19)85407-8 | doi-access = free }}

{{cite journal | vauthors = Ficner R, Huber R | title = Refined crystal structure of phycoerythrin from Porphyridium cruentum at 0.23-nm resolution and localization of the gamma subunit | journal = European Journal of Biochemistry | volume = 218 | issue = 1 | pages = 103–106 | date = November 1993 | pmid = 8243457 | doi = 10.1111/j.1432-1033.1993.tb18356.x | doi-access = free }}

{{cite journal | vauthors = Six C, Thomas JC, Garczarek L, Ostrowski M, Dufresne A, Blot N, Scanlan DJ, Partensky F | display-authors = 6 | title = Diversity and evolution of phycobilisomes in marine Synechococcus spp.: a comparative genomics study | journal = Genome Biology | volume = 8 | issue = 12 | pages = R259 | date = 2007 | pmid = 18062815 | pmc = 2246261 | doi = 10.1186/gb-2007-8-12-r259 | name-list-style = amp | doi-access = free }}

}}

• {{MeshName|Phycoerythrin}}

{{Plant Pigments}}

Category:Proteins

Category:Photosynthetic pigments

Category:Fluorescent proteins

Category:Cyanobacteria proteins

Category:Red algae