PAR CLIP ref name pmid20371350 cite journal author Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T. title Transcriptome wide identification of RNA binding protein and microRNA target sites by PAR CLIP. journal Cell volume 141 issue 1 pages 129 141 year 2010 pmid 20371350 doi 10.1016 j.cell.2010.03.009 pmc 2861495 ref Photoactivatable Ribonucleoside Enhanced Crosslinking and Immunoprecipitation is a novel method, used for identifying the binding sites of cellular RNA binding proteins RBPs and microRNA containing ribonucleoprotein complexes miRNPs . The method relies on the incorporation of photoreactive ribonucleoside analogs, such as 4 thiouridine 4 SU and 6 thioguanosine 6 SG into nascent RNA transcripts by living cells. Irradiation of the cells by UV light of 365 nm induces efficient crosslinking of photoreactive nucleoside labeled cellular RNAs to interacting RBPs. Immunoprecipitation of the RBP of interest is followed by isolation of the crosslinked and coimmunoprecipitated RNA. The isolated RNA is converted into a cDNA library and deep sequenced using next generation sequencing technology ref name pmid20371350 ref Cite pmid 20644507 ref . Recently, PAR CLIP have been applied to determine the transcriptome wide binding sites of several known RBPs and microRNA containing ribonucleoprotein complexes at high resolution ref name pmid20371350 ref name pmid21037263 cite journal author Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH. title starBase a database for exploring microRNA mRNA interaction maps from Argonaute CLIP Seq and Degradome Seq data. journal Nucl. Acids Res. volume 39 issue Database issue pages D202 D209 year 2011 pmid 21037263 doi 10.1093 nar gkq1056 pmc 3013664 ref . External links http starbase.sysu.edu.cn starBase database a database for exploring protein RNA and miRNA target interactions from PAR CLIP CLIP Seq , HITS C ... more details
Photo reactive amino acid analogs are artificial analogs of natural amino acids that can be used for crosslinking of protein complexes. ref cite journal author Suchanek, M., Radzikowska, A., and Thiele, C. date 2005 title Photo leucine and photo methionine allow identification of protein protein interactions in living cells journal Nature Methods volume 2 pmid 15782218 pages 261 268 doi 10.1038 nmeth752 issue 4 ref Photo reactive amino acid analogs may be incorporated into proteins and peptides in vivo or in vitro . Photo reactive amino acid analogs in common use are Photochemistry photoreactive diazirine analogs to leucine and methionine , and p benzoylphenylalanine. Upon exposure to ultraviolet light , they are activated and covalently bind to interacting proteins that are within a few angstrom s of the photo reactive amino acid analog. L Photo Leucine and L Photo Methionine are analogs of the naturally occurring L Leucine and L Methionine amino acids that are endogenously incorporated into the primary sequence of proteins during synthesis using the normal translation machinery. They are then ultraviolet light UV activated to covalently crosslink proteins within protein protein interaction domains in their native in vivo environment. The method enables the determination and characterization of both stable and transient protein interactions in cells without the addition of chemical crosslinkers and associated solvents that can adversely affect the cell biology being studied in the experiment. When used in combination with limiting media that is devoid of leucine and methionine, the photo activatable derivatives are treated like naturally occurring amino acids by the cellular protein synthesis machinery. As a result, they can be substituted for leucine or methionine in the primary structure of proteins. Photo leucine and photo methionine derivatives contain diazirine rings that are activated when exposed to UV light to become reactive intermediates that form covalen ... more details
Image Quantum efficiency graph for WFPC2 en.svg thumb right 300px A graph showing variation of quantum efficiency with wavelength of a CCD chip in the Hubble Space Telescope s Wide Field and Planetary Camera 2 . Quantum efficiency QE is a quantity defined for a photosensitive device such as photographic film or a charge coupled device CCD as the percentage of photon s hitting the photoreactive surface that will produce an electron hole pair . ref http www.photonics.com Directory Dictionary Definition.aspx?type 2&DictionaryID 6488 Definition of quantum efficiency in Photonics Dictionary ref It is an accurate measurement of the device s electrical sensitivity to light. Since the energy of a photon depends on more precisely, is inversely proportional to its wavelength , QE is often measured over a range of different wavelengths to characterize a device s efficiency at each photon energy. Photographic film typically has a QE of much less than 10 , while CCDs can have a QE of well over 90 at some wavelengths. The quantum efficiency of a solar cell is a very important measure for solar cells as it gives information on the current that a given cell will produce when illuminated by a particular wavelength. If the quantum efficiency is integrated summed over the whole Solar radiation solar electromagnetic spectrum , one can evaluate the current that a cell will produce when exposed to the solar spectrum. The ratio between this current and the highest possible current if the QE was 100 over the whole spectrum gives the electrical efficiency of the solar cell. With solar cells, one often measures the external quantum efficiency EQE, sometimes also simply referred to as QE , which is the current obtained outside the device per incoming photon. math text Efficiency frac text output text input math math text EQE frac text electrons sec text photons sec frac text current text charge of 1 electron text total power of photons text energy of one photon math The external quantum effic ... more details
Retinylidene proteins are a family of proteins that use retinal as chromophore for light reception. Proteins of this family are also called opsin s. They are the molecular basis for a variety of light sensing systems from phototaxis in flagellate s to eyesight in animal s. Structure All rhodopsins consist of two building blocks, a protein moiety and a reversibly covalent ly bound non protein Cofactor biochemistry cofactor , retinal retinaldehyde . The protein structure of rhodopsin consists of a bundle of seven Transmembrane helix transmembrane helices that form an internal pocket binding the photoreactive chromophore. They form a superfamily with other membrane bound receptors containing seven transmembrane domains, for example odor and chemokine receptors. ref name Sakmar cite journal author Sakmar T title Structure of rhodopsin and the superfamily of seven helical receptors the same and not the same journal Curr Opin Cell Biol volume 14 issue 2 pages 189 95 year 2002 pmid 11891118 doi 10.1016 S0955 0674 02 00306 X ref Mechanism of light reception Instead of being activated by binding chemical ligand s like their relatives, rhodopsins contain retinal which changes conformation in reaction to light via photoisomerization and thus are activated by light. The retinal molecule can take on several different Cis trans isomerism cis trans isomeric forms, such as all trans , 11 cis and 13 cis . Photoisomerization light dependent isomerization of retinal from cis to trans or vice versa induces a conformational change in the receptor protein. This change acts as a molecular switch to activate a signal transduction mechanism within the cell. Depending on the type of rhodopsin, it either opens an ion channel for example in bacteria or activates an associated G protein and triggers a second messenger cascade for example in animal eyes . Types of rhodopsins Retinylidene proteins or rhodopsins are present in many species from bacteria to algae and animals. They can be divided in ... more details
About the visual rhodopsin of vertebrates other types of rhodopsin retinylidene protein PBB geneid 6010 Rhodopsin , also known as visual purple , is a biological pigment of the retina that is responsible for both the formation of the photoreceptor cell s and the first events in the perception of light . Rhodopsins belong to the G protein coupled receptor family and are extremely sensitive to light, enabling vision in low light conditions. ref name Litmann 1996 cite book author Litmann BJ, Mitchell DC authorlink editor Lee AG others title Rhodopsin and G Protein Linked Receptors, Part A Vol 2, 1996 2 Vol Set edition language publisher JAI Press location Greenwich, Conn year 1996 origyear pages 1 32 quote isbn 1 55938 659 2 chapter Rhodopsin structure and function doi url accessdate ref Exposed to light, the pigment immediately Photobleaching photobleaches , and it takes about 30 minutes ref name Stuart 1996 cite book author Stuart JA, Brige RR authorlink editor Lee AG others title Rhodopsin and G Protein Linked Receptors, Part A Vol 2, 1996 2 Vol Set edition language publisher JAI Press location Greenwich, Conn year 1996 origyear pages 33 140 quote isbn 1 55938 659 2 chapter Characterization of the primary photochemical events in bacteriorhodopsin and rhodopsin doi url accessdate ref to regenerate fully in humans. Structure Rhodopsin consists of the Moiety chemistry protein moiety opsin and a reversibly covalent ly bound Cofactor biochemistry cofactor , retinal . Opsin, a bundle of seven transmembrane helices connected to each other by protein loops, binds retinal a photoreactive chromophore , which is located in a central pocket on the seventh helix at a lysine residue. Retinal lies horizontally with relation to the membrane. Each outer segment disc contains thousands of visual pigment molecules. About half the opsin is within the lipid bilayer . Retinal is produced in the retina from Vitamin A , from dietary beta carotene . Isomerization of 11 cis retinal into all ... more details
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