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Topic: Chromophore

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	Chromophore - Wikipedia, the free encyclopedia
		A chromophore is a region in a molecule where the energy difference between two different molecular orbitals falls within the range of the visible spectrum.
		The metal complex chromophores arise from the splitting of d-orbitals by binding of a transition metal to ligands.
		A common motif in biochemistry is chromophores consisting of four pyrrole rings.
	en.wikipedia.org /wiki/Chromophore (305 words)

	RedOrbit - Science - QM/MM Study of Energy Storage and Molecular Rearrangements Due to the Primary Event in Vision (Site not responding. Last check: 2007-10-08)
		Furthermore, the wavelength of maximum ahsorbance of the retinyl chromophore in rhodopsin is significantly shifted relative to the absorption of retinal in solutions and approximately coincides with the wavelength of maximum intensity of the solar spectrum (~500 nm).
		Other steric constraints for chromophore rearrangements in the rhodopsin binding pocket are responsible for blocking the motion of the β-ionone ring during isomerization, inducing torsional strain in the polyene chain.
		The retinyl chromophore and the protein chain beyond the Schiff linkage are represented by brown and gray tubes, respectively.
	www.redorbit.com /news/display/?id=104500 (7108 words)

	Olympus FluoView Resource Center: The Fluorescent Protein Color Palette
		In all cases, the first step in maturation of the chromophore is a series of torsional adjustments that relocate the carboxyl carbon of the amino acid at position 65 so that it is in close proximity to the amino nitrogen of the glycine residue at position 67 (Gly67) in the polypeptide backbone.
		The DsRed chromophore is similar in structure to that found in native green fluorescent protein, but is modified through the oxidation of a second backbone bond to extend the conjugated pi-electron system to include the phenylalanine amino acid residue at position 65 (preceding the chromophore) in the peptide chain.
		Light-induced changes to the autocatalytic chromophores, including photoactivation and photoconversion, may serve as a highly evolved photo-protection mechanism to assist these organisms in the useful dissipation of high-energy sunlight, especially the damaging shorter wavelengths, via the absorption and subsequent fluorescence re-emission of longer and safer wavelengths.
	www.olympusconfocal.com /applications/fpcolorpalette.html (10016 words)

	Olympus FluoView Resource Center: Optical Highlighter Fluorescent Proteins
		Protein chromophores that can be activated to initiate fluorescence emission from a quiescent state (a process known as photoactivation), or are capable of being optically converted from one fluorescence emission bandwidth to another (photoconversion), represent perhaps the most promising approach to the in vivo investigation of protein lifetimes, transport, and turnover rates.
		When the protein is illuminated with high-intensity ultraviolet or violet light, however, the chromophore population undergoes photoconversion and shifts predominately to the anionic form, reversing the relative extinction coefficient ratio of the major and minor absorption peaks.
		Light-induced changes to the autocatalytic chromophores, including photoactivation and photoconversion, may serve as a highly evolved photoprotection mechanism to assist these organisms in the useful dissipation of high-energy sunlight, especially the damaging shorter wavelengths, via the absorption and subsequent fluorescence re-emission of longer and safer wavelengths.
	www.olympusconfocal.com /applications/opticalhighlighters.html (10266 words)

	Crystal structure of neocarzinostatin, an antitumor protein-chromophore complex -- Kim et al. 262 (5136): 1042 -- ... (Site not responding. Last check: 2007-10-08)
		Neocarzinostatin is composed of a labile chromophore with DNA-cleaving activity and a stabilizing protein.
		The chromophore displays marked nonlinearity of the triple bonds and is bound noncovalently in a pocket formed by the two protein domains.
		The amino sugar and carbonate groups of the chromophore are solvent exposed, whereas the epoxide, acetylene groups, and carbon C-12, the site of nucleophilic thiol addition during chromophore activation, are unexposed.
	www.sciencemag.org /cgi/content/abstract/262/5136/1042 (508 words)

	Chromophore Synthesis (Site not responding. Last check: 2007-10-08)
		In addition to polymeric chromophores, we are sythesizing molecular chromophores.
		In some cases, the chromophores are designed to be added to a fiber much like traditional dyestuffs.
		In others, we are attaching the chromophores to the surface of films and fibers in a highly organized manner.
	facweb.furman.edu /~thanks/ntc/ChromoSyn1.html (70 words)

	Synthesis of key sandramycin analogs: systematic examination of the intercalation chromophore.
		The preparation and examination of 2-22 constituting a systematic study of the chromophore of sandramycin (1) are detailed.
		The exception to this generalization was 4 which lacks the sandramycin chromophore phenol.
		Additionally, the first disclosure of the HIV-1 reverse transcriptase inhibitory activity of sandramycin (1) as well as that of its key analogs are described and define the chromophore structural features required for their exceptional potency.
	www.aegis.com /aidsline/1998/jul/M9871151.html (541 words)

	The Heme-Oxygenase Family Required for Phytochrome Chromophore Biosynthesis Is Necessary for Proper Photomorphogenesis ...
		Muramoto T, Kohchi T, Yokota A, Hwang I, Goodman HM (1999) The Arabidopsis photomorphogenic mutant hy1 is deficient in phytochrome chromophore biosynthesis as a result of a mutation in a plastid heme oxygenase.
		Terry MJ, Kendrick RE (1996) The aurea and yellow-green-2 mutants of tomato are deficient in phytochrome chromophore synthesis.
		Terry MJ, McDowell MT, Lagarias JC (1995) (3Z)- and (3E)-phytochromobilin are intermediates in the biosynthesis of the phytochrome chromophore.
	www.plantphysiol.org /cgi/content/full/126/2/656 (7216 words)

	Studies of Single Green Fluorescent Proteins (GFP) in Gels
		A protein composed of 238 amino acids, GFP folds such that the chromophore is isolated inside a compact barrel structure.
		This blinking behavior likely results from ground state dynamics between at least two states of the chromophore, only one of which is capable of being excited at 488 nm and producing fluorescence.
		Mutation of individual amino acid residues near the chromophore should allow fine-tuning of the potential barrier separating the anionic and neutral states, thus altering their relative ground and excited state stabilities.
	www.stanford.edu /group/moerner/blinking.html (671 words)

	Chromophore aggregates (Site not responding. Last check: 2007-10-08)
		We are applying absorption and resonance Raman spectroscopies to study the structural and optical properties of chromophore aggregates.
		Our main focus is on aggregates of the organic "push-pull" chromophores that are being explored as the optically active media in polymers for nonlinear optical applications.
		For device applications the chromophores must be present at high concentration (5-50% by mass) in the polymer, where interchromophore interactions may substantially modify their properties.
	faculty.ucmerced.edu /amkelley/dimer.html (516 words)

	Green Fluorescent Protein (GFP) - Structure (Site not responding. Last check: 2007-10-08)
		The chromophore is located in the middle of the beta-barrel, it is occasionally referred to as the “light in the can”.
		The chromophore of GFP is responsible for its fluorescence.
		The biggest difference between green fluorescent protein and it's red analog, DsRed, is that the chromophore of DsRed has an extra double bond (drawn in yellow) which extends the chromophores conjugation and causes the red-shift.
	www.conncoll.edu /ccacad/zimmer/GFP-ww/GFP3.htm (258 words)

	Chemical nature of the light emitter of the Aequorea green fluorescent protein -- Niwa et al. 93 (24): 13617 -- ...
		To establish the chemical structure of the chromophore, the purified GFP was digested with lysyl endopeptidase/proteinase
		of the chromophore was not altered by the digestion and that the
		The similarity of the GFP chromophore structure with compound 1 is further seen in the absorption spectra of compound
	www.pnas.org /cgi/content/full/93/24/13617 (4204 words)

	Photoreceptor for Curling Behavior in Peranema trichophorum and Evolution of Eukaryotic Rhodopsins -- Saranak and ...
		of the native chromophore with the retinal analog n-hexenal.
		The spectra are shown on the same relative sensitivity scale, and the scales are in a standard proportion, where a 1-eV shift is the same length as 2 log sensitivity units (12).
		Light-induced charge redistribution in the retinal chromophore is required for initiating the bacteriorhodopsin photocycle.
	ec.asm.org /cgi/content/full/4/10/1605 (5858 words)

	Genes for Production of the Enediyne Antitumor Antibiotic C-1027 in Streptomyces globisporus Are Clustered with the ...
		Structures of C-1027 chromophore and the benzenoid diradical intermediate proposed to initiate DNA cleavage.
		Biosynthesis of NCS chrom A, the chromophore of the antitumor antibiotic neocarzinostatin.
		A comparison of DNA cleavage by neocarzinostatin chromophore and its aglycon: evaluating the role of the carbohydrate residue.
	aac.asm.org /cgi/content/full/44/2/382 (6154 words)

	GFP Cloned and Sequenced
		The chromophore in the GFPs is covalently bound and is formed by modification of certain aa residues within the polypeptide.
		The cyclized chromophore is formed from the trimer Ser-dehydroTyr-Gly within the polypeptide by an unknown mechanism.
		Perhaps energy-transfer occurs between it and the chromophore in the native protein preventing the Trp fluorescence (320-350 nm).
	www.bio.davidson.edu /Courses/molbio/restricted/02GFPseq/GFPseq.html (2673 words)

	FEBS Abstract
		The chromophore is an intrinsic part of the protein backbone, it is formed by an autocatalytic cyclization.
		The chromophore only fluoresces when it is located in the correctly folded GFP beta-barrel.
		Computational methods have been used to establish that (i) the chromophore cavity of wild-type GFP is not complementary with a planar chromophore, (ii) the tau one-bond-flip (OBF) in the chromophore model, 4-hydroxybenzylidene-2,3-dimethylimidazolidinone displaces a larger volume than the hula-twist (HT) or the phi OBF.
	www.blackwellpublishing.com /febsabstracts2005/abstract.asp?id=40113 (198 words)

	Photorefractive Organic Polymer System Functionalized with a Nonlinear Optical Chromophore Boronate
		wt.% the chromophore concentration because the incompatibility of the polar dye CB and the non-polar, plasticized polymer matrix.
		Neher and K. Meerholz, “Influence of glass transition temperature and chromophore content on the steady state performance of poly(N-vinylcarbazole)-based photorefractive polymers”, Adv.
		Hendrickx, D. Steenwinkel, A. Persoons and A. Watanabe, “Photorefractive Polysilanes functionalized with a nonlinear optical chromophore”, Macromolecules, 32 (1999) 2232-2238.
	www.azom.com /Details.asp?ArticleID=3116 (3493 words)

	Red Fluorescent Protein
		hybridized, too, but it's plane is perpendicular to the chromophore and thus cannot contribute to a larger resonance system (use the mouse to bring the molecule into proper aspect!).
		In the mature tetrameric protein only half of the chromophores are oxidized in the second step, so really there is a mixture of green and red fluorescent dyes.
		of this residue is turned inward to form water mediated hydrogen bridges to the chromophore and therefore is not available to form the beta sheet.
	www.biologie.uni-hamburg.de /lehre/bza/light/1g7k/1g7ktext.htm (567 words)

	Occupancy of the Chromophore Binding Site of Opsin Activates Visual Transduction in Rod Photoreceptors -- Kefalov et ...
		in the chromophore pocket of opsin to produce a complex that is
		to this scheme, photoisomerization of the chromophore from the
		The contrast between the chromophore pockets of rods and cones is not limited to the interaction with
	www.jgp.org /cgi/content/full/113/3/491 (6586 words)

	Rhodopsin: Structural Basis of Molecular Physiology -- Menon et al. 81 (4): 1659 -- Physiological Reviews
		the 11-cis- to all-trans-form of the RET chromophore is the primary
		The RET chromophore is shown in magenta, and the side chains of Lys-296 and Glu-113 are shown to highlight the Schiff base region of the RET binding pocket.
		The position of the cyclohexenyl ring of the chromophore is largely constrained on the cytoplasmic side of the binding pocket
	physrev.physiology.org /cgi/content/full/81/4/1659 (10457 words)

	Nature of the Chromophore Binding Site of Bacteriorhodopsin: The Potential Role of Arg82 as a Principal Counterion -- ...
		be in the electrostatic vicinity of the chromophore.
		In all cases, the chromophore has been minimized by using MNDO/PM3 semiempirical molecular orbital theory, and if additional water molecules improved agreement with experiment, these additional water molecules are shown in lighter colors (one water molecule was added to 1AP9 and three water molecules to 1AT9).
		The vertical axis monitors the distance between the chromophore imine nitrogen atom and the closest nitrogen atom on the Arg
	www.biophysj.org /cgi/content/full/76/5/2370 (7116 words)

	Peter Tonge
		In order that changes in fluorescence not be misinterpreted, it is important to determine the changes in chromophore structure resulting from irradiation and to analyze the spectroscopic properties of the different chromophore structures.
		Consequently, a complete understanding of the photophysical properties of the chromophore is fundamental to GFP applications.
		In addition, we are constructing an expression system to introduce isotopic labels and unnatural amino acids into the GFP chromophore to study the mechanism of chromophore formation.
	www.sunysb.edu /chemistry/faculty/ptonge.htm (610 words)

	National Partnership for Advanced Computational Infrastructure: Archives
		This rigidity extends to the immediate surrounding of the chromophore where a very stable arrangement of hydrogen bonds and water positions was found.
		Three different mechanisms are known that influence the absorption spectrum of GFP: (a) protein mutations that shift excitation wavelengths and alter transition dipole moments through electrostatic interaction with the chromophore, (b) protein mutations that alter the equilibrium between neutral and anionic forms of the chromophore, and (c) possible conformational transitions of the protein.
		Nobody has been able to fully characterize this network in detail, either by experiment or by calculations." Upon excitation of the neutral chromophore, it is likely to facilitate a proton shuttle between the hydroxyl tip of the chromophore and a nearby glutamate residue, Glu222.
	www.npaci.edu /online/v4.14/gfp.html (1398 words)

	The pvc Gene Cluster of Pseudomonas aeruginosa: Role in Synthesis of the Pyoverdine Chromophore and Regulation by PtxR ...
		The pvc Gene Cluster of Pseudomonas aeruginosa: Role in Synthesis of the Pyoverdine Chromophore and Regulation by PtxR and PvdS -- Stintzi et al.
		The pvc Gene Cluster of Pseudomonas aeruginosa: Role in Synthesis of the Pyoverdine Chromophore and Regulation by PtxR and PvdS
		for pyoverdine biosynthesis (44), presumably for the chromophore
	jb.asm.org /cgi/content/full/181/13/4118 (3964 words)

	Pacific Wave Communications Material Technology (Site not responding. Last check: 2007-10-08)
		PWC has developed a series of new NLO chromophores that provide the required thermal and chemical stability properties without sacrificing molecular non-linearity.
		The polymer serves as a matrix to host the chromophore molecules and to stabilize the poling induced chromophore alignment.
		It is compatible with the CPW-1 chromophore as observed from the absence of phase separation during the elevated temperature electric poling.
	www.pacificwaveind.com /html/f-pwc_material.htm (806 words)

	Gene transcription analysis of Saccharomyces cerevisiae exposed to neocarzinostatin protein- chromophore complex ...
		Gene transcription analysis of Saccharomyces cerevisiae exposed to neocarzinostatin protein- chromophore complex reveals evidence of DNA damage, a potential mechanism of resistance, and consequences of prolonged exposure -- Schaus et al.
		The small-molecule component of NCS, NCS chromophore, is bound noncovalently in a cleft of the binding protein (7) and
		Nucleophilic activation of the chromophore, principally with thiols
	www.pnas.org /cgi/content/full/98/20/11075 (4868 words)

	CHROMOPHORE STRUCTURE IN THE PHOTOCYCLE OF THE CYANOBACTERIAL PHYTOCHROME CPH1 -- van Thor et al., ...
		CHROMOPHORE STRUCTURE IN THE PHOTOCYCLE OF THE CYANOBACTERIAL PHYTOCHROME CPH1 -- van Thor et al., 10.1529/biophysj.106.084335 -- Biophysical Journal
		The chromophore conformations of the red- and far-red light
		for the C and D rings of the chromophore.
	www.biophysj.org /cgi/content/abstract/biophysj.106.084335v1 (268 words)

	A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome : Nature
		Phytochromes consist of an amino-terminal region that covalently binds a single bilin chromophore, followed by a carboxy-terminal dimerization domain that often transmits the light signal through a histidine kinase relay.
		Here we describe the three-dimensional structure of the chromophore-binding domain of Deinococcus radiodurans phytochrome assembled with its chromophore biliverdin in the Pr ground state.
		Our model, refined to 2.5 Å resolution, reaffirms Cys 24 as the chromophore attachment site, locates key amino acids that form a solvent-shielded bilin-binding pocket, and reveals an unusually formed deep trefoil knot that stabilizes this region.
	www.nature.com /nature/journal/v438/n7066/abs/nature04118.html (302 words)

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