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ref: -0 tags: protein engineering structure evolution date: 02-23-2021 19:57 gmt revision:1 [0] [head]

From Protein Structure to Function with Bioinformatics

  • Dense and useful resource!
  • Few new folds have been discovered since 2010 -- the total number of extand protein folds is around 100,000. Evolution re-uses existing folds + the protein fold space is highly convergent. Amazing. link

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ref: -2011 tags: two photon cross section fluorescent protein photobleaching Drobizhev gcamp date: 11-04-2020 18:07 gmt revision:9 [8] [7] [6] [5] [4] [3] [head]

PMID-21527931 Two-photon absorption properties of fluorescent proteins

  • Significant 2-photon cross section of red fluorescent proteins (same chromophore as DsRed) in the 700 - 770nm range, accessible to Ti:sapphire lasers ...
    • This corresponds to a S 0S nS_0 \rightarrow S_n transition
    • But but, photobleaching is an order of magnitude slower when excited by the direct S 0S 1S_0 \rightarrow S_1 transition (but the fluorophores can be significantly less bright in this regime).
      • Quote: the photobleaching of DsRed slows down by an order of magnitude when the excitation wavelength is shifted to the red, from 750 to 950 nm (32).
    • See also PMID-18027924
  • Further work by same authors: Absolute Two-Photon Absorption Spectra and Two-Photon Brightness of Orange and Red Fluorescent Proteins
    • " TagRFP possesses the highest two-photon cross section, σ2 = 315 GM, and brightness, σ2φ = 130 GM, where φ is the fluorescence quantum yield. At longer wavelengths, 1000–1100 nm, tdTomato has the largest values, σ2 = 216 GM and σ2φ = 120 GM, per protein chain. Compared to the benchmark EGFP, these proteins present 3–4 times improvement in two-photon brightness."
    • "Single-photon properties of the FPs are poor predictors of which fluorescent proteins will be optimal in two-photon applications. It follows that additional mutagenesis efforts to improve two-photon cross section will benefit the field."
  • 2P cross-section in both the 700-800nm and 1000-1100 nm range corresponds to the chromophore polarizability, and is not related to 1p cross section.
  • This can be useflu for multicolor imaging: excitation of the higher S0 → Sn transition of TagRFP simultaneously with the first, S0 → S1, transition of mKalama1 makes dual-color two-photon imaging possible with a single excitation laser wavelength (13)
  • Why are red GECIs based on mApple (rGECO1) or mRuby (RCaMP)? dsRed2 or TagRFP are much better .. but maybe they don't have CP variants.
  • from https://elifesciences.org/articles/12727

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ref: -0 tags: Lucy Flavin mononucelotide FAD FMN fluorescent protein reporter date: 10-17-2019 19:54 gmt revision:1 [0] [head]

PMID-25906065 LucY: A Versatile New Fluorescent Reporter Protein

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ref: -2016 tags: fluorescent proteins photobleaching quantum yield piston GFP date: 06-19-2019 14:33 gmt revision:0 [head]

PMID-27240257 Quantitative assessment of fluorescent proteins.

  • Cranfill PJ1,2, Sell BR1, Baird MA1, Allen JR1, Lavagnino Z2,3, de Gruiter HM4, Kremers GJ4, Davidson MW1, Ustione A2,3, Piston DW
  • Model bleaching as log(F)=αlog(P)+clog(F) = -\alpha log(P) + c or k bleach=bI αk_{bleach} = b I^{\alpha} where F is the fluorescence intensity, P is the illumination power, and b and c are constants.
    • Most fluorescent proteins have α\alpha > 1, which means superlinear photobleaching -- more power, bleaches faster.
  • Catalog the degree to which each protein tends to form aggregates by tagging to the ER and measuring ER morphology. Fairly thorough -- 10k cells each FP.

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ref: -2019 tags: super-resolution microscopy fluorescent protein molecules date: 05-28-2019 16:02 gmt revision:3 [2] [1] [0] [head]

PMID-30997987 Chemistry of Photosensitive Fluorophores for Single-Molecule Localization Microscopy

  • Excellent review of all the photo-convertable, photo-switchable, and more complex (photo-oxidation or reddening) of both proteins and small molecule fluorophore.
    • E.g. PA-GFP is one of the best -- good photoactivation quantum yield, good N ~ 300
    • Other small molecules, like Alexa Fluor 647 have a photon yield > 6700, which can be increased with triplet quenchers and antioxidants.
  • Describes the chemical mechanism of the various photo switching -- review is targeted at (bio)chemists interested in getting into imaging.
  • Emphasize that critical figures of merit are photoactivation quantum yield Φ pa\Phi_{pa} and N, overall photon yield before photobleaching.
  • See also Colorado lecture

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ref: -0 tags: voltage sensitive dyes fluorescent protein date: 01-02-2013 05:08 gmt revision:0 [head]

PMID-20622860 Imaging brain electric signals with genetically targeted voltage-sensitive fluorescent proteins.

  • Interesting: Most fluorescent fusion proteins form intracellular aggregates during long-term expression in mammalian neurons, although this effect appears to be minimal in Aequorea victoria–derived fluorescent proteins.
  • See also {1185}

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ref: Sakai-2001.06 tags: voltage scensitive fluorescent protein flourophore VSFP1 endoscope date: 01-24-2012 06:07 gmt revision:5 [4] [3] [2] [1] [0] [head]

http://www.blackwell-synergy.com/doi/full/10.1046/j.0953-816x.2001.01617.x PMID-11454036[0]


[0] Sakai R, Repunte-Canonigo V, Raj CD, Knöpfel T, Design and characterization of a DNA-encoded, voltage-sensitive fluorescent protein.Eur J Neurosci 13:12, 2314-8 (2001 Jun)
[1] van Roessel P, Brand AH, Imaging into the future: visualizing gene expression and protein interactions with fluorescent proteins.Nat Cell Biol 4:1, E15-20 (2002 Jan)
[2] Guerrero G, Siegel MS, Roska B, Loots E, Isacoff EY, Tuning FlaSh: redesign of the dynamics, voltage range, and color of the genetically encoded optical sensor of membrane potential.Biophys J 83:6, 3607-18 (2002 Dec)
[3] Jung JC, Mehta AD, Aksay E, Stepnoski R, Schnitzer MJ, In vivo mammalian brain imaging using one- and two-photon fluorescence microendoscopy.J Neurophysiol 92:5, 3121-33 (2004 Nov)
[4] Sjulson L, Miesenböck G, Optical recording of action potentials and other discrete physiological events: a perspective from signal detection theory.Physiology (Bethesda) 22no Issue 47-55 (2007 Feb)

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ref: Graves-2001.04 tags: sleep memory REM protein synthesis review date: 03-25-2009 15:23 gmt revision:1 [0] [head]

PMID-11250009[0] Sleep and memory: a molecular perspective.

  • inhibition of protein synthesis is most effective if it occurs at a time post-training when rapid eye movement (REM) sleep is required for memory consolidation
  • The neurochemical changes that occur across sleep/wake states, especially the cholinergic changes that occur in the hippocampus during REM sleep, might provide a mechanism by which sleep modulates specific cellular signaling pathways involved in hippocampus-dependent memory storage.
    • REM sleep could influence the consolidation of hippocampus-dependent long-term memory if it occurs during windows that are sensitive to cholinergic or serotonergic signaling.
    • PKA activation seems important to hippocampal long-term memory
    • NMDA affects PKA through Ca2+ to adenyl cyclase
    • 5-HT_1A receptor negatively coupled to adenyl cyclase (AC)
    • 5-HT concentrations go down in hippocampus during sleep ?


[0] Graves L, Pack A, Abel T, Sleep and memory: a molecular perspective.Trends Neurosci 24:4, 237-43 (2001 Apr)

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ref: notes-0 tags: grain protein growing framing feed oats alfalfa barley corn wheat date: 06-18-2008 15:14 gmt revision:0 [head]

I found this on my computer tucked away into a dusty corner. Such fascinating information should not be left hidden -

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ref: Walker-2005.12 tags: algae transfection transformation protein synthesis bioreactor date: 03-21-2008 17:22 gmt revision:1 [0] [head]

Microalgae as bioreactors PMID-16136314

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ref: bookmark-0 tags: petaflop gigaflop RIKEN protein folding MDGRAPE date: 09-17-2007 14:55 gmt revision:0 [head]

pretty impressive project, especially considering how much time and money they spent ($15 m, 6 man-months to do the verilog (only!)) http://www.hotchips.org/archives/hc16/3_Tue/1_HC16_Sess6_Pres1_bw.pdf