Prediction of no oxidizable cysteines
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Prediction of NO Oxidizable Cysteines. Larry Grant Dr. Jamil Momand Cal State L.A. Redox-based protein regulation. similar to phosphorylation. reversible detectable Plays a major role in many physiological processes. inflammation, cell channel signaling, protease activity.

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Prediction of no oxidizable cysteines l.jpg

Prediction of NO Oxidizable Cysteines

Larry Grant

Dr. Jamil Momand

Cal State L.A.


S nitrosylation l.jpg

Redox-based protein regulation.

similar to phosphorylation.

reversible

detectable

Plays a major role in many physiological processes.

inflammation, cell channel signaling, protease activity

S-nitrosylation


Copp project l.jpg
COPP Project

  • Cysteine Oxidation Prediction Program

    • Will be web-based

    • Capable of predicting cysteine reactivity based on primary sequence and/or structure data.

      • 4 kinds of reactivity



My project l.jpg
My Project

  • Generate parameters based on sequence information to predict NO susceptibility.

  • Stamler et, al have proposed a short motiff based on 27 sequences.

    • (Lys,Arg,His,Asp,Glu) – Cys – (Asp/Glu)


Extracting parameters l.jpg
Extracting parameters…

  • Data Mining

    • Target of 100-150 oxidizable thiols

      • 71 s-nitrosylated Cys from 63 different proteins.

-20………-10…………..-1C+1….…+10……...…+20


Psipred analyzer l.jpg
PSIPRED Analyzer

  • Three major functions:

    • Average confidence

    • Secondary structure frequency

    • Residue frequency


Slide8 l.jpg

H H H H C C C C C C

6 6 6 6 6 6 6 6 6 6

Green = Polar Blue = Basic

Black = Hydrophobic Red = Acidic


The future l.jpg
The future C C

  • Support Vector Machines

    • relative solvent accessibility

      • minimum of 1.3 Å2

    • hydrophobicity, acidity, side-chain length


References l.jpg
References C C

  • Stamler, et al. “(S)NO signals: translocation, regulation, and a consensus motif.”Neuron. 1997 May;18(5):691-6.

  • Sanchez, et al. “Prediction of reversibly oxidized protein cysteine thiols using protein structure properties.” Protein Sci. 2008 Mar;17(3):473-81.

  • Hess, et al. “Protein S-nitrosylation - Purview and Parameters.” Nat Rev Mol Cell Biol. 2005 Feb;6(2):150-66.


Acknowledgements l.jpg

Thank you for all of your help: C C

Dr. Momand

Dr. Sharp

Dr. Warter-Perez

Dr. Johnston

Ronnie Cheng

My fellow interns.

Funded by:

Acknowledgements