rerun of essentials of week 1-3
DESCRIPTION
Rerun of essentials of week 1-3. Protein structure analysis, comparison, and prediction. Structure comparison. Structure relates to function. Structure comparison has the same role as sequence alignment: transfer of information. - PowerPoint PPT PresentationTRANSCRIPT
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Rerun of essentials of week 1-3
Protein structure analysis, comparison, and prediction
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Structure comparison
Structure relates to function. Structure comparison has the same role as sequence alignment: transfer of information.
Done with structures, though, the transfer of information has much higher quality.
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Non-bonded interactions
Lennard-Jones potential Coulomb potential
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Protein detailsTorsion angle
Ramachandran plot
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Action = Reaction
Ramachandran plots for Glu and Asp found in loops.Who is who and why?
Keep in mind that SFB is Bioinformatics 1 for the mature scientists …
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Hydrogen bonds
Paradoxically, hydrogen bonds are bad for the Folded <-> Unfolded equilibrium (assuming we call folded good and unfolded bad…). Why?
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Salt bridgesSalt bridges work over a longer distance than other interactions (Coulomb goes with 1/r^2).So, salt bridges are easier to engineer than hydrogen bonds.This example shows a hydrogen bonded salt bridge.Salt bridges work less well in high salt solutions. (why?).
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Cys-cys bonds
Cysteine bridges are used for stability by small proteins, or by toxins that have to escape the innate immune system. Free cysteines are dangerous for a protein, so paired cysteines either don’t mutate or mutate in tandem. They either work thermodynamically by destabilizing the unfolded form, or kinetically by keeping surface loops from unfolding locally.
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Accessibility
Buried hydrophobic surface is worth about 20 J/Å2 (and don’t forget that there are two surfaces touching each other)… So, one carbon fully buried is worth 2*20*4*π*1.82~3200 J/Mole ~ 1kCal/Mole (again using Belgium calculus, that is)
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