SEMINAR @ SISSA, SBP, Fabrizio Marinelli 4 maggio 2007

[Barbara Corzani]

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STATISTICAL AND BIOLOGICAL PHYSICS SEMINAR
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Dott. Fabrizio Marinelli
(SISSA)

Title:
"Cluster analysis of folding free energy surface: thermodynamics and kinetics of the TRP cage miniprotein folding."


Fri 4 May 2007  @ 02.00 p.m.

SISSA - Basement floor - room A
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Abstract:
This work give an hint on TRP cage folding process supporting the hypotesis of a multistate process instead of a two state one.
Using bias-exchange metadynamics the folding free energy surface of TRP cage was calculated using 5 general collective variables.
To explore the topology of this surface the markov cluster analysis algorithm was used yelding several structural coherent free energy basins, consistent with a multistate folding model.
Enthalpy calculation allowed to extrapolate temperature dependent properties (i.e. CD at 222 nm, TRP SASA, t-jump fluorescence experiment) to validate our calculations with available experimental results.
A diffusion model was used to simulate the kinetic properties by means of
kinetic montecarlo algorithm giving a folding time in the order of 1-2 us , in good agreement with the experimental value of 4 us founded by Linlin Qiu et.
all (J.AM.CHEM.SOC.2002,124,12952-12953).