Berlin 2005 – wissenschaftliches Programm
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AKB: Biologische Physik
AKB 90: Protein Folding and Molecular Dynamics
AKB 90.2: Vortrag
Mittwoch, 9. März 2005, 14:15–14:30, TU H2013
A DFT-GGA based thermodynamic analysis of the secondary structure of proteins — •Lars Ismer1, Joel Ireta1, Matthias Scheffler1, and Jörg Neugebauer2 — 1Fritz-Haber-Institut der MPG, Faradayweg 4-6, 14195 Berlin — 2Theoretische Physik, Universität Paderborn, Warburger Str. 100, 33098 Paderborn
Studies of the thermodynamic stability of the secondary structure of proteins are important for understanding the protein folding process. We have therefore estimated the free energy change to fold a fully extended structure (FES) into the α-helical conformation for isolated infinite poly-glycine (Gly) and -alanine (Ala) chains. The calculations have been performed employing DFT-GGA, a plane-wave pseudo-potential approach and the harmonic approximation. Our results reveal [1], that this approach leads to a significantly improved description of thermodynamic data with respect to previous studies based on empirical force fields. Further we find, that the enthalpy to transform an α-helix into an FES strongly reduces with increasing temperature: at room temperature the free energy difference for Gly is close to zero within the numerical error bar (0.5 kcal/mol), whereas for Ala the α-helix is by 1.0 kcal/mol more stable. We conclude, without recoursing to any empirical input parameters, that an isolated Ala-FES will even at room temperature spontaneously fold into an α-helix.
[1] L.Ismer, J. Ireta, S. Boeck and J. Neugebauer, submitted to Phys. Rev. E