Regensburg 2004 – scientific programme
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SYLS: Life Sciences on the Nanometer Scale - Physics Meets Biology
SYLS 3: Symposium "Life Sciences on the Nanometer Scale - Physics Meets Biology"
SYLS 3.22: Poster
Wednesday, March 10, 2004, 16:00–18:30, B
Ab-initio vibrational analysis of the secondary structure of proteins — •Lars Ismer1, Joel Ireta1 und Jörg Neugebauer2 — 1FHI Berlin — 2Universität Paderborn
For a detailed understanding of protein functionality an accurate description of their dynamical properties is crucial. However, so far ab-initio based studies on realistic structures going beyond the primary structure are rare, particularly with respect to vibrational properties. We have therefore performed a full ab-initio DFT-PBE based harmonic vibrational analysis of infinite poly-alanine and -glycine chains in two different secondary conformations: the infinite α -helical conformation, as model for the most ubiquitous native secondary conformation stabilized by hydrogen bonds (hb) and the fully extended conformation (FES), as a reference system where hb’s are absent. By comparing the phonon dispersion relation of α -helix and FES we were able to extract a direct "fingerprint" of the hb’s and their cooperativity in specific high frequent vibrational branches. We also observed that constraining the peptide chain to the helical conformation leads to significant blue-shifts in the low frequent backbone vibrations. A thermodynamic analysis based on these results revealed that the vibrational contributions of the free energy significantly lower the stability of the α -helix with respect to the FES by about 0.8 kcal/mol at 300K.