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BP: Fachverband Biologische Physik

BP 5: Proteins

BP 5.4: Vortrag

Montag, 23. März 2009, 15:15–15:30, ZEU 260

Sequence-specific size, structure, and stability of tight protein knots — •Joachim Dzubiella — Physik, TU München

Approximately 1% of protein structures display knots in their native fold. Nothing however, is known about their function. By using all-atom computer simulations we show that tightened protein knots (TPKs) exhibit a bulky size in quantitative agreement with recent atomic force microscopy (AFM) pulling and a complex stability behavior. TPKs are thus capable of blocking peptide transport through narrow (~ 2 nm) biological pores in a sequence-dependent way. Hydrophobic side chains shield the knot core from the polar solvent, leading to an exceptionally strong H-bonding and water trapping capability of TPKs. This kinetically arrests knot diffusion along the peptide, and is controllable by the tightening force in special cases. Intriguingly, macroscopic tight knot structures are reproduced microscopically and can be tuned by sequence. Our findings may explain a function of knots in proteins, challenge previous mathematical and physical studies of macromolecular knots, and are readily verifiable in AFM or optical tweezer experiments.