An account on the factors determining the extra stability of the β–hairpin from B1 domain of protein G

Abstract

The folding–unfolding of a 16 residue polypeptide, a β–hairpin in B1 domain of protein G is investigated here to account for the factors assisting the extra stability of the polypeptide in the presence of an explicit solvent and even when a denaturant like urea is present in the medium. It is observed here that the backbone H–bond network well defines the folded state and is even capable of forming the folded state, but it is not the only criteria for making a stable β–hairpin fold. Factors such as the side chain H–bonds and the alignment of the certain hydrophobic group side chains play a prominent role in preserving the β–hairpin structure and thus providing an extra stability to the hairpin architecture. It is also affirmed that the mentioned hydrophobic groups side chain interactions are very crucial in holding the β–hairpin together and without which the hairpin collapses completely. We also confirm that the denaturant urea acts on the GB1–hairpin backbone H–bonds and in the presence of strong hydrophobic interactions with a consistent side chain H–bonding network, the denaturation being comparatively a slower process with respect to the protein devoid of the side chain interactions.

Communicated by Ramaswamy H. Sarma

Keywords:

• Molecular dynamics
• protein folding
• hydrophobic interactions
• β–hairpin
• replica exchange molecular dynamics

Acknowledgements

The authors thank IIT Palakkad for providing us with CHANDRA supercomputing facility.

Disclosure statement

No potential conflict of interest was reported by the authors.