Kink Formation Dynamics in a Single α-helical Protein

Abstract

Protein folding remains an open problem despite the progress in understanding the process rate and the success in folding prediction for some small proteins. The reason is the absence of a constructive theoretical framework, both general and specific enough.In earlier papers, we have argued that protein-folding dynamics can be described in terms of solitons of a generalized discrete non-linear Schrodinger equation (GDNLSE) obtained from the energy function in terms of bond and torsion angles [1]. The soliton manifestation is the pattern helix--loop--helix in the secondary structure of the protein, which explains the importance of understanding loop formation in helical proteins and the kink assignment to it [2]. We propose a new mechanism for this process based on the energy transmission along the chain---a disturbance in the latter leads to energy accumulation sufficient to form a kink. We present first insights into the process dynamics by all-atom molecular-dynamics analysis of unfolding of a single alpha-helical protein–--one chain of the core structure of gp41 from the HIV envelope glycoprotein (PDB ID: 1AIK). We suggest an adequate quantification of the side-chain orientation dynamics and also identify some force-field related artefacts.