A theoretical study of the effects of intrahelical and interhelical interactions on the helix-coil transitions of various single polypetides in water

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The biological activity of a protein molecule strictly depends on its conformation. The helix-coil transition of a single chain polypeptide segment is an important factor in the determination of a protein molecule's conformation and has been implicated in a variety of physiologically important processes. In this work, a modified form of Dr.J. A. McCammon's simplified polypeptide model is utilized tostudy the importance of polypeptide hydrophobic content, alpha-helical amphipathicity, intrahelical electrostatic interactions, interhelical potential interactions andsurface binding to various fixed alpha-helical polypeptides of differing hydrophobic content to the coil-helix transition of various single chain polypeptide homopolymers and heteropolymers. This work demonstrates that in the absence of a site available for binding, as the hydrophobic content of a polypeptide chain increases, so does the likelihood of both post-nucleation alpha-helical chain state propagation and random coil to total alpha-helix transition. The most favorable state is the all random coil state independent of the residue type content of the polypeptide, in this circumstance. Depending on the relative positions of oppositely charged residues in a polypeptide chain, salt-bridge formation tends to increase the probability of post nucleation chain state propagation and shift K1 toward 1H, as defined by the equilibrium state model. In the presence of a site available for binding, R, the likelihood of both hydrophobic and hydrophobically amphipathic ligand types undergoing 1 to R binding, as well as coil to helix transition is almost completely dependent on the overall hydrophobicity of R. The nucleation of 1 is more likely to occur in the bound state. As the hydrophobic content of the binding site increases, so does the favorability of the coil-helix transition of an amphipathic polypeptide. Based on the calculations drawn from this study, the factors effecting the coil to helix transition of the polypeptide chains ofinterest in this work may indeed play significant roles in a variety of physiologically important processes.