Mathematical modelling of helical protein structure
We review recent work on modelling helical parts of protein structure mathematically. We use classical calculus of variations and consider mathematical energies dependent on the curvature and torsion of the protein backbone curve. We demonstrate classes of mathematical energies for which a given helix, or all helices, are extremisers. A future goal is to find within these energies some which permit less regular protein backbone curves, as also observed in nature. As a step in this direction we incorporate a new function into the model, dependent on position along the backbone curve, which permits some allowance for variability in structure due to different amino acid components, side chains, or obstacles.
McCoy, J. A. (2011). Mathematical modelling of helical protein structure. In L. M. Haggerty (Eds.), Protein Structure (pp. 105-121). New York: Nova Science Publishers.