title: Discrete Frenet frame, inflection point solitons, and curve visualization with applications to folded proteins.
abstract: We develop a transfer matrix formalism to visualize the framing of discrete piecewise linear curves in three-dimensional space. Our approach is based on the concept of an intrinsically discrete curve. This enables us to more effectively describe curves that in the limit where the length of line segments vanishes approach fractal structures in lieu of continuous curves. We verify that in the case of differentiable curves the continuum limit of our discrete equation reproduces the generalized Frenet equation. In particular, we draw attention to the conceptual similarity between inflection points where the curvature vanishes and topologically stable solitons. As an application we consider folded proteins, their Hausdorff dimension is known to be fractal. We explain how to employ the orientation of C(β) carbons of amino acids along a protein backbone to introduce a preferred framing along the backbone. By analyzing the experimentally resolved fold geometries in the Protein Data Bank we observe that this C(β) framing relates intimately to the discrete Frenet framing. We also explain how inflection points (a.k.a. soliton centers) can be located in the loops and clarify their distinctive rôle in determining the loop structure of folded proteins.
authors.affiliation: Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden.
authors.forename: Shuangwei
authors.initials: S
authors.lastname: Hu
authors.forename: Martin
authors.initials: M
authors.lastname: Lundgren
authors.forename: Antti J
authors.initials: AJ
authors.lastname: Niemi
mesh_terms: D003196:Computer Graphics; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins