Consequences of non-uniformity in the stoichiometry of component fractions within one and two loops models of alpha-helical peptides

Authors: Schmidt, Walter; Hapeman, Cathleen; WACHIRA, JAMES - Morgan State University; THOMAS, CLAYTON - Morgan State University

Submitted to: Journal of Biophysical Chemistry
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/1/2014
Publication Date: 11/1/2014
Publication URL: http://handle.nal.usda.gov/10113/4114165
Citation: Schmidt, W.F., Hapeman, C.J., Wachira, J., Thomas, C.G. 2104. Consequences of non-uniformity in the stoichiometry of component fractions within one and two loops models of alpha-helical peptides. Biophysical Chemistry. 5:125-133.

Interpretive Summary: Feathers are composed at the microscopic level of keratin proteins with different morphological shapes, such as strong flexible fibers and tough rigid quills. The flexible fibers are referred to as alpha helices, while the rigid quills are referred to as beta sheets. The major form that occurs in keratin is the alpha helix. At the molecular level, keratin flexibility vs. rigidity is related to the closeness and uniformity of specific Nitrogen and Carbon atoms in the protein backbone. In this study, we identified the recurring sequence of atoms required to create an alpha helix structure, and demonstrate that the angles between these atoms (-34.1o, 177.2o, and -69.3o) alone are able to generate the redundant helical shape. This research will be of interest to other scientists.

Technical Abstract: Atoms in biomolecular structures like alpha helices contain an array of distances and angles which include abundant multiple patterns of redundancies. Thus all peptides backbones contain the three atom sequence N-C*C, whereas the repeating set of a four atom sequences (N-C*C-N, C*-C-N-C*, and C-N-C*-C) are also present. From N, C* and C in a backbone sequence to next atom of the same atom type, an array of dihedral angles are generated which may or may not be uniform over any specific number of steps in the sequence. An eleven atom peptide backbone sequence precisely generates one loop of an alpha helix. Using the simple criteria of self-consistency, three specific dihedral angles (-34.1o, 177.2o, and -69.3o) precisely generates the same alpha helix. The dihedral angles and resulting pattern are the same for any number of backbone atoms (loops and/or fractions of a loop) larger/longer than 5-6 atoms. Pattern recognition models containing only three atom sequences appear insufficient to predict uniformity over six atoms. A molecular model to explain the mechanism for this four atom three bond uniformity in dihedral angles is proposed. Wavefront Topology System enables calculating an electrostatic density map that repeat every set of four atoms of the same atom type in a peptide backbone. The electrostatic density in every loop of 11 backbone atoms is periodic amide to amide, and C* to C* albeit not at the same frequency. The beginning and end of an alpha helix occurs when the uniformity of periodicity of dihedral angles is disrupted or interrupted.