NMR-Observed Atomic Bond Length Stability Supports a Dimensionality Shift in Protein Main Chain 3D Structure Description and Representation

Abstract

<p class=MsoListParagraph style=margin-left:.25in;mso-add-space:auto; text-indent:-.25in;mso-char-indent-count:0;mso-list:l0 level1 lfo1;mso-mirror-indents: yes> 1. Abstract <p class=MsoListParagraph style=margin-left:.25in;mso-add-space:auto; text-indent:-.25in;mso-char-indent-count:0;mso-list:l0 level1 lfo1;mso-mirror-indents: yes> To date, the Cartesian ( x, y, z ) coordinate system is the default system in the Protein Data Bank to specify atomic positions in protein structures. Presented here is an alternative spherical coordinate system approach for a three-dimensional lossless deconstruction of protein main chain structures experimentally determined by NMR spectroscopy. To the default Cartesian system and a previously reported global spherical approach, this alternative local spherical approach provides a geometric description of the three-dimensional structure of protein main chains, which requires only two parameters ( θ and <span style=font-size:10.0pt;font-family: times= new= roman,serif;mso-fareast-font-family:calibri;mso-fareast-theme-font:= minor-latin;color:red=>φ ) , instead of the default three, i.e., x, y, z . Intrinsically a simpler approach than the default and previously reported approaches, this 2018 one induces a dimensionality shift from three to two, allowing it to find its potential application in significantly increasing the efficiency of protein structure-centered researches. <span style=font-size:11.0pt;font-family: times= new= roman,serif;mso-fareast-font-family:times= roman=>2. Keywords: Atomic Bond Length Stability; Dimensionality Shift; Frequency Distribution; Protein Main Chain Structure; Spherical Coordinate System