More precise model of α-helix and transmembrane α-helical peptide backbone structure

Walter F. Schmidt, Clayton G. Thomas

Agricultural Research Service, USA Department of Agriculture, Beltsville, USA.
Department of Engineering, Morgan State University, Baltimore, USA.

DOI: 10.4236/jbpc.2012.34036                

Abstract

The 3-D structure of the β-adrenergic receptor with a molecular weight of 55,000 daltons is available from crystallographic data. Within one of the seven transmembrane ion channel helices in the β₂-receptor, one loop of a helix ACADL has previously been proposed as the site that explains β₂ activity (fights acute bronchitis) whereas ASADL in the β₁-receptor at the corresponding site explains β₁-activity (cardiac stimulation). The α-agonist responsible for this selective reaction is only 0.5% of the receptor molecular weight, and only 1.5% of the weight of the trans-membrane portion of the receptor. The understanding of the mechanism by which a small molecule on binding to a site on one single loop of a helix produces a specific agonist activity on an entire transmembrane ion channel is uncertain. A model of an α-helix is presented in which of pitch occurs at angles both smaller and larger than 180° n. Consequently, atomic coordinates in a peptide backbone α-helix match the data points of individual atom (and atom types) in the backbone. More precisely, eleven atoms in peptide backbone routinely equal one loop of a helix, instead of eleven amino acid residues equaling three loops of a helix; therefore, an α-helix can begin (or end) at any specific atom in a peptide backbone, not just at any specific amino acid. Wavefront Topology System and Finite Element Methods calculate this specific helical shape based only upon circumference, pitch, and phase. Only external forces which specifically affect circumference, pitch and/or phase (e.g. from agonist binding) can/will alter the shape of an α-helix.

Keywords

Helix; Alpha-Helix; Circumference; Pitch, phase; peptide backbone; Wavefront Topology System; Finite Element Method

Conflicts of Interest

The authors declare no conflicts of interest.

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