Enlarged Curvature, Torsion and Torque in Helical Conformations and the Stability and Growth of α-Peptide under the Isochoric and Isobaric Conditions: Variatonal Optimization

Abstract

The torsional deformation behavior of an elastic bar with a circular cross-section was investigated by applying invariant dyadic analysis, where the small finite displacement functions advocated by Saint-Venant (1855) were fully employed. It was found that the previously overlooked circumferential shear force field generated by pure torsion on the side walls of a bar produces an unusual torque term induced by the skew-symmetric part of the deformation tensor and exhibits quadratic length dependence along the z-axis of the bar. The adaptation of this torque term for a helical conformation of α-peptides creates moments acting on the circular cross-sections and is directed along the surface normal of circular cross-sections, which coincides with the tangent vector of the helix. The projection of this torque along the z-axis of the helix varies quadratically with the azimuthal angle. The radial component of the unusual torque, which also lies along the principal normal vector of the helix, starts to perform a precession motion by tracking a spiral orbit around the z-axis, whereas its apex angle decreases asymptotically with the azimuthal angle and finally reaches a finite value depending on the height of the helix along the z-axis. The ordinary torque terms, which are also deduced from the self- and anti-self-conjugate parts of the deformation tensor, have magnitudes half that of the full torque term reported in the literature. The present results were applied to the helical conformation of α-peptides designated by {3.611} to show that the mechanical stability of strained open-ended helical conformations can be successfully achieved by spontaneous readjustments of the surface and bulk Helmholtz free energies under isothermal isochoric conditions. It has been demonstrated that the main contribution to the mechanical stability of α-peptide 3.611 cannot come alone from the electrostatic dipole-dipole interaction potential of the anti-align excess dipole pairs but also from the surface Helmholtz free energy, which is characterized by a binding free energy of -15.5 eV/molecule (-32.56 Kcal/mole) for an alpha-peptide composed of 11 amino acid residues with a critical arc length of approximately 10 nm, assuming that the shear modulus is G = 1GPa and the surface Helmholtz specific free energy density is fs = 800 erg/cm2. This result was in excellent agreement with the experimental observations of the AH-1 conformation of (Glu)n Cys at pH 8. The present theory indicates that only two excess permanent anti-align dipole pairs for one α-Helical peptide molecule is requirement to stabilize the whole secondary structure of the protein that is exposed to heavy torsional deformation during the folding processes which amounts to 7.75 eV/molecule stored electrostatic energy compared to the interfacial Helmholtz free energy of -23.25 eV/molecule, which is exposed to hydrophobic