Protein chains in tight-binding framework

Abstract

Context: This research assesses the band structure and density of states for three unique conformations of protein chains, examined in both finite and infinite configurations. Under a constant temperature, the band structure and density of states reveal flat energy dispersion curves and discrete energy levels for the finite protein conformations, which are ascribed to the presence of localized states within these structures. Conversely, the infinite protein chain demonstrates a continuous band structure due to its periodic nature, resulting in narrow-gap semiconducting behavior across all conformations. The influence of temperature on the energy spectra of the systems, regardless of the configuration type, leads to alterations in both the peak heights and positions for all three protein conformations.

Methods: The exploration of the electronic properties of protein chains is performed using the tight-binding Hamiltonian method in conjunction with Green's function formalism. The primary emphasis is placed on protein chains consisting of thirty-six amino acids, characterized by a straightforward structural arrangement, where amino acids are interconnected through covalent bonds, while the other two conformations exhibit a more complex structural configuration, with amino acids linked by both peptide bonds and non-covalent interactions.

Keywords: Band structures; Density of states; Green’s function; Protein; Tight-binding.