Electronic structure of protein–RNA coupling: a tight-binding perspective

Abstract

In this work, we perform a detailed theoretical investigation into the electronic interactions governing protein–RNA complexes by employing a tight-binding Hamiltonian framework coupled by Green’s function methods. The RNA molecule is represented as a half-ladder network of nitrogenous bases, allowing us to evaluate three different protein structural conformations while assessing how multiple contact sites and fluctuating hopping integrals influence the system’s electronic behavior. To capture coherent electronic phenomena and suppress thermal broadening artifacts, we calculate the energy band structures (BS) and density of states (DOS) at low temperatures. Furthermore, both uniform and random configurations of hopping parameters are introduced within the RNA framework to simulate sequence diversity and structural variations. Our numerical findings demonstrate that protein–RNA binding induces notable energy level shifts and reorganizes the DOS profiles, where the intensity and location of these spectral modifications are dictated by the number of interface points, the specific protein shape, and the magnitude of the hopping links. This research emphasizes the crucial role of backbone coupling and outlines the overarching patterns of protein-induced electron delocalization along the RNA strand. Although the selected parameter sets and the low-temperature environment act as conceptual models rather than exact physiological duplicates, they offer meaningful perspectives on the underlying electronic features of these biomolecular assemblies. Ultimately, this theoretical approach establishes a robust basis for interpreting the qualitative electronic responses of biological systems, charting a path for subsequent models that integrate ambient environmental noise, base-to-base interactions, and direct empirical testing.