Structure and Dynamics of the Bcl-2 Promoter G-Quadruplex using the Drude Polarizable Force Field

Abstract

G-quadruplexes (GQ) are noncanonical nucleic acid structures that form in guanine-rich sequences and exist in a variety of topological forms. The guanine bases in GQ arrange in a square planar configuration and stack to form tetrads via Hoogsteen hydrogen bonding and coordination of ions like K+. These highly ordered secondary structures are implicated in the regulation of gene expression and genome maintenance, and alterations to their structures contribute to diseases such as cancer. The B-cell CLL/lymphoma 2 (bcl-2) oncogene is associated with a variety of cancers and its promoter features a GQ that arises due to two consecutive substitutions of guanine with thymine. Understanding the forces driving GQ folding and stabilization is required for developing novel therapeutics that target these structures. To develop a greater understanding of the atomistic details in the bcl-2 GQ, we performed molecular dynamics simulations using the CHARMM36 additive and Drude-2017 polarizable force fields. In the classical Drude oscillator model, electronic degrees of freedom are modeled as negatively charged particles attached harmonically to all heavy atoms. This approach overcomes limitations of nonpolarizable force fields, which approximate average polarization via assignment of partial charges. We performed simulations of the mutant bcl-2 promoter GQ and created the wild-type sequence by reverting the point mutations. The wild-type sequence was then thermally denatured and allowed to re-fold to determine the structural differences between the mutant bcl-2 GQ and the native, wild-type fold. Our analysis provides insight into the stability of the bcl-2 GQ structure, backbone conformational ensembles in dihedral space, base-ion interaction energetics, and the magnitude and fluctuation of dipole moments. These simulations illustrate that polarization is integral for tetrad stability and suggests that the Drude force field is essential for simulating GQ structures.