Structural Biology

Proteins are sensitive to electrostatic charges from amino acid side chains that change with conformation. But molecular

dynamics (MD) simulations of protein folding and unfolding are based on classical force fi elds with electrostatic interaction

represented by fi xed point charges. Quantum mechanics (QM) modifi cation of point charges during conformational changes is

required but is impractical because of computational costs. Computation costs aside, even if point charges were continuously

updated, the eff ect on protein folding and unfolding would be insignifi cant compared to the more fundamental QM eff ect

of the Planck law on the heat capacity of atoms. In this regard, proteins are generally thought to unfold upon increasing

temperature based on the classical assumption the constituent atoms have heat capacity. But the Planck law requires the heat

capacity of the atom to vanish with conservation proceeding by creating EM radiation that by the photoelectric eff ect removes

electrons to positively charge the protein atoms. What this means is the heat thought to induce unfolding by increasing the

temperature of proteins is actually conserved by producing charge that unfolds the protein by Coulomb repulsion. To illustrate

QM induced charge, the MD simulation of folding and unfolding using for a simple 5-atom protein is illustrated in Figure 1.

Initially, the protein in the form of a semi-circle relaxes under L-J forces but does not unfold. L-J stands for Lennard-Jones.

Unfolding occurs upon applying QM induced repulsive positive charge (0.5-1 electron charges) on each atom. Folding back to

an intermediate cluster occurs by relaxing the protein with L-J forces alone without QM induced charge. Th e protein returns

to an inverted semi-circular shape by unfolding the cluster by applying the QM induced repulsive charge. How the protein

constantly modifi es QM induced charge is discussed.