Journal of Proteomics & Bioinformatics
Open Access
ISSN: 0974-276X
+44 1223 790975
ISSN: 0974-276X
+44 1223 790975
Thomas Prevenslik
QED Radiations Discovery Bay, China
Scientific Tracks Abstracts: J Proteomics Bioinform
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 fields with electrostatic interaction represented by fixed point charges. Quantum mechanics (QM) modification 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 effect on protein folding and unfolding would be insignificant compared to the more fundamental QM effect 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 effect 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. The protein returns to an inverted semi-circular shape by unfolding the cluster by applying the QM induced repulsive charge. How the protein constantly modifies QM induced charge is discussed. Recent Publications 1. Changge Ji and Ye Mei (2014) Some Practical approaches to treating electrostatic polarization of proteins. Accounts of Chemical Research 47(9):2795-803. 2. Weber J K and Pande V S (2012) Protein folding is mechanistically robust. Biophysical Journal 102: 859�??867. 3. Torshin I Y and Harrison R W (2003) Protein folding: search for basic physical models. Scientific World Journal 3:623�??635. 4. Allen M P and Tildesley, D J (1987) Computer Simulation of Liquids, Oxford University Press. ISBN: 9780198803201.