A critical assessment of the role of topology on protein thermal stability

For several decades, experimental and computational studies have been used to investigate the potential functional role of knots in protein structures. A property that has attracted considerable attention is thermal stability, i.e., the extent to which a protein retains its native conformation and biological activity at high temperatures, without undergoing denaturation or aggregation. Thermal stability is quantified by the melting temperature $T_m$, an equilibrium property that corresponds to the peak of heat capacity in differential scanning calorimetry experiments. Since protein energy does not depend on the topological state, equilibrium properties such as $T_m$ should not depend on the topology, provided that the exploration of the equilibrium space is ergodic. However, experimental and computational results reported in the literature provide conflicting views on this problem, with some studies reporting an enhancement of thermal stability for certain knotted proteins. Here, we use extensive Monte Carlo simulations of a simple C-alpha protein model of protein YibK to show in a comprehensive manner that $T_m$ does not depend on the topological state of the protein.