Role of topology in 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 <a:math xmlns:a="http://www.w3.org/1998/Math/MathML"> <a:msub> <a:mi>T</a:mi> <a:mi>m</a:mi> </a:msub> </a:math> , an equilibrium property that corresponds to the peak of heat capacity in differential scanning calorimetry (DSC) experiments. Experimental and computational studies report conflicting effects of knotting on protein thermal stability [M. A. Soler and P. F. N. Faísca, ;Y.-C. Chuang, I.-C. Hu, P.-C. Lyu, and S.-T. D. Hsu, ]. Here, we use extensive Monte Carlo simulations of a simple C-alpha model of protein YibK, with energetics modeled by the Go potential, to show that <b:math xmlns:b="http://www.w3.org/1998/Math/MathML"> <b:msub> <b:mi>T</b:mi> <b:mi>m</b:mi> </b:msub> </b:math> does not depend on the topological state of the protein. Our simulations further support the view that the discrepancy between the experimental and computational results stems from a pronounced separation of timescales for unknotting and unfolding that is inherent to deeply knotted proteins like YibK. In particular, the timescale separation implies that the complete unfolding-untying transition may not be accessible within the duration of a DSC experiment, whose apparent <c:math xmlns:c="http://www.w3.org/1998/Math/MathML"> <c:msub> <c:mi>T</c:mi> <c:mi>m</c:mi> </c:msub> </c:math> measurements likely reflect a nonequilibrium distribution lacking unfolded states that are also unknotted.