Stabilizing Effect of Inherent Knots on Proteins Revealed by Molecular Dynamics Simulations

A growing number of proteins are identified to be knotted in their native structures, with such entangled topological feature being expected to play stabilizing roles maintaining both the global fold and the nature of proteins. However, the molecular mechanism underlying the stabilizing effect is ambiguous. Here, we combine unbiased and mechanical atomistic molecular dynamics (MD) simulations to investigate how a protein is stabilized by an inherent knot by directly comparing chemical, thermal and mechanical denaturing properties of two proteins having the same sequence and secondary structures but differing in the presence or absence of an inherent knot.

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