Prediction of the optimal set of contacts to fold the smallest knotted protein

Abstract

Knotted protein chains represent a new motif in protein folds. They have been linked to various diseases, and recent extensive analysis of the Protein Data Bank shows that they constitute 1.5% of all deposited protein structures. Despite thorough theoretical and experimental investigations, the role of knots in proteins still remains elusive. Nonetheless, it is believed that knots play an important role in mechanical and thermal stability of proteins. Here, we perform a comprehensive analysis of native, shadow-specific and non-native interactions which describe free energy landscape of the smallest knotted protein (PDB id 2efv). We show that the addition of shadow-specific contacts in the loop region greatly enhances folding kinetics, while the addition of shadow-specific contacts along the C-terminal region (H3 or H4) results in a new folding route with slower kinetics. By means of direct coupling analysis (DCA) we predict non-native contacts which also can accelerate kinetics. Next, we show that the length of the C-terminal knot tail is responsible for the shape of the free energy barrier, while the influence of the elongation of the N-terminus is not significant. Finally, we develop a concept of a minimal contact map sufficient for 2efv protein to fold and analyze properties of this protein using this map.

Knotted proteins: Tie etiquette in structural biology

“…Nevertheless, it would be interesting to test this prediction in experiments in vitro. The importance of the contact map for efficient knotting was addressed in (108) in the context of off-lattice simulations of protein MJ0366.…”

Knots in soft condensed matter

“…Relaxation of this residue from the native-state trans conformation to a cis conformation when denatured, induces strong hysteresis in the unfolding-folding cycle. In a computational study, Dabrowski-Tumanski et al [12] pick apart the interactions in the smallest knotted protein (2efv in the Protein Data Bank) to determine how they affect knotting and folding. The native contact interactions are sufficient for the knotted structure to fold, but an additional subset of "native-like" contacts in the loop region greatly enhances the kinetics, and certain non-native contacts accelerate the rate still further.…”

In Search of Functional Advantages of Knots in Proteins

“…Most of them form simple trefoil knots, but there are also proteins forming more complex knots such as figure-of-eight, pretzel-like pentaknot and Stevedore’s knot [1, 4–6]. It should be stressed here that these knots are not results of some accidental entanglements of long polypeptide chains but their complex structure and topology is entirely dictated by their sequence [7, 8]. However, folding of knotted proteins is much slower and thus less efficient than of unknotted analogues [7–9].…”