Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2ouf-knot

Abstract

While fast folding of small proteins has been relatively well characterized by experiments and theories, much less is known for slow folding of larger proteins, for which recent experiments suggested quite complex and rich folding behaviors. Here, we address how the energy landscape theory can be applied to these slow folding reactions. Combining the perfect-funnel approximation with a multiscale method, we first extended our previous atomic-interaction based coarse grained (AICG) model to take into account local flexibility of protein molecules. Using this model, we then investigated the energy landscapes and folding routes of two proteins with complex topologies: a multidomain protein adenylate kinase (AKE) and a knotted protein 2ouf-knot. In the AKE folding, consistent with experimental results, the kinetic free energy surface showed several substates between the fully unfolded and native states. We characterized the structural features of these substates and transitions among them, finding temperature-dependent multiroute folding. For protein 2ouf-knot, we found that the improved atomic-interaction based coarse-grained model can spontaneously tie a knot and fold the protein with a probability up to 96%. The computed folding rate of the knotted protein was much slower than that of its unknotted counterpart, in agreement with experimental findings. Similar to the AKE case, the 2ouf-knot folding exhibited several substates and transitions among them. Interestingly, we found a dead-end substate that lacks the knot, thus suggesting backtracking mechanisms.

Folding pathway of a multidomain protein depends on its topology of domain connectivity

“…Whereas the multiplicity and flexibility of folding pathways have been investigated for multidomain proteins (3,4,15,16,33), questions still remain, particularly with regard to how the different types of folding mechanisms of multidomain proteins, folding through multiple or flexible pathways, or folding along a single sequential pathway can be distinguished from the energy landscape perspective. Using a simple structurebased model, we have shown that the folding mechanism is determined by the balance between the tendency to prevent the steep decrease of entropy through the association of discontinuous parts of the chain and the tendency to promote energy stabilization through the formation of compact domains.…”

“…folding intermediates | internal friction | eWSME model T opology of protein conformation, or the spatial arrangement of structural units and the chain connectivity among them, is a key determinant of the folding mechanisms of proteins (1)(2)(3)(4)(5). However, predicting a folding pathway is a subtle problem when a protein comprises multiple regions of cooperative structure formation (i.e., foldons or domains).…”

Physicochemical bases for protein folding, dynamics, and protein-ligand binding

“…In addition, when the folding process reaches the glass transition state, the intermediates have only a few paths towards the native structure [61]. It is worth noting that although the folding funnel model was established originally based on studies of small and fast-folding proteins, it can also be used to describe and explain the folding process of large and complex proteins [64].…”

Near-Atomic Structural Model for Bacterial DNA Replication Initiation Complex and its Functional Insights

“…Our simulations in the initial part used coarse-grained models where each amino acid in proteins was modeled by one particle located at Cα position (34) and each nucleotide in DNA was represented by three particles, each representing sugar, phosphate, and base (35,36). The protein energy function is based on native structure information at atomic resolution (SI Appendix, SI Methods provides details).…”