Modeling of Multicolor Single-Molecule Förster Resonance Energy-Transfer Experiments on Protein Folding.

Using a coarse-grained, C-model of BBL protein, a multicolor single-molecule Förster resonance energy transfer (FRET) experiment is modeled. Three fluorophores are introduced, which, for simplicity, are associated with C beads. Two fluorophores are placed at the ends of protein chain and the third one at the middle of the chain.

Turbulence in protein folding: Vorticity, scaling and diffusion of probability flows.

Recently, when studying folding of a SH3 domain, we discovered that the flows of transitions between protein states can be surprisingly similar to turbulent fluid flows. This similarity was not restricted by a vortex pattern of the flow fields but extended to a spatial correlation of flow fluctuations, resulting, in particular, in the structure functions such as in the Kolmogorov theory of homogeneous and isotropic turbulence. Here, we undertake a detailed analysis of spatial distribution of folding flows and their similarity to turbulent fluid flows.

Temperature evolution of Trp-cage folding pathways: An analysis by dividing the probability flux field into stream tubes.

Owing to its small size and very fast folding rate, the Trp-cage miniprotein has become a benchmark system to study protein folding. Two folding pathways were found to be characteristic of this protein: pathway I, in which the hydrophobic collapse precedes the formation of α-helix, and pathway II, in which the events occur in the reverse order. At the same time, the relative contribution of these pathways at different temperatures as well as the nature of transition from one pathway to the other remain unclear.

A hydrodynamic view of the first-passage folding of Trp-cage miniprotein.

We study folding of Trp-cage miniprotein in the conditions when the native state of the protein is stable and unfolding events are improbable, which corresponds to physiological conditions. Using molecular dynamics simulations with an implicit solvent model, an ensemble of folding trajectories from unfolded (practically extended) states of the protein to the native state was generated. To get insight into the folding kinetics, the free energy surface and kinetic network projected on this surface were constructed.