Statistical Learning from Single-Molecule Experiments: Support Vector Machines and Expectation-Maximization Approaches to Understanding Protein Unfolding Data

Structural Mechanisms of Forced Unfolding of Double-Stranded Fibrin Oligomers

Fibrin forms a polymeric scaffold of blood clots, which are subjected to deformation in their dynamic environment. The extensible fibrin network allows fibers to stretch without breaking, but the mechanisms of their forced elongation are not understood. We combined atomic force microscopy, computer simulations, and Machine Learning to explore the nanomechanics of double-stranded cross-linked fibrin oligomers (FO). From the experimental force-extension profiles, the median 63 pN unfolding force and median 8.1 nm peak-to-peak distance with corresponding 56 pN and 11.4 nm interquartile ranges indicate substantial scatter due to ∼3-5 nm extension fluctuation of the triple α-helical coiled-coils. From simulations, unraveling of FO is determined by coupled dissociation of the D:D interface, γ-nodules unfolding, and reversible unfolding-refolding of the coiled-coils. These can occur as single structural transitions (60% of the time) or mixed transitions (40% of the time), with an alternating order of strands in which unfolding transitions occur, i.e., if the previous transition takes place in one strand, the next transition occurs in the other strand. The double-stranded FO are less extensible but stiffer and more stable compared with the single-stranded oligomers. These findings provide important insights into the biomechanics and dynamic structural properties of fibrin necessary to understand the (sub)molecular origin of fibrin extensibility.

Single-molecule mechanical studies of chaperones and their clients

Single-molecule force spectroscopy provides access to the mechanics of biomolecules. Recently, magnetic and laser optical tweezers were applied in the studies of chaperones and their interaction with protein clients. Various aspects of the chaperone-client interactions can be revealed based on the mechanical probing strategies. First, when a chaperone is probed under load, one can examine the inner workings of the chaperone while it interacts with and works on the client protein. Second, when protein clients are probed under load, the action of chaperones on folding clients can be studied in great detail. Such client folding studies have given direct access to observing actions of chaperones in real-time, like foldase, unfoldase, and holdase activity. In this review, we introduce the various single molecule mechanical techniques and summarize recent single molecule mechanical studies on heat shock proteins, chaperone-mediated folding on the ribosome, SNARE folding, and studies of chaperones involved in the folding of membrane proteins. An outlook on significant future developments is given.