Zu Thur Yew

The structure of a folding intermediate provides insight into differences in immunoglobulin amyloidogenicity.

Folding intermediates play a key role in defining protein folding and assembly pathways as well as those of misfolding and aggregation. Yet, due to their transient nature, they are poorly accessible to high-resolution techniques. Here, we made use of the intrinsically slow folding reaction of an antibody domain to characterize its major folding intermediate in detail. Furthermore, by a single point mutation we were able to trap the intermediate in equilibrium and characterize it at atomic resolution. The intermediate exhibits the basic β-barrel topology, yet some strands are distorted. Surprisingly, two short strand-connecting helices conserved in constant antibody domains assume their completely native structure already in the intermediate, thus providing a scaffold for adjacent strands. By transplanting these helical elements into β2-microglobulin, a highly homologous member of the same superfamily, we drastically reduced its amyloidogenicity. Thus, minor structural differences in an intermediate can shape the folding landscape decisively to favor either folding or misfolding.

Non-native interactions are critical for mechanical strength in PKD domains.

Summary Experimental observation has led to the commonly held view that native state protein topology is the principle determinant of mechanical strength. However, the PKD domains of polycystin-1 challenge this assumption: they are stronger than predicted from their native structure. Molecular dynamics simulations suggest that force induces rearrangement to an intermediate structure, with nonnative hydrogen bonds, that resists unfolding. Here we test this hypothesis directly by introducing mutations designed to prevent formation of these nonnative interactions. We find that these mutations, which only moderately destabilize the native state, reduce the mechanical stability dramatically. The results demonstrate that nonnative interactions impart significant mechanical stability, necessary for the mechanosensor function of polycystin-1. Remarkably, such nonnative interactions result from force-induced conformational change: the PKD domain is strengthened by the application of force.

Complex Unfolding Kinetics of Single-Domain Proteins in the Presence of Force

Single-molecule force spectroscopy is providing unique, and sometimes unexpected, insights into the free-energy landscapes of proteins. Despite the complexity of the free-energy landscapes revealed by mechanical probes, forced unfolding experiments are often analyzed using one-dimensional models that predict a logarithmic dependence of the unfolding force on the pulling velocity. We previously found that the unfolding force of the protein filamin at low pulling speed did not decrease logarithmically with the pulling speed. Here we present results from a large number of unfolding simulations of a coarse-grain model of the protein filamin under a broad range of constant forces. These show that a two-path model is physically plausible and produces a deviation from the behavior predicted by one-dimensional models analogous to that observed experimentally. We also show that the analysis of the distributions of unfolding forces (p[F]) contains crucial and exploitable information, and that a proper description of the unfolding of single-domain proteins needs to account for the intrinsic multidimensionality of the underlying free-energy landscape, especially when the applied perturbation is small.

Free-Energy Landscapes of Proteins in the Presence and Absence of Force

The equilibrium properties of the fourth immunoglobulin domain of filamin from Dictyostelium discoideum (ddFLN4) in the absence and presence of a small force (0-6 pN) pulling the termini apart is characterized through atomistic numerical simulation. The equilibrium free-energy landscape of ddFLN4 is found to change in a complex fashion that cannot be described in terms of one-dimensional projections as usually done in the interpretation of mechanical (un)folding experiments. Nonequilibrium unfolding simulations reveal that the major unfolding intermediate corresponds to a marginally populated state at equilibrium that only appears when a force larger than 4 pN is applied. Finally, we show that if the free-energy difference between states is taken to be linear in the applied force, the proportionality coefficient is not the difference in the end-to-end distance between pair of states as generally assumed even though the data can be reasonably fitted. The present results suggest that mechanical unfolding experiments may reveal states that are not accessible in the absence of force. Thus, special care should be taken when trying to interpret both equilibrium and nonequilibrium mechanical (un)folding experiments in light of the (un)folding properties in the absence of a force.

Fluctuation power spectra reveal dynamical heterogeneity of peptides

Characterizing the conformational properties and dynamics of biopolymers and their relation to biological activity and function is an ongoing challenge. Single molecule techniques have provided a rich experimental window on these properties, yet they have often relied on simple one-dimensional projections of a multidimensional free energy landscape for a practical interpretation of the results. Here, we study three short peptides with different structural propensity (alpha helical, beta hairpin, and random coil) in the presence (or absence) of a force applied to their ends using Langevin dynamics simulation and an all-atom model with implicit solvation. Each peptide produces fluctuation power spectra with a characteristic dynamic fingerprint consistent with persistent structural motifs of helices, hairpins, and random coils. The spectra for helix formation shows two well-defined relaxation modes, corresponding to local relaxation and cooperative coil to uncoil interconversion. In contrast, both the hairpin and random coil are polymerlike, showing a broad and continuous range of relaxation modes giving characteristic power laws of omega(-5/4) and omega(-3/2), respectively; the -5/4 power law for hairpins is robust and has not been previously observed. Langevin dynamics simulations of diffusers on a potential of mean force derived from the atomistic simulations fail to reproduce the fingerprints of each peptide motif in the power spectral density, demonstrating explicitly that such information is lacking in such one-dimensional projections. Our results demonstrate the yet unexploited potential of single molecule fluctuation spectroscopy to probe more fine scaled properties of proteins and biological macromolecules and how low dimensional projections may cause the loss of relevant information.

Free‐energy Landscapes of Proteins in the Presence of a Small Force

The unfolding of proteins induced by a large mechanical force pulling the termini apart have been widely investigated during the past decade. In contrast, the equilibrium properties of a protein in the presence of a small force have not been clearly determined or related to the nonequilibrium response of the same protein under a large force. We show through atomistic numerical simulations that the equilibrium free‐energy landscape of an immunoglobulin domain changes in a complex fashion that cannot be described in terms of one‐dimensional projections, as generally assumed in the interpretation of mechanical (un)folding experiments, or predicted from the unperturbed free‐energy landscape. We also show that the assumption that the relative free‐energy between a pair of states varies linearly with the force leads to parameters that do not correspond to those computed from the equilibrium simulations.