The successful integration of proteins into bionanomaterials with specific and desired function requires an accurate understanding of their material properties. Two such important properties are their mechanical stability and malleability. While single molecule manipulation techniques 15 now routinely provide access to these, there is a need to move towards predictive tools that can rationally identify proteins with desired material properties. We provide a comprehensive review of the available experimental data on the single molecule characterisation of proteins using the 20 atomic force microscope. We uncover a number of empirical relationships between the measured mechanical stability of a protein and its malleability which provide a set of simple tools which might be employed to estimate properties of previously uncharacterised proteins. 25

Single-molecule force spectroscopy has emerged as a powerful approach to examine the stability and dynamics of single proteins. We have completed force extension experiments on the small cold shock protein B from Thermotoga maritima, using a specially constructed chimeric polyprotein. The protein's simple topology, which is distinct from the mechanically well-characterized β-grasp and immunoglobulin (Ig)-like folds, in addition to the wide range of structural homologues resulting from its ancient origin, provides an attractive model protein for single-molecule force spectroscopy studies. We have determined that the protein has mechanical stability, unfolding at greater than 70 pN at a pulling velocity of 100 nm s(-1). We reveal features of the unfolding energy landscape by measuring the dependence of the mechanical stability on pulling velocity, in combination with Monte Carlo simulations. We show that the cold shock protein has mechanically robust, yet malleable, features that may be important in providing the protein with stability and flexibility to function over a range of environmental conditions. These results provide insights into the relationship between the secondary structure and topology of a protein and its mechanical strength. This lays the foundation for the investigation of the effects of changes in environmental conditions on the mechanical and dynamic properties of cold shock proteins.

The ability of thermophilic and hyperthermophilic proteins to maintain their native structure, yet be dynamic and flexible is a key determinant of their ability to function at the extremes of environmental temperatures found on Earth. An understanding of the design principles governing their material properties is important in the development of biomaterials which are able to withstand such extreme conditions. Single molecule force spectroscopy is used to characterise the mechanical flexibility of cold shock protein B from a hyperthermophilic organism, Thermotoga maritima, in the temperature range from 5-40 C. We measure temperature-dependent changes in features of the unfolding energy landscape of this protein by studying the pulling speed dependence of the unfolding force with temperature in combination with Monte Carlo simulations. We find that the position of the transition state to unfolding shifts away from the native state with increased temperature, reflecting a reduction in the spring constant of the protein and an increase in the malleability of the structure. The mechanical robustness and malleability of this cold shock protein over the temperature range studied, provides an insight into the dynamical properties of hyperthermophilic proteins and lays the foundations for further studies using this highly structurally conserved protein family.

Proteins from extremophilic organisms provide excellent model systems to determine the role of non-covalent interactions in defining protein stability and dynamics as well as being attractive targets for the development of robust biomaterials. Hyperthermophilic proteins have a prevalence of salt bridges, relative to their mesophilic homologues, which are thought to be important for enhanced thermal stability. However, the impact of salt bridges on the mechanical properties of proteins is far from understood. Here, a combination of protein engineering, biophysical characterisation, single molecule force spectroscopy (SMFS) and molecular dynamics (MD) simulations directly investigates the role of salt bridges in the mechanical stability of two cold shock proteins; BsCSP from the mesophilic organism Bacillus subtilis and TmCSP from the hyperthermophilic organism Thermotoga maritima. Single molecule force spectroscopy shows that at ambient temperatures TmCSP is mechanically stronger yet, counter-intuitively, its native state can withstand greater deformation before unfolding (i.e. it is mechanically soft) compared with BsCSP. MD simulations were used to identify the location and quantify the population of salt bridges, and reveal that TmCSP contains a larger number of highly occupied salt bridges than BsCSP. To test the hypothesis that salt-bridges endow these mechanical properties on the hyperthermophilic CSP, a charged triple mutant (CTM) variant of BsCSP was generated by grafting an ionic cluster from TmCSP into the BsCSP scaffold. As expected CTM is thermodynamically more stable and mechanically softer than BsCSP. We show that a grafted ionic cluster can increase the mechanical softness of a protein and speculate that it could provide a mechanical recovery mechanism and that it may be a design feature applicable to other proteins.

The heat-shock protein 90 (Hsp90) molecular chaperones are highly conserved across species. However, their dynamic properties can vary significantly from organism to organism. Here we used high-precision optical tweezers to analyze the mechanical properties and folding of different Hsp90 orthologs, namely bacterial Hsp90 (HtpG) and Hsp90 from the endoplasmic reticulum (ER) (Grp94), as well as from the cytosol of the eukaryotic cell (Hsp82). We find that the folding rates of Hsp82 and HtpG are similar, while the folding of Grp94 is slowed down by misfolding of the N-terminal domain. Furthermore, the domain interactions mediated by the charged linker, involved in the conformational cycles of all three orthologs, are much stronger for Grp94 than for Hsp82, keeping the N-terminal domain and the middle domain in close proximity. Thus, the ER resident Hsp90 ortholog differs from the cytosolic counterparts in basic functionally relevant structural properties.

The molecular chaperone Hsp90 is an important regulator of proteostasis. It has remained unclear why S. cerevisiae possesses two Hsp90 isoforms, the constitutively expressed Hsc82 and the stress-inducible Hsp82. Here, we report distinct differences despite a sequence identity of 97%. Consistent with its function under stress conditions, Hsp82 is more stable and refolds more efficiently than Hsc82. The two isoforms also differ in their ATPases and conformational cycles. Hsc82 is more processive and populates closed states to a greater extent. Variations in the N-terminal ATP-binding domain modulate its dynamics and conformational cycle. Despite these differences, the client interactomes are largely identical, but isoform-specific interactors exist both under physiological and heat shock conditions. Taken together, changes mainly in the N-domain create a stress-specific, more resilient protein with a shifted activity profile. Thus, the precise tuning of the Hsp90 isoforms preserves the basic mechanism but adapts it to specific needs.

We report the development of a terahertz pulsed spectroscopic imaging system based on the concept of compressive sensing. A single-point terahertz detector, together with a set of 40 optimized two-dimensional binary masks, was used to measure the terahertz waveforms transmitted through a sample. Terahertz time- and frequency-domain images of the sample comprising 20×20 pixels were subsequently reconstructed. We demonstrate that both the spatial distribution and the spectral characteristics of a sample can be obtained by this means. Compared with conventional terahertz pulsed imaging, no raster scanning of the object is required, and ten times fewer terahertz spectra need be taken. It is therefore ideal for real-time imaging applications.

Single-molecule force spectroscopy using an atomic force microscope (AFM) can be used to measure the average unfolding force of proteins in a constant velocity experiment. In combination with Monte Carlo simulations and through the application of the Zhurkov-Bell model, information about the parameters describing the underlying unfolding energy landscape of the protein can be obtained. Using this approach, we have completed protein unfolding experiments on the polyprotein (I 27) 5 over a range of pulling velocities. In agreement with previous work, we find that the observed number of protein unfolding events observed in each approach-retract cycle varies between one and five, due to the nature of the interactions between the polyprotein, the AFM tip, and the substrate, and there is an unequal unfolding probability distribution. We have developed a Monte Carlo simulation that incorporates the impact of this unequal unfolding probability distribution on the median unfolding force and the calculation of the protein unfolding energy landscape parameters. These results show that while there is a significant, unequal unfolding probability distribution, the unfolding energy landscape parameters obtained from use of the Zhurkov-Bell model are not greatly affected. This result is important because it demonstrates that the minimum acceptance criteria typically used in force extension experiments are justified and do not skew the calculation of the unfolding energy landscape parameters. We further validate this approach by determining the error in the energy landscape parameters for two extreme cases, and we provide suggestions for methods that can be employed to increase the level of accuracy in single-molecule experiments using polyproteins.