Protein folding occurs as a set of transitions between structural states within an energy landscape. An oversimplified view of the folding process emerges when transiently populated states are undetected because of limited instrumental resolution. Using force spectroscopy optimized for 1-μs resolution, we reexamined the unfolding of individual bacteriorhodopsin molecules in native lipid bilayers. The experimental data reveal the unfolding pathway in unprecedented detail. Numerous newly detected intermediates—many separated by as few as 2– 3 amino acids—exhibited complex dynamics, including frequent refolding and state occupancies of <10 μs. Equilibrium measurements between such states enabled the folding free-energy landscape to be deduced. These results sharpen the picture of the mechanical unfolding of membrane proteins and, more broadly, enable experimental access to previously obscured protein dynamics.

For the broadest dissemination of solid-state dynamic nuclear polarization (ssDNP) enhanced NMR as a material characterization tool, the ability to employ generic mono-nitroxide radicals as spin probes is critical. A better understanding of the factors contributing to ssDNP efficiency is needed to rationally optimize the experimental condition for the practically accessible spin probes at hand. This study seeks to advance the mechanistic understanding of ssDNP by examining the effect of electron spin dynamics on ssDNP performance at liquid helium temperatures (4-40 K). The key observation is that bi-radicals and mono-radicals can generate comparable nuclear spin polarization at 4 K and 7 T, which is in contrast to the observation for ssDNP at liquid nitrogen temperatures (80-150 K) that finds bi-radicals to clearly outperform mono-radicals. To rationalize this observation, we analyze the change in the DNP-induced nuclear spin polarization (Pn) and the characteristic ssDNP signal buildup time as a function of electron spin relaxation rates that are modulated by the mono- and bi-radical spin concentration. Changes in Pn are consistent with a systematic variation in the product of the electron spin-lattice relaxation time and the electron spin flip-flop rate that constitutes an integral saturation factor of an inhomogeneously broadened EPR spectrum. We show that the comparable Pn achieved with both radical species can be reconciled with a comparable integral EPR saturation factor. Surprisingly, the largest Pn is observed at an intermediate spin concentration for both mono- and bi-radicals. At the highest radical concentration, the stronger inter-electron spin dipolar coupling favors ssDNP, while oversaturation diminishes Pn, as experimentally verified by the observation of a maximum Pn at an intermediate, not the maximum, microwave (μw) power. At the maximum μw power, oversaturation reduces the electron spin population differential that must be upheld between electron spins that span a frequency difference matching the (1)H NMR frequency-characteristic of the cross effect DNP. This new mechanistic insight allows us to rationalize experimental conditions where generic mono-nitroxide probes can offer competitive ssDNP performance to that of custom designed bi-radicals, and thus helps to vastly expand the application scope of ssDNP for the study of functional materials and solids.

The microfossil record suggests that cyanobacteria or cyanobacteria-like prokaryotes were present on the primitive Earth in the Archaean era more than 3.5 billion years ago (28). The exquisite preservation of these microfossils is thought to reflect the intrinsic stability of the extracellular polysaccharide (EPS) and its ability to bind heavy metals as well as resist degradation (13). Extant cyanobacteria dominate the microbial populations of many extreme environments including soda lakes (Spirulina, Cyanospira), the nutrient-poor open ocean (Trichodesmium), thermal springs (Synechococcus and Mastigocladis), and the cold dry polar deserts (Chroococcidiopsis) (35). In these environments the cyanobacteria produce copious amounts of EPSs in the form of sheaths, slimes, and capsules. Very little is known about the diversity, mode of synthesis, structure, or properties of these biopolymers (19). A recent review emphasized the potential role of EPSs in the desiccation tolerance of prokaryotes (23). However, much further research is needed to resolve the specific mechanisms which biopolymers contribute to such a complex process.The terrestrial cyanobacterium Nostoc commune has a marked capacity for desiccation tolerance and can survive storage at Ϫ400 MPa (0% relative humidity) for centuries (23). The cells produce large amounts of an unusual excreted polysaccharide that contributes in at least four ways to the marked stabilization of cells during prolonged storage in the air-dried state, at low or high temperatures. First, the glycan inhibits fusion of membrane vesicles during desiccation and freezedrying (10) and acts as an immobilization matrix for a range of secreted enzymes which remain fully active after long-term air-dried storage (11,27,32). Second, the glycan provides a structural and/or molecular scaffold with rheological properties which can accommodate the rapid biophysical and physiological changes in the community upon rehydration and during recovery from desiccation. The glycan swells from brittle dried crusts to cartilaginous structures within minutes of rehydration. Third, the glycan matrix contains both lipid-and watersoluble UV radiation-absorbing pigments which protect the cell from photodegradation (12). Fourth, although epiphytes colonize the surfaces of Nostoc colonies, there is no penetration of the glycan due in part to a silicon-and calcium-rich pellicle and inherent resistance of the glycan to enzymatic breakdown. Preliminary structural work on one water-soluble UV-absorbing pigment (released from the glycan by acid hydrolysis) indicated the presence of an oligosaccharide (4), raising the possibility that the pigment may be covalently linked to the glycan in the desiccated state.An understanding of the biochemical and biophysical properties of such biopolymers and the isolation of genes and enzymes required for their synthesis and modification can lead to an understanding of the underlying principles of extremophile stability. Furthermore, one can envision the utilization of such materials f...

Atomic-force-microscopy (AFM)-based single-molecule force spectroscopy (SMFS) is a powerful yet accessible means to characterize mechanical properties of biomolecules. Historically, accessibility relies upon the nonspecific adhesion of biomolecules to a surface and a cantilever and, for proteins, the integration of the target protein into a polyprotein. However, this assay results in a low yield of high-quality data, defined as the complete unfolding of the polyprotein. Additionally, nonspecific surface adhesion hinders studies of α–helical proteins, which unfold at low forces and low extensions. Here, we overcame these limitations by merging two developments: (i) a polyprotein with versatile, genetically encoded short peptide tags functionalized via a mechanically robust Hydrazino-Pictet Spengler ligation and (ii) the efficient site-specific conjugation of biomolecules to PEG-coated surfaces. Heterobifunctional anchoring of this polyprotein construct and DNA via copper-free click chemistry to PEG-coated substrates and a strong but reversible streptavidin-biotin linkage to PEG-coated AFM tips enhanced data quality and throughput. For example, we achieved a 75-fold increase in the yield of high-quality data and repeatedly probed the same individual polyprotein to deduce its dynamic force spectrum in just 2 h. The broader utility of this polyprotein was demonstrated by measuring three diverse target proteins: an α-helical protein (calmodulin), a protein with internal cysteines (rubredoxin), and a computationally designed three-helix bundle (α3D). Indeed, at low loading rates, α3D represents the most mechanically labile protein yet characterized by AFM. Such efficient SMFS studies on a commercial AFM enable the rapid characterization of macromolecular folding over a broader range of proteins and a wider array of experimental conditions (pH, temperature, denaturants). Further, by integrating these enhancements with optical traps, we demonstrate how efficient bioconjugation to otherwise nonstick surfaces can benefit diverse single-molecule studies.

We present our experimental setup for both dynamic nuclear polarization (DNP) and electron paramagnetic resonance (EPR) detection at 7 T using a quasi-optical bridge for propagation of the 200 GHz beam and our initial results obtained at 4 K. Our quasi-optical bridge allows the polarization of the microwave beam to be changed from linear to circular. Only the handedness of circular polarization in the direction of the Larmor precession is absorbed by the electron spins, so a gain in effective microwave power of two is expected for circular vs. linear polarization. Our results show an increase in DNP signal enhancement of 28% when using circularly vs. linearly polarized radiation. We measured a maximum signal enhancement of 65 times that of thermal polarization for a (13)C labeled urea sample corresponding to 3% nuclear spin polarization. Since the time constant for nuclear spin polarization buildup during microwave irradiation is 10 times faster than the (13)C nuclear spin T(1), the actual gain in detection sensitivity with DNP is much greater.

Atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) is widely used to mechanically measure the folding and unfolding of proteins. However, the temporal resolution of a standard commercial cantilever is 50–1000 μs, masking rapid transitions and short-lived intermediates. Recently, SMFS with 0.7-μs temporal resolution was achieved using an ultrashort (L = 9 μm) cantilever on a custom-built, high-speed AFM. By micromachining such cantilevers with a focused ion beam, we optimized them for SMFS rather than tapping-mode imaging. To enhance usability and throughput, we detected the modified cantilevers on a commercial AFM retrofitted with a detection laser system featuring a 3-μm circular spot size. Moreover, individual cantilevers were reused over multiple days. The improved capabilities of the modified cantilevers for SMFS were showcased by unfolding a polyprotein, a popular biophysical assay. Specifically, these cantilevers maintained a 1-μs response time while eliminating cantilever ringing (Q ≅ 0.5). We therefore expect such cantilevers, along with the instrumentational improvements to detect them on a commercial AFM, to accelerate high-precision AFM-based SMFS studies.

We present the first observation of self-amplified spontaneous emission (SASE) in a free-electron laser (FEL) in the vacuum ultraviolet regime at 109 nm wavelength (11 eV). The observed free-electron laser gain (approximately 3000) and the radiation characteristics, such as dependency on bunch charge, angular distribution, spectral width, and intensity fluctuations, are all consistent with the present models for SASE FELs.

The structural organization of the functionally relevant, hexameric oligomer of green-absorbing proteorhodopsin (G-PR) was obtained from double electron-electron resonance (DEER) spectroscopy utilizing conventional nitroxide spin labels and recently developed Gd3+ -based spin labels. G-PR with nitroxide or Gd3+ labels was prepared using cysteine mutations at residues Trp58 and Thr177. By combining reliable measurements of multiple interprotein distances in the G-PR hexamer with computer modeling, we obtained a structural model that agrees with the recent crystal structure of the homologous blue-absorbing PR (B-PR) hexamer. These DEER results provide specific distance information in a membrane-mimetic environment and across loop regions that are unresolved in the crystal structure. In addition, the X-band DEER measurements using nitroxide spin labels suffered from multispin effects that, at times, compromised the detection of next-nearest neighbor distances. Performing measurements at high magnetic fields with Gd3+ spin labels increased the sensitivity considerably and alleviated the difficulties caused by multispin interactions.