Dynamic measurement of single protein's mechanical properties

Spatially-resolved nanometer-scale measurement of cartilage extracellular matrix mobility

OBJECTIVE

Tissues have complex structures, comprised of solid and fluid phases. Improved understanding of interactions between joint fluid and extracellular matrix (ECM) is required in models of cartilage mechanics. X-ray photon correlation spectroscopy (XPCS) directly measures nanometer-scale dynamics and can provide insight into biofluid-biosolid interactions in cartilage. This study applies XPCS to evaluate dynamic interactions between intact cartilage and biofluids.

DESIGN

Cartilage biopsies were collected from bovine femoral condyles. During XPCS measurements, cartilage samples were exposed to different fluids: deionized water, PBS, synovial fluid, or sonicated synovial fluid. ECM-biofluid interactions were also assessed at different length scales and different depths from the cartilage surface.

RESULTS

Using XPCS, cartilage ECM mobility was detected at length scales from 50 to 207 nm. As length scale decreased, time scale for autocorrelation decay decreased, suggesting smaller ECM components are more mobile. ECM dynamics were slowed by dehydrating the sample, demonstrating XPCS assesses matrix mobility in hydrated environments. At all length scales, the matrix was more mobile in deionized water and slowest in synovial fluid. Using the 207 nm length scale assessment, ECM dynamics in synovial fluid were fastest at the cartilage surface and progressively slowed as depth into the sample increased, demonstrating XPCS can assess spatial distribution of ECM dynamics. Finally, ECM mobility increased for degraded synovial fluid.

CONCLUSIONS

This study demonstrates the potential of XPCS to provide unique insights into nanometer-scale cartilage ECM mobility in a spatially resolved manner and illustrates the importance of biosolid-biofluid interactions in dictating ECM dynamics.

Nano-Mechanical Characterization of Ataxia Telangiectasia Cells Treated with Dexamethasone

Ataxia telangiectasia is a rare genetic disease and no therapy is currently available. Glucocorticoid analogues have been shown to improve the neurological symptoms of treated patients. In the present study ataxia telangiectasia and wild type cells were used as a cellular model and treated with dexamethasone. The cells were subsequently investigated for membrane and whole cell mechanical properties by atomic force microscopy. In addition, cytoskeleton protein dynamics and nuclear shapes were assayed by fluorescence microscopy, while western blots were used to assess actin and tubulin content. At the macro level, dexamethasone directly modified the cell shape, Young's modulus and cytoskeleton protein dynamics. At the nano level, the roughness of the cell surface and the local nano-mechanical proprieties were found to be affected by Dexa. Our results show that ataxia telangiectasia and wild type cells are affected by Dexa, although there are dissimilarities in some macro-level and nano-level features between the tested cell lines. The Young's modulus of the cells appears to depend mainly on nuclear shape, with a slight contribution from the tested cytoskeleton proteins. The current study proposes that dexamethasone influences ataxia telangiectasia cell membranes contents, cell components and cell shape.

Protein high-force pulling simulations yield low-force results

All-atom explicit-solvent molecular dynamics simulations are used to pull with extremely large constant force (750–3000 pN) on three small proteins. The introduction of a nondimensional timescale permits direct comparison of unfolding across all forces. A crossover force of approximately 1100 pN divides unfolding dynamics into two regimes. At higher forces, residues sequentially unfold from the pulling end while maintaining the remainder of the protein force-free. Measurements of hydrodynamic viscous stresses are made easy by the high speeds of unfolding. Using an exact low-Reynolds-number scaling, these measurements can be extrapolated to provide, for the first time, an estimate of the hydrodynamic force on low-force unfolding. Below 1100 pN, but surprisingly still at extremely large applied force, intermediate states and cooperative unfoldings as seen at much lower forces are observed. The force-insensitive persistence of these structures indicates that decomposition into unfolded fragments requires a large fluctuation. This finding suggests how proteins are constructed to resist transient high force. The progression of helix and sheet unfolding is also found to be insensitive to force. The force-insensitivity of key aspects of unfolding opens the possibility that numerical simulations can be accelerated by high applied force while still maintaining critical features of unfolding.

Nanotechnological characterization of human serum albumin adsorption on wet synthetic polymer dialysis membrane surfaces

The objective of the present study was to evaluate the characteristics of protein adsorption on the inner surface of various dialysis membranes, to develop protein adsorption-resistant biocompatible dialysis membranes. The adsorption force of human serum albumin (HSA) on the inner surface of a dialysis membrane and the smoothness of the membrane were evaluated from a nanoscale perspective by atomic force microscopy. The content ratio of the hydrophilic polymer, polyvinylpyrrolidone (PVP), was determined by attenuated total reflection Fourier transform infrared spectroscopy. Nine synthetic-polymer dialysis membranes on the market made of polysulfone (PSF), polyethersulfone (PES), polyester polymer-alloy (PEPA), and ethylene vinylalcohol (EVAL) were used in the present study. The HSA adsorption force on the surface of the hydrophobic polymer PEPA membrane was higher than that on the hydrophilic polymer EVAL membrane surface. It has been considered beneficial, for decreasing the HSA adsorption force, to cover a hydrophobic polymer membrane surface with PVP. However, there were some areas on PVP-containing membrane surfaces at which much higher HSA adsorption forces were observed. The HSA adsorption force gave a nearly linear correlation with the surface roughness on the PSF membrane surface. However, the HSA adsorption force was uncorrelated with the PVP content ratio for any of the PSF membrane surfaces tested. In conclusion, protein adsorption can be minimized by the use of dialysis membranes made of hydrophobic polymers containing PVP with a smooth surface.

Periodic forces trigger a complex mechanical response in ubiquitin

Mechanical forces govern physiological processes in all living organisms. Many cellular forces, for example, those generated in cyclic conformational changes of biological machines, have repetitive components. In apparent contrast, little is known about how dynamic protein structures respond to periodic mechanical information. Ubiquitin is a small protein found in all eukaryotes. We developed molecular dynamics simulations to unfold single and multimeric ubiquitins with periodic forces. By using a coarse-grained representation, we were able to model forces with periods about 2 orders of magnitude longer than the protein's relaxation time. We found that even a moderate periodic force weakened the protein and shifted its unfolding pathways in a frequency- and amplitude-dependent manner. A complex dynamic response with secondary structure refolding and an increasing importance of local interactions was revealed. Importantly, repetitive forces with broadly distributed frequencies elicited very similar molecular responses compared to fixed-frequency forces. When testing the influence of pulling geometry on ubiquitin's mechanical stability, it was found that the linkage involved in the mechanical degradation of cellular proteins renders the protein remarkably insensitive to periodic forces. We also devised a complementary kinetic energy landscape model that traces these observations and explains periodic-force, single-molecule measurements. In turn, this analytical model is capable of predicting dynamic protein responses. These results provide new insights into ubiquitin mechanics and a potential mechanical role during protein degradation, as well as first frameworks for dynamic protein stability and the modeling of repetitive mechanical processes.

Nanomechanical strength mechanisms of hierarchical biological materials and tissues

Biological protein materials (BPMs), intriguing hierarchical structures formed by assembly of chemical building blocks, are crucial for critical functions of life. The structural details of BPMs are fascinating: They represent a combination of universally found motifs such as alpha-helices or beta-sheets with highly adapted protein structures such as cytoskeletal networks or spider silk nanocomposites. BPMs combine properties like strength and robustness, self-healing ability, adaptability, changeability, evolvability and others into multi-functional materials at a level unmatched in synthetic materials. The ability to achieve these properties depends critically on the particular traits of these materials, first and foremost their hierarchical architecture and seamless integration of material and structure, from nano to macro. Here, we provide a brief review of this field and outline new research directions, along with a review of recent research results in the development of structure-property relationships of biological protein materials exemplified in a study of vimentin intermediate filaments.

Hierarchies, multiple energy barriers, and robustness govern the fracture mechanics of alpha-helical and beta-sheet protein domains

The fundamental fracture mechanisms of biological protein materials remain largely unknown, in part, because of a lack of understanding of how individual protein building blocks respond to mechanical load. For instance, it remains controversial whether the free energy landscape of the unfolding behavior of proteins consists of multiple, discrete transition states or the location of the transition state changes continuously with the pulling velocity. This lack in understanding has thus far prevented us from developing predictive strength models of protein materials. Here, we report direct atomistic simulation that over four orders of magnitude in time scales of the unfolding behavior of alpha-helical (AH) and beta-sheet (BS) domains, the key building blocks of hair, hoof, and wool as well as spider silk, amyloids, and titin. We find that two discrete transition states corresponding to two fracture mechanisms exist. Whereas the unfolding mechanism at fast pulling rates is sequential rupture of individual hydrogen bonds (HBs), unfolding at slow pulling rates proceeds by simultaneous rupture of several HBs. We derive the hierarchical Bell model, a theory that explicitly considers the hierarchical architecture of proteins, providing a rigorous structure-property relationship. We exemplify our model in a study of AHs, and show that 3-4 parallel HBs per turn are favorable in light of the protein's mechanical and thermodynamical stability, in agreement with experimental findings that AHs feature 3.6 HBs per turn. Our results provide evidence that the molecular structure of AHs maximizes its robustness at minimal use of building materials.

Distribution of olfactory marker protein on a tissue section of vomeronasal organ measured by AFM

Distribution of olfactory marker protein (OMP) on a tissue section of vomeronasal organ (VNO) was successfully measured by atomic force microscopy (AFM). Anti-OMP antibodies were covalently crosslinked with the tip of the AFM and were used as a probe to observe the distribution of OMP on a tissue section. First, force measurements were performed using a glass surface on which OMP was covalently immobilized to verify the success of tip modification. Clear differences of interaction forces were observed between a specific pair and the control experiments, indicating that the tip preparation succeeded. Next, distributions of OMP on the tissue section were observed by AFM and were compared with immunohistochemical observations. For large scale observation, a microbead was used as a probe in the AFM measurements. The results of the AFM measurements were well overlapped with that of immunohistochemistry, confirming the reliability of our method. A mapping of the AFM measurement with high resolution was also successfully obtained, which showed an advantage of the application of the AFM measurement in analysis of proteins on the tissue section.

Viscoelastic properties of single poly(ethylene glycol) molecules

The viscoelastic properties of single poly(ethylene glycol) (PEG) molecules were measured by analysis of thermally and magnetically driven oscillations of an atomic force microscope (AFM) cantilever/molecule system. The molecular and monomer stiffness and friction of the PEG polymer were derived using a simple harmonic oscillator (SHO) model. Excellent agreement between the values of these two parameters obtained by the two approaches indicates the validity of the SHO model under the experimental regimes and the excellent reproducibility of the techniques. A sharp minimum in the monomeric friction is seen at around 180 pN applied force which we propose is due to a force induced change in the shape of the energy landscape describing the conformational transition of PEG from a helical to a planar state, which in turn affects the timescale of the transition and therefore modifies the measured internal friction. A knowledge of the viscoelastic response of PEG monomers is particularly important since PEG is widely used as a linker molecule for tethering groups of interest to the AFM tip in force spectroscopy experiments, and we show here that care must be exercised because of the force-dependent viscoelastic properties of these linkers.

Entropy and barrier-controlled fluctuations determine conformational viscoelasticity of single biomolecules

Biological macromolecules have complex and nontrivial energy landscapes, endowing them with a unique conformational adaptability and diversity in function. Hence, understanding the processes of elasticity and dissipation at the nanoscale is important to molecular biology and emerging fields such as nanotechnology. Here we analyze single molecule fluctuations in an atomic force microscope, using a generic model of biopolymer viscoelasticity that includes local "internal" conformational dissipation. Comparing two biopolymers, dextran and cellulose (polysaccharides with and without local bistable transitions), demonstrates that signatures of simple conformational change are minima in both the elastic and internal friction constants around a characteristic force. A novel analysis of dynamics on a bistable energy landscape provides a simple explanation: an elasticity driven by the entropy, and friction by a barrier-controlled hopping time of populations between states, which is surprisingly distinct to the well-known relaxation time. This nonequilibrium microscopic analysis thus provides a means of quantifying new dynamical features of the energy landscape of the glucopyranose ring, revealing an unexpected underlying roughness and information on the shape of the barrier of the chair-boat transition in dextran. The results presented herein provide a basis toward probing the viscoelasticity of macromolecular conformational transitions on more complex energy landscapes, such as during protein folding.

Frequency modulation atomic force microscopy reveals individual intermediates associated with each unfolded I27 titin domain

In this study, we apply a dynamic atomic force microscopy (AFM) technique, frequency modulation (FM) detection, to the mechanical unfolding of single titin I27 domains and make comparisons with measurements made using the AFM contact or static mode method. Static mode measurements revealed the well-known force transition occurring at 100-120 pN in the first unfolding peak, which was less clear, or more often absent, in the subsequent unfolding peaks. In contrast, some FM-AFM curves clearly resolved a force transition associated with each of the unfolding peaks irrespective of the number of observed unfolded domains. As expected for FM-AFM, the frequency shift response of the main unfolding peaks and their intermediates could only be detected when the oscillation amplitudes used were smaller than the interaction lengths being measured. It was also shown that the forces measured for the dynamical interaction of the FM-AFM technique were significantly lower than those measured using the static mode. This study highlights the potential for using dynamic AFM for investigating biological interactions, including protein unfolding and the detection of novel unfolding intermediates.

Imaging and detecting molecular interactions of single transmembrane proteins

Single-molecule atomic force microscopy (AFM) provides novel ways to characterize structure-function relationships of native membrane proteins. High-resolution AFM-topographs allow observing substructures of single membrane proteins at sub-nanometer resolution as well as their conformational changes, oligomeric state, molecular dynamics and assembly. Complementary to AFM imaging, single-molecule force spectroscopy experiments allow detecting molecular interactions established within and between membrane proteins. The sensitivity of this method makes it possible to detect the interactions that stabilize secondary structures such as transmembrane alpha-helices, polypeptide loops and segments within. Changes in temperature or protein-protein assembly do not change the position of stable structural segments, but influence their stability established by collective molecular interactions. Such changes alter the probability of proteins to choose a certain unfolding pathway. Recent examples have elucidated unfolding and refolding pathways of membrane proteins as well as their energy landscapes. We review current and future potential of these approaches to reveal insights into membrane protein structure, function, and unfolding as we recognize that they could help answering key questions in the molecular basis of certain neuro-pathological dysfunctions.

Nanorheology measurement on single circularly permuted green fluorescent protein molecule

The force measurement mode of an atomic force microscope (AFM) has enabled us to measure the mechanical properties of biological materials at the single molecular level. In a conventional quasi-static force measurement on a single circularly permuted green fluorescent protein (cpGFP), we could unfold it by unraveling several sub-domains in a distinct sawtooth pattern at a slow stretching speed. In order to elucidate more detailed conformational changes at each extension length, we further measured dynamic relax-stress response of cpGFP molecules. In this measurement, several cycles of sinusoidal movement were applied to the sample during the stretching process. We found the protein molecule showed in-phase response to the sinusoidal input in most case of measurements.

Molecular force modulation spectroscopy revealing the dynamic response of single bacteriorhodopsins

Recent advances in atomic force microscopy allowed globular and membrane proteins to be mechanically unfolded on a single-molecule level. Presented is an extension to the existing force spectroscopy experiments. While unfolding single bacteriorhodopsins from native purple membranes, small oscillation amplitudes (6-9 nm) were supplied to the vertical displacement of the cantilever at a frequency of 3 kHz. The phase and amplitude response of the cantilever-protein system was converted to reveal the elastic (conservative) and viscous (dissipative) contributions to the unfolding process. The elastic response (stiffness) of the extended parts of the protein were in the range of a few tens pN/nm and could be well described by the derivative of the wormlike chain model. Discrete events in the viscous response coincided with the unfolding of single secondary structure elements and were in the range of 1 microNs/m. In addition, these force modulation spectroscopy experiments revealed novel mechanical unfolding intermediates of bacteriorhodopsin. We found that kinks result in a loss of unfolding cooperativity in transmembrane helices. Reconstructing force-distance spectra by the integration of amplitude-distance spectra verified their position, offering a novel approach to detect intermediates during the forced unfolding of single proteins.

Investigation of interparticle forces in natural waters: effects of adsorbed humic acids on iron oxide and alumina surface properties

The nature of interparticle forces acting on colloid particle surfaces with adsorbed surface films of the internationally used humic acid standard material, Suwannee River Humic Acid (SHA), has been investigated using an atomic force microscope (AFM). Two particle surfaces were used, alumina and a hydrous iron oxide film coated onto silica particles. Adsorbed SHA dominated the interactive forces for both surface types when present. At low ionic strength and pH > 4, the force curves were dominated by electrostatic repulsion of the electrical double layers, with the extent of repulsion decreasing as electrolyte (NaCl) concentration increased, scaling with the Debye length (kappa(-1)) of the electrolyte according to classical theory. At pH approximately 4, electrostatic forces were largely absent, indicating almost complete protonation of carboxylic acid (-COOH) functional groups on the adsorbed SHA. Under these conditions and also at high electrolyte concentration ([NaCl] > 0.1 M), the absence of electrostatic forces allowed observation of repulsion forces arising from steric interaction of adsorbed SHA as the oxide surfaces approached closely to each other (separation < 10 nm). This steric barrier shrank as electrolyte concentration increased, implying tighter coiling of the adsorbed SHA molecules. In addition, adhesive bridging between surfaces was observed only in the presence of SHA films, implying a strong energy barrier to spontaneous detachment of the surfaces from each other once joined. This adhesion was especially strong in the presence of Ca2+ which appears to bridge SHA layers on each surface. Overall, our results show that SHA is a good model for the NOM adsorbed on colloids.

Dynamics of a partially stretched protein molecule studied using an atomic force microscope

The dynamics of a single protein molecule subjected to forced mechanical unfolding was investigated in a millisecond time domain using a custom-made atomic force microscope (AFM) apparatus, which allows simultaneous measurements of an average tensile force applied to a single molecule and its mechanical response with respect to an external oscillation. Our target protein was genetically engineered bovine carbonic anhydrase II (BCA) which is a monomeric globular protein, and it has been shown that the as-expressed BCA from Escherichia coli contains two conformational isomers, one with enzymatic activity (type I) and the other without (type II). An interesting feature observed from the dynamic measurements was that when the type I BCA conformer was extended, it often exhibited a clear out-of-phase response against an external oscillation. The type II BCA conformer, however, always exhibited an in-phase response to the external oscillation. This relationship between different types of BCA and their dynamical behaviors was evidently observed around the discontinuous transition point from type I to II.

Quantification of cell adhesion force with AFM: distribution of vitronectin receptors on a living MC3T3-E1 cell

Distribution of vitronectin (VN) receptors on a living murine osteoblastic cell was successfully measured by atomic force microscopy (AFM). First, the distribution of the integrin beta(5) subunit which constitutes a part of the VN receptor on the cell was confirmed by conventional immunohistochemistry after fixing the cell. To visualize the distribution of the receptor on a living cell by an independent and potentially a more quantitative method, the AFM was used with a microbead attached to the cantilever tip to increase the area of contact and VN was immobilized on the microbead. Force measurements were then performed over a large area of a living murine osteoblastic cell using the microbead covered with VN.

Forces between colloid particles in natural waters

The origin and nature of interparticle forces acting on colloid surfaces in natural waters has been examined using an atomic force microscope. Natural colloids were represented by a surface film of iron oxide precipitated onto spherical SiO2 particles, and the effects of adsorbed natural organic matter (NOM), solution pH, and ionic composition on the force-separation curves were investigated. NOM from both riverine and marine environments was strongly adsorbed to the iron oxide surface. Under conditions of low ionic strength, the interparticle forces were dominated by electrostatic repulsion arising from negative functional groups on the NOM, except at very small separations (<10 nm) where repulsive forces arising from steric interference of the NOM molecules were also present. At high ionic strength (e.g., seawater) or low pH, the electrostatic forces were largely absent, allowing steric repulsion forces to dominate. In addition, adhesive bridging between surfaces by adsorbed NOM was observed, creating a strong energy barrier to spontaneous disaggregation of colloid aggregates. Our results demonstrate that adsorbed NOM dominates the surface forces and thus stability with respect to aggregation of natural water colloids.

The importance of being knotted: effects of the C-terminal knot structure on enzymatic and mechanical properties of bovine carbonic anhydrase II

In order to better understand the contribution of the knotted folding pattern to the enzymatic and mechanical properties of carbonic anhydrases, we replaced Gln-253 of bovine carbonic anhydrase II with Cys, which allowed us to measure the mechanical strength of the protein against tensile deformation by avoiding knot tightening. The expressed protein, to our surprise, turned out to contain two conformational isomers, one capable of binding an enzymatic inhibitor and the other not, which led to their separation through affinity chromatography. In near- and far-UV circular dichroism and fluorescence spectra, the separated conformers were very similar to each other and to the wild-type enzyme, indicating that they both had native-like conformations. We describe new evidence which supports the notion that the difference between the two conformers is likely to be related to the completeness of the C-terminal knot formation.