A versatile "multiple fishhooks" approach for the study of ligand-receptor interactions using single-molecule atomic force microscopy

In situ quantitative determination of the intermolecular attraction between amines and a graphene surface using atomic force microscopy

The adsorption of pollutants on carbonaceous environmental media has been widely studied via batch sorption experiments and spectroscopic characterization. However, the molecular interactions between pollutants and interfacial sites on carbonaceous materials have only been indirectly investigated. To comprehend the adsorption mechanisms in situ, we applied atomic force microscopy force spectroscopy (AFM-FS) to quantitatively determine the molecular interactions between typical amines (methylamines and N-methylaniline) and the surface of highly oriented pyrolytic graphite (HOPG), which was supported by the single molecule interaction derived from density functional theory and batch adsorption experiments. This method achieved direct and in situ characterization of the molecular interactions in the adsorption process. The molecular interactions between the amines and the adsorption sites on the graphite surface were affected by pH and peaked at pH 7 due to strong cation-π interactions. When the pH was 11, the attractions were weak due to a lack of cation-π interaction, whereas, when the pH was 3, the competitive occupation of hydronium ions on the surface reduced the attraction between the amines and HOPG. Based on AFM-FS, the single molecule force of methylamine and N-methylaniline on the graphite surface was estimated to be 0.224 nN and 0.153 nN, respectively, which was consistent with density functional theory (DFT) calculations. This study broadens our comprehension of cation-π interactions between amines and electron-rich aromatic compounds at the micro/nanoscale.

Role of the copper ion in pseudoazurin during the mechanical unfolding process

Metalloproteins require the corresponding metal cofactors to exert their proper function. The presence of metal cofactors in the metalloprotein makes it more difficult to investigate its folding and unfolding process. In this study, we employed atomic-force-microscopy-based single-molecule force spectroscopy to reveal the unfolding process of pseudoazurin (PAZ) that belongs to blue copper proteins. Our study shows that holo-PAZ requires a higher rupture force for mechanical unfolding comparing with the apo-PAZ. This result demonstrates that the copper atom not only enables PAZ access to transfer electron, but should also have an influence on its stability. The results also suggest that the electronic configuration of the metal cofactors has a striking effect on the strength of the organometallic bonds. Moreover, the results also reveal that there is an intermediate state during the unfolding process of PAZ. This study provides insight into the characteristics of metalloproteins and leads to a better knowledge of their interaction at the individual molecule level.

Next Generation Methods for Single-Molecule Force Spectroscopy on Polyproteins and Receptor-Ligand Complexes

Single-molecule force spectroscopy with the atomic force microscope provides molecular level insights into protein function, allowing researchers to reconstruct energy landscapes and understand functional mechanisms in biology. With steadily advancing methods, this technique has greatly accelerated our understanding of force transduction, mechanical deformation, and mechanostability within single- and multi-domain polyproteins, and receptor-ligand complexes. In this focused review, we summarize the state of the art in terms of methodology and highlight recent methodological improvements for AFM-SMFS experiments, including developments in surface chemistry, considerations for protein engineering, as well as theory and algorithms for data analysis. We hope that by condensing and disseminating these methods, they can assist the community in improving data yield, reliability, and throughput and thereby enhance the information that researchers can extract from such experiments. These leading edge methods for AFM-SMFS will serve as a groundwork for researchers cognizant of its current limitations who seek to improve the technique in the future for in-depth studies of molecular biomechanics.

Blue light-induced low mechanical stability of ruthenium-based coordination bonds: an AFM-based single-molecule force spectroscopy study

A HA–Ru^II complex was conjugated to a hyaluronan polymer through amide bonds. In AFM experiments using the “multi-fishhook” approach, the cantilever tip made contact with the polymeric molecule, resulting in stretching, indicated by sawtooth-like force-extension curves.

Injectable dynamic covalent hydrogels of boronic acid polymers cross-linked by bioactive plant-derived polyphenols

We report here the development of hydrogels formed at physiological conditions using PEG (polyethylene glycol) based polymers modified with boronic acids (BAs) as backbones and the plant derived polyphenols ellagic acid (EA), epigallocatechin gallate (EGCG), tannic acid (TA), nordihydroguaiaretic acid (NDGA), rutin trihydrate (RT), rosmarinic acid (RA) and carminic acid (CA) as linkers. Rheological frequency sweep and single molecule force spectroscopy (SMFS) experiments show that hydrogels linked with EGCG and TA are mechanically stiff, arising from the dynamic covalent bond formed by the polyphenol linker and boronic acid functionalized polymer. Stability tests of the hydrogels in physiological conditions revealed that gels linked with EA, EGCG, and TA are stable. We furthermore showed that EA- and EGCG-linked hydrogels can be formed via in situ gelation in pH 7.4 buffer, and provide long-term steady state release of bioactive EA. In vitro experiments showed that EA-linked hydrogel significantly reduced the viability of CAL-27 human oral cancer cells via gradual release of EA.

How Do We Know when Single-Molecule Force Spectroscopy Really Tests Single Bonds?

Single-molecule force spectroscopy makes it possible to measure the mechanical strength of single noncovalent receptor-ligand-type bonds. A major challenge in this technique is to ensure that measurements reflect bonds between single biomolecules because the molecules cannot be directly observed. This perspective evaluates different methodologies for identifying and reducing the contribution of multiple molecule interactions to single-molecule measurements to help the reader design experiments or assess publications in the single-molecule force spectroscopy field. We apply our analysis to the large body of literature that purports to measure the strength of single bonds between biotin and streptavidin as a demonstration that measurements are only reproducible when the most reliable methods for ensuring single molecules are used.

Interactions between shape-persistent macromolecules as probed by AFM

Water-soluble shape-persistent cyclodextrin (CD) polymers with amino-functionalized end groups were prepared starting from diacetylene-modified cyclodextrin monomers by a combined Glaser coupling/click chemistry approach. Structural perfection of the neutral CD polymers and inclusion complex formation with ditopic and monotopic guest molecules were proven by MALDI-TOF and UV-vis measurements. Small-angle neutron and X-ray (SANS/SAXS) scattering experiments confirm the stiffness of the polymer chains with an apparent contour length of about 130 Å. Surface modification of planar silicon wafers as well as AFM tips was realized by covalent bound formation between the terminal amino groups of the CD polymer and a reactive isothiocyanate-silane monolayer. Atomic force measurements of CD polymer decorated surfaces show enhanced supramolecular interaction energies which can be attributed to multiple inclusion complexes based on the rigidity of the polymer backbone and the regular configuration of the CD moieties. Depending on the geometrical configuration of attachment anisotropic adhesion characteristics of the polymer system can be distinguished between a peeling and a shearing mechanism.

Influence of molecular dipole orientations on long-range exponential interaction forces at hydrophobic contacts in aqueous solutions

Strong and particularly long ranged (>100 nm) interaction forces between apposing hydrophobic lipid monolayers are now well understood in terms of a partial turnover of mobile lipid patches, giving rise to a correlated long-range electrostatic attraction. Here we describe similarly strong long-ranged attractive forces between self-assembled monolayers of carboranethiols, with dipole moments aligned either parallel or perpendicular to the surface, and hydrophobic lipid monolayers deposited on mica. We compare the interaction forces measured at very different length scales using atomic force microscope and surface forces apparatus measurements. Both systems gave a long-ranged exponential attraction with a decay length of 2.0 ± 0.2 nm for dipole alignments perpendicular to the surface. The effect of dipole alignment parallel to the surface is larger than for perpendicular dipoles, likely due to greater lateral correlation of in-plane surface dipoles. The magnitudes and range of the measured interaction forces also depend on the surface area of the probe used: At extended surfaces, dipole alignment parallel to the surface leads to a stronger attraction due to electrostatic correlations of freely rotating surface dipoles and charge patches on the apposing surfaces. In contrast, perpendicular dipoles at extended surfaces, where molecular rotation cannot lead to large dipole correlations, do not depend on the scale of the probe used. Our results may be important to a range of scale-dependent interaction phenomena related to solvent/water structuring on dipolar and hydrophobic surfaces at interfaces.

Single molecule evidence for the adaptive binding of DOPA to different wet surfaces

3,4-Dihydroxyphenylalanine (DOPA) is the noncanonical amino acid widely found in mussel holdfast proteins, which is proposed to be responsible for their strong wet adhesion. This feature has also inspired the successful development of a range of DOPA-containing synthetic polymers for wet adhesions and surface coating. Despite the increasing applications of DOPA in material science, the underlying mechanism of DOPA-wet surface interactions remains unclear. In this work, we studied DOPA-surface interactions one bond at a time using atomic force microscope (AFM) based single molecule force spectroscopy. With our recently developed "multiple fishhook" protocol, we were able to perform high-throughput quantification of the binding strength of DOPA to various types of surfaces for the first time. We found that the dissociation forces between DOPA and nine different types of organic and inorganic surfaces are all in the range of 60-90 pN at a pulling speed of 1000 nm s(-1), suggesting the strong and versatile binding capability of DOPA to different types of surfaces. Moreover, by constructing the free energy landscape for the rupture events, we revealed several distinct binding modes between DOPA and different surfaces, which are directly related to the chemistry nature of the surfaces. These results explain the molecular origin of the versatile binding ability of DOPA. Moreover, we could quantitatively predict the relationship between DOPA contents and the binding strength based on the measured rupture kinetics. These serve as the bases for the quantitative prediction of the relationship between DOPA contents and adhesion strength to different wet surfaces, which is important for the design of novel DOPA based materials.

Single-chain mechanics of poly(N,N-diethylacrylamide) and poly(N-isopropylacrylamide): comparative study reveals the effect of hydrogen bond donors

The single-chain mechanics of two similar thermosensitive polymers, poly(N,N-diethylacrylamide) (PDEAM) and poly(N-isopropylacrylamide) (PNIPAM), have been studied by atomic force microscopy-based single-molecule force spectroscopy (SMFS). In a typical nonpolar organic solvent, octane, both of the polymers show the same inherent elasticity, although they have different substitutional groups. However, the mechanics of the two polymers presents large differences in water. The energies needed for the rearrangement of the bound water during elongation at room temperature are estimated by the SMFS method at the single-chain level, which is ~1.13 ± 0.10 and ~5.19 ± 0.10 kJ/mol for PDEAM and PNIPAM, respectively. In addition, PNIPAM shows a temperature-dependent single-chain mechanics when the temperature is increased across the lower critical solution temperature (LCST), while PDEAM does not. These differences observed in aqueous solution originate from the different structures of the two polymers. With a hydrogen bond donor in the amide group, PNIPAM will be more hydrated when T < LCST. When T > LCST, PNIPAM will have larger changes in both conformation and hydration. These findings also suggest that PNIPAM is a good candidate for a thermo-driven single-molecule motor, while PDEAM is not.

Elastic repulsion from polymer brush layers exhibiting high protein repellency

Hydrophilic poly(2-methacryloyloxyethyl phosphorylcholine) (PMPC) and poly(2-hydroxyethyl methacrylate) (PHEMA) brush layers with different thicknesses and graft densities were prepared to construct a model surface to elucidate protein-surface interactions. In particular, we focused on the steric repulsion of hydrophilic polymer layers as one of the surface properties that strongly influence protein adsorption and employed force-versus-distance (f-d) curve measurements obtained via atomic force microscopy to quantitatively evaluate the steric repulsion force, which is also referred to as the "elastic repulsion energy." We also analyzed direct interactions between the surface and proteins via the f-d curve, because these interactions trigger the protein-adsorption phenomenon. Protein-surface interactions were extremely suppressed at surfaces with high elastic repulsion energies and highly dense polymer brush structures, which is in contrast to those at surfaces with low elastic repulsion energies and low density of the grafted polymer layers. These results indicate that the elastic repulsion from the grafted polymer layer at the surface is an important parameter for controlling protein-surface interactions and protein adsorption phenomenon.

Hydrodynamic force depends not only on the viscosity of solution but also on the molecular weights of viscogens

Many cellular processes, such as the diffusion of biomacromolecules, the movement of molecular motors, and the conformational dynamics of proteins, are subjected to hydrodynamic forces because of the high viscosities of cellular environments. However, it is still unknown how hydrodynamic forces are related to the physical properties of different viscogens. Here, using the atomic force microscope-based force spectroscopy technique, we directly measured the hydrodynamic forces acting on a moving cantilever in various viscogen solutions. We found that the hydrodynamic force is not only dependent on the viscosity but also related to the molecular weight of viscogens. Counterintuitively, at the same macroscopic viscosity, the hydrodynamic force rises with the increasing molecular weight of viscogens, although the local microscopic viscosity of the solution decreases. This finding provides insights into the origin of hydrodynamic forces in biomolecule solutions and could inspire many force-spectroscopy-based techniques to measure the molecular weight and conformational changes of biomacromolecules in biological settings directly.