Visualizing and manipulating individual protein molecules

Single-particle virology

The development of advanced experimental methodologies, such as optical tweezers, scanning-probe and super-resolved optical microscopies, has led to the evolution of single-molecule biophysics, a field of science that allows direct access to the mechanistic detail of biomolecular structure and function. The extension of single-molecule methods to the investigation of particles such as viruses permits unprecedented insights into the behavior of supramolecular assemblies. Here we address the scope of viral exploration at the level of individual particles. In an era of increased awareness towards virology, single-particle approaches are expected to facilitate the in-depth understanding, and hence combating, of viral diseases.

Attractive and repulsive polymer-mediated forces between scale-free surfaces

We consider forces acting on objects immersed in, or attached to, long fluctuating polymers. The confinement of the polymer by the obstacles results in polymer-mediated forces that can be repulsive (due to loss of entropy) or attractive (if some or all surfaces are covered by adsorbing layers). The strength and sign of the force in general depends on the detailed shape and adsorption properties of the obstacles but assumes simple universal forms if characteristic length scales associated with the objects are large. This occurs for scale-free shapes (such as a flat plate, straight wire, or cone) when the polymer is repelled by the obstacles or is marginally attracted to it (close to the depinning transition where the absorption length is infinite). In such cases, the separation h between obstacles is the only relevant macroscopic length scale, and the polymer-mediated force equals Ak_{B}T/h, where T is temperature. The amplitude A is akin to a critical exponent, depending only on geometry and universality of the polymer system. The value of A, which we compute for simple geometries and ideal polymers, can be positive or negative. Remarkably, we find A=0 for ideal polymers at the adsorption transition point, irrespective of shapes of the obstacles, i.e., at this special point there is no polymer-mediated force between obstacles (scale free or not).

Assessment of the nature interactions of β-amyloid protein by a nanoprobe method

We present a method based on atomic force microscopy (AFM) to assess the work of adhesion between the interfaces of gold AFM tips functionalized with three peptides derived from β-sheet breaker LPFFD [CLPFFD-NH2 (i0) and their isomers CDLPFF-NH2 (i1) and CLPDFF-NH2 (i2)], and the beta-amyloid protein (Aβ1-42). β-Amyloid protein was deposited onto a highly oriented graphite (HOPG) surface as protofibrils and fibrils. The presence of the residues Leu (L), Phe (F), and Phe (F), which are also present in the native sequence, confirm that the peptides are able to bind to the aggregates of Aβ1-42 fibrils and protofibrils. Force of adhesion data were directly obtained from the maximum force on retraction, and the work of adhesion was calculated from the Jhonson-Kendall-Roberts model (JKR-Model). Both the polar and dispersive contributions to the surface energy of the peptides i0, i1, and i2, as well as Aβ1-42 fibrils and protofibrils, were determined by means of measuring the contact angle and using the two-fluid method. The macroscopic energies of the functionalized gold surfaces do not differ significantly between isomers, which confirms the similar nature of the peptides i0, i1, and i2 but suggests that the macroscopic measurements are not able to distinguish specific sequences. The nanoprobe reveals a typical adhesion work value associated with the interaction of protofibrils with i0 and i2; this value is three times higher than that of i1. The difference is attributed to the hydrophobic nature of protofibrils, the predominant exposition of hydrophobic residues of the peptides i0 and i2, with respect to i1, and the degree of functionalization. i0 and i2 presented a slight adhesion with Aβ fibrils, which is associated with the exposed hydrophilic groups of these fibrils (onto HOPG) compared to the protofibrils. However, i1 showed interaction with both Aβ fibrils and protofibrils. For this, we propose an explanation based on the fact that the peptide i1 locates itself adjacent to the gold surface of the probe, concealing their hydrophobic groups and therefore decreasing the probability of interaction with Aβ fibrils and protofibrils. The peptide-gold nano probe represents a useful tool to study the nanobiointeractions of functionalized nanoparticles with amyloid aggregates.

Entropic forces exerted on a rough wall by a grafted semiflexible polymer

We study the entropic force due to a fluctuating semiflexible polymer that is grafted from one end and confined by a rigid and rough wall from the other end. We show how roughness of the wall modifies the entropic force. In addition to the perpendicular force that is present in the case of a flat wall, roughness of the wall adds a lateral component to the force. Both perpendicular and lateral components of the force are examined for different values of amplitude and wavelength of the roughness and at different temperatures. The lateral force is controlled by the local slope of the wall while the perpendicular force is only sensitive to the curvature of the wall. We show that for small compression, the entropic force is increased by increasing the curvature of the confining wall. In addition to the biophysical relevance, the results may also be useful in developing an AFM-based experimental technique for probing the roughness of surfaces.

Breaking the resolution limit in light microscopy

The advancement in fluorescence microscopy has dramatically enhanced the obtainable optical resolution enabling the users to inspect the structures of interest at finer and finer level of detail. This chapter describes some of these methods and how they break the classical resolution limit. The labeling of targets, such as individual genetic loci, specific proteins, or organelles, is possible inside living cells, which led to the extensive use of fluorescence microscopy in life sciences. Other microscopic modes usually lack this high specificity but sometimes provide other useful information such as the orientation of molecular species in polarization microscopy. Modes, such as differential interference contrast, phase contrast, or dark field, are useful to discriminate and follow cells or structures within them without the need for specific labeling. However, classically the resolution of all of these light microscopic modes was far below that of the electron microscope, and only some recent approaches have made significant progress in resolution increase. Recently, many microscopy methods have dramatically enhanced the resolution. Gradually, these methods are now applied to solve biological problems. The most promising approaches are all based on fluorescence and use either nonlinear interaction of light with the sample (STED, nonlinear structured illumination, dynamic saturation optical microscopy, or saturation in the time domain) or precise localization of individual particles or molecules with subsequent image generation.

Polymer-mediated entropic forces between scale-free objects

The number of configurations of a polymer is reduced in the presence of a barrier or an obstacle. The resulting loss of entropy adds a repulsive component to other forces generated by interaction potentials. When the obstructions are scale invariant shapes (such as cones, wedges, lines, or planes) the only relevant length scales are the polymer size R(0) and characteristic separations, severely constraining the functional form of entropic forces. Specifically, we consider a polymer (single strand or star) attached to the tip of a cone, at a separation h from a surface (or another cone). At close proximity, such that h << R(0), separation is the only remaining relevant scale and the entropic force must take the form F = Ak(B)T/h. The amplitude A is universal and can be related to exponents η governing the anomalous scaling of polymer correlations in the presence of obstacles. We use analytical, numerical, and ε-expansion techniques to compute the exponent η for a polymer attached to the tip of the cone (with or without an additional plate or cone) for ideal and self-avoiding polymers. The entropic force is of the order of 0.1 pN at 0.1 μm for a single polymer and can be increased for a star polymer.

Adhesion, stretching, and electrical charge assessment of dermatan sulfate molecules by colloidal probes

Electrical and mechanical properties of dermatan sulfate (DS) molecules are studied in an aqueous environment as a function of pH. DS molecules linked at various points distributed on the surface of mica previously silanizated along with a suitable functionalized microsphere, attached to the cantilever of an atomic force microscope (AFM), provided suitable surfaces for testing interactions through the colloidal probe methodology. The repulsive force between the surfaces indicated that the charge of DS increases with pH as a result of the gradual deprotonation of acidic groups. Pulling experiments revealed increasing adhesion of DS to the monolayer as a function of pH, presumably due both to the electrical nature of the interaction between these molecules and the progressive increase of the charge of DS with pH. Serrations exhibited by the force in pulling experiments indicate that more than a single DS molecule is stretched at the same time. In addition, pulling force remained significant even at extensions that went beyond the average contour length of a single DS molecule, which suggests the existence of a significant link between DS molecules.

Effect of chemical cross-linking on the mechanical properties of elastomeric peptides studied by single molecule force spectroscopy

Mechanical properties of animal tissues are mainly provided by the assembly of single elastomeric proteins into a complex network of filaments. Even if the overall elastic properties of such a reticulated structure depend on the mechanical characteristics of the constituents, it is not the only aspect to be considered. In addition, the aggregation mechanism has to be clarified to attain a full knowledge of the molecular basis of the elastic properties of natural nanostructured materials. This aim is even more crucial in the process of rational design of biomaterials with selected mechanical properties, in which not only the mechanics of single molecules but also of their assemblies has to be cared of. In this study, this aspect was approached by means of single molecule stretching experiments. In particular, the effect of chemical cross-linking on the mechanical properties of a naturally inspired elastomeric peptide was investigated. Accordingly, we observed that, in order to preserve the elastic properties of the single filament, the two strands of the dimer have to interact with each other. The results thus confirm that the influence of the aggregation process on the mechanical properties of a molecular assembly cannot be neglected.

Combined atomic force microscopy and fluorescence microscopy

The atomic force microscope (AFM) is a high-resolution scanning-probe instrument which has become an important tool for cellular and molecular biophysics in recent years, but lacks the time resolution and functional specificities offered by fluorescence microscopic techniques. The advantages of both methods may be exploited by combining and synchronizing them. In this paper, the biological applications of AFM, fluorescence, and their combinations are briefly reviewed, and the assembly and utilization of a spatially and temporally synchronized AFM and total internal reflection fluorescence microscope are described. The application of the method is demonstrated on a fluorescently labeled cell culture.

Optical manipulation for single-cell studies

In the last decade optical manipulation has evolved from a field of interest for physicists to a versatile tool widely used within life sciences. This has been made possible in particular due to the development of a large variety of imaging techniques that allow detailed information to be gained from investigations of single cells. The use of multiple optical traps has high potential within single-cell analysis since parallel measurements provide good statistics. Multifunctional optical tweezers are, for instance, used to study cell heterogeneity in an ensemble, and force measurements are used to investigate the mechanical properties of individual cells. Investigations of molecular motors and forces on the single-molecule level have led to discoveries that would have been difficult to make with other techniques. Optical manipulation has prospects within the field of cell signalling and tissue engineering. When combined with microfluidic systems the chemical environment of cells can be precisely controlled. Hence the influence of pH, salt concentration, drugs and temperature can be investigated in real time. Fast advancing technical developments of automated and user-friendly optical manipulation tools and cross-disciplinary collaboration will contribute to the routinely use of optical manipulation techniques within the life sciences.

Atomic force microscopy of the morphology and mechanical behaviour of barnacle cyprid footprint proteins at the nanoscale

Barnacles are a major biofouler of man-made underwater structures. Prior to settlement, cypris larvae explore surfaces by reversible attachment effected by a 'temporary adhesive'. During this exploratory behaviour, cyprids deposit proteinaceous 'footprints' of a putatively adhesive material. In this study, footprints deposited by Balanus amphitrite cyprids were probed by atomic force microscopy (AFM) in artificial sea water (ASW) on silane-modified glass surfaces. AFM images obtained in air yielded better resolution than in ASW and revealed the fibrillar nature of the secretion, suggesting that the deposits were composed of single proteinaceous nanofibrils, or bundles of fibrils. The force curves generated in pull-off force experiments in sea water consisted of regions of gradually increasing force, separated by sharp drops in extension force manifesting a characteristic saw-tooth appearance. Following the relaxation of fibrils stretched to high strains, force-distance curves in reverse stretching experiments could be described by the entropic elasticity model of a polymer chain. When subjected to relaxation exceeding 500 ms, extended footprint proteins refolded, and again showed saw-tooth unfolding peaks in subsequent force cycles. Observed rupture and hysteresis behaviour were explained by the 'sacrificial bond' model. Longer durations of relaxation (>5 s) allowed more sacrificial bond reformation and contributed to enhanced energy dissipation (higher toughness). The persistence length for the protein chains (L(P)) was obtained. At high elongation, following repeated stretching up to increasing upper strain limits, footprint proteins detached at total stretched length of 10 microm.

Interrogation of Single Synthetic Polymer Chains and Polysaccharides by AFM-Based Force Spectroscopy

This contribution reviews selected mechanical experiments on individual flexible macromolecules using single-molecule force spectroscopy (SMFS) based on atomic force microscopy. Focus is placed on the analysis of elasticity and conformational changes in single polymer chains upon variation of the external environment, as well as on conformational changes induced by the mechanical stress applied to individual macromolecular chains. Various experimental strategies regarding single-molecule manipulation and SMFS testing are discussed, as is theoretical analysis through single-chain elasticity models derived from statistical mechanics. Moreover, a complete record, reported to date, of the parameters obtained when applying the models to fit experimental results on synthetic polymers and polysaccharides is presented.

Downscaling functional bioassays by single-molecule techniques

In this short review we examine the potential of single-molecule assays in drug development and in basic research to provide new types of information at the smallest assay scales. A key advantage of many single-molecule assays is the requirement for conservative amounts of precious sample compared to conventional assays. In addition, they measure processes that are not observed directly in molecular ensembles. These advantages are balanced currently by difficulties in assay setup, preparation and equipment expense. However, future developments will ameliorate these drawbacks with the production of simpler, less expensive experimental systems for single-molecule assays.

Exploring mechanochemical processes in the cell with optical tweezers

Force and torque, stress and strain or work are examples of mechanical and elastic actions which are intimately linked to chemical reactions in the cell. Optical tweezers are a light-based method which allows the real-time manipulation of single molecules and cells to measure their interactions. We describe the technique, briefly reviewing the operating principles and the potential capabilities to the study of biological processes. Additional emphasis is given to the importance of fluctuations in biology and how single-molecule techniques allow access to them. We illustrate the applications by addressing experimental configurations and recent progresses in molecular and cell biology.

Visions for novel biophysical elucidations of extracellular matrix networks

The extracellular matrix consists of multifunctional molecules, which are composed of a large numbers of different domains. Clearly these domains and even the entire molecules do not function independently as isolated species, but interact with each other in large networks. In many cases specific regions of the networks may be considered as molecular machines in which the different molecules are arranged in highly defined spatial structures and act in a dynamic, concerted fashion. At present most structural information is limited to single molecules, and dynamics have been measured mainly for pairs of interacting partners in solution. Work needs to be extended to large integrated systems and the functions of molecular machines need to be explored. Electron tomography, fluorescence resonance energy transfer, and other biophysical techniques are very promising.

A toy model of polymer stretching

We present an extremely simplified model of multiple-domain polymer stretching in an atomic force microscopy experiment. We portray each module as a binary set of contacts and decompose the system energy into a harmonic term (the cantilever) and long-range interaction terms inside each domain. Exact equilibrium computations and Monte Carlo simulations qualitatively reproduce the experimental sawtooth pattern of force-extension profiles, corresponding (in our model) to first-order phase transitions. We study the influence of the coupling induced by the cantilever and the pulling speed on the relative heights of the force peaks. The results suggest that the increasing height of the critical force for subsequent unfolding events is an out-of-equilibrium effect due to a finite pulling speed. The dependence of the average unfolding force on the pulling speed is shown to reproduce the experimental logarithmic law.

Single-molecule experiments in biological physics: methods and applications

I review single-molecule experiments (SMEs) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SMEs it is possible to manipulate molecules one at a time and measure distributions describing molecular properties, characterize the kinetics of biomolecular reactions and detect molecular intermediates. SMEs provide additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SMEs it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level, emphasizing the importance of SMEs to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SMEs from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOTs), magnetic tweezers (MTs), biomembrane force probes (BFPs) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation) and proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SMEs to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.

Mechanical manipulation of Alzheimer’s amyloid β1–42 fibrils

The 39- to 42-residue-long amyloid beta-peptide (Abeta-peptide) forms filamentous structures in the neuritic plaques found in the neuropil of Alzheimer's disease patients. The assembly and deposition of Abeta-fibrils is one of the most important factors in the pathogenesis of this neurodegenerative disease. Although the structural analysis of amyloid fibrils is difficult, single-molecule methods may provide unique insights into their characteristics. In the present work, we explored the nanomechanical properties of amyloid fibrils formed from the full-length, most neurotoxic Abeta1-42 peptide, by manipulating individual fibrils with an atomic force microscope. We show that Abeta-subunit sheets can be mechanically unzipped from the fibril surface with constant forces in a reversible transition. The fundamental unzipping force (approximately 23 pN) was significantly lower than that observed earlier for fibrils formed from the Abeta1-40 peptide (approximately 33 pN), suggesting that the presence of the two extra residues (Ile and Ala) at the peptide's C-terminus result in a mechanical destabilization of the fibril. Deviations from the constant force transition may arise as a result of geometrical constraints within the fibril caused by its left-handed helical structure. The nanomechanical fingerprint of the Abeta1-42 is further influenced by the structural dynamics of intrafibrillar interactions.

Spatially and temporally synchronized atomic force and total internal reflection fluorescence microscopy for imaging and manipulating cells and biomolecules

The atomic force microscope is a high-resolution scanning-probe instrument which has become an important tool for cellular and molecular biophysics in recent years but lacks the time resolution and functional specificities offered by fluorescence microscopic techniques. To exploit the advantages of both methods, here we developed a spatially and temporally synchronized total internal reflection fluorescence and atomic force microscope system. The instrument, which we hereby call STIRF-AFM, is a stage-scanning device in which the mechanical and optical axes are coaligned to achieve spatial synchrony. At each point of the scan the sample topography (atomic force microscope) and fluorescence (photon count or intensity) information are simultaneously recorded. The tool was tested and validated on various cellular (monolayer cells in which actin filaments and intermediate filaments were fluorescently labeled) and biomolecular (actin filaments and titin molecules) systems. We demonstrate that with the technique, correlated sample topography and fluorescence images can be recorded, soft biomolecular systems can be mechanically manipulated in a targeted fashion, and the fluorescence of mechanically stretched titin can be followed with high temporal resolution.