The interplay between chemistry and mechanics in the transduction of a mechanical signal into a biochemical function

Decomposition of Forces in Protein: Methodology and General Properties

In contrast to the central role played by the structure of biomolecules, the complementary force-based view has received little attention in past studies. Here, we proposed a simple method for the force decomposition of multibody interactions and provided some techniques to analyze and visualize the general behavior of forces in proteins. It was shown that atomic forces fluctuate at a magnitude of about 3000 pN, which is huge in the context of cell biology. Remarkably, the average scalar product between atomic force and displacement universally approximates -3kBT. This is smaller by an order of magnitude than the simple product of their fluctuation magnitudes due to the unexpectedly weak correlation between the directions of force and displacement. The pairwise forces are highly anisotropic, with elongated fluctuation ellipsoids. Residue-residue forces can be attractive or repulsive (despite being more likely to be attractive), forming some kind of tensegrity structure stabilized by a complicated network of forces. Being able to understand and predict the interaction network provides a basis for rational drug design and uncovering molecular recognition mechanisms.

Understanding and Regulating Cell-Matrix Interactions Using Hydrogels of Designable Mechanical Properties

Similar to natural tissues, hydrogels contain abundant water, so they are considered as promising biomaterials for studying the influence of the mechanical properties of extracellular matrices (ECM) on various cell functions. In recent years, the growing research on cellular mechanical response has revealed that many cell functions, including cell spreading, migration, tumorigenesis and differentiation, are related to the mechanical properties of ECM. Therefore, how cells sense and respond to the extracellular mechanical environment has gained considerable attention. In these studies, hydrogels are widely used as the in vitro model system. Hydrogels of tunable stiffness, viscoelasticity, degradability, plasticity, and dynamical properties have been engineered to reveal how cells respond to specific mechanical features. In this review, we summarize recent process in this research direction and specifically focus on the influence of the mechanical properties of the ECM on cell functions, how cells sense and respond to the extracellular mechanical environment, and approaches to adjusting the stiffness of hydrogels.

Amphiphilic cationic cyclodextrin nanovesicles: a versatile cue for guiding cell adhesion

It is well known that amphiphilic cationic β-cyclodextrins (amβCDs) form nanovesicles able to release their cargo in aqueous solution upon applying different stimuli. In addition they can be selectively positioned onto substrates by unconventional soft lithography. This makes them a powerful tool for designing environments where different cues can be externally supplied to the cells helping to achieve good control of their fate. Lithographically controlled wetting (LCW) of amβCD nanovesicles loaded with fluorescein isothiocyanate (FITC), amβCD/FITC, has been used here to fabricate geometrically functionalized surfaces, thus achieving multiscale control of the cell environment. The amβCD functionalization was strongly influenced by the surface energy of the underlying substrates that, according to their hydrophobicity, orient the amβCD in a different way, thus "offering" different portions to the cells. The structure of the pattern was characterized both over large scales exploiting the FITC fluorescence and at the nanoscale by atomic force microscopy. Cell guidance and aCD/FITC cell internalization were demonstrated in human neuroblastoma SHSY5Y cells.

Effect of disulphide loop length on mechanochemical structural stability of macromolecules

Polymer chains folded with a single disulphide loop are shown to present distinct rates of mechanochemical fragmentation.

Can Dissipative Properties of Single Molecules Be Extracted from a Force Spectroscopy Experiment?

We performed dynamic force spectroscopy of single dextran and titin I27 molecules using small-amplitude and low-frequency (40-240 Hz) dithering of an atomic force microscope tip excited by a sine wave voltage fed onto the tip-carrying piezo. We show that for such low-frequency dithering experiments, recorded phase information can be unambiguously interpreted within the framework of a transparent theoretical model that starts from a well-known partial differential equation to describe the dithering of an atomic force microscope cantilever and a single molecule attached to its end system, uses an appropriate set of initial and boundary conditions, and does not exploit any implicit suggestions. We conclude that the observed phase (dissipation) signal is due completely to the dissipation related to the dithering of the cantilever itself (i.e., to the change of boundary conditions in the course of stretching). For both cases, only the upper bound of the dissipation of a single molecule has been established as not exceeding 3⋅10(-7)kg/s. We compare our results with previously reported measurements of the viscoelastic properties of single molecules, and we emphasize that extreme caution must be taken in distinguishing between the dissipation related to the stretched molecule and the dissipation that originates from the viscous damping of the dithered cantilever. We also present the results of an amplitude channel data analysis, which reveal that the typical values of the spring constant of a I27 molecule at the moment of module unfolding are equal to 4±1.5mN/m, and the typical values of the spring constant of dextran at the moment of chair-boat transition are equal to 30-50mN/m.

Stretching of red blood cells using an electro-optics trap

The stretching stiffness of Red Blood Cells (RBCs) was investigated using a combination of an AC dielectrophoretic apparatus and a single-beam optical tweezer. The experiments were performed at 10 MHz, a frequency high enough to avoid conductivity losses, but below the second turnover point between positive and negative dielectrophoresis. By measuring the geometrical parameters of single healthy human RBCs as a function of the applied voltage, the elastic modulus of RBCs was determined (µ = 1.80 ± 0.5 µN/m) and compared with similar values of the literature got by other techniques. The method is expected to be an easy-to-use, alternative tool to determine the mechano-elastic properties of living cells, and, on this basis, to distinguish healthy and diseased cells.

Calculation and visualization of atomistic mechanical stresses in nanomaterials and biomolecules

Many biomolecules have machine-like functions, and accordingly are discussed in terms of mechanical properties like force and motion. However, the concept of stress, a mechanical property that is of fundamental importance in the study of macroscopic mechanics, is not commonly applied in the biomolecular context. We anticipate that microscopical stress analyses of biomolecules and nanomaterials will provide useful mechanistic insights and help guide molecular design. To enable such applications, we have developed Calculator of Atomistic Mechanical Stress (CAMS), an open-source software package for computing atomic resolution stresses from molecular dynamics (MD) simulations. The software also enables decomposition of stress into contributions from bonded, nonbonded and Generalized Born potential terms. CAMS reads GROMACS topology and trajectory files, which are easily generated from AMBER files as well; and time-varying stresses may be animated and visualized in the VMD viewer. Here, we review relevant theory and present illustrative applications.

Polymer brushes: routes toward mechanosensitive surfaces

Soft nanotechnology involves both understanding the behavior of soft matter and using these components to build useful nanoscale structures and devices. However, molecular scale properties such as Brownian motion, diffusion, surface forces, and conformational flexibility dominate the chemistry and physics in soft nanotechnology, and therefore the design rules for generating functional structures from soft, self-assembled materials are still developing. Biological motors illustrate how wet nanoscale machines differ from their macroscopic counterparts. These molecular machines convert chemical energy into mechanical motion through an isothermal process: chemical reactions generate chemical potential and diffusion of ions, leading to conformational changes in proteins and the production of mechanical force. Because the actuation steps form a thermodynamic cycle that is reversible, the application of mechanical forces can also generate a chemical potential. This reverse process of mechanotransduction is the underlying sensing and signaling mechanism for a wide range of physiological phenomena such as hearing, touch, and growth of bone. Many of the biological systems that respond to mechanical stimuli do this via complex stress-activated ion channels or remodeling of the actin cytoskeleton. These biological actuation and mechanosensing processes are rather different from nano- and microelectromechanical systems (NEMS and MEMS) produced via semiconductor fabrication technologies. In our group, we are working to emulate biological mechanotransduction by systematically developing building blocks based on polymer brushes. In this soft nanotechnology approach to mechanotransduction, the chemical building blocks are polymer chains whose conformational changes and actuation can be investigated at a very basic level in polymer brushes, particularly polyelectrolyte brushes. Because these polymer brushes are easily accessible synthetically with control over parameters such as composition, chain length, and chain density, brushes provide a robust platform to study the coupling of mechanical forces with conformational changes of the chains. This Account provides an overview of our recent research in the design of mechanosensitive polymer brushes starting with the demonstration of nanoactuators and leading to our first attempts toward the creation of artificial mechanotransduction elements. As the brushes collapse in response to external triggers such as pH and ion concentration, polyelectrolyte brushes provide stimuli-responsive films. These collapse transitions lead to the generation of mechanical forces, and by reversing the chain of events, we designed a mechanically responsive film with a chemical output. Having reported an initial proof-of-principle experiment, we think that the stage is set for the preparation of more elaborate mechanosensitive surfaces.

Mechanochemistry: one bond at a time

Single-molecule force-clamp spectroscopy offers a novel platform for mechanically denaturing proteins by applying a constant force to a polyprotein. A powerful emerging application of the technique is that, by introducing a disulfide bond in each protein module, the chemical kinetics of disulfide bond cleavage under different stretching forces can be probed at the single-bond level. Even at forces much lower than that which can rupture the chemical bond, the breaking of the S-S bond at the presence of various chemical reducing agents is significantly accelerated. Our previous work demonstrated that the rate of thiol/disulfide exchange reaction is force-dependent and well-described by an Arrhenius term of the form r = A(exp((FΔx(r) - E(a))/k(B)T)[nucleophile]). From Arrhenius fits to the force dependency of the reduction rate, we measured the bond elongation parameter, Δx(r), along the reaction coordinate to the transition state of the S(N)2 reaction cleaved by different nucleophiles and enzymes, never before observed by any other technique. For S-S cleavage by various reducing agents, obtaining the Δx(r) value can help depicting the energy landscapes and elucidating the mechanisms of the reactions at the single-molecule level. Small nucleophiles, such as 1,4-dl-dithiothreitol (DTT), tris(2-carboxyethyl)phosphine (TCEP), and l-cysteine, react with the S-S bond with monotonically increasing rates under the applied force, while thioredoxin enzymes exhibit both stretching-favored and -resistant reaction-rate regimes. These measurements demonstrate the power of the single-molecule force-clamp spectroscopy approach in providing unprecedented access to chemical reactions.

Hooke: an open software platform for force spectroscopy

SUMMARY

Hooke is an open source, extensible software intended for analysis of atomic force microscope (AFM)-based single molecule force spectroscopy (SMFS) data. We propose it as a platform on which published and new algorithms for SMFS analysis can be integrated in a standard, open fashion, as a general solution to the current lack of a standard software for SMFS data analysis. Specific features and support for file formats are coded as independent plugins. Any user can code new plugins, extending the software capabilities. Basic automated dataset filtering and semi-automatic analysis facilities are included.

AVAILABILITY

Software and documentation are available at (http://code.google.com/p/hooke). Hooke is a free software under the GNU Lesser General Public License.

Conformational equilibria in monomeric alpha-synuclein at the single-molecule level

Human α-Synuclein (αSyn) is a natively unfolded protein whose aggregation into amyloid fibrils is involved in the pathology of Parkinson disease. A full comprehension of the structure and dynamics of early intermediates leading to the aggregated states is an unsolved problem of essential importance to researchers attempting to decipher the molecular mechanisms of αSyn aggregation and formation of fibrils. Traditional bulk techniques used so far to solve this problem point to a direct correlation between αSyn's unique conformational properties and its propensity to aggregate, but these techniques can only provide ensemble-averaged information for monomers and oligomers alike. They therefore cannot characterize the full complexity of the conformational equilibria that trigger the aggregation process. We applied atomic force microscopy–based single-molecule mechanical unfolding methodology to study the conformational equilibrium of human wild-type and mutant αSyn. The conformational heterogeneity of monomeric αSyn was characterized at the single-molecule level. Three main classes of conformations, including disordered and “β-like” structures, were directly observed and quantified without any interference from oligomeric soluble forms. The relative abundance of the “β-like” structures significantly increased in different conditions promoting the aggregation of αSyn: the presence of Cu²⁺, the pathogenic A30P mutation, and high ionic strength. This methodology can explore the full conformational space of a protein at the single-molecule level, detecting even poorly populated conformers and measuring their distribution in a variety of biologically important conditions. To the best of our knowledge, we present for the first time evidence of a conformational equilibrium that controls the population of a specific class of monomeric αSyn conformers, positively correlated with conditions known to promote the formation of aggregates. A new tool is thus made available to test directly the influence of mutations and pharmacological strategies on the conformational equilibrium of monomeric αSyn.

Natively unstructured proteins defy the classical “one sequence–one structure” paradigm of protein science. In pathological conditions, monomers of these proteins can aggregate in the cell, a process that underlies neurodegenerative diseases such as Alzheimer and Parkinson. A key step in the aggregation process—the formation of misfolded intermediates—remains obscure. To shed light on this process, we characterized the folding and conformational diversity of αSyn, a natively unstructured protein involved in Parkinson disease, by mechanically stretching single molecules of this protein and recording their mechanical properties. These experiments permitted us to observe directly and quantify three main classes of conformations that, under in vitro physiological conditions, exist simultaneously in the αSyn sample. We found that one class of conformations, “β-like” structures, is directly related to αSyn aggregation. In fact, their relative abundance increases drastically in three different conditions known to promote the formation of αSyn fibrils. We expect that a critical concentration of αSyn with a “β-like” structure must be reached to trigger fibril formation. This critical concentration is therefore controlled by a chemical equilibrium. Novel pharmacological strategies can now be tailored to act upstream, before the aggregation process ensues, by targeting this equilibrium. To this end, single-molecule force spectroscopy can be an effective tool to tailor and test new pharmacological agents.

A single-molecule study detects structured and unstructured conformers in equilibrium in monomeric α-synuclein. The β-like conformers increase with pathological mutations and under other conditions known to promote aggregation.