Hidden complexity in the mechanical properties of titin

Interdomain Linker Effect on the Mechanical Stability of Ig Domains in Titin

Titin is the largest protein in humans, composed of more than one hundred immunoglobulin (Ig) domains, and plays a critical role in muscle’s passive elasticity. Thus, the molecular design of this giant polyprotein is responsible for its mechanical function. Interestingly, most of these Ig domains are connected directly with very few interdomain residues/linker, which suggests such a design is necessary for its mechanical stability. To understand this design, we chose six representative Ig domains in titin and added nine glycine residues (9G) as an artificial interdomain linker between these Ig domains. We measured their mechanical stabilities using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) and compared them to the natural sequence. The AFM results showed that the linker affected the mechanical stability of Ig domains. The linker mostly reduces its mechanical stability to a moderate extent, but the opposite situation can happen. Thus, this effect is very complex and may depend on each particular domain’s property.

Single-Molecule Force Spectroscopy Studies of Missense Titin Mutations That Are Likely Causing Cardiomyopathy

The giant muscle protein titin plays important roles in heart function. Mutations in titin have emerged as a major cause of familial cardiomyopathy. Missense mutations have been identified in cardiomyopathy patients; however, it is challenging to distinguish disease-causing mutations from benign ones. Given the importance of titin mechanics in heart function, it is critically important to elucidate the mechano-phenotypes of cardiomyopathy-causing mutations found in the elastic I-band part of cardiac titin. Using single-molecule atomic force microscopy (AFM) and equilibrium chemical denaturation, we investigated the mechanical and thermodynamic effects of two missense mutations, R57C-I94 and S22P-I84, found in the elastic I-band part of cardiac titin that were predicted to be likely causing cardiomyopathy by bioinformatics analysis. Our AFM results showed that mutation R57C had a significant destabilization effect on the I94 module. R57C reduced the mechanical unfolding force of I94 by ∼30-40 pN, accelerated the unfolding kinetics, and decelerated the folding. These effects collectively increased the unfolding propensity of I94, likely resulting in altered titin elasticity. In comparison, S22P led to only modest destabilization of I84, with a decrease in unfolding force by ∼10 pN. It is unlikely that such a modest destabilization would lead to a change in titin elasticity. These results will serve as the first step toward elucidating mechano-phenotypes of cardiomyopathy-causing mutations in the elastic I-band.

Dependence of Work on the Pulling Speed in Mechanical Ligand Unbinding

In single-molecule force spectroscopy, the rupture force F_max required for mechanical unfolding of a biomolecule or for pulling a ligand out of a binding site depends on the pulling speed V and, in the linear Bell-Evans regime, F_max ∼ ln(V). Recently, it has been found that non-equilibrium work W is better than F_max in describing relative ligand binding affinity, but the dependence of W on V remains unknown. In this paper, we developed an analytical theory showing that in the linear regime, W ∼ c₁ ln(V) + c₂ ln²(V), where c₁ and c₂ are constants. This quadratic dependence was also confirmed by all-atom steered molecular dynamics simulations of protein-ligand complexes. Although our theory was developed for ligand unbinding, it is also applicable to other processes, such as mechanical unfolding of proteins and other biomolecules, due to its universality.

Reconstruction of mechanical unfolding and refolding pathways of proteins with atomic force spectroscopy and computer simulations

Most proteins in proteomes are large, typically consist of more than one domain and are structurally complex. This often makes studying their mechanical unfolding pathways challenging. Proteins composed of tandem repeat domains are a subgroup of multi-domain proteins that, when stretched, display a saw-tooth pattern in their mechanical unfolding force extension profiles due to their repetitive structure. However, the assignment of force peaks to specific repeats undergoing mechanical unraveling is complicated because all repeats are similar and they interact with their neighbors and form a contiguous tertiary structure. Here, we describe in detail a combination of experimental and computational single-molecule force spectroscopy methods that proved useful for examining the mechanical unfolding and refolding pathways of ankyrin repeat proteins. Specifically, we explain and delineate the use of atomic force microscope-based single molecule force spectroscopy (SMFS) to record the mechanical unfolding behavior of ankyrin repeat proteins and capture their unusually strong refolding propensity that is responsible for generating impressive refolding force peaks. We also describe Coarse Grain Steered Molecular Dynamic (CG-SMD) simulations which complement the experimental observations and provide insights in understanding the unfolding and refolding of these proteins. In addition, we advocate the use of novel coiled-coils-based mechanical polypeptide probes which we developed to demonstrate the vectorial character of folding and refolding of these repeat proteins. The combination of AFM-based SMFS on native and CC-equipped proteins with CG-SMD simulations is powerful not only for ankyrin repeat polypeptides, but also for other repeat proteins and more generally to various multidomain, non-repetitive proteins with complex topologies.

The Non-dominant AAA+ Ring in the ClpAP Protease Functions as an Anti-stalling Motor to Accelerate Protein Unfolding and Translocation

ATP-powered unfoldases containing D1 and D2 AAA+ rings play important roles in protein homeostasis, but uncertainty about the function of each ring remains. Here we use single-molecule optical tweezers to assay mechanical unfolding and translocation by a variant of the ClpAP protease containing an ATPase-inactive D1 ring. This variant displays substantial mechanical defects in both unfolding and translocation of protein substrates. Notably, when D1 is hydrolytically inactive, ClpAP often stalls for times as long as minutes, and the substrate can back-slip through the enzyme when ATP concentrations are low. The inactive D1 variant also has more difficulty traveling in the N-to-C direction on a polypeptide track than it does moving in a C-to-N direction. These results indicate that D1 normally functions as an auxiliary/regulatory motor to promote uninterrupted enzyme advancement that is fueled largely by the D2 ring.

Mechanical Unfolding of Single Polyubiquitin Molecules Reveals Evidence of Dynamic Disorder

Mechanical unfolding of single polyubiquitin molecules subjected to a constant stretching force showed nonexponentiality in the measured probability density of unfolding (waiting time distribution) and the survival probability of the folded state during the course of the measurements. These observations explored the relevance of disorder present in the system under study with implications for a static disorder approach to rationalize the experimental results. Here, an approach for dynamic disorder is presented based on Zwanzig's fluctuating bottleneck (FB) model, in which the rate of the reaction is controlled by the passage through the cross-sectional area of the bottleneck. The radius of the latter undergoes stochastic fluctuations that in turn is described in terms of the end-to-end distance fluctuations of the Rouse-like dynamics using a non-Markovian generalized Langevin equation with a memory kernel and Gaussian colored noise. Our results are comprised of analytical expressions for the survival probability and waiting time distribution, which show excellent agreement with the experimental data throughout the range of the applied forces. In addition, by fitting the survival probabilities at different stretching forces, we quantify two system parameters, namely, the average free energy ΔG _av and the average distance to the transition state Δx _av, both perfectly recovered the experimental estimates. These agreements validate the present model of polymer dynamics, which captures the very essence of dynamic disorder in single-molecule pulling experiments.

Monitoring Unfolding of Titin I27 Single and Bi Domain with High-Pressure NMR Spectroscopy

A complete description of the pathways and mechanisms of protein folding requires a detailed structural and energetic characterization of the folding energy landscape. Simulations, when corroborated by experimental data yielding global information on the folding process, can provide this level of insight. Molecular dynamics (MD) has often been combined with force spectroscopy experiments to decipher the unfolding mechanism of titin immunoglobulin-like single or multidomain, the giant multimodular protein from sarcomeres, yielding information on the sequential events during titin unfolding under stretching. Here, we used high-pressure NMR to monitor the unfolding of titin I27 Ig-like single domain and tandem. Because this method brings residue-specific information on the folding process, it can provide quasiatomic details on this process without the help of MD simulations. Globally, the results of our high-pressure analysis are in agreement with previous results obtained by the combination of experimental measurements and MD simulation and/or protein engineering, although the intermediate folding state caused by the early detachment of the AB β-sheet, often reported in previous works based on MD or force spectroscopy, cannot be detected. On the other hand, the A'G parallel β-sheet of the β-sandwich has been confirmed as the Achilles heel of the three-dimensional scaffold: its disruption yields complete unfolding with very similar characteristics (free energy, unfolding volume, kinetics rate constants) for the two constructs.

Mechanical unfolding of spectrin reveals a super-exponential dependence of unfolding rate on force

We investigated the mechanical unfolding of single spectrin molecules over a broad range of loading rates and thus unfolding forces by combining magnetic tweezers with atomic force microscopy. We find that the mean unfolding force increases logarithmically with loading rate at low loading rates, but the increase slows at loading rates above 1pN/s. This behavior indicates an unfolding rate that increases exponentially with the applied force at low forces, as expected on the basis of one-dimensional models of protein unfolding. At higher forces, however, the increase of the unfolding rate with the force becomes faster than exponential, which may indicate anti-Hammond behavior where the structures of the folded and transition states become more different as their free energies become more similar. Such behavior is rarely observed and can be explained by either a change in the unfolding pathway or as a reflection of a multidimensional energy landscape of proteins under force.

Folding pathway of an Ig domain is conserved on and off the ribosome

Most proteins need to fold into a specific 3D structure to function. The mechanism by which isolated proteins fold has been thoroughly studied by experiment and theory. However, in the cell proteins do not fold in isolation but are synthesized as linear chains by the ribosome during translation. It is therefore natural to ask at which point during synthesis proteins fold, and whether this differs from the folding of isolated protein molecules. By studying folding of a well-characterized protein domain, titin I27, stalled at different points during translation, we show that it already folds in the mouth of the ribosome exit tunnel and that the mechanism is almost identical to that of the isolated protein.

Proteins that fold cotranslationally may do so in a restricted configurational space, due to the volume occupied by the ribosome. How does this environment, coupled with the close proximity of the ribosome, affect the folding pathway of a protein? Previous studies have shown that the cotranslational folding process for many proteins, including small, single domains, is directly affected by the ribosome. Here, we investigate the cotranslational folding of an all-β Ig domain, titin I27. Using an arrest peptide-based assay and structural studies by cryo-EM, we show that I27 folds in the mouth of the ribosome exit tunnel. Simulations that use a kinetic model for the force dependence of escape from arrest accurately predict the fraction of folded protein as a function of length. We used these simulations to probe the folding pathway on and off the ribosome. Our simulations—which also reproduce experiments on mutant forms of I27—show that I27 folds, while still sequestered in the mouth of the ribosome exit tunnel, by essentially the same pathway as free I27, with only subtle shifts of critical contacts from the C to the N terminus.

Switching of the folding-energy landscape governs the allosteric activation of protein kinase A

Protein kinases are dynamic molecular switches that sample multiple conformational states. The regulatory subunit of PKA harbors two cAMP-binding domains [cyclic nucleotide-binding (CNB) domains] that oscillate between inactive and active conformations dependent on cAMP binding. The cooperative binding of cAMP to the CNB domains activates an allosteric interaction network that enables PKA to progress from the inactive to active conformation, unleashing the activity of the catalytic subunit. Despite its importance in the regulation of many biological processes, the molecular mechanism responsible for the observed cooperativity during the activation of PKA remains unclear. Here, we use optical tweezers to probe the folding cooperativity and energetics of domain communication between the cAMP-binding domains in the apo state and bound to the catalytic subunit. Our study provides direct evidence of a switch in the folding-energy landscape of the two CNB domains from energetically independent in the apo state to highly cooperative and energetically coupled in the presence of the catalytic subunit. Moreover, we show that destabilizing mutational effects in one CNB domain efficiently propagate to the other and decrease the folding cooperativity between them. Taken together, our results provide a thermodynamic foundation for the conformational plasticity that enables protein kinases to adapt and respond to signaling molecules.

Structural-elastic determination of the force-dependent transition rate of biomolecules

The force-dependent unfolding/refolding of protein domains and ligand-receptor association/dissociation are crucial for mechanosensitive functions, while many aspects of how force affects the transition rate still remain poorly understood. Here, we report a new analytical expression of the force-dependent rate of molecules for transitions overcoming a single barrier. Unlike previous models derived in the framework of Kramers theory that requires a presumed one-dimensional free energy landscape, our model is derived based on the structural-elastic properties of molecules which are not restricted by the shape and dimensionality of the underlying free energy landscape. Importantly, the parameters of this model provide direct information on the structural-elastic features of the molecules between their transition and initial states. We demonstrate the applications of this model by applying it to explain force-dependent transition kinetics for several molecules and predict the structural-elastic properties of the transition states of these molecules.

History, rare, and multiple events of mechanical unfolding of repeat proteins

Mechanical unfolding of proteins consisting of repeat domains is an excellent tool to obtain large statistics. Force spectroscopy experiments using atomic force microscopy on proteins presenting multiple domains have revealed that unfolding forces depend on the number of folded domains (history) and have reported intermediate states and rare events. However, the common use of unspecific attachment approaches to pull the protein of interest holds important limitations to study unfolding history and may lead to discarding rare and multiple probing events due to the presence of unspecific adhesion and uncertainty on the pulling site. Site-specific methods that have recently emerged minimize this uncertainty and would be excellent tools to probe unfolding history and rare events. However, detailed characterization of these approaches is required to identify their advantages and limitations. Here, we characterize a site-specific binding approach based on the ultrastable complex dockerin/cohesin III revealing its advantages and limitations to assess the unfolding history and to investigate rare and multiple events during the unfolding of repeated domains. We show that this approach is more robust, reproducible, and provides larger statistics than conventional unspecific methods. We show that the method is optimal to reveal the history of unfolding from the very first domain and to detect rare events, while being more limited to assess intermediate states. Finally, we quantify the forces required to unfold two molecules pulled in parallel, difficult when using unspecific approaches. The proposed method represents a step forward toward more reproducible measurements to probe protein unfolding history and opens the door to systematic probing of rare and multiple molecule unfolding mechanisms.

Multi-modal mechanophores based on cinnamate dimers

Mechanochemistry offers exciting opportunities for molecular-level engineering of stress-responsive properties of polymers. Reactive sites, sometimes called mechanophores, have been reported to increase the material toughness, to make the material mechanochromic or optically healable. Here we show that macrocyclic cinnamate dimers combine these productive stress-responsive modes. The highly thermally stable dimers dissociate on the sub-second timescale when subject to a stretching force of 1-2 nN (depending on isomer). Stretching a polymer of the dimers above this force more than doubles its contour length and increases the strain energy that the chain absorbs before fragmenting by at least 600 kcal per mole of monomer. The dissociation produces a chromophore and dimers are reformed upon irradiation, thus allowing optical healing of mechanically degraded parts of the material. The mechanochemical kinetics, single-chain extensibility, toughness and potentially optical properties of the dissociation products are tunable by synthetic modifications.

Studying the mechanical responses of proteins using magnetic tweezers

The mechanical stability of proteins has been extensively studied using AFM as a single-molecule force spectroscopy method. While this has led to many important results, these studies have been mainly limited to fast unfolding at a high-force regime due to the rapid mechanical drift in most AFM stretching experiments. Therefore, there is a gap between the knowledge obtained at a high-force regime and the mechanical properties of proteins at a lower force regime which is often more physiologically relevant. Recent studies have demonstrated that this gap can be addressed by stretching single protein molecules using magnetic tweezers, due to the excellent mechanical stability this technology offers. Here we review magnetic tweezers technology and its current application in studies of the force-dependent stability and interactions of proteins.

High-speed atomic force microscopy imaging of live mammalian cells

Direct imaging of morphological dynamics of live mammalian cells with nanometer resolution under physiological conditions is highly expected, but yet challenging. High-speed atomic force microscopy (HS-AFM) is a unique technique for capturing biomolecules at work under near physiological conditions. However, application of HS-AFM for imaging of live mammalian cells was hard to be accomplished because of collision between a huge mammalian cell and a cantilever during AFM scanning. Here, we review our recent improvements of HS-AFM for imaging of activities of live mammalian cells without significant damage to the cell. The improvement of an extremely long (~3 μm) AFM tip attached to a cantilever enables us to reduce severe damage to soft mammalian cells. In addition, a combination of HS-AFM with simple fluorescence microscopy allows us to quickly locate the cell in the AFM scanning area. After these improvements, we demonstrate that developed HS-AFM for live mammalian cells is possible to image morphogenesis of filopodia, membrane ruffles, pits open-close formations, and endocytosis in COS-7, HeLa cells as well as hippocampal neurons.

Probing Small Molecule Binding to Unfolded Polyprotein Based on its Elasticity and Refolding

Unfolded protein, a disordered structure found before folding of newly synthesized protein or after protein denaturation, is a substrate for binding by many cellular factors such as heat-stable proteins, chaperones, and many small molecules. However, it is challenging to directly probe such interactions in physiological solution conditions because proteins are largely in their folded state. In this work we probed small molecule binding to mechanically unfolded polyprotein using sodium dodecyl sulfate (SDS) as an example. The effect of binding is quantified based on changes in the elasticity and refolding of the unfolded polyprotein in the presence of SDS. We show that this single-molecule mechanical detection of binding to unfolded polyprotein can serve, to our knowledge, as a novel label-free assay with a great potential to study many factors that interact with unfolded protein domains, which underlie many important biological processes.

Transient misfolding dominates multidomain protein folding

Neighbouring domains of multidomain proteins with homologous tandem repeats have divergent sequences, probably as a result of evolutionary pressure to avoid misfolding and aggregation, particularly at the high cellular protein concentrations. Here we combine microfluidic-mixing single-molecule kinetics, ensemble experiments and molecular simulations to investigate how misfolding between the immunoglobulin-like domains of titin is prevented. Surprisingly, we find that during refolding of tandem repeats, independent of sequence identity, more than half of all molecules transiently form a wide range of misfolded conformations. Simulations suggest that a large fraction of these misfolds resemble an intramolecular amyloid-like state reported in computational studies. However, for naturally occurring neighbours with low sequence identity, these transient misfolds disappear much more rapidly than for identical neighbours. We thus propose that evolutionary sequence divergence between domains is required to suppress the population of long-lived, potentially harmful misfolded states, whereas large populations of transient misfolded states appear to be tolerated.

Single molecule kinetics investigations and molecular simulations are useful tools in elucidating protein assembly mechanisms. Here, the authors use these to show that even naturally occurring tandem repeats undergo transient misfolding and that assembly is much more complex than we previously understood.

Polyproteins in structural biology

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Structures have been determined for natural and recombinant polyproteins.

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Native HIV Gag polyprotein architecture was revealed by cryo-EM of immature capsids.

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Recombinant polyprotein technology has resolved sample preparation bottlenecks.

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The high-resolution structure of influenza polymerase has been solved.

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Single-molecule analysis of polyproteins revealed their folding characteristics.

Polyproteins are chains of covalently conjoined smaller proteins that occur in nature as versatile means to organize the proteome of viruses including HIV. During maturation, viral polyproteins are typically cleaved into the constituent proteins with different biological functions by highly specific proteases, and structural analyses at defined stages of this maturation process can provide clues for antiviral intervention strategies. Recombinant polyproteins that use similar mechanisms are emerging as powerful tools for producing hitherto inaccessible protein targets such as the influenza polymerase, for high-resolution structure determination by X-ray crystallography. Conversely, covalent linking of individual protein subunits into single polypeptide chains are exploited to overcome sample preparation bottlenecks. Moreover, synthetic polyproteins provide a promising tool to dissect dynamic folding of polypeptide chains into three-dimensional architectures in single-molecule structure analysis by atomic force microscopy (AFM). The recent use of natural and synthetic polyproteins in structural biology and major achievements are highlighted in this contribution.

Higher impact energy in traumatic brain injury interferes with noncovalent and covalent bonds resulting in cytotoxic brain tissue edema as measured with computational simulation

BACKGROUND

Cytotoxic brain tissue edema is a complicated secondary consequence of ischemic injury following cerebral diseases such as traumatic brain injury and stroke. To some extent the pathophysiological mechanisms are known, but far from completely. In this study, a hypothesis is proposed in which protein unfolding and perturbation of nucleotide structures participate in the development of cytotoxic edema following traumatic brain injury (TBI).

METHODS

An advanced computational simulation model of the human head was used to simulate TBI. The consequences of kinetic energy transfer following an external dynamic impact were analyzed including the intracranial pressure (ICP), strain level, and their potential influences on the noncovalent and covalent bonds in folded protein structures.

RESULTS

The result shows that although most of the transferred kinetic energy is absorbed in the skin and three bone layers, there is a substantial amount of energy reaching the gray and white matter. The kinetic energy from an external dynamic impact has the theoretical potential to interfere not only with noncovalent but also covalent bonds when high enough. The induced mechanical strain and pressure may further interfere with the proteins, which accumulate water molecules into the interior of the hydrophobic structures of unfolded proteins. Simultaneously, the noncovalent energy-rich bonds in nucleotide adenosine-triphosphates may be perturbed as well.

CONCLUSIONS

Based on the analysis of the numerical simulation data, the kinetic energy from an external dynamic impact has the theoretical potential to interfere not only with noncovalent, but also with covalent bonds when high enough. The subsequent attraction of increased water molecules into the unfolded protein structures and disruption of adenosine-triphosphate bonds could to some extent explain the etiology to cytotoxic edema.

Thermodynamics of force-dependent folding and unfolding of small protein and nucleic acid structures

In this paper, we outline the theoretical framework for understanding the equilibrium force-dependent folding and unfolding transitions of protein domains and small nucleic acid structures, both having small rigid folded structures and highly flexible unfolded polymeric chain conformations. A complete statistical description of the state described by the probability function ρ(ξ)(n,x), is obtained, where n is an index denoting the structural state, and x is the extension of the molecule. ξ denotes an external constraint applied to the molecule, which is either a constant force or a harmonic spring attached to one end of the molecule. The extension probability distribution regardless of the structural state: , the free energy landscape: -kBT ln(ρ(ξ)(x)), and the probability of the states regardless of the extension: , are analyzed using the force-dependent structural transitions of the classic titin I27 domain as an example. The impact of different external constraints is also discussed.

Dynamics of equilibrium folding and unfolding transitions of titin immunoglobulin domain under constant forces

The mechanical stability of force-bearing proteins is crucial for their functions. However, slow transition rates of complex protein domains have made it challenging to investigate their equilibrium force-dependent structural transitions. Using ultra stable magnetic tweezers, we report the first equilibrium single-molecule force manipulation study of the classic titin I27 immunoglobulin domain. We found that individual I27 in a tandem repeat unfold/fold independently. We obtained the force-dependent free energy difference between unfolded and folded I27 and determined the critical force (∼5.4 pN) at which unfolding and folding have equal probability. We also determined the force-dependent free energy landscape of unfolding/folding transitions based on measurement of the free energy cost of unfolding. In addition to providing insights into the force-dependent structural transitions of titin I27, our results suggest that the conformations of titin immunoglobulin domains can be significantly altered during low force, long duration muscle stretching.

Long-tip high-speed atomic force microscopy for nanometer-scale imaging in live cells

Visualization of morphological dynamics of live cells with nanometer resolution under physiological conditions is highly desired, but challenging. It has been demonstrated that high-speed atomic force microscopy is a powerful technique for visualizing dynamics of biomolecules under physiological conditions. However, application of high-speed atomic force microscopy for imaging larger objects such as live mammalian cells has been complicated because of the collision between the cantilever and samples. Here, we demonstrate that attaching an extremely long (~3 μm) and thin (~5 nm) tip by amorphous carbon to the cantilever allows us to image the surface structure of live cells with the spatiotemporal resolution of nanometers and seconds. We demonstrate that long-tip high-speed atomic force microscopy is capable of imaging morphogenesis of filopodia, membrane ruffles, pit formation, and endocytosis in COS-7, HeLa cells and hippocampal neurons.

Direct observation of multimer stabilization in the mechanical unfolding pathway of a protein undergoing oligomerization

Understanding how protein oligomerization affects the stability of monomers in self-assembled structures is crucial to the development of new protein-based nanomaterials and protein cages for drug delivery. Here, we use single-molecule force spectroscopy (AFM-SMFS), protein engineering, and computer simulations to evaluate how dimerization and tetramerization affects the stability of the monomer of Streptavidin, a model homotetrameric protein. The unfolding force directly relates to the folding stability, and we find that monomer of Streptavidin is mechanically stabilized by 40% upon dimerization, and that it is stabilized an additional 24% upon tetramerization. We also find that biotin binding increases stability by another 50% as compared to the apo-tetrameric form. We used the distribution of unfolding forces to extract properties of the underlying energy landscape and found that the distance to the transition state is decreased and the barrier height is increased upon multimerization. Finally, we investigated the origin of the strengthening by ligand binding. We found that, rather than being strengthened through intramolecular contacts, it is strengthened due to the contacts provided by the biotin-binding loop that crosses the interface between the dimers.

Induction of insulin-like growth factor 1 splice forms by subfragments of myofibrillar proteins

Expression of insulin-like growth factor 1 (IGF-1) mRNAs splice forms was recently shown to be stimulated by myofibrillar proteins released from the damaged muscle. In this study, we report that individual subfragments of titin and myomesin composed of Fn type III and Ig-like domains can activate expression of two IGF-1 splice forms in cultured myoblasts, both at protein and mRNA levels. Competition studies showed that each of the domain-types interacts with its own receptor. Induction of IGF-1 expression caused by domains of different types showed dissimilar sensitivity to inhibitors of regulatory cascades. The effect of Fn type III domains was more sensitive to inhibition of Ca(2+)/calmodulin dependent protein kinase, whereas the effect of Ig-like domains showed greater sensitivity to the inhibition of the adenylyl cyclase-cAMP-PKA pathway.

A structure-based model fails to probe the mechanical unfolding pathways of the titin I27 domain

We discuss the use of a structure based Cα-Go model and Langevin dynamics to study in detail the mechanical properties and unfolding pathway of the titin I27 domain. We show that a simple Go-model does detect correctly the origin of the mechanical stability of this domain. The unfolding free energy landscape parameters x(u) and ΔG(‡), extracted from dependencies of unfolding forces on pulling speeds, are found to agree reasonably well with experiments. We predict that above v = 10(4) nm/s the additional force-induced intermediate state is populated at an end-to-end extension of about 75 Å. The force-induced switch in the unfolding pathway occurs at the critical pulling speed v(crit) ≈ 10(6)-10(7) nm/s. We argue that this critical pulling speed is an upper limit of the interval where Bell's theory works. However, our results suggest that the Go-model fails to reproduce the experimentally observed mechanical unfolding pathway properly, yielding an incomplete picture of the free energy landscape. Surprisingly, the experimentally observed intermediate state with the A strand detached is not populated in Go-model simulations over a wide range of pulling speeds. The discrepancy between simulation and experiment is clearly seen from the early stage of the unfolding process which shows the limitation of the Go model in reproducing unfolding pathways and deciphering the complete picture of the free energy landscape.

Reconstructing folding energy landscapes by single-molecule force spectroscopy

Folding may be described conceptually in terms of trajectories over a landscape of free energies corresponding to different molecular configurations. In practice, energy landscapes can be difficult to measure. Single-molecule force spectroscopy (SMFS), whereby structural changes are monitored in molecules subjected to controlled forces, has emerged as a powerful tool for probing energy landscapes. We summarize methods for reconstructing landscapes from force spectroscopy measurements under both equilibrium and nonequilibrium conditions. Other complementary, but technically less demanding, methods provide a model-dependent characterization of key features of the landscape. Once reconstructed, energy landscapes can be used to study critical folding parameters, such as the characteristic transition times required for structural changes and the effective diffusion coefficient setting the timescale for motions over the landscape. We also discuss issues that complicate measurement and interpretation, including the possibility of multiple states or pathways and the effects of projecting multiple dimensions onto a single coordinate.

Single-molecule force spectroscopy reveals force-enhanced binding of calcium ions by gelsolin

Force is increasingly recognized as an important element in controlling biological processes. Forces can deform native protein conformations leading to protein-specific effects. Protein–protein binding affinities may be decreased, or novel protein–protein interaction sites may be revealed, on mechanically stressing one or more components. Here we demonstrate that the calcium-binding affinity of the sixth domain of the actin-binding protein gelsolin (G6) can be enhanced by mechanical force. Our kinetic model suggests that the calcium-binding affinity of G6 increases exponentially with force, up to the point of G6 unfolding. This implies that gelsolin may be activated at lower calcium ion levels when subjected to tensile forces. The demonstration that cation–protein binding affinities can be force-dependent provides a new understanding of the complex behaviour of cation-regulated proteins in stressful cellular environments, such as those found in the cytoskeleton-rich leading edge and at cell adhesions.

The application of force can influence biological processes such as ligand and protein–protein binding, with mechanical stress typically hindering such interactions. Here, the authors use atomic force microscopy to show that the binding of calcium to gelsolin can be improved under stress.

Mechanisms of enhanced force production in lengthening (eccentric) muscle contractions

In contrast to isometric and shortening contractions, many observations made on actively lengthening muscles cannot be readily explained with the sliding filament and cross-bridge theory. Specifically, residual force enhancement, the persistent increase in force following active muscle lengthening, beyond what one would expect based on muscle length, has not been explained satisfactorily. Here, we summarize the experimental evidence on residual force enhancement, critically evaluate proposed mechanisms for the residual force enhancement, and propose a mechanism for residual force enhancement that explains all currently agreed upon experimental observations. The proposed mechanism is based on the engagement of the structural protein titin upon muscle activation and an increase in titin's resistance to active compared with passive stretching. This change in resistance from the passive to the active state is suggested to be based on 1) calcium binding by titin upon activation, 2) binding of titin to actin upon activation, and 3) as a consequence of titin-actin binding—a shift toward stiffer titin segments that are used in active compared with passive muscle elongation. Although there is some experimental evidence for the proposed mechanism, it must be stressed that much of the details proposed here remain unclear and should provide ample research opportunities for scientists in the future. Nevertheless, the proposed mechanism for residual force enhancement explains all basic findings in this area of research.

Model studies of force-dependent kinetics of multi-barrier reactions

According to transition state theory, the rate of a reaction that traverses multiple energy barriers is determined by the least stable (rate-determining) transition state. The preceding ('inner') energy barriers are kinetically 'invisible' but mechanistically significant. Here we show experimentally and computationally that the reduction rate of organic disulphides by phosphines in water, which in the absence of force proceeds by an equilibrium formation of a thiophosphonium intermediate, measured as a function of force applied on the disulphide moiety yields a usefully accurate estimate of the height of the inner barrier. We apply varying stretching force to the disulphide by incorporating it into a series of increasingly strained macrocycles. This force accelerates the reduction, even though the strain-free rate-determining step is orthogonal to the pulling direction. The observed rate-force correlation is consistent with the simplest model of force-dependent kinetics of a multi-barrier reaction.

Improving single molecule force spectroscopy through automated real-time data collection and quantification of experimental conditions

The benefits of single molecule force spectroscopy (SMFS) clearly outweigh the challenges which include small sample sizes, tedious data collection and introduction of human bias during the subjective data selection. These difficulties can be partially eliminated through automation of the experimental data collection process for atomic force microscopy (AFM). Automation can be accomplished using an algorithm that triages usable force-extension recordings quickly with positive and negative selection. We implemented an algorithm based on the windowed fast Fourier transform of force-extension traces that identifies peaks using force-extension regimes to correctly identify usable recordings from proteins composed of repeated domains. This algorithm excels as a real-time diagnostic because it involves <30 ms computational time, has high sensitivity and specificity, and efficiently detects weak unfolding events. We used the statistics provided by the automated procedure to clearly demonstrate the properties of molecular adhesion and how these properties change with differences in the cantilever tip and protein functional groups and protein age.

High-speed AFM and applications to biomolecular systems

Directly observing individual protein molecules in action at high spatiotemporal resolution has long been a holy grail for biological science. This is because we long have had to infer how proteins function from the static snapshots of their structures and dynamic behavior of optical makers attached to the molecules. This limitation has recently been removed to a large extent by the materialization of high-speed atomic force microscopy (HS-AFM). HS-AFM allows us to directly visualize the structure dynamics and dynamic processes of biological molecules in physiological solutions, at subsecond to sub-100-ms temporal resolution, without disturbing their function. In fact, dynamically acting molecules such as myosin V walking on an actin filament and bacteriorhodopsin in response to light are successfully visualized. In this review, we first describe theoretical considerations for the highest possible imaging rate of this new microscope, and then highlight recent imaging studies. Finally, the current limitation and future challenges to explore are described.

Mechanical unfolding of human telomere G-quadruplex DNA probed by integrated fluorescence and magnetic tweezers spectroscopy

Single-molecule techniques facilitate analysis of mechanical transitions within nucleic acids and proteins. Here, we describe an integrated fluorescence and magnetic tweezers instrument that permits detection of nanometer-scale DNA structural rearrangements together with the application of a wide range of stretching forces to individual DNA molecules. We have analyzed the force-dependent equilibrium and rate constants for telomere DNA G-quadruplex (GQ) folding and unfolding, and have determined the location of the transition state barrier along the well-defined DNA-stretching reaction coordinate. Our results reveal the mechanical unfolding pathway of the telomere DNA GQ is characterized by a short distance (<1 nm) to the transition state for the unfolding reaction. This mechanical unfolding response reflects a critical contribution of long-range interactions to the global stability of the GQ fold, and suggests that telomere-associated proteins need only disrupt a few base pairs to destabilize GQ structures. Comparison of the GQ unfolded state with a single-stranded polyT DNA revealed the unfolded GQ exhibits a compacted non-native conformation reminiscent of the protein molten globule. We expect the capacity to interrogate macromolecular structural transitions with high spatial resolution under conditions of low forces will have broad application in analyses of nucleic acid and protein folding.

High-speed atomic force microscopy

High-speed atomic force microscopy (HS-AFM) has been developed as a nano-dynamics visualization technique. This microscopy permits direct observation of structure dynamics and dynamic processes of biological molecules in physiological solutions, at a subsecond to sub-100 ms temporal resolution and an ∼2 nm lateral and a 0.1 nm vertical resolution. Importantly, tip-sample interactions do not disturb the biomolecules' functions. Various functioning proteins including myosin V walking on an actin filament and bacteriorhodopsin responding to light have been successfully visualized with HS-AFM. In the quest for understanding the functional mechanisms of proteins, inferences no longer have to be made from static snapshots of molecular structures and dynamic behavior of optical markers attached to proteins. High-resolution molecular movies obtained from HS-AFM observations reveal the details of molecules' dynamic behavior in action, without the need for intricate analyses and interpretations. In this review, I first describe the fundamentals behind the achieved high imaging rate and low invasiveness to samples, and then highlight recent imaging studies. Finally, future studies are briefly described.

Direct observation of a force-induced switch in the anisotropic mechanical unfolding pathway of a protein

Many biological processes generate force, and proteins have evolved to resist and respond to tension along different force axes. Single-molecule force spectroscopy allows for molecular insight into the behavior of proteins under force and the mechanism of protein folding in general. Here, we have used src SH3 to investigate the effect of different pulling axes under the low-force regime afforded by an optical trap. We find that this small cooperatively folded protein shows an anisotropic response to force; the protein is more mechanically resistant to force applied along a longitudinal axis compared to force applied perpendicular to the terminal β strand. In the longitudinal axis, we observe an unusual biphasic behavior revealing a force-induced switch in the unfolding mechanism suggesting the existence of two parallel unfolding pathways. A site-specific variant can selectively affect one of these pathways. Thus, even this simple two-state protein demonstrates a complex mechanical unfolding trajectory, accessing multiple unfolding pathways under the low-force regime of the optical trap; the specific unfolding pathway depends on the perturbation axis and the applied force.