Examining the influence of linkers and tertiary structure in the forced unfolding of multiple-repeat spectrin molecules

α-Helices propagating from stable nucleators exhibit unconventional thermal folding

Although the effect of thermal perturbations on protein structure has long been modeled in helical peptides, several details, such as the relation between the thermal stabilities of the propagating and nucleating segments of helices, remain elusive. We had earlier reported on the helix-nucleating propensities of covalent H-bond surrogate-constrained α-turns. Here, we analyze the thermal stabilities of helices that propagate along peptides appended to these α-helix nucleators using their NMR and far-UV CD spectra. Unconventional thermal folding of these helix models reveals that the helical fold in propagating backbones resists thermal perturbations as long as their nucleating template is intact. The threshold temperature of such resistance is also influenced by the extent of similarity between the natures of helical folds in the nucleating and propagating segments. Correlations between helicities and rigidities of helix-nucleating and helix-propagating segments reveal subtle interdependence, which explains cooperativity and residual helix formation during protein folding.

Mechanical behavior of actin and spectrin subjected to high strain rate: A molecular dynamics simulation study

Recent nanoscopy and super-resolution microscopy studies have substantiated the structural contribution of periodic actin-spectrin lattice to the axonal cytoskeleton of neuron. However, sufficient mechanical insight is not present for spectrin and actin-spectrin network, especially in high strain rate scenario. To quantify the mechanical behavior of actin-spectrin cytoskeleton in such conditions, this study determines individual stretching characteristics of actin and spectrin at high strain rate by molecular dynamics (MD) simulation. The actin-spectrin separation criteria are also determined. It is found that both actin and spectrin have high stiffness when susceptible to high strain rate and show strong dependence on applied strain rate. The stretching stiffness of actin and forced unfolding mechanism of spectrin are in harmony with the current literature. Actin-spectrin model provides novel insight into their interaction and separation stretch. It is shown that the region vulnerable to failure is the actin-spectrin interface at lower strain rate, while it is the inter-repeat region of spectrin at higher strain rate.

Targeting spectrin redox switches to regulate the mechanoproperties of red blood cells

The mechanical properties of red blood cells (RBCs) are fundamental for their physiological role as gas transporters. RBC flexibility and elasticity allow them to survive the hemodynamic changes in the different regions of the vascular tree, to dynamically contribute to the flow thereby decreasing vascular resistance, and to deform during the passage through narrower vessels. RBC mechanoproperties are conferred mainly by the structural characteristics of their cytoskeleton, which consists predominantly of a spectrin scaffold connected to the membrane via nodes of actin, ankyrin and adducin. Changes in redox state and treatment with thiol-targeting molecules decrease the deformability of RBCs and affect the structure and stability of the spectrin cytoskeleton, indicating that the spectrin cytoskeleton may contain redox switches. In this perspective review, we revise current knowledge about the structural and functional characterization of spectrin cysteine redox switches and discuss the current lines of research aiming to understand the role of redox regulation on RBC mechanical properties. These studies may provide novel functional targets to modulate RBC function, blood viscosity and flow, and tissue perfusion in disease conditions.

When Stiffness Matters: Mechanosensing in Heart Development and Disease

During embryonic morphogenesis, the heart undergoes a complex series of cellular phenotypic maturations (e.g., transition of myocytes from proliferative to quiescent or maturation of the contractile apparatus), and this involves stiffening of the extracellular matrix (ECM) acting in concert with morphogenetic signals. The maladaptive remodeling of the myocardium, one of the processes involved in determination of heart failure, also involves mechanical cues, with a progressive stiffening of the tissue that produces cellular mechanical damage, inflammation, and ultimately myocardial fibrosis. The assessment of the biomechanical dependence of the molecular machinery (in myocardial and non-myocardial cells) is therefore essential to contextualize the maturation of the cardiac tissue at early stages and understand its pathologic evolution in aging. Because systems to perform multiscale modeling of cellular and tissue mechanics have been developed, it appears particularly novel to design integrated mechano-molecular models of heart development and disease to be tested in ex vivo reconstituted cells/tissue-mimicking conditions. In the present contribution, we will discuss the latest implication of mechanosensing in heart development and pathology, describe the most recent models of cell/tissue mechanics, and delineate novel strategies to target the consequences of heart failure with personalized approaches based on tissue engineering and induced pluripotent stem cell (iPSC) technologies.

Mechanical Unfolding of Spectrin Repeats Induces Water-Molecule Ordering

Mechanical processes are involved at many stages of the development of living cells, and often external forces applied to a biomolecule result in its unfolding. Although our knowledge of the unfolding mechanisms and the magnitude of the forces involved has evolved, the role that water molecules play in the mechanical unfolding of biomolecules has not yet been fully elucidated. To this end, we investigated with steered molecular dynamics simulations the mechanical unfolding of dystrophin's spectrin repeat 1 and related the changes in the protein's structure to the ordering of the surrounding water molecules. Our results indicate that upon mechanically induced unfolding of the protein, the solvent molecules become more ordered and increase their average number of hydrogen bonds. In addition, the unfolded structures originating from mechanical pulling expose an increasing amount of the hydrophobic residues to the solvent molecules, and the uncoiled regions adapt a convex surface with a small radius of curvature. As a result, the solvent molecules reorganize around the protein's small protrusions in structurally ordered waters that are characteristic of the so-called "small-molecule regime," which allows water to maintain a high hydrogen bond count at the expense of an increased structural order. We also determined that the response of water to structural changes in the protein is localized to the specific regions of the protein that undergo unfolding. These results indicate that water plays an important role in the mechanically induced unfolding of biomolecules. Our findings may prove relevant to the ever-growing interest in understanding macromolecular crowding in living cells and their effects on protein folding, and suggest that the hydration layer may be exploited as a means for short-range allosteric communication.

The mechano-sensing role of the unique SH3 insertion in plakin domains revealed by Molecular Dynamics simulations

The plakin family of proteins, important actors in cross-linking force-bearing structures in the cell, contain a curious SH3 domain insertion in their chain of spectrin repeats (SRs). While SH3 domains are known to mediate protein-protein interactions, here, its canonical binding site is autoinhibited by the preceding SR. Under force, however, this SH3 domain could be released, and possibly launch a signaling cascade. We performed large-scale force-probe molecular dynamics simulations, across two orders of magnitude of loading rates, to test this hypothesis, on two prominent members of the plakin family: desmoplakin and plectin, obligate proteins at desmosomes and hemidesmosomes, respectively. Our simulations show that force unravels the SRs and abolishes the autoinhibition of the SH3 domain, an event well separated from the unfolding of this domain. The SH3 domain is free and fully functional for a significant portion of the unfolding trajectories. The rupture forces required for the two proteins significantly decrease when the SH3 domain is removed, which implies that the SH3 domain also stabilizes this junction. Our results persist across all simulations, and support a force-sensing as well as a stabilizing role of the unique SH3 insertion, putting forward this protein family as a new class of mechano-sensors.

The nesprin-cytoskeleton interface probed directly on single nuclei is a mechanically rich system

The cytoskeleton provides structure and plays an important role in cellular function such as migration, resisting compression forces, and transport. The cytoskeleton also reacts to physical cues such as fluid shear stress or extracellular matrix remodeling by reorganizing filament associations, most commonly focal adhesions and cell-cell cadherin junctions. These mechanical stimuli can result in genome-level changes, and the physical connection of the cytoskeleton to the nucleus provides an optimal conduit for signal transduction by interfacing with nuclear envelope proteins, called nesprins, within the LINC (linker of the nucleus to the cytoskeleton) complex. Using single-molecule on single nuclei assays, we report that the interactions between the nucleus and the cytoskeleton, thought to be nesprin-cytoskeleton interactions, are highly sensitive to force magnitude and direction depending on whether cells are historically interfaced with the matrix or with cell aggregates. Application of ∼10-30 pN forces to these nesprin linkages yielded structural transitions, with a base transition size of 5-6 nm, which are speculated to be associated with partial unfoldings of the spectrin domains of the nesprins and/or structural changes of histones within the nucleus.

Effect of Chain Conformation on the Single-Molecule Melting Force in Polymer Single Crystals: Steered Molecular Dynamics Simulations Study

Understanding the relationship between polymer chain conformation as well as the chain composition within the single crystal and the mechanical properties of the corresponding single polymer chain will facilitate the rational design of high performance polymer materials. Here three model systems of polymer single crystals, namely poly(ethylene oxide) (PEO), polyethylene (PE), and nylon-66 (PA66) have been chosen to study the effects of chain conformation, helical (PEO) versus planar zigzag conformation (PE, PA66), and chain composition (PE versus PA66) on the mechanical properties of a single polymer chain. To do that, steered molecular dynamics simulations were performed on those polymer single crystals by pulling individual polymer chains out of the crystals. Our results show that the patterns of force-extension curve as well as the chain moving mode are closely related to the conformation of the polymer chain in the single crystal. In addition, hydrogen bonds can enhance greatly the force required to stretch the polymer chain out of the single crystal. The dynamic breaking and reformation of multivalent hydrogen bonds have been observed for the first time in PA66 at the single molecule level.

A novel strain energy relationship for red blood cell membrane skeleton based on spectrin stiffness and its application to micropipette deformation

Red blood cell (RBC) membrane skeleton is a closed two-dimensional elastic network of spectrin tetramers with nodes formed by short actin filaments. Its three-dimensional shape conforms to the shape of the bilayer, to which it is connected through vertical linkages to integral membrane proteins. Numerous methods have been devised over the years to predict the response of the RBC membrane to applied forces and determine the corresponding increase in the skeleton elastic energy arising either directly from continuum descriptions of its deformation, or seeking to relate the macroscopic behavior of the membrane to its molecular constituents. In the current work, we present a novel continuum formulation rooted in the molecular structure of the membrane and apply it to analyze model deformations similar to those that occur during aspiration of RBCs into micropipettes. The microscopic elastic properties of the skeleton are derived by treating spectrin tetramers as simple linear springs. For a given local deformation of the skeleton, we determine the average bond energy and define the corresponding strain energy function and stress-strain relationships. The lateral redistribution of the skeleton is determined variationally to correspond to the minimum of its total energy. The predicted dependence of the length of the aspirated tongue on the aspiration pressure is shown to describe the experimentally observed system behavior in a quantitative manner by taking into account in addition to the skeleton energy an energy of attraction between RBC membrane and the micropipette surface.

Crystal structure of a rigid four-spectrin-repeat fragment of the human desmoplakin plakin domain

The plakin protein family serves to connect cell-cell and cell-matrix adhesion molecules to the intermediate filament cytoskeleton. Desmoplakin (DP) is an integral part of desmosomes, where it links desmosomal cadherins to the intermediate filaments. The 1056-amino-acid N-terminal region of DP contains a plakin domain common to members of the plakin family. Plakin domains contain multiple copies of spectrin repeats (SRs). We determined the crystal structure of a fragment of DP, residues 175-630, consisting of four SRs and an inserted SH3 domain. The four repeats form an elongated, rigid structure. The SH3 domain is present in a loop between two helices of an SR and interacts extensively with the preceding SR in a manner that appears to limit inter-repeat flexibility. The intimate intramolecular association of the SH3 domain with the preceding SR is also observed in plectin, another plakin protein, but not in α-spectrin, suggesting that the SH3 domain of plakins contributes to the stability and rigidity of this subfamily of SR-containing proteins.

Multiscale simulation of erythrocyte membranes

To quantitatively predict the mechanical response and mechanically induced remodeling of red blood cells, we developed a multiscale method to correlate distributions of internal stress with overall cell deformation. This method consists of three models at different length scales: in the complete cell level the membrane is modeled as two distinct layers of continuum shells using finite element method (Level III), in which the skeleton-bilayer interactions are depicted as a slide in the lateral (i.e., in-plane) direction (caused by the mobility of the skeleton-bilayer pinning points) and a normal contact force; the constitutive laws of the inner layer (the protein skeleton) are obtained from a molecular-based model (Level II); the mechanical properties of the spectrin (Sp, a key component of the skeleton), including its folding/unfolding reactions, are obtained with a stress-strain model (Level I). Model verification is achieved through comparisons with existing numerical and experimental studies in terms of the resting shape of the cell as well as cell deformations induced by micropipettes and optical tweezers. Detailed distributions of the interaction force between the lipid bilayer and the skeleton that may cause their dissociation and lead to phenomena such as vesiculation are predicted. Specifically, our model predicts correlation between the occurrence of Sp unfolding and increase in the mechanical load upon individual skeleton-bilayer pinning points. Finally a simulation of the necking process after skeleton-bilayer dissociation, a precursor of vesiculation, is conducted.

Discovery through the computational microscope

All-atom molecular dynamics simulations have become increasingly popular as a tool to investigate protein function and dynamics. However, researchers are concerned about the short time scales covered by simulations, the apparent impossibility to model large and integral biomolecular systems, and the actual predictive power of the molecular dynamics methodology. Here we review simulations that were in the past both hotly disputed and considered key successes, namely of proteins with mainly mechanical functions (titin, fibrinogen, ankyrin, and cadherin). The simulation work covered shows how state-of-the-art modeling alleviates some of the prior concerns and how unrefuted discoveries are made through the "computational microscope."

Mechanical signaling on the single protein level studied using steered molecular dynamics

Efficient communication between the cell and its external environment is of the utmost importance to the function of multicellular organisms. While signaling events can be generally characterized as information exchange by means of controlled energy conversion, research efforts have hitherto mainly been concerned with mechanisms involving chemical and electrical energy transfer. Here, we review recent computational efforts addressing the function of mechanical force in signal transduction. Specifically, we focus on the role of steered molecular dynamics (SMD) simulations in providing details at the atomic level on a group of protein domains, which play a fundamental role in signal exchange by responding properly to mechanical strain. We start by giving a brief introduction to the SMD technique and general properties of mechanically stable protein folds, followed by specific examples illustrating three general regimes of signal transfer utilizing mechanical energy: purely mechanical, mechanical to chemical, and chemical to mechanical. Whenever possible the physiological importance of the example at hand is stressed to highlight the diversity of the processes in which mechanical signaling plays a key role. We also provide an overview of future challenges and perspectives for this rapidly developing field.

Structural and dynamic study of the tetramerization region of non-erythroid alpha-spectrin: a frayed helix revealed by site-directed spin labeling electron paramagnetic resonance

The N-terminal region of alpha-spectrin is responsible for its association with beta-spectrin in a heterodimer, forming functional tetramers. Non-erythroid alpha-spectrin (alphaII-spectrin) has a significantly higher association affinity for beta-spectrin than the homologous erythroid alpha-spectrin (alphaI-spectrin). We have previously determined the solution structure of the N-terminal region of alphaI-spectrin by NMR methods, but currently no structural information is available for alphaII-spectrin. We have used cysteine scanning, spin labeling electron paramagnetic resonance (EPR), and isothermal titration calorimetry (ITC) methods to study the tetramerization region of alphaII-spectrin. EPR data clearly show that, in alphaII-spectrin, the first nine N-terminal residues were unstructured, followed by an irregular helix (helix C'), frayed at the N-terminal end, but rigid at the C-terminal end, which merges into the putative triple-helical structural domain. The region corresponding to the important unstructured junction region linking helix C' to the first structural domain in alphaI-spectrin was clearly structured. On the basis of the published model for aligning helices A', B', and C', important interactions among residues in helix C' of alphaI- and alphaII-spectrin and helices A' and B' of betaI- and betaII-spectrin are identified, suggesting similar coiled coil helical bundling for spectrin I and II in forming tetramers. The differences in affinity are likely due to the differences in the conformation of the junction regions. Equilibrium dissociation constants of spin-labeled alphaII and betaI complexes from ITC measurements indicate that residues 15, 19, 37, and 40 are functionally important residues in alphaII-spectrin. Interestingly, all four corresponding homologous residues in alphaI-spectrin (residues 24, 28, 46, and 49) have been reported to be clinically significant residues involved in hematological diseases.

Molecular epitopes of the ankyrin-spectrin interaction

Isoforms of ankyrin and its binding partner spectrin are responsible for a number of interactions in a variety of human cells. Conflicting evidence, however, had identified two different, non-overlapping human erythroid ankyrin subdomains, Zu5 and 272, as the minimum binding region for beta-spectrin. Complementary studies on the ankyrin-binding domain of spectrin have been somewhat more conclusive yet have not presented binding in terms of well-phased, integral numbers of spectrin repeats. Thus, the objective of this study was to clearly define and characterize the minimal ankyrin-spectrin binding epitopes. Circular dichroism (CD) wavelength spectra of the aforementioned ankyrin subdomains show that these fragments are 30-60% unstructured. In contrast, human erythroid beta-spectrin repeats 13, 14, 15, and 16 (prepared in all combinations of two adjacent repeats) demonstrated proper folding and stability as determined by CD and tryptophan wavelength and heat denaturation scans. Native polyacrylamide gel electrophoresis (PAGE) gel shifts as well as affinity pull-down assays implicated Zu5 and beta-spectrin repeats 14-15 as the minimum binding epitopes. These results were confirmed by analytical ultracentrifugation to sedimentation equilibrium by which a 1:1 complex was obtained if and only if Zu5 was mixed with beta-spectrin constructs containing repeats 14 and 15 in tandem. Surface plasmon resonance yielded a K D of 15.2 nM for binding of beta-spectrin fragments to the ankyrin subdomain Zu5, accounting for all of the binding observed between the intact molecules. Collectively, these results show the 14th and 15th beta-spectrin repeats comprise the minimal, phased region of beta-spectrin, which binds ankyrin at the Zu5 subdomain with high affinity.

How force might activate talin's vinculin binding sites: SMD reveals a structural mechanism

Upon cell adhesion, talin physically couples the cytoskeleton via integrins to the extracellular matrix, and subsequent vinculin recruitment is enhanced by locally applied tensile force. Since the vinculin binding (VB) sites are buried in the talin rod under equilibrium conditions, the structural mechanism of how vinculin binding to talin is force-activated remains unknown. Taken together with experimental data, a biphasic vinculin binding model, as derived from steered molecular dynamics, provides high resolution structural insights how tensile mechanical force applied to the talin rod fragment (residues 486–889 constituting helices H1–H12) might activate the VB sites. Fragmentation of the rod into three helix subbundles is prerequisite to the sequential exposure of VB helices to water. Finally, unfolding of a VB helix into a completely stretched polypeptide might inhibit further binding of vinculin. The first events in fracturing the H1–H12 rods of talin1 and talin2 in subbundles are similar. The proposed force-activated α-helix swapping mechanism by which vinculin binding sites in talin rods are exposed works distinctly different from that of other force-activated bonds, including catch bonds.

For cell survival, most eukaryotic cells need to be mechanically anchored to their environment. This is done by transmembrane proteins, including integrins, which externally bind to the extracellular matrix and on the cell interior to the contractile cytoskeleton via scaffolding proteins. One essential scaffolding protein is talin, which binds to integrins via its head and to the cytoskeletal filament f-actin via its rodlike tail. As cells apply tensile forces to newly formed adhesion sites, proteins that are part of such force-bearing networks get stretched and might change their structure and thus function. One of many proteins that are recruited to newly formed adhesions is vinculin, and vinculin recruitment is upregulated by tensile mechanical force—but how? Since talin's vinculin binding sites are buried in its native structure, we used steered molecular dynamics here to derive a high resolution structural model of how tensile mechanical forces might activate talin's vinculin binding sites. Once tensile forces break up the talin rod into helix subbundles, an event that we find here to constitute the main energy barrier, we propose how the strain-induced gradual exposure of the vinculin-binding helices finally allows for their activation and enables helix swapping with the vinculin head.

The allosteric role of the Ca2+ switch in adhesion and elasticity of C-cadherin

Modular proteins such as titin, fibronectin, and cadherin are ubiquitous components of living cells. Often involved in signaling and mechanical processes, their architecture is characterized by domains containing a variable number of heterogeneous "repeats" arranged in series, with either flexible or rigid linker regions that determine their elasticity. Cadherin repeats arranged in series are unique in that linker regions also feature calcium-binding motifs. While it is well known that the extracellular repeats of cadherin proteins mediate cell-cell adhesion in a calcium-dependent manner, the molecular mechanisms behind the influence of calcium in adhesion dynamics and cadherin's mechanical response are not well understood. Here we show, using molecular dynamics simulations, how calcium ions control the structural integrity of cadherin's linker regions, thereby affecting cadherin's equilibrium dynamics, the availability of key residues involved in cell-cell adhesion, and cadherin's mechanical response. The all-atom, multi-nanosecond molecular dynamics simulations involved the entire C-cadherin extracellular domain solvated in water (a 345,000 atom system). Equilibrium simulations show that the extracellular domain maintains its crystal conformation (elongated and slightly curved) when calcium ions are present. In the absence of calcium ions, however, it assumes a disordered conformation. The conserved residue Trp(2), which is thought to insert itself into a hydrophobic pocket of another cadherin molecule (thereby providing the basis for cell-cell adhesion), switches conformation from exposed to intermittently buried upon removal of calcium ions. Furthermore, the overall mechanical response of C-cadherin's extracellular domain is characterized at low force by changes in shape (tertiary structure elasticity), and at high force by unraveling of secondary structure elements (secondary structure elasticity). This mechanical response is modulated by calcium ions at both low and high force, switching from a stiff, rod-like to a soft, spring-like behavior upon removal of ions. The simulations provide an unprecedented molecular view of calcium-mediated allostery in cadherins, also illustrating the general principles of linker-mediated elasticity of modular proteins relevant not only for cell-cell adhesion and sound transduction, but also muscle elasticity.

Unique elastic properties of the spectrin tetramer as revealed by multiscale coarse-grained modeling

The force-extension profile of tetrameric spectrin is determined by using multiscale computer simulation. Fluctuation results of atomistic simulations of double spectrin repeat units (DSRU) are used to systematically build a coarse-grained (CG) model for the tetrameric form of spectrin. It is found that the spectrin tetramer can be modeled as a soft polymer with a unique flat force-extension profile over the range of biologically important lengths. It is also concluded that in the cytoskeletal network of the red blood cell the tetramer is in an "overcompressed" state. These findings are in contrast to the commonly used models of spectrin tetramer elasticity, namely the "entropic spring" polymer models. From these results, it is concluded that stable intact helical linker regions are needed to maintain the soft elasticity of the spectrin tetramer.

Spectrin folding versus unfolding reactions and RBC membrane stiffness

Spectrin (Sp), a key component of the erythrocyte membrane, is routinely stretched to near its fully folded contour length during cell deformations. Such dynamic loading may induce domain unfolding as suggested by recent experiments. Herein we develop a model to describe the folding/unfolding of spectrin during equilibrium or nonequilibrium extensions. In both cases, our model indicates that there exists a critical extension beyond which unfolding occurs. We further deploy this model, together with a three-dimensional model of the junctional complex in the erythrocyte membrane, to explore the effect of Sp unfolding on the membrane's mechanical properties, and on the thermal fluctuation of membrane-attached beads. At large deformations our results show a distinctive strain-induced unstiffening behavior, manifested in the slow decrease of the shear modulus, and accompanied by an increase in bead fluctuation. Bead fluctuation is also found to be influenced by mode switching, a phenomenon predicted by our three-dimensional model. The amount of stiffness reduction, however, is modest compared with that reported in experiments. A possible explanation for the discrepancy is the occurrence of spectrin head-to-head disassociation which is also included within our modeling framework and used to analyze bead motion as observed via experiment.

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

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

Transient violations of the second law of thermodynamics in protein unfolding examined using synthetic atomic force microscopy and the fluctuation theorem

The synthetic atomic force microscopy (AFM) method is developed to simulate a periodically replicated atomistic system subject to force and length fluctuations characteristic of an AFM experiment. This new method is used to examine the forced-extension and subsequent rupture of the alpha-helical linker connecting periodic images of a spectrin protein repeat unit. A two-dimensional potential of mean force (PMF) along the length and a reaction coordinate describing the state of the linker was calculated. This PMF reveals that the basic material properties of the spectrin repeat unit are sensitive to the state of linker, an important feature that cannot be accounted for in a one-dimensional PMF. Furthermore, nonequilibrium simulations were generated to examine the rupture event in the context of the fluctuation theorem. These atomistic simulations demonstrate that trajectories which are in apparent violation of the second law can overcome unfolding barriers at significantly reduced rupture forces.

Single-Molecule Experiments in Vitro and in Silico

Single-molecule force experiments in vitro enable the characterization of the mechanical response of biological matter at the nanometer scale. However, they do not reveal the molecular mechanisms underlying mechanical function. These can only be readily studied through molecular dynamics simulations of atomic structural models: "in silico" (by computer analysis) single-molecule experiments. Steered molecular dynamics simulations, in which external forces are used to explore the response and function of macromolecules, have become a powerful tool complementing and guiding in vitro single-molecule experiments. The insights provided by in silico experiments are illustrated here through a review of recent research in three areas of protein mechanics: elasticity of the muscle protein titin and the extracellular matrix protein fibronectin; linker-mediated elasticity of the cytoskeleton protein spectrin; and elasticity of ankyrin repeats, a protein module found ubiquitously in cells but with an as-yet unclear function.