Hierarchical extensibility in the PEVK domain of skeletal-muscle titin

Structure of the ISW1a complex bound to the dinucleosome

Nucleosomes are basic repeating units of chromatin and form regularly spaced arrays in cells. Chromatin remodelers alter the positions of nucleosomes and are vital in regulating chromatin organization and gene expression. Here we report the cryo-EM structure of chromatin remodeler ISW1a complex from Saccharomyces cerevisiae bound to the dinucleosome. Each subunit of the complex recognizes a different nucleosome. The motor subunit binds to the mobile nucleosome and recognizes the acidic patch through two arginine residues, while the DNA-binding module interacts with the entry DNA at the nucleosome edge. This nucleosome-binding mode provides the structural basis for linker DNA sensing of the motor. Notably, the Ioc3 subunit recognizes the disk face of the adjacent nucleosome through interacting with the H4 tail, the acidic patch and the nucleosomal DNA, which plays a role in the spacing activity in vitro and in nucleosome organization and cell fitness in vivo. Together, these findings support the nucleosome spacing activity of ISW1a and add a new mode of nucleosome remodeling in the context of a chromatin environment.

Stretching the story of titin and muscle function

The discovery of the giant protein titin, also known as connectin, dates almost half a century back. In this review, I recapitulate major advances in the discovery of the titin filaments and the recognition of their properties and function until today. I briefly discuss how our understanding of the layout and interactions of titin in muscle sarcomeres has evolved and review key facts about the titin sequence at the gene (TTN) and protein levels. I also touch upon properties of titin important for the stability of the contractile units and the assembly and maintenance of sarcomeric proteins. The greater part of my discussion centers around the mechanical function of titin in skeletal muscle. I cover milestones of research on titin's role in stretch-dependent passive tension development, recollect the reasons behind the enormous elastic diversity of titin, and provide an update on the molecular mechanisms of titin elasticity, details of which are emerging even now. I reflect on current knowledge of how muscle fibers behave mechanically if titin stiffness is removed and how titin stiffness can be dynamically regulated, such as by posttranslational modifications or calcium binding. Finally, I highlight novel and exciting, but still controversially discussed, insight into the role titin plays in active tension development, such as length-dependent activation and contraction from longer muscle lengths.

Contributions of Titin and Collagen to Passive Stress in Muscles from mdm Mice with a Small Deletion in Titin’s Molecular Spring

Muscular dystrophy with myositis (mdm) is a naturally occurring mutation in the mouse Ttn gene that results in higher passive stress in muscle fibers and intact muscles compared to wild-type (WT). The goal of this study was to test whether alternative splicing of titin exons occurs in mdm muscles, which contain a small deletion in the N2A-PEVK regions of titin, and to test whether splicing changes are associated with an increase in titin-based passive tension. Although higher levels of collagen have been reported previously in mdm muscles, here we demonstrate alternative splicing of titin in mdm skeletal muscle fibers. We identified Z-band, PEVK, and C-terminus Mex5 exons as splicing hotspots in mdm titin using RNA sequencing data and further reported upregulation in ECM-associated genes. We also treated skinned mdm soleus fiber bundles with trypsin, trypsin + KCl, and trypsin + KCL + KI to degrade titin. The results showed that passive stress dropped significantly more after trypsin treatment in mdm fibers (11 ± 1.6 mN/mm²) than in WT fibers (4.8 ± 1 mN/mm²; p = 0.0004). The finding that treatment with trypsin reduces titin-based passive tension more in mdm than in WT fibers supports the hypothesis that exon splicing leads to the expression of a stiffer and shorter titin isoform in mdm fibers. After titin extraction by trypsin + KCl + KI, mdm fibers (6.7 ± 1.27 mN/mm²) had significantly higher collagen-based passive stress remaining than WT fibers (2.6 ± 1.3 mN/mm²; p = 0.0014). We conclude that both titin and collagen contribute to higher passive tension of mdm muscles.

CARs-DB: A Database of Cryptic Amyloidogenic Regions in Intrinsically Disordered Proteins

Proteome-wide analyses suggest that most globular proteins contain at least one amyloidogenic region, whereas these aggregation-prone segments are thought to be underrepresented in intrinsically disordered proteins (IDPs). In recent work, we reported that intrinsically disordered regions (IDRs) indeed sustain a significant amyloid load in the form of cryptic amyloidogenic regions (CARs). CARs are widespread in IDRs, but they are necessarily exposed to solvent, and thus they should be more polar and have a milder aggregation potential than conventional amyloid regions protected inside globular proteins. CARs are connected with IDPs function and, in particular, with the establishment of protein-protein interactions through their IDRs. However, their presence also appears associated with pathologies like cancer or Alzheimer’s disease. Given the relevance of CARs for both IDPs function and malfunction, we developed CARs-DB, a database containing precomputed predictions for all CARs present in the IDPs deposited in the DisProt database. This web tool allows for the fast and comprehensive exploration of previously unnoticed amyloidogenic regions embedded within IDRs sequences and might turn helpful in identifying disordered interacting regions. It contains >8,900 unique CARs identified in a total of 1711 IDRs. CARs-DB is freely available for users and can be accessed at http://carsdb.ppmclab.com. To validate CARs-DB, we demonstrate that two previously undescribed CARs selected from the database display full amyloidogenic potential. Overall, CARs-DB allows easy access to a previously unexplored amyloid sequence space.

Regulation of Poly-E Motif Flexibility by pH, Ca2+ and the PPAK Motif

The disordered PEVK region of titin contains two main structural motifs: PPAK and poly-E. The distribution of these motifs in the PEVK region contributes to the elastic properties of this region, but the specific mechanism of how these motifs work together remains unclear. Previous work from our lab has demonstrated that 28-amino acid peptides of the poly-E motif are sensitive to shifts in pH, becoming more flexible as the pH decreases. We extend this work to longer poly-E constructs, including constructs containing PPAK motifs. Our results demonstrate that longer poly-E motifs have a much larger range of pH sensitivity and that the inclusion of the PPAK motif reduces this sensitivity. We also demonstrate that binding calcium can increase the conformational flexibility of the poly-E motif, though the PPAK motif can block this calcium-dependent change. The data presented here suggest a model where PPAK and calcium can alter the stiffness of the poly-E motif by modulating the degree of charge repulsion in the glutamate clusters.

Identification of the domains within the N2A region of titin that regulate binding to actin

Titin, the largest muscle protein, plays an important role in passive tension, sarcomeric integrity and cell signaling within the muscle. Recent work has also highlighted a role for titin in active muscle and the N2A region found in skeletal muscle titin and in some isoforms of cardiac titin has been linked to this function. The N2A region is a multi-domain region composed of four immunoglobulin domains (I80-I83) and a disordered region called the insertion sequence. Previously, our lab has shown that the N2A region binds F-actin in a calcium dependent manner, but it is not known which domains within this region are critical for this binding to occur. In this work, we have used co-sedimentation to demonstrate that only constructs containing the I80 domain are capable of binding F-actin. In addition, binding was only observed in constructs containing at least 3 immunoglobulin domains suggesting a length-dependence to binding. Finally, the calcium-dependence of N2A binding is lost when I83 is not present, consistent with the calcium stabilization that has been reported for this domain. Based on these results, we propose that I80 is critical for initiating binding to F-actin and that I83 is responsible for the calcium dependence.

Protein Unfolding: Denaturant vs. Force

While protein refolding has been studied for over 50 years since the pioneering work of Christian Anfinsen, there have been a limited number of studies correlating results between chemical, thermal, and mechanical unfolding. The limited knowledge of the relationship between these processes makes it challenging to compare results between studies if different refolding methods were applied. Our current work compares the energetic barriers and folding rates derived from chemical, thermal, and mechanical experiments using an immunoglobulin-like domain from the muscle protein titin as a model system. This domain, I83, has high solubility and low stability relative to other Ig domains in titin, though its stability can be modulated by calcium. Our experiments demonstrated that the free energy of refolding was equivalent with all three techniques, but the refolding rates exhibited differences, with mechanical refolding having slightly faster rates. This suggests that results from equilibrium-based measurements can be compared directly but care should be given comparing refolding kinetics derived from refolding experiments that used different unfolding methods.

The effects of an activation-dependent increase in titin stiffness on whole muscle properties using finite element modeling

Active state titin's effects have been studied predominantly in sarcomere or muscle fiber segment level and an understanding of its functional effects in the context of a whole muscle, and the mechanism of those is lacking. By representing experimentally observed calcium induced stiffening and actin-titin interaction induced reduced free spring length effects of active state titin in our linked fiber-matrix mesh finite element model, our aim was to study the mechanism of effects and particularly to determine the functionally more effective active state titin model. Isolated EDL muscle of the rat was modeled and three cases were studied: passive state titin (no change in titin constitutive equation in the active state), active state titin-I (constitutive equation involves a higher stiffness in the active state) and active state titin-II (constitutive equation also involves a strain shift coefficient accounting for titin's reduced free spring length). Isometric muscle lengthening was imposed (initial to long length, l_m = 28.7 mm to 32.7 mm). Compared to passive state titin, (i) active state titin-I and II elevates muscle total (l_m = 32.7 mm: 14% and 29%, respectively) and active (l_m = 32.7 mm: 37.5% and 77.4%, respectively) forces, (ii) active state titin-II also shifts muscle's optimum length to a longer length (l_m = 29.6 mm), (iii) active state titin-I and II limits sarcomere shortening (l_m = 32.7 mm: up to 10% and 20%, respectively). Such shorter sarcomere effect characterizes active state titin's mechanism of effects. These effects become more pronounced and functionally more effective if not only calcium induced stiffening but also a reduced free spring length of titin is accounted for.

The Poly-E motif in Titin's PEVK region undergoes pH dependent conformational changes

The muscle protein titin plays a crucial role in passive elasticity and the disordered PEVK region within titin is central to that function. The PEVK region is so named due to its high proline, glutamate, valine and lysine content and the high charge density in this region results in a lack of organized structure within this domain. The PEVK region is highly extensible but the molecular interactions that contribute to the elastic nature of the PEVK still remain poorly described. The PEVK region is formed by two unique sequence motifs. The PPAK motif is a 26 to 28 amino acid sequence that contains a mixture of charged and hydrophobic residues and is the primary building block for the PEVK region. Poly-E sequence motifs vary in length and contain clusters of 3–4 glutamic acids distributed throughout the motif. In this study, we derived two 28-residue peptides from the human titin protein sequence and measured their structural characteristics over a range of pHs. Our results demonstrate that the poly-E peptide undergoes a shift from a more rigid and elongated state to a more collapsed state as pH decreases with the midpoint of this transition being at pH ~5.5. Interestingly, a similar conformational shift is not observed in the PPAK peptide. These results suggest that the poly-E motif might provide a nucleating site for the PEVK when the muscle is not in an extended state.

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Poly-E peptides have a more extended conformation at pH 7.0 than PPAK peptides.

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Poly-E peptides assume a more relaxed conformation below pH 6.

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PPAK peptides do not show any conformational sensitivity to changes in pH.

Genetics of Muscle Stiffness, Muscle Elasticity and Explosive Strength

Muscle stiffness, muscle elasticity and explosive strength are the main components of athletes' performance and they show a sex-based as well as ethnicity variation. Muscle stiffness is thought to be one of the risk factors associated with sports injuries and is less common in females than in males. These observations may be explained by circulating levels of sex hormones and their specific receptors. It has been shown that higher levels of estrogen are associated with lower muscle stiffness responsible for suppression of collagen synthesis. It is thought that these properties, at least in part, depend on genetic factors. Particularly, the gene encoding estrogen receptor 1 (ESR1) is one of the candidates that may be associated with muscle stiffness. Muscle elasticity increases with aging and there is evidence suggesting that titin (encoded by the TTN gene), a protein that is expressed in cardiac and skeletal muscles, is one of the factors responsible for elastic properties of the muscles. Mutations in the TTN gene result in some types of muscular dystrophy or cardiomyopathy. In this context, TTN may be regarded as a promising candidate for studying the elastic properties of muscles in athletes. The physiological background of explosive strength depends not only on the muscle architecture and muscle fiber composition, but also on the central nervous system and functionality of neuromuscular units. These properties are, at least partly, genetically determined. In this context, the ACTN3 gene code for α-actinin 3 has been widely researched.

Deleting Titin's C-Terminal PEVK Exons Increases Passive Stiffness, Alters Splicing, and Induces Cross-Sectional and Longitudinal Hypertrophy in Skeletal Muscle

The Proline, Glutamate, Valine and Lysine-rich (PEVK) region of titin constitutes an entropic spring that provides passive tension to striated muscle. To study the functional and structural repercussions of a small reduction in the size of the PEVK region, we investigated skeletal muscles of a mouse with the constitutively expressed C-terminal PEVK exons 219-225 deleted, the Ttn^Δ219-225 model (MGI: Ttn^{TM 2.1Mgot} ). Based on this deletion, passive tension in skeletal muscle was predicted to be increased by ∼17% (sarcomere length 3.0 μm). In contrast, measured passive tension (sarcomere length 3.0 μm) in both soleus and EDL muscles was increased 53 ± 11% and 62 ± 4%, respectively. This unexpected increase was due to changes in titin, not to alterations in the extracellular matrix, and is likely caused by co-expression of two titin isoforms in Ttn^Δ219-225 muscles: a larger isoform that represents the Ttn^Δ219-225 N2A titin and a smaller isoform, referred to as N2A2. N2A2 represents a splicing adaption with reduced expression of spring element exons, as determined by titin exon microarray analysis. Maximal tetanic tension was increased in Ttn^Δ219-225 soleus muscle (WT 240 ± 9; Ttn^Δ219-225 276 ± 17 mN/mm²), but was reduced in EDL muscle (WT 315 ± 9; Ttn^Δ219-225 280 ± 14 mN/mm²). The changes in active tension coincided with a switch toward slow fiber types and, unexpectedly, faster kinetics of tension generation and relaxation. Functional overload (FO; ablation) and hindlimb suspension (HS; unloading) experiments were also conducted. Ttn^Δ219-225 mice showed increases in both longitudinal hypertrophy (increased number of sarcomeres in series) and cross-sectional hypertrophy (increased number of sarcomeres in parallel) in response to FO and attenuated cross-sectional atrophy in response to HS. In summary, slow- and fast-twitch muscles in a mouse model devoid of titin's PEVK exons 219-225 have high passive tension, due in part to alterations elsewhere in splicing of titin's spring region, increased kinetics of tension generation and relaxation, and altered trophic responses to both functional overload and unloading. This implicates titin's C-terminal PEVK region in regulating passive and active muscle mechanics and muscle plasticity.

Differences in stability and calcium sensitivity of the Ig domains in titin's N2A region

Titin is a large filamentous protein that spans half a sarcomere, from Z-disk to M-line. The N2A region within the titin molecule exists between the proximal immunoglobulin (Ig) region and the PEVK region and protein-protein interactions involving this region are required for normal muscle function. The N2A region consists of four Ig domains (I80-I83) with a 105 amino acid linker region between I80 and I81 that has a helical nature. Using chemical stability measurements, we show that predicted differences between the adjacent Ig domains (I81-I83) correlate with experimentally determined differences in chemical stability and refolding kinetics. Our work further shows that I83 has the lowest ΔG_unfolding , which is increased in the presence of calcium (pCa 4.3), indicating that Ca²⁺ plays a role in stabilizing this immunoglobulin domain. The characteristics of N2A's three Ig domains provide insight into the stability of the binding sites for proteins that interact with the N2A region. This work also provides insights into how Ca²⁺ might influence binding events involving N2A.

Contracting striated muscle has a dynamic I-band spring with an undamped stiffness 100 times larger than the passive stiffness

KEY POINTS

Fast sarcomere-level mechanics in contracting intact fibres from frog skeletal muscle reveal an I-band spring with an undamped stiffness 100 times larger than the known static stiffness. This undamped stiffness remains constant in the range of sarcomere length 2.7-3.1 µm, showing the ability of the I-band spring to adapt its length to the width of the I-band. The stiffness and tunability of the I-band spring implicate titin as a force contributor that, during contraction, allows weaker half-sarcomeres to equilibrate with in-series stronger half-sarcomeres, preventing the development of sarcomere length inhomogeneity. This work opens new possibilities for the detailed in situ description of the structural-functional basis of muscle dysfunctions related to mutations or site-directed mutagenesis in titin that alter the I-band stiffness.

ABSTRACT

Force and shortening in the muscle sarcomere are due to myosin motors from thick filaments pulling nearby actin filaments toward the sarcomere centre. Thousands of serially linked sarcomeres in muscle make the shortening (and the shortening speed) macroscopic, while the intrinsic instability of in-series force generators is likely prevented by the cytoskeletal protein titin that connects the thick filament with the sarcomere end, working as an I-band spring that accounts for the rise of passive force with sarcomere length (SL). However, current estimates of titin stiffness, deduced from the passive force-SL relation and single molecule mechanics, are much smaller than what is required to avoid the development of large inhomogeneities among sarcomeres. In this work, using 4 kHz stiffness measurements on a population of sarcomeres selected along an intact fibre isolated from frog skeletal muscle contracting at different SLs (temperature 4°C), we measure the undamped stiffness of an I-band spring that at SL > 2.7 µm attains a maximum constant value of ∼6 pN nm-1 per half-thick filament, two orders of magnitude larger than expected from titin-related passive force. We conclude that a titin-like dynamic spring in the I-band, made by an undamped elastic element in-series with damped elastic elements, adapts its length to the SL with kinetics that provide force balancing among serially linked sarcomeres during contraction. In this way, the I-band spring plays a fundamental role in preventing the development of SL inhomogeneity.

Titin as a force-generating muscle protein under regulatory control

Titin has long been recognized as a mechanical protein in muscle cells that has a main function as a molecular spring in the contractile units, the sarcomeres. Recent work suggests that the titin spring contributes to muscle contraction in a more active manner than previously thought. In this review, we highlight this property, specifically the ability of the immunoglobulin-like (Ig) domains of titin to undergo unfolding-refolding transitions when isolated titin molecules or skeletal myofibrils are held at physiological force levels. Folding of titin Ig domains under force is a hitherto unappreciated, putative source of work production in muscle cells, which could work in synergy with the actomyosin system to maximize the energy delivered by a stretched, actively contracting muscle. This review also focuses on the mechanisms shown to modulate titin-based viscoelastic forces in skeletal muscle cells, including chaperone binding, titin oxidation, phosphorylation, Ca²⁺ binding, and interaction with actin filaments. Along the way, we discuss which of these modulatory mechanisms might contribute to the phenomenon of residual force enhancement relevant for eccentric muscle contractions. Finally, a brief perspective is added on the potential for the alterations in titin-based force to dynamically alter mechano-chemical signaling pathways in the muscle cell. We conclude that titin from skeletal muscle is a determinant of both passive and active tension and a bona fide mechanosensor, whose stiffness is tuned by various independent mechanisms.

Crystal structure of Zen4 in the apo state reveals a missing conformation of kinesin

Kinesins hydrolyse ATP to transport intracellular cargoes along microtubules. Kinesin neck linker (NL) functions as the central mechano-chemical coupling element by changing its conformation through the ATPase cycle. Here we report the crystal structure of kinesin-6 Zen4 in a nucleotide-free, apo state, with the NL initial segment (NIS) adopting a backward-docked conformation and the preceding α6 helix partially melted. Single-molecule fluorescence resonance energy transfer (smFRET) analyses indicate the NIS of kinesin-1 undergoes similar conformational changes under tension in the two-head bound (2HB) state, whereas it is largely disordered without tension. The backward-docked structure of NIS is essential for motility of the motor. Our findings reveal a key missing conformation of kinesins, which provides the structural basis of the stable 2HB state and offers a tension-based rationale for an optimal NL length to ensure processivity of the motor.

The increase in non-cross-bridge forces after stretch of activated striated muscle is related to titin isoforms

Skeletal muscles present a non-cross-bridge increase in sarcomere stiffness and tension on Ca(2+) activation, referred to as static stiffness and static tension, respectively. It has been hypothesized that this increase in tension is caused by Ca(2+)-dependent changes in the properties of titin molecules. To verify this hypothesis, we investigated the static tension in muscles containing different titin isoforms. Permeabilized myofibrils were isolated from the psoas, soleus, and heart ventricle from the rabbit, and tested in pCa 9.0 and pCa 4.5, before and after extraction of troponin C, thin filaments, and treatment with the actomyosin inhibitor blebbistatin. The myofibrils were tested with stretches of different amplitudes in sarcomere lengths varying between 1.93 and 3.37 μm for the psoas, 2.68 and 4.21 μm for the soleus, and 1.51 and 2.86 μm for the ventricle. Using gel electrophoresis, we confirmed that the three muscles tested have different titin isoforms. The static tension was present in psoas and soleus myofibrils, but not in ventricle myofibrils, and higher in psoas myofibrils than in soleus myofibrils. These results suggest that the increase in the static tension is directly associated with Ca(2+)-dependent change in titin properties and not associated with changes in titin-actin interactions.

Self-recovering caddisfly silk: energy dissipating, Ca(2+)-dependent, double dynamic network fibers

Single fibers of the sticky underwater larval silk of the casemaker caddisfly (H. occidentalis) are viscoelastic, display large strain cycle hysteresis, and self-recover 99% of their initial stiffness and strength within 120 min. Mechanical response to cyclical strains suggested viscoelasticity is due to two independent, self-recovering Ca(2+)-crosslinked networks. The networks display distinct pH dependence. The first network is attributed to Ca(2+)-stabilized phosphoserine motifs in H-fibroin, the second to Ca(2+) complexed carboxylate groups in the N-terminus of H-fibroin and a PEVK-like protein. These assignments were corroborated by IR spectroscopy. The results are consolidated into a multi-network model in which reversible rupture of the Ca(2+)-crosslinked domains at a critical stress results in pseudo-plastic deformation. Slow refolding of the domains results in nearly full recovery of fiber length, stiffness, and strength. The fiber toughening, energy dissipation, and recovery mechanisms, are highly adaptive for the high energy aquatic environment of caddisfly larvae.

Non-crossbridge forces in activated striated muscles: a titin dependent mechanism of regulation?

When skeletal muscles are stretched during activation in the absence of myosin-actin interactions, the force increases significantly. The force remains elevated throughout the activation period. The mechanism behind this non-crossbridge force, referred to as static tension, is unknown and generates debate in the literature. It has been suggested that the static tension is caused by Ca(2+)-induced changes in the properties of titin molecules that happens during activation and stretch, but a comprehensive evaluation of such possibility is still lacking. This paper reviews the general characteristics of the static tension, and evaluates the proposed mechanism by which titin may change the force upon stretch. Evidence is presented suggesting that an increase in intracellular Ca(2+) concentration leads to Ca(2+) binding to the PEVK region of titin. Such binding increases titin stiffness, which increases the overall sarcomere stiffness and causes the static tension. If this form of Ca(2+)-induced increase in titin stiffness is confirmed in future studies, it may have large implications for understating of the basic mechanisms of muscle contraction.

Cross-species mechanical fingerprinting of cardiac myosin binding protein-C

Cardiac myosin binding protein-C (cMyBP-C) is a member of the immunoglobulin (Ig) superfamily of proteins and consists of 8 Ig- and 3 fibronectin III (FNIII)-like domains along with a unique regulatory sequence referred to as the MyBP-C motif or M-domain. We previously used atomic force microscopy to investigate the mechanical properties of murine cMyBP-C expressed using a baculovirus/insect cell expression system. Here, we investigate whether the mechanical properties of cMyBP-C are conserved across species by using atomic force microscopy to manipulate recombinant human cMyBP-C and native cMyBP-C purified from bovine heart. Force versus extension data obtained in velocity-clamp experiments showed that the mechanical response of the human recombinant protein was remarkably similar to that of the bovine native cMyBP-C. Ig/Fn-like domain unfolding events occurred in a hierarchical fashion across a threefold range of forces starting at relatively low forces of ~50 pN and ending with the unfolding of the highest stability domains at ~180 pN. Force-extension traces were also frequently marked by the appearance of anomalous force drops suggestive of additional mechanical complexity such as structural coupling among domains. Both recombinant and native cMyBP-C exhibited a prominent segment ~100 nm-long that could be stretched by forces <50 pN before the unfolding of Ig- and FN-like domains. Combined with our previous observations of mouse cMyBP-C, these results establish that although the response of cMyBP-C to mechanical load displays a complex pattern, it is highly conserved across species.

Low-force transitions in single titin molecules reflect a memory of contractile history

Titin is a giant elastomeric muscle protein that has been suggested to function as a sensor of sarcomeric stress and strain, but the mechanisms by which it does so are unresolved. To gain insight into its mechanosensory function we manipulated single titin molecules with high-resolution optical tweezers. Discrete, step-wise transitions, with rates faster than canonical Ig domain unfolding occurred during stretch at forces as low as 5 pN. Multiple mechanisms and molecular regions (PEVK, proximal tandem-Ig, N2A) are likely to be involved. The pattern of transitions is sensitive to the history of contractile events. Monte-Carlo simulations of our experimental results predicted that structural transitions begin before the complete extension of the PEVK domain. High-resolution atomic force microscopy (AFM) supported this prediction. Addition of glutamate-rich PEVK domain fragments competitively inhibited the viscoelastic response in both single titin molecules and muscle fibers, indicating that PEVK domain interactions contribute significantly to sarcomere mechanics. Thus, under non-equilibrium conditions across the physiological force range, titin extends by a complex pattern of history-dependent discrete conformational transitions, which, by dynamically exposing ligand-binding sites, could set the stage for the biochemical sensing of the mechanical status of the sarcomere.

Structure of giant muscle proteins

Giant muscle proteins (e.g., titin, nebulin, and obscurin) play a seminal role in muscle elasticity, stretch response, and sarcomeric organization. Each giant protein consists of multiple tandem structural domains, usually arranged in a modular fashion spanning 500 kDa to 4 MDa. Although many of the domains are similar in structure, subtle differences create a unique function of each domain. Recent high and low resolution structural and dynamic studies now suggest more nuanced overall protein structures than previously realized. These findings show that atomic structure, interactions between tandem domains, and intrasarcomeric environment all influence the shape, motion, and therefore function of giant proteins. In this article we will review the current understanding of titin, obscurin, and nebulin structure, from the atomic level through the molecular level.

Conformational dynamics of titin PEVK explored with FRET spectroscopy

The proline-, glutamate-, valine-, and lysine-rich (PEVK) domain of the giant muscle protein titin is thought to be an intrinsically unstructured random-coil segment. Various observations suggest, however, that the domain may not be completely devoid of internal interactions and structural features. To test the validity of random polymer models for PEVK, we determined the mean end-to-end distances of an 11- and a 21-residue synthetic PEVK peptide, calculated from the efficiency of the fluorescence resonance energy transfer (FRET) between an N-terminal intrinsic tryptophan donor and a synthetically added C-terminal IAEDANS acceptor obtained in steady-state and time-resolved experiments. We find that the contour-length scaling of mean end-to-end distance deviates from predictions of a purely statistical polymer chain. Furthermore, the addition of guanidine hydrochloride decreased, whereas the addition of salt increased the FRET efficiency, pointing at the disruption of structure-stabilizing interactions. Increasing temperature between 10 and 50°C increased the normalized FRET efficiency in both peptides but with different trajectories, indicating that their elasticity and conformational stability are different. Simulations suggest that whereas the short PEVK peptide displays an overall random structure, the long PEVK peptide retains residual, loose helical configurations. Transitions in the local structure and dynamics of the PEVK domain may play a role in the modulation of passive muscle mechanics.

The neck linker of kinesin 1 seems optimally designed to approach the largest stepping velocity: a simulation study of an ideal model

The neck linker is widely believed to play a critical role in the hand-over-hand walking of conventional kinesin 1. Experiments have shown that change of the neck linker length will significantly change the stepping velocity of the motor. In this paper, we studied this length effect based on a highly simplified chemically powered ratchet model. In this model, we assume that the chemical steps (ATP hydrolysis, ADP and P(i) release, ATP binding, neck linker docking) are fast enough under conditions far from equilibrium and the mechanical steps (detachment, diffusional search and re-attachment of the free head) are rate-limiting in kinesin walking. According to this model, and regarding the neck linker as a worm-like-chain polypeptide, we can calculate the steady state stepping velocity of the motor for different neck linker lengths. Our results show, under the actual values of binding energy between kinesin head and microtubule (~15k(B)T) and the persistence length of neck linker (~0.5 nm), that there is an optimal neck linker length (~14-16 a.a.) corresponding to the maximal velocity, which implies that the length of the wild-type neck linker (~15 a.a.) might be optimally designed for kinesin 1 to approach the largest stepping velocity.

Comparative biomechanics of thick filaments and thin filaments with functional consequences for muscle contraction

The scaffold of striated muscle is predominantly comprised of myosin and actin polymers known as thick filaments and thin filaments, respectively. The roles these filaments play in muscle contraction are well known, but the extent to which variations in filament mechanical properties influence muscle function is not fully understood. Here we review information on the material properties of thick filaments, thin filaments, and their primary constituents; we also discuss ways in which mechanical properties of filaments impact muscle performance.

Modular structure of smooth muscle Myosin light chain kinase: hydrodynamic modeling and functional implications

Smooth muscle myosin light chain kinase (smMLCK) is a calcium-calmodulin complex-dependent enzyme that activates contraction of smooth muscle. The polypeptide chain of rabbit uterine smMLCK (Swiss-Prot entry P29294) contains the catalytic/regulatory domain, three immunoglobulin-related motifs (Ig), one fibronectin-related motif (Fn3), a repetitive, proline-rich segment (PEVK), and, at the N-terminus, a unique F-actin-binding domain. We have evaluated the spatial arrangement of these domains in a recombinant 125 kDa full-length smMLCK and its two catalytically active C-terminal fragments (77 kDa, residues 461-1147, and 61 kDa, residues 461-1002). Electron microscopic images of smMLCK cross-linked to F-actin show particles at variable distances (11-55 nm) from the filament, suggesting that a well-structured C-terminal segment of smMLCK is connected to the actin-binding domain by a long, flexible tether. We have used structural homology and molecular dynamics methods to construct various all-atom representation models of smMLCK and its two fragments. The theoretical sedimentation coefficients computed with HYDROPRO were compared with those determined by sedimentation velocity. We found agreement between the predicted and observed sedimentation coefficients for models in which the independently folded catalytic domain, Fn3, and Ig domains are aligned consecutively on the long axis of the molecule. The PEVK segment is modeled as an extensible linker that enables smMLCK to remain bound to F-actin and simultaneously activate the myosin heads of adjacent myosin filaments at a distance of >or=40 nm. The structural properties of smMLCK may contribute to the elasticity of smooth muscle cells.

Dynamic strength of titin's Z-disk end

Titin is a giant filamentous protein traversing the half sarcomere of striated muscle with putative functions as diverse as providing structural template, generating elastic response, and sensing and relaying mechanical information. The Z-disk region of titin, which corresponds to the N-terminal end of the molecule, has been thought to be a hot spot for mechanosensing while also serving as anchorage for its sarcomeric attachment. Understanding the mechanics of titin's Z-disk region, particularly under the effect of binding proteins, is of great interest. Here we briefly review recent findings on the structure, molecular associations, and mechanics of titin's Z-disk region. In addition, we report experimental results on the dynamic strength of titin's Z1Z2 domains measured by nanomechanical manipulation of the chemical dimer of a recombinant protein fragment.

Tuning passive mechanics through differential splicing of titin during skeletal muscle development

During postnatal development, major changes in mechanical properties of skeletal muscle occur. We investigated passive properties of skeletal muscle in mice and rabbits that varied in age from 1 day to approximately 1 year. Neonatal skeletal muscle expressed large titin isoforms directly after birth, followed by a gradual switch toward progressively smaller isoforms that required weeks-to-months to be completed. This suggests an extremely high plasticity of titin splicing during skeletal muscle development. Titin exon microarray analysis showed increased expression of a large group of exons in neonatal muscle, when compared to adult muscle transcripts, with the majority of upregulated exons coding for the elastic proline-glutamate-valine-lysine (PEVK) region of titin. Protein analysis supported expression of a significantly larger PEVK segment in neonatal muscle. In line with these findings, we found >50% lower titin-based passive stiffness of neonatal muscle when compared to adult muscle. Inhibiting 3,5,3'-tri-iodo-L-thyronine and 3,5,3',5'-tetra-iodo-L-thyronine secretion did not alter isoform switching, suggesting no major role for thyroid hormones in regulating differential titin splicing during postnatal development. In summary, our work shows that stiffening of skeletal muscle during postnatal development occurs through a decrease in titin isoform size, due mainly to a marked restructuring of the PEVK region of titin.

Role of titin in skeletal muscle function and disease

This review covers recent developments in the titin field. Most recent reviews have discussed titin's role in cardiac function: here we will mainly focus on skeletal muscle, and discuss recent advances in the understanding of titin's role in skeletal muscle function and disease.

Muscle giants: molecular scaffolds in sarcomerogenesis

Myofibrillogenesis in striated muscles is a highly complex process that depends on the coordinated assembly and integration of a large number of contractile, cytoskeletal, and signaling proteins into regular arrays, the sarcomeres. It is also associated with the stereotypical assembly of the sarcoplasmic reticulum and the transverse tubules around each sarcomere. Three giant, muscle-specific proteins, titin (3-4 MDa), nebulin (600-800 kDa), and obscurin (approximately 720-900 kDa), have been proposed to play important roles in the assembly and stabilization of sarcomeres. There is a large amount of data showing that each of these molecules interacts with several to many different protein ligands, regulating their activity and localizing them to particular sites within or surrounding sarcomeres. Consistent with this, mutations in each of these proteins have been linked to skeletal and cardiac myopathies or to muscular dystrophies. The evidence that any of them plays a role as a "molecular template," "molecular blueprint," or "molecular ruler" is less definitive, however. Here we review the structure and function of titin, nebulin, and obscurin, with the literature supporting a role for them as scaffolding molecules and the contradictory evidence regarding their roles as molecular guides in sarcomerogenesis.

Insights into the Mechanical Properties of the Kinesin Neck Linker Domain from Sequence Analysis and Molecular Dynamics Simulations

The 14-18 amino acid kinesin neck linker domain links the core motor to the coiled-coil dimerization domain. One puzzle is that the neck linker appears too short for the 4 nm distance each linker must stretch to enable an 8 nm step - when modeled as an entropic spring, high inter-head forces are predicted when both heads are bound to the microtubule. We addressed this by analyzing the length of the neck linker across different kinesin families and using molecular dynamics simulations to model the extensibility of Kinesin-1 and Kinesin-2 neck linkers. The force-extension profile from molecular dynamics agrees with the Worm Like Chain (WLC) model for Kinesin-1 and supports the puzzling prediction that extending the neck linker 4 nm requires forces multiple times the motor stall force. Despite being 3 amino acids longer, simulations suggest that extending the Kinesin-2 neck linker by 4 nm requires similarly high forces. A possible resolution to this dilemma is that helix α-6 may unwind to enable the two-head bound state. Finally, simulations suggest that cis/trans isomerization of a conserved proline residue in Kinesin-2 accounts for the differing predictions of molecular dynamics and the WLC model, and may contribute to motor regulation in vivo.

The myofibrillar protein, projectin, is highly conserved across insect evolution except for its PEVK domain

All striated muscles respond to stretch by a delayed increase in tension. This physiological response, known as stretch activation, is, however, predominantly found in vertebrate cardiac muscle and insect asynchronous flight muscles. Stretch activation relies on an elastic third filament system composed of giant proteins known as titin in vertebrates or kettin and projectin in insects. The projectin insect protein functions jointly as a "scaffold and ruler" system during myofibril assembly and as an elastic protein during stretch activation. An evolutionary analysis of the projectin molecule could potentially provide insight into how distinct protein regions may have evolved in response to different evolutionary constraints. We mined candidate genes in representative insect species from Hemiptera to Diptera, from published and novel genome sequence data, and carried out a detailed molecular and phylogenetic analysis. The general domain organization of projectin is highly conserved, as are the protein sequences of its two repeated regions-the immunoglobulin type C and fibronectin type III domains. The conservation in structure and sequence is consistent with the proposed function of projectin as a scaffold and ruler. In contrast, the amino acid sequences of the elastic PEVK domains are noticeably divergent, although their length and overall unusual amino acid makeup are conserved. These patterns suggest that the PEVK region working as an unstructured domain can still maintain its dynamic, and even its three-dimensional, properties, without the need for strict amino acid conservation. Phylogenetic analysis of the projectin proteins also supports a reclassification of the Hymenoptera in relation to Diptera and Coleoptera.

Function and structure of inherently disordered proteins

The application of bioinformatics methodologies to proteins inherently lacking 3D structure has brought increased attention to these macromolecules. Here topics concerning these proteins are discussed, including their prediction from amino acid sequence, their enrichment in eukaryotes compared to prokaryotes, their more rapid evolution compared to structured proteins, their organization into specific groups, their structural preferences, their half-lives in cells, their contributions to signaling diversity (via high contents of multiple-partner binding sites, post-translational modifications, and alternative splicing), their distinct functional repertoire compared to that of structured proteins, and their involvement in diseases.

Structure-function relations of the giant elastic protein titin in striated and smooth muscle cells

The striated muscle sarcomere contains, in addition to thin and thick filaments, a third myofilament comprised of titin. The extensible region of titin spans the I-band region of the sarcomere and develops passive force in stretched sarcomeres. This force positions the A-bands in the middle of the sarcomere, maintains sarcomere length homogeneity and, importantly, is responsible for myocardial passive tension that determines diastolic filling. Recent work suggests that smooth muscle expresses a truncated titin isoform with a short extensible region that is predicted to develop high passive force levels. Several mechanisms for tuning the titin-based passive tension have been discovered that involve alternative splicing as well as posttranslational modification, mechanisms that are at play both during normal muscle function as well as during disease.

Secondary and tertiary structure elasticity of titin Z1Z2 and a titin chain model

The giant protein titin, which is responsible for passive elasticity in muscle fibers, is built from approximately 300 regular immunoglobulin-like (Ig) domains and FN-III repeats. While the soft elasticity derived from its entropic regions, as well as the stiff mechanical resistance derived from the unfolding of the secondary structure elements of Ig- and FN-III domains have been studied extensively, less is known about the mechanical elasticity stemming from the orientation of neighboring domains relative to each other. Here we address the dynamics and energetics of interdomain arrangement of two adjacent Ig-domains of titin, Z1, and Z2, using molecular dynamics (MD) simulations. The simulations reveal conformational flexibility, due to the domain-domain geometry, that lends an intermediate force elasticity to titin. We employ adaptive biasing force MD simulations to calculate the energy required to bend the Z1Z2 tandem open to identify energetically feasible interdomain arrangements of the Z1 and Z2 domains. The finding is cast into a stochastic model for Z1Z2 interdomain elasticity that is generalized to a multiple domain chain replicating many Z1Z2-like units and representing a long titin segment. The elastic properties of this chain suggest that titin derives so-called tertiary structure elasticity from bending and twisting of its domains. Finally, we employ steered molecular dynamics simulations to stretch individual Z1 and Z2 domains and characterize the so-called secondary structure elasticity of the two domains. Our study suggests that titin's overall elastic response at weak force stems from a soft entropic spring behavior (not described here), from tertiary structure elasticity with an elastic spring constant of approximately 0.001-1 pN/A and, at strong forces, from secondary structure elasticity.

Functional genomics of chicken, mouse, and human titin supports splice diversity as an important mechanism for regulating biomechanics of striated muscle

Titin is a giant filamentous elastic protein that spans from the Z-disk to M-band regions of the sarcomere. The I-band region of titin is extensible and develops passive force in stretched sarcomeres. This force has been implicated as a factor involved in regulating cardiac contraction. To better understand the adaptation in the extensible region of titin, we report the sequence and annotation of the chicken and mouse titin genes and compare them to the human titin gene. Our results reveal a high degree of conservation within the genomic region encoding the A-band segment of titin, consistent with the structural similarity of vertebrate A-bands. In contrast, the genomic region encoding the Z-disk and I-band segments is highly divergent. This is most prominent within the central I-band segment, where chicken titin has fewer but larger PEVK exons (up to 1,992 bp). Furthermore, in mouse titin we found two LINE repeats that are inserted in the Z-disk and I-band regions, the regions that account for most of the splice isoform diversity. Transcript studies show that a group of 55 I-band exons is differentially expressed in chicken titin. Consistent with a large degree of titin isoform plasticity and variation in PEVK content, chicken skeletal titins range in size from approximately 3,000 to approximately 3,700 kDa and vary greatly in passive mechanical properties. Low-angle X-ray diffraction experiments reveal significant differences in myofilament lattice spacing that correlate with titin isoform expression. We conclude that titin splice diversity regulates structure and biomechanics of the sarcomere.

Interaction forces between F-actin and titin PEVK domain measured with optical tweezers

Titin is a giant protein that determines the elasticity of striated muscle and is thought to play important roles in numerous regulatory processes. Previous studies have shown that titin's PEVK domain interacts with F-actin, thereby creating viscous forces of unknown magnitude that may modulate muscle contraction. Here we measured, with optical tweezers, the forces necessary to dissociate F-actin from individual molecules of recombinant PEVK fragments rich either in polyE or PPAK motifs. Rupture forces at a stretch rate of 250 nm/s displayed a wide, nonnormal distribution with a peak at approximately 8 pN in the case of both fragments. Dynamic force spectroscopy experiments revealed low spontaneous off-rates that were increased even by low forces. The loading-rate dependence of rupture force was biphasic for polyE in contrast with the monophasic response observed for PPAK. Analysis of the molecular lengths at which rupture occurred indicated that there are numerous actin-binding regions along the PEVK fragments' contour, suggesting that the PEVK domain is a promiscuous actin-binding partner. The complexity of PEVK-actin interaction points to an adaptable viscoelastic mechanism that safeguards sarcomeric structural integrity in the relaxed state and modulates thixotropic behavior during contraction.

Titin as a Giant Scaffold for Integrating Stress and Src Homology Domain 3-mediated Signaling Pathways

The richness of proline sequences in titins qualifies these giant proteins as the largest source of intrinsically disordered structures in nature. An extensive search and analysis for Src homology domain 3 (SH3) ligand motifs revealed a myriad of broadly distributed SH3 ligand motifs, with the highest density in the PEVK segments of human titin. Besides the canonical class I and II motifs with opposite orientations, novel overlapping motifs consisting of one or more of each canonical motif are abundant. Experimentally, the binding affinity and critical residues of these putative titin-based SH3 ligands toward nebulin SH3 and other SH3-containing proteins in muscle and non-muscle cell extracts were validated with peptide array technology and by the sarcomere distribution of SH3-containing proteins. A 28-mer overlapping motif-containing PEVK module binds to nebulin SH3 in and around the canonical cleft, especially to the acidic residues in the loops, as revealed by NMR titration. Molecular dynamics and molecular docking studies indicated that the overlapping motif can bind in opposite orientations with comparable energy and contact areas and predicts correctly orientation-specific contacts in NMR data. We propose that the overlap ligand motifs are a new class of ligands with innate ability to dictate SH3 domain orientation and to facilitate the rate, strength, and stereospecificity of receptor interactions. Proline-rich sequences of titins are candidates as major hubs of SH3-dependent signaling pathways. The interplay of elasticity and dense clustering of mixed receptor orientations in titin PEVK segment have important implications for the mechanical sensing, force sensitivity, and inter-adapter interactions in signaling pathways.

Mechanical properties of cardiac titin’s N2B-region by single-molecule atomic force spectroscopy

Titin is a giant protein responsible for passive-tension generation in muscle sarcomeres. Here, we used single-molecule AFM force spectroscopy to investigate the mechanical characteristics of a recombinant construct from the human cardiac-specific N2B-region, which harbors a 572-residue unique sequence flanked by two immunoglobulin (Ig) domains on either side. Force-extension curves of the N2B-construct revealed mean unfolding forces for the Ig-domains similar to those of a recombinant fragment from the distal Ig-region in titin (I91-98). The mean contour length of the N2B-unique sequence was 120 nm, but there was a bimodal distribution centered at approximately 95 nm (major peak) and 180 nm (minor peak). These values are lower than expected if the N2B-unique sequence were a permanently unfolded entropic spring, but are consistent with the approximately 100 nm maximum extension of that segment measured in isolated stretched cardiomyofibrils. A contour-length below 200 nm would be reasonable, however, if the N2B-unique sequence were stabilized by a disulphide bridge, as suggested by several disulphide connectivity prediction algorithms. Since the N2B-unique sequence can be phosphorylated by protein kinase A (PKA), which lowers titin-based stiffness, we studied whether addition of PKA (+ATP) affects the mechanical properties of the N2B-construct, but found no changes. The softening effect of PKA on N2B-titin may require specific conditions/factors present inside the cardiomyocytes.

Elasticity of peptide omega bonds

We calculated the changes of the free energy profile of the peptidyl-prolyl torsional angle of the dipeptide valine-proline under pulling forces by simulations. Using a dynamic model built on the equilibrium properties of this system and previously studied dynamic properties of cis-trans isomerization of other dipeptides, we calculated the dynamic viscoelasticity of this degree of freedom. The results show significant differences between how thermal and mechanical forces alter the equilibrium and the dynamics of the isomerization transition. The former does not change the barrier heights but changes the prefactor of the kinetics owing to temperature effects, while the latter changes minima and thus the population. The force that is required to "excite" this degree of freedom is small. Compared to other systems, we found that this degree of freedom becomes already quite rigid at several hertz, which is a much lower value due to the high barrier of the cis-trans isomerization. We also found that the tensile elastic modulus of densely packed omega bonds is at the order of GPa, which is comparable to that of polymer materials. These results give mechanical properties of polyproline elasticity of a local nature and provide guidance for future experimental designs.