Myosin head configuration in relaxed fish muscle: resting state myosin heads must swing axially by up to 150 A or turn upside down to reach rigor

Interacting-heads motif explains the X-ray diffraction pattern of relaxed vertebrate skeletal muscle

Electron microscopy (EM) shows that myosin heads in thick filaments isolated from striated muscles interact with each other and with the myosin tail under relaxing conditions. This "interacting-heads motif" (IHM) is highly conserved across the animal kingdom and is thought to be the basis of the super-relaxed state. However, a recent X-ray modeling study concludes, contrary to expectation, that the IHM is not present in relaxed intact muscle. We propose that this conclusion results from modeling with a thick filament 3D reconstruction in which the myosin heads have radially collapsed onto the thick filament backbone, not from absence of the IHM. Such radial collapse, by about 3-4 nm, is well established in EM studies of negatively stained myosin filaments, on which the reconstruction was based. We have tested this idea by carrying out similar X-ray modeling and determining the effect of the radial position of the heads on the goodness of fit to the X-ray pattern. We find that, when the IHM is modeled into a thick filament at a radius 3-4 nm greater than that modeled in the recent study, there is good agreement with the X-ray pattern. When the original (collapsed) radial position is used, the fit is poor, in agreement with that study. We show that modeling of the low-angle region of the X-ray pattern is relatively insensitive to the conformation of the myosin heads but very sensitive to their radial distance from the filament axis. We conclude that the IHM is sufficient to explain the X-ray diffraction pattern of intact muscle when placed at the appropriate radius.

Analysis methods and quality criteria for investigating muscle physiology using x-ray diffraction

X-ray diffraction studies of muscle have been tremendously powerful in providing fundamental insights into the structures of, for example, the myosin and actin filaments in a variety of muscles and the physiology of the cross-bridge mechanism during the contractile cycle. However, interpretation of x-ray diffraction patterns is far from trivial, and if modeling of the observed diffraction intensities is required it needs to be performed carefully with full knowledge of the possible pitfalls. Here, we discuss (1) how x-ray diffraction can be used as a tool to monitor various specific muscle properties and (2) how to get the most out of the rest of the observed muscle x-ray diffraction patterns by modeling where the reliability of the modeling conclusions can be objectively tested. In other x-ray diffraction methods, such as protein crystallography, the reliability of every step of the process is estimated and quoted in published papers. In this way, the quality of the structure determination can be properly assessed. To be honest with ourselves in the muscle field, we need to do as near to the same as we can, within the limitations of the techniques that we are using. We discuss how this can be done. We also use test cases to reveal the dos and don’ts of using x-ray diffraction to study muscle physiology.

The muscle M3 x-ray diffraction peak and sarcomere length: No evidence for disordered myosin heads out of actin overlap

X-ray diffraction studies of muscle have provided a wealth of information on muscle structure and physiology, and the meridian of the diffraction pattern is particularly informative. Reconditi et al. (2014. J. Physiol.https://doi.org/10.1113/jphysiol.2013.267849) performed superb experiments on changes to the M3 meridional peak as a function of sarcomere length (SL). They found that the M3 intensity dropped almost linearly as sarcomere length increased at least to about SL = 3.0 µm, and that it followed the same track as tension, pointing toward zero at the end of overlap at ∼3.6 µm. They concluded that, just as tension could only be generated by overlapped myosin heads, so ordered myosin heads contributing to the M3 intensity could only occur in the overlap region of the A-band, and that nonoverlapped heads must be highly disordered. Here we show that this conclusion is not consistent with x-ray diffraction theory; it would not explain their observations. We discuss one possible reason for the change in M3 intensity with increasing sarcomere length in terms of increasing axial misalignment of the myosin filaments that at longer sarcomere lengths is limited by the elastic stretching of the M-band and titin.

The Transient Mechanics of Muscle Require Only a Single Force-Producing Cross-Bridge State and a 100 Å Working Stroke

Simple Summary

With modern increased computational power, newly developed computer programs can be used to simulate how muscle contracts. Here, we created, in silico, a “virtual” muscle that includes modelled myosin cross-bridges, and, using statistical mechanical methods, we calculated the macroscopic response of the muscle during contraction and as a result of applied transients. Good fits to many experimental observations were obtained with this simple model with one attached force-producing state and using a single cross-bridge step size of 100 Å.

Abstract

An informative probe of myosin cross-bridge behaviour in active muscle is a mechanical transient experiment where, for example, a fully active muscle initially held at constant length is suddenly shortened to a new fixed length, providing a force transient, or has its load suddenly reduced, providing a length transient. We describe the simplest cross-bridge mechanical cycle we could find to model these transients. We show using the statistical mechanics of 50,000 cross-bridges that a simple cycle with two actin-attached cross-bridge states, one producing no force and the other producing force, will explain much of what has been observed experimentally, and we discuss the implications of this modelling for our understanding of how muscle works. We show that this same simple model will explain, reasonably well, the isotonic mechanical and X-ray transients under different loads observed by Reconditi et al. (2004, Nature 428, 578) and that there is no need to invoke different cross-bridge step sizes under these different conditions; a step size of 100 Å works well for all loads. We do not claim that this model provides a total mechanical explanation of how muscle works. However, we do suggest that only if there are other observations that cannot be explained by this simple model should something more complicated be considered.

Special Issue: The Actin-Myosin Interaction in Muscle: Background and Overview

Muscular contraction is a fundamental phenomenon in all animals; without it life as we know it would be impossible. The basic mechanism in muscle, including heart muscle, involves the interaction of the protein filaments myosin and actin. Motility in all cells is also partly based on similar interactions of actin filaments with non-muscle myosins. Early studies of muscle contraction have informed later studies of these cellular actin-myosin systems. In muscles, projections on the myosin filaments, the so-called myosin heads or cross-bridges, interact with the nearby actin filaments and, in a mechanism powered by ATP-hydrolysis, they move the actin filaments past them in a kind of cyclic rowing action to produce the macroscopic muscular movements of which we are all aware. In this special issue the papers and reviews address different aspects of the actin-myosin interaction in muscle as studied by a plethora of complementary techniques. The present overview provides a brief and elementary introduction to muscle structure and function and the techniques used to study it. It goes on to give more detailed descriptions of what is known about muscle components and the cross-bridge cycle using structural biology techniques, particularly protein crystallography, electron microscopy and X-ray diffraction. It then has a quick look at muscle mechanics and it summarises what can be learnt about how muscle works based on the other studies covered in the different papers in the special issue. A picture emerges of the main molecular steps involved in the force-producing process; steps that are also likely to be seen in non-muscle myosin interactions with cellular actin filaments. Finally, the remarkable advances made in studying the effects of mutations in the contractile assembly in causing specific muscle diseases, particularly those in heart muscle, are outlined and discussed.

Mammalian muscle fibers may be simple as well as slow

Squire and Luther consider new evidence for a simple lattice structure in mammalian skeletal muscle.

The Interacting Head Motif Structure Does Not Explain the X-Ray Diffraction Patterns in Relaxed Vertebrate (Bony Fish) Skeletal Muscle and Insect (Lethocerus) Flight Muscle

Unlike electron microscopy, which can achieve very high resolution but to date can only be used to study static structures, time-resolved X-ray diffraction from contracting muscles can, in principle, be used to follow the molecular movements involved in force generation on a millisecond timescale, albeit at moderate resolution. However, previous X-ray diffraction studies of resting muscles have come up with structures for the head arrangements in resting myosin filaments that are different from the apparently ubiquitous interacting head motif (IHM) structures found by single particle analysis of electron micrographs of isolated myosin filaments from a variety of muscle types. This head organization is supposed to represent the super-relaxed state of the myosin filaments where adenosine triphosphate (ATP) usage is minimized. Here we have tested whether the interacting head motif structures will satisfactorily explain the observed low-angle X-ray diffraction patterns from resting vertebrate (bony fish) and invertebrate (insect flight) muscles. We find that the interacting head motif does not, in fact, explain what is observed. Previous X-ray models fit the observations much better. We conclude that the X-ray diffraction evidence has been well interpreted in the past and that there is more than one ordered myosin head state in resting muscle. There is, therefore, no reason to question some of the previous X-ray diffraction results on myosin filaments; time-resolved X-ray diffraction should be a reliable way to follow crossbridge action in active muscle and may be one of the few ways to visualise the molecular changes in myosin heads on a millisecond timescale as force is actually produced.

Monitoring the myosin crossbridge cycle in contracting muscle: steps towards 'Muscle-the Movie'

Some vertebrate muscles (e.g. those in bony fish) have a simple lattice A-band which is so well ordered that low-angle X-ray diffraction patterns are sampled in a simple way amenable to crystallographic techniques. Time-resolved X-ray diffraction through the contractile cycle should provide a movie of the molecular movements involved in muscle contraction. Generation of 'Muscle-The Movie' was suggested in the 1990s and since then efforts have been made to work out how to achieve it. Here we discuss how a movie can be generated, we discuss the problems and opportunities, and present some new observations. Low angle X-ray diffraction patterns from bony fish muscles show myosin layer lines that are well sampled on row-lines expected from the simple hexagonal A-band lattice. The 1st, 2nd and 3rd myosin layer lines at d-spacings of around 42.9 nm, 21.5 nm and 14.3 nm respectively, get weaker in patterns from active muscle, but there is a well-sampled intensity remnant along the layer lines. We show here that the pattern from the tetanus plateau is not a residual resting pattern from fibres that have not been fully activated, but is a different well-sampled pattern showing the presence of a second, myosin-centred, arrangement of crossbridges within the active crossbridge population. We also show that the meridional M3 peak from active muscle has two components of different radial widths consistent with (i) active myosin-centred (probably weak-binding) heads giving a narrow peak and (ii) heads on actin in strong states giving a broad peak.

Do Actomyosin Single-Molecule Mechanics Data Predict Mechanics of Contracting Muscle?

In muscle, but not in single-molecule mechanics studies, actin, myosin and accessory proteins are incorporated into a highly ordered myofilament lattice. In view of this difference we compare results from single-molecule studies and muscle mechanics and analyze to what degree data from the two types of studies agree with each other. There is reasonable correspondence in estimates of the cross-bridge power-stroke distance (7–13 nm), cross-bridge stiffness (~2 pN/nm) and average isometric force per cross-bridge (6–9 pN). Furthermore, models defined on the basis of single-molecule mechanics and solution biochemistry give good fits to experimental data from muscle. This suggests that the ordered myofilament lattice, accessory proteins and emergent effects of the sarcomere organization have only minor modulatory roles. However, such factors may be of greater importance under e.g., disease conditions. We also identify areas where single-molecule and muscle data are conflicting: (1) whether force generation is an Eyring or Kramers process with just one major power-stroke or several sub-strokes; (2) whether the myofilaments and the cross-bridges have Hookean or non-linear elasticity; (3) if individual myosin heads slip between actin sites under certain conditions, e.g., in lengthening; or (4) if the two heads of myosin cooperate.

Myosin and Actin Filaments in Muscle: Structures and Interactions

In the last decade, improvements in electron microscopy and image processing have permitted significantly higher resolutions to be achieved (sometimes <1 nm) when studying isolated actin and myosin filaments. In the case of actin filaments the changing structure when troponin binds calcium ions can be followed using electron microscopy and single particle analysis to reveal what happens on each of the seven non-equivalent pseudo-repeats of the tropomyosin α-helical coiled-coil. In the case of the known family of myosin filaments not only are the myosin head arrangements under relaxing conditions being defined, but the latest analysis, also using single particle methods, is starting to reveal the way that the α-helical coiled-coil myosin rods are packed to give the filament backbones.

FIT2D: a multi-purpose data reduction, analysis and visualization program

FIT2D is one of the principal area detector data reduction, analysis and visualization programs used at the European Synchrotron Radiation Facility and is also used by more than 400 research groups worldwide, including many other synchrotron radiation facilities. It has been developed for X-ray science, but is applicable to other structural techniques and is used in analysing electron diffraction data and microscopy, and neutron diffraction and scattering data. FIT2D works for both interactive and `batch'-style data processing. Calibration and correction of detector distortions, integration of two-dimensional data to a variety of one-dimensional scans, and one- and two-dimensional model fitting are the main uses. Many other general-purpose image processing and image visualization operations are available. Commands are available through a `graphical user interface' and operations common to certain types of analysis are grouped within `interfaces'. Executable versions for most workstation and personal computer systems, and web page documentation, are available at http://www.esrf.eu/computing/scientific/FIT2D.

The intriguing dual lattices of the Myosin filaments in vertebrate striated muscles: evolution and advantage

Myosin filaments in vertebrate striated muscle have a long roughly cylindrical backbone with cross-bridge projections on the surfaces of both halves except for a short central bare zone. In the middle of this central region the filaments are cross-linked by the M-band which holds them in a well-defined hexagonal lattice in the muscle A-band. During muscular contraction the M-band-defined rotation of the myosin filaments around their long axes influences the interactions that the cross-bridges can make with the neighbouring actin filaments. We can visualise this filament rotation by electron microscopy of thin cross-sections in the bare-region immediately adjacent to the M-band where the filament profiles are distinctly triangular. In the muscles of teleost fishes, the thick filament triangular profiles have a single orientation giving what we call the simple lattice. In other vertebrates, for example all the tetrapods, the thick filaments have one of two orientations where the triangles point in opposite directions (they are rotated by 60° or 180°) according to set rules. Such a distribution cannot be developed in an ordered fashion across a large 2D lattice, but there are small domains of superlattice such that the next-nearest neighbouring thick filaments often have the same orientation. We believe that this difference in the lattice forms can lead to different contractile behaviours. Here we provide a historical review, and when appropriate cite recent work related to the emergence of the simple and superlattice forms by examining the muscles of several species ranging back to primitive vertebrates and we discuss the functional differences that the two lattice forms may have.

Head-head interactions of resting myosin crossbridges in intact frog skeletal muscles, revealed by synchrotron x-ray fiber diffraction

The intensities of the myosin-based layer lines in the x-ray diffraction patterns from live resting frog skeletal muscles with full thick-thin filament overlap from which partial lattice sampling effects had been removed were analyzed to elucidate the configurations of myosin crossbridges around the thick filament backbone to nanometer resolution. The repeat of myosin binding protein C (C-protein) molecules on the thick filaments was determined to be 45.33 nm, slightly longer than that of myosin crossbridges. With the inclusion of structural information for C-proteins and a pre-powerstroke head shape, modeling in terms of a mixed population of regular and perturbed regions of myosin crown repeats along the filament revealed that the myosin filament had azimuthal perturbations of crossbridges in addition to axial perturbations in the perturbed region, producing pseudo-six-fold rotational symmetry in the structure projected down the filament axis. Myosin crossbridges had a different organization about the filament axis in each of the regular and perturbed regions. In the regular region that lacks C-proteins, there were inter-molecular interactions between the myosin heads in axially adjacent crown levels. In the perturbed region that contains C-proteins, in addition to inter-molecular interactions between the myosin heads in the closest adjacent crown levels, there were also intra-molecular interactions between the paired heads on the same crown level. Common features of the interactions in both regions were interactions between a portion of the 50-kDa-domain and part of the converter domain of the myosin heads, similar to those found in the phosphorylation-regulated invertebrate myosin. These interactions are primarily electrostatic and the converter domain is responsible for the head-head interactions. Thus multiple head-head interactions of myosin crossbridges also characterize the switched-off state and have an important role in the regulation or other functions of myosin in thin filament-regulated muscles as well as in the thick filament-regulated muscles.

Myosin heads contribute to the maintenance of filament order in relaxed rabbit muscle

Raising the temperature of rabbit skeletal muscle from ∼0°C to ∼20°C has been shown to enhance the helical organization of the myosin heads and to change the intensities of the 10 and 11 equatorial reflections. We show here by time-resolved x-ray diffraction combined with temperature jump that the movement of the heads to enhance the organized myosin helix occurs at the same fast rate as the change in the intensities of the equatorial reflections. However, model calculations indicate that the change in the equatorials cannot be explained simply in terms of the movement of myosin heads. Analysis of electron micrographs of transverse sections of relaxed muscle fibers cryofixed at ∼5°C and ∼35°C shows that in addition to the reorganization of the heads the thin and thick filaments are less constrained to their positions in the hexagonal filament lattice in the warm muscle than in the cold. Incorporating the changes in filament order in model calculations reconciles these with the observed changes in equatorial reflections. We suggest the thin filaments in the cold muscle are boxed into their positions by the thermal movement of the disordered myosin heads. In the warmer muscle, the packed-down heads leave the thin filaments more room to diffuse laterally.

Shape and flexibility in the titin 11-domain super-repeat

Titin is a giant protein of striated muscle with important roles in the assembly, intracellular signalling and passive mechanical properties of sarcomeres. The molecule consists principally of approximately 300 immunoglobulin and fibronectin domains arranged in a chain more than 1 mum long. The isoform-dependent N-terminal part of the molecule forms an elastic connection between the end of the thick filament and the Z-line. The larger, constitutively expressed C-terminal part is bound to the thick filament. Through most of the thick filament part, the immunoglobulin and fibronectin domains are arranged in a repeating pattern of 11 domains termed the 'large super-repeat'. There are 11 contiguous copies of the large super-repeat making up a segment of the molecule nearly 0.5 mum long. We have studied a set of two-domain and three-domain recombinant fragments from the large super-repeat region by electron microscopy, synchrotron X-ray solution scattering and analytical ultracentrifugation, with the goal of reconstructing the overall structure of this part of titin. The data illustrate different average conformations in different domain pairs, which correlate with differences in interdomain linker lengths. They also illustrate interdomain bending and flexibility around average conformations. Overall, the data favour a helical conformation in the super-repeat. They also suggest that this region of titin is dimerized when bound to the thick filament.

Muscle myosin filaments: cores, crowns and couplings

Myosin filaments in muscle, carrying the ATPase myosin heads that interact with actin filaments to produce force and movement, come in multiple varieties depending on species and functional need, but most are based on a common structural theme. The now successful journeys to solve the ultrastructures of many of these myosin filaments, at least at modest resolution, have not been without their false starts and erroneous sidetracks, but the picture now emerging is of both diversity in the rotational symmetries of different filaments and a degree of commonality in the way the myosin heads are organised in resting muscle. Some of the remaining differences may be associated with how the muscle is regulated. Several proteins in cardiac muscle myosin filaments can carry mutations associated with heart disease, so the elucidation of myosin filament structure to understand the effects of these mutations has a clear and topical clinical relevance.

A mathematical analysis of obstructed diffusion within skeletal muscle

Molecules are transported through the myofilament lattice of skeletal muscle fibers during muscle activation. The myofilaments, along with the myosin heads, sarcoplasmic reticulum, t-tubules, and mitochondria, obstruct the diffusion of molecules through the muscle fiber. In this work, we studied the process of obstructed diffusion within the myofilament lattice using Monte Carlo simulation, level-set and homogenization theory. We found that these intracellular obstacles significantly reduce the diffusion of material through skeletal muscle and generate diffusion anisotropy that is consistent with experimentally observed slower diffusion in the radial than the longitudinal direction. Our model also predicts that protein size has a significant effect on the diffusion of material through muscle, which is consistent with experimental measurements. Protein diffusion on the myofilament lattice is also anomalous (i.e., it does not obey Brownian motion) for proteins that are close in size to the myofilament spacing. The obstructed transport of Ca2+ and ATP-bound Ca2+ through the myofilament lattice also generates smaller Ca2+ transients. In addition, we used homogenization theory to discover that the nonhomogeneous distribution in the troponin binding sites has no effect on the macroscopic Ca2+ dynamics. The nonuniform sarcoplasmic reticulum Ca2+-ATPase pump distribution also introduces small asymmetries in the myoplasmic Ca2+ transients.

Neutron diffraction measurements of skeletal muscle using the contrast variation technique: analysis of the equatorial diffraction patterns

Among various methods for structural studies of biological macromolecules, neutron scattering and diffraction have a unique feature in that the contrast between the scattering length density of the molecules and that of the solvent can be varied easily by changing the D2O content in the solvent. This "contrast variation" technique enables one to obtain information on variations of scattering length density of the molecules of interest. Here, in order to explore the possibilities of the contrast variation technique in neutron fiber diffraction, neutron diffraction measurements of skeletal muscles were performed. The neutron fiber diffraction patterns from frog sartorius muscles were measured in various D2O concentrations in the relaxed state where no tension of muscle is produced, and in the rigor state where all myosin heads of the thick filaments bind tightly to actin in the thin filaments. It was shown that in both states, there were reflections having distinct contrast matching points, indicating a variation in the scattering length density of the protein regions in the unit cell of the muscle structure. Analysis of the equatorial reflections by the two-dimensional projected scattering length density map calculations by Fourier synthesis and model calculations provided the phase information of the equatorial reflections, with which the projected scattering length density maps of the unit cell of the hexagonal filament array in both states were calculated. The analysis showed that the scattering length density of the thick filament region was higher than that of the thin filament region, and that the scattering length density of the thick filament backbone changed as muscle went from the relaxed state into the rigor state.

Understanding the organisation and role of myosin binding protein C in normal striated muscle by comparison with MyBP-C knockout cardiac muscle

Myosin binding protein C (MyBP-C) is a component of the thick filament of striated muscle. The importance of this protein is revealed by recent evidence that mutations in the cardiac gene are a major cause of familial hypertrophic cardiomyopathy. Here we investigate the distribution of MyBP-C in the A-bands of cardiac and skeletal muscles and compare this to the A-band structure in cardiac muscle of MyBP-C-deficient mice. We have used a novel averaging technique to obtain the axial density distribution of A-bands in electron micrographs of well-preserved specimens. We show that cardiac and skeletal A-bands are very similar, with a length of 1.58 ± 0.01 μm. In normal cardiac and skeletal muscle, the distributions are very similar, showing clearly the series of 11 prominent accessory protein stripes in each half of the A-band spaced axially at 43-nm intervals and starting at the edge of the bare zone. We show by antibody labelling that in cardiac muscle the distal nine stripes are the location of MyBP-C. These stripes are considerably suppressed in the knockout mouse hearts as expected. Myosin heads on the surface of the thick filament in relaxed muscle are thought to be arranged in a three-stranded quasi-helix with a mean 14.3-nm axial cross bridge spacing and a 43 nm helix repeat. Extra “forbidden” meridional reflections, at orders of 43 nm, in X-ray diffraction patterns of muscle have been interpreted as due to an axial perturbation of some levels of myosin heads. However, in the MyBP-C-deficient hearts these extra meridional reflections are weak or absent, suggesting that they are due to MyBP-C itself or to MyBP-C in combination with a head perturbation brought about by the presence of MyBP-C.

Towards a unified theory of muscle contraction. I: foundations

Molecular models of contractility in striated muscle require an integrated description of the action of myosin motors, firstly in the filament lattice of the half-sarcomere. Existing models do not adequately reflect the biochemistry of the myosin motor and its sarcomeric environment. The biochemical actin-myosin-ATP cycle is reviewed, and we propose a model cycle with two 4- to 5-nm working strokes, where phosphate is released slowly after the first stroke. A smaller third stroke is associated with ATP-induced detachment from actin. A comprehensive model is defined by applying such a cycle to all myosin-S1 heads in the half-sarcomere, subject to generic constraints as follows: (a) all strain-dependent kinetics required for actin-myosin interactions are derived from reaction-energy landscapes and applied to dimeric myosin, (b) actin-myosin interactions in the half-sarcomere are controlled by matching rules derived from the structure of the filaments, so that each dimer may be associated with a target zone of three actin sites, and (c) the myosin and actin filaments are treated as elastically extensible. Numerical predictions for such a model are presented in the following paper.

Myosin filament 3D structure in mammalian cardiac muscle

A number of cardiac myopathies (e.g. familial hypertrophic cardiomyopathy and dilated cardiomyopathy) are linked to mutations in cardiac muscle myosin filament proteins, including myosin and myosin binding protein C (MyBP-C). To understand the myopathies it is necessary to know the normal 3D structure of these filaments. We have carried out 3D single particle analysis of electron micrograph images of negatively stained isolated myosin filaments from rabbit cardiac muscle. Single filament images were aligned and divided into segments about 2 × 430 Å long, each of which was treated as an independent ‘particle’. The resulting 40 Å resolution 3D reconstruction showed both axial and azimuthal (no radial) myosin head perturbations within the 430 Å repeat, with successive crown rotations of approximately 60°, 60° and 0°, rather than the regular 40° for an unperturbed helix. However, it is shown that the projecting density peaks appear to start at low radius from origins closer to those expected for an unperturbed helical filament, and that the azimuthal perturbation especially increases with radius. The head arrangements in rabbit cardiac myosin filaments are very similar to those in fish skeletal muscle myosin filaments, suggesting a possible general structural theme for myosin filaments in all vertebrate striated muscles (skeletal and cardiac).

The structure of isolated cardiac Myosin thick filaments from cardiac Myosin binding protein-C knockout mice

Mutations in the thick filament associated protein cardiac myosin binding protein-C (cMyBP-C) are a major cause of familial hypertrophic cardiomyopathy. Although cMyBP-C is thought to play both a structural and a regulatory role in the contraction of cardiac muscle, detailed information about the role of this protein in stability of the thick filament and maintenance of the ordered helical arrangement of the myosin cross-bridges is limited. To address these questions, the structure of myosin thick filaments isolated from the hearts of wild-type mice containing cMyBP-C (cMyBP-C(+/+)) were compared to those of cMyBP-C knockout mice lacking this protein (cMyBp-C(-/-)). The filaments from the knockout mice hearts lacking cMyBP-C are stable and similar in length and appearance to filaments from the wild-type mice hearts containing cMyBP-C. Both wild-type and many of the cMyBP-C(-/-) filaments display a distinct 43 nm periodicity. Fourier transforms of electron microscope images typically show helical layer lines to the sixth layer line, confirming the well-ordered arrangement of the cross-bridges in both sets of filaments. However, the "forbidden" meridional reflections, thought to derive from a perturbation from helical symmetry in the wild-type filament, are weaker or absent in the transforms of the cMyBP-C(-/-) myocardial thick filaments. In addition, the cross-bridge array in the absence of cMyBP-C appears more easily disordered.

The CCP13 FibreFix program suite: semi-automated analysis of diffraction patterns from non-crystalline materials

The extraction of useful information from recorded diffraction patterns from non-crystalline materials is non-trivial and is not a well defined operation. Unlike protein crystallography where one expects to see well behaved diffraction spots in predictable positions defined by standard space groups, the diffraction patterns from non-crystalline materials are very diverse. They can range from uniaxially oriented fibre patterns which are completely sampled as Bragg peaks, but rotationally averaged around the fibre axis, to fibre patterns that are completely unsampled, to either kind of pattern with considerable axial misalignment (disorientation), to liquid-like order and even to mixtures of these various structure types. In the case of protein crystallography, the specimen is generated artificially and only used if the degree of order is sufficient to yield a three-dimensional density map of high enough resolution to be interpreted sensibly. However, with non-crystalline diffraction, many of the specimens of interest are naturally occurring (e.g. cellulose, rubber, collagen, muscle, hair, silk) and to elucidate their structure it is necessary to extract structural information from the materials as they actually are and to whatever resolution is available. Even when synthetic fibres are generated from purified components (e.g. nylon, polyethylene, DNA, polysaccharides, amyloids etc.) and diffraction occurs to high resolution, it is rarely possible to obtain perfect uniaxial alignment. The CCP13 project was established in the 1990s to generate software which will be generally useful for analysis of non-crystalline diffraction patterns. Various individual programs were written which allowed separate steps in the analysis procedure to be carried out. Many of these programs have now been integrated into a single user-friendly package known as FibreFix, which is freely downloadable from http://www.ccp13.ac.uk. Here the main features of FibreFix are outlined and some of its applications are illustrated.

Axial dispositions and conformations of myosin crossbridges along thick filaments in relaxed and contracting states of vertebrate striated muscles by X-ray fiber diffraction

X-ray diffraction patterns from live vertebrate striated muscles were analyzed to elucidate the detailed structural models of the myosin crown arrangement and the axial disposition of two-headed myosin crossbridges along the thick filaments in the relaxed and contracting states. The modeling studies were based upon the previous notion that individual myosin filaments had a mixed structure with two regions, a "regular" and a "perturbed". In the relaxed state the distributions and sizes of the regular and perturbed regions on myosin filaments, each having its own axial periodicity for the arrangement of crossbridge crowns within the basic period, were similar to those reported previously. A new finding was that in the contracting state, this mixed structure was maintained but the length of each region, the periodicities of the crowns and the axial disposition of two heads of a crossbridge were altered. The perturbed regions of the crossbridge repeat shifted towards the Z-bands in the sarcomere without changing the lengths found in the relaxed state, but in which the intervals between three successive crowns within the basic period became closer to the regular 14.5-nm repeat in the contracting state. In high resolution modeling for a myosin head, the two heads of a crossbridge were axially tilted in opposite directions along the three-fold helical tracks of myosin filaments and their axial orientations were different from each other in perturbed and regular regions in both states. Under relaxing conditions, one head of a double-headed crossbridge pair appeared to be in close proximity to another head in a pair at the adjacent crown level in the axial direction in the regular region. In the perturbed region this contact between heads occurred only on the narrower inter-crown levels. During contraction, one head of a crossbridge oriented more perpendicular to the fiber axis and the partner head flared axially. Several factors that significantly influence the intensities of the myosin based-meridional reflections and their relative contributions are discussed.

Refined structure of bony fish muscle myosin filaments from low-angle X-ray diffraction data

Application of X-ray diffraction methods to the elucidation of the arrangement of the myosin heads on myosin filaments in resting muscles is made simpler when the muscles themselves are well ordered in 3D. Bony fish muscle for the vertebrates and insect flight muscle for the invertebrates are the muscles of choice for this analysis. The rich, well-sampled, low-angle X-ray diffraction pattern from bony fish muscle has previously been modelled with an R-factor of 3.4% between observed and calculated transforms on the assumption that the two heads in one myosin molecule have the same shape. However, recent evidence from other kinds of analysis of other muscles has shown that this assumption may not be valid. There is evidence that the motor domain of one head in each pair may interact with the neck region of the second head. This possibility has been tested directly in the present analysis which extends the X-ray modelling of fish muscle myosin filaments by permitting independent shape changes of the two heads in one molecule. The new model, with a computed R-factor of 1.19% against 56 independent reflections, shows that in fish muscle also there is a marked asymmetry in the organisation of each head pair.

3D structure of relaxed fish muscle myosin filaments by single particle analysis

To understand the structural changes involved in the force-producing myosin cross-bridge cycle in vertebrate muscle it is necessary to know the arrangement and conformation of the myosin heads at the start of the cycle (i.e. the relaxed state). Myosin filaments isolated from goldfish muscle under relaxing conditions and viewed in negative stain by electron microscopy (EM) were divided into segments and subjected to three-dimensional (3D) single particle analysis without imposing helical symmetry. This allowed the known systematic departure from helicity characteristic of vertebrate striated muscle myosin filaments to be preserved and visualised. The resulting 3D reconstruction reveals details to about 55 A resolution of the myosin head density distribution in the three non-equivalent head 'crowns' in the 429 A myosin filament repeat. The analysis maintained the well-documented axial perturbations of the myosin head crowns and revealed substantial azimuthal perturbations between crowns with relatively little radial perturbation. Azimuthal rotations between crowns were approximately 60 degrees , 60 degrees and 0 degrees , rather than the regular 40 degrees characteristic of an unperturbed helix. The new density map correlates quite well with the head conformations analysed in other EM studies and in the relaxed fish muscle myosin filament structure modelled from X-ray fibre diffraction data. The reconstruction provides information on the polarity of the myosin head array in the A-band, important in understanding the geometry of the myosin head interaction with actin during the cross-bridge cycle, and supports a number of conclusions previously inferred by other methods. The observed azimuthal head perturbations are consistent with the X-ray modelling results from intact muscle, indicating that the observed perturbations are an intrinsic property of the myosin filaments and are not induced by the proximity of actin filaments in the muscle A-band lattice. Comparison of the axial density profile derived in this study with the axial density profile of the X-ray model of the fish myosin filaments which was restricted to contributions from the myosin heads allows the identification of a non-myosin density peak associated with the azimuthally perturbed head crown which can be interpreted as a possible location for C-protein or X-protein (MyBP-C or -X). This position for C-protein is also consistent with the C-zone interference function deduced from previous analysis of the meridional X-ray pattern from frog muscle. It appears that, along with other functions, C-(X-) protein may have the role of slewing the heads of one crown so that they do not clash with the neighbouring actin filaments, but are readily available to interact with actin when the muscle is activated.

The mammalian cardiac muscle thick filament: crossbridge arrangement

Although skeletal muscle thick filaments have been extensively studied, information on the structure of cardiac thick filaments is limited. Since cardiac muscle differs in many physiological properties from skeletal muscle it is important to elucidate the structure of the cardiac thick filament. The structure of isolated and negatively stained rabbit cardiac thick filaments has been analyzed from computed Fourier transforms and image analysis. The transforms are detailed, showing a strong set of layer lines corresponding to a 42.9 nm quasi-helical repeat. The presence of relatively strong "forbidden" meridional reflections not expected from ideal helical symmetry on the second, fourth, fifth, seventh, eighth, and tenth layer lines suggest that the crossbridge array is perturbed from ideal helical symmetry. Analysis of the phase differences for the primary reflections on the first layer line of transforms from 15 filaments showed an average difference of 170 degrees, close to the value of 180 degrees expected for an odd-stranded structure. Computer-filtered images of the isolated thick filaments unequivocally demonstrate a three-stranded arrangement of the crossbridges on the filaments and provide evidence that the crossbridge arrangement is axially perturbed from ideal helical symmetry.

Single particle analysis: a new approach to solving the 3D structure of myosin filaments

Knowledge of the structure of muscle myosin filaments is essential for a proper understanding of sarcomere structure and how myosin heads interact with the actin filaments to produce force and movement. Two principal methods have been used to define the myosin head arrays in filaments in the relaxed state, namely modelling from low-angle X-ray diffraction data and image processing of electron micrographs of isolated filaments. Analysis of filament images by 3D helical reconstruction, which imposes total helical symmetry on the structure, is very effective in some cases, but it relies on the existence of very highly ordered preparations of straight filaments. Resolutions achieved to date are about 70 angstroms. Modelling of X-ray diffraction data recorded from whole relaxed fish or insect muscles has also been used as an independent method. Although the resolution of the diffraction data is often also about 70 angstroms, the effective resolution of the modelling is very much higher than this because additional very high resolution data (e.g. from protein crystallography) is included in the analysis. However, the X-ray diffraction method has to date provided only limited data on non-myosin thick filament proteins such as C-protein and titin and it cannot provide the polarity of the myosin head arrangement. Both the helical reconstruction and X-ray diffraction techniques have advantages and disadvantages, but their disadvantages are avoided in the new approach of single particle analysis of electron micrograph data. Even using the same micrographs as for helical reconstruction, the resolution can be extended by this method to about 50 angstroms or better. In addition, it is not necessary to assume that the myosin filaments are helical; a significant advantage in the case of vertebrate myosin filaments where there is a known crossbridge perturbation. Here we describe the principles of all these approaches, but particularly that of single particle analysis. We outline the application of single particle analysis to myosin filaments from vertebrate skeletal and insect flight (IFM) muscle myosin filaments.

New X-ray diffraction observations on vertebrate muscle: organisation of C-protein (MyBP-C) and troponin and evidence for unknown structures in the vertebrate A-band

Previous low-angle X-ray diffraction studies of various vertebrate skeletal muscles have shown the presence of two rich layer-line patterns, one from the myosin heads and based on a 429 A axial repeat, and one from actin filaments and based on a repeat of about 360-370 A. In addition, meridional intensities have been seen from C-protein (MyBP-C; at about 440 A and its higher orders) and troponin (at about 385 A and its orders). Using preparations of intact, relaxed, bony fish fin muscles and the ID-02 low-angle X-ray camera at the ESRF with a 10 m camera length we have now seen numerous, hitherto unreported, sampled, X-ray layer-lines many of which do not fit onto the previously observed repeats and which require interpretation. The new reflections all fall on the normal ("vertical") hexagonal lattice row-lines in the highly sampled, almost "crystalline", low-angle diffraction X-ray patterns from bony fish muscle, indicating that they all arise from the muscle A-band. However, they do not fall on a single axial repeat. In direct confirmation of our previous analysis, some of these new reflections are explained by the interaction in resting muscle between the N-terminal ends of myosin-bound C-protein molecules with adjacent actin filaments, possibly through the Pro-Ala-rich region. Other newly observed reflections lie on a much longer repeat, but they are most easily interpreted in terms of the arrangement of troponin on the actin filaments. If this is so, then the implication is that the actin filaments and their troponin complexes are systematically arranged in the fish muscle A-band lattice relative to the myosin head positions, and that these newly observed X-ray reflections, when fully analysed, will report on the shape and distribution of troponin molecules in the resting muscle A-band. The less certain contributions of titin and nebulin to these new reflections have also been tested and are described. Many of the new reflections do not appear to come from these known structures. There must be structural features of the A-band that have not yet been described.

Bifunctional rhodamine probes of Myosin regulatory light chain orientation in relaxed skeletal muscle fibers

The orientation of the regulatory light chain (RLC) region of the myosin heads in relaxed skinned fibers from rabbit psoas muscle was investigated by polarized fluorescence from bifunctional rhodamine (BR) probes cross-linking pairs of cysteine residues introduced into the RLC. Pure 1:1 BR-RLC complexes were exchanged into single muscle fibers in EDTA rigor solution for 30 min at 30 degrees C; approximately 60% of the native RLC was removed and stoichiometrically replaced by BR-RLC, and >85% of the BR-RLC was located in the sarcomeric A-bands. The second- and fourth-rank order parameters of the orientation distributions of BR dipoles linking RLC cysteine pairs 100-108, 100-113, 108-113, and 104-115 were calculated from polarized fluorescence intensities, and used to determine the smoothest RLC orientation distribution-the maximum entropy distribution-consistent with the polarized fluorescence data. Maximum entropy distributions in relaxed muscle were relatively broad. At the peak of the distribution, the "lever" axis, linking Cys707 and Lys843 of the myosin heavy chain, was at 70-80 degrees to the fiber axis, and the "hook" helix (Pro830-Lys843) was almost coplanar with the fiber and lever axes. The temperature and ionic strength of the relaxing solution had small but reproducible effects on the orientation of the RLC region.

Helical order in tarantula thick filaments requires the "closed" conformation of the myosin head

Myosin heads are helically ordered on the thick filament surface in relaxed muscle. In mammalian and avian filaments this helical arrangement is dependent on temperature and it has been suggested that helical order is related to ATP hydrolysis by the heads. To test this hypothesis, we have used electron microscopy and image analysis to study the ability and temperature dependence of analogs of ATP and ADP.Pi to induce helical order in tarantula thick filaments. ATP or analogs were added to rigor myofibrils or purified thick filaments at 22 degrees C and 4 degrees C and the samples negatively stained. The ADP.Pi analogs ADP.AlF4 and ADP.Vi, and the ATP analogs ADP.BeFx, AMPPNP and ATPgammaNH2, all induced helical order in tarantula thick filaments, independent of temperature. In the absence of nucleotide, or in the presence of ADP or the ATP analog, ATPgammaS, there was no helical ordering. According to crystallographic and tryptophan fluorescence studies, all of these analogs, except ATPgammaS and ADP, induce the "closed" conformation of the myosin head (in which the gamma phosphate pocket is closed). We suggest that helical order requires the closed conformation of the myosin head but is not dependent on the hydrolysis of ATP.

MusLABEL: a program to model striated muscle A-band lattices, to explore crossbridge interaction geometries and to simulate muscle diffraction patterns

The program MusLABEL has been devised as a simple aid both in understanding the origin and appearance of fibre diffraction patterns from helical structures and also to simulate the structure and some features of the diffraction patterns from striated muscles and their filament components. Helices are common as preferred conformations in both natural and synthetic macromolecules (e.g. DNA, alpha -helices, polysaccharides, synthetic polymers), and they also occur frequently in extended macromolecular aggregates (e.g. actin filaments, myosin filaments, microtubules, amyloid filaments etc). For this reason, a simple way of visualising the kinds of diffraction patterns that these filament structures can give, particularly for the actin and myosin filaments in muscle, can have educational value and can also be useful as a quick means of evaluating possible symmetries in structural interpretations of diffraction data before embarking on full helical diffraction analysis. A feature of the MusLABEL program is that, when a particular kind of A-band lattice has been set up, for example for vertebrate striated muscle or insect flight muscle, additional parameters can be defined both to describe the limits to the azimuthal and axial ranges over which a myosin head can search for an actin binding site and also to describe the size and position of an actin 'target area' assuming that the azimuthal position of an actin monomer has a large effect in determining whether or not a myosin head can bind to it. By this means the effects of lattice geometry on head attachment can be explored and the diffraction effects of specific labelling patterns on actin can be calculated and simulated. The MusLABEL program, running under Microsoft Windows, is available free on the CCP13 website (www.ccp13.ac.uk) where further documentation is given.

Structural evidence for the interaction of C-protein (MyBP-C) with actin and sequence identification of a possible actin-binding domain

C-protein (MyBP-C) is a myosin-binding protein that is usually seen in two sets of seven to nine positions in the C-zones in each half of the vertebrate striated muscle A-band. Skeletal muscle C-protein is a modular structure containing ten sub-domains (C1 to C10) of which seven are immunoglobulin-type domains and three (C6, C7 and C9) are fibronectin-like domains. Cardiac muscle C-protein has an extra N-terminal domain (C0) and also some sequence insertions, one of which provides phosphorylation sites. It is conceivable that C-protein has both a structural and regulatory role within the sarcomere. The precise mode of binding of C-protein to the myosin filament has not been determined. However, detailed ultrastructural studies have suggested that C-protein, which binds to myosin, can give rise to a longer periodicity (about 435A) than the intrinsic myosin filament repeat of 429A. The reason for this has remained a puzzle for over 25 years. Here we show by modelling and computation that the presence of this longer periodicity could be explained if the myosin-binding part of C-protein binds to myosin with the expected 429A repeat, but if there are systematic interactions of the N-terminal end of C-protein with the neighbouring actin filaments in the hexagonal lattice of filaments in the A-band. We also show that if they occur these interactions would probably only arise in defined muscle states. Further analysis of the MyBP-C sequence identifies a possible actin-binding domain in the Pro-Ala-rich sequence found at the N terminus of skeletal MyBP-C and between domains C0 and C1 in the cardiac sequence.

Myosin head configuration in relaxed insect flight muscle: x-ray modeled resting cross-bridges in a pre-powerstroke state are poised for actin binding

Low-angle x-ray diffraction patterns from relaxed insect flight muscle recorded on the BioCAT beamline at the Argonne APS have been modeled to 6.5 nm resolution (R-factor 9.7%, 65 reflections) using the known myosin head atomic coordinates, a hinge between the motor (catalytic) domain and the light chain-binding (neck) region (lever arm), together with a simulated annealing procedure. The best head conformation angles around the hinge gave a head shape that was close to that typical of relaxed M*ADP*Pi heads, a head shape never before demonstrated in intact muscle. The best packing constrained the eight heads per crown within a compact crown shelf projecting at approximately 90 degrees to the filament axis. The two heads of each myosin molecule assume nonequivalent positions, one head projecting outward while the other curves round the thick filament surface to nose against the proximal neck of the projecting head of the neighboring molecule. The projecting heads immediately suggest a possible cross-bridge cycle. The relaxed projecting head, oriented almost as needed for actin attachment, will attach, then release Pi followed by ADP, as the lever arm with a purely axial change in tilt drives approximately 10 nm of actin filament sliding on the way to the nucleotide-free limit of its working stroke. The overall arrangement appears well designed to support precision cycling for the myogenic oscillatory mode of contraction with its enhanced stretch-activation response used in flight by insects equipped with asynchronous fibrillar flight muscles.

Direct modeling of x-ray diffraction pattern from skeletal muscle in rigor

Available high-resolution structures of F-actin, myosin subfragment 1 (S1), and their complex, actin-S1, were used to calculate a 2D x-ray diffraction pattern from skeletal muscle in rigor. Actin sites occupied by myosin heads were chosen using a "principle of minimal elastic distortion energy" so that the 3D actin labeling pattern in the A-band of a sarcomere was determined by a single parameter. Computer calculations demonstrate that the total off-meridional intensity of a layer line does not depend on disorder of the filament lattice. The intensity of the first actin layer A1 line is independent of tilting of the "lever arm" region of the myosin heads. Myosin-based modulation of actin labeling pattern leads not only to the appearance of the myosin and "beating" actin-myosin layer lines in rigor diffraction patterns, but also to changes in the intensities of some actin layer lines compared to random labeling. Results of the modeling were compared to experimental data obtained from small bundles of rabbit muscle fibers. A good fit of the data was obtained without recourse to global parameter search. The approach developed here provides a background for quantitative interpretation of the x-ray diffraction data from contracting muscle and understanding structural changes underlying muscle contraction.

Mammalian cardiac muscle thick filaments: their periodicity and interactions with actin

Cardiac muscle has been extensively studied, but little information is available on the detailed macromolecular structure of its thick filament. To elucidate the structure of these filaments I have developed a procedure to isolate the cardiac thick filaments for study by electron microscopy and computer image analysis. This procedure uses chemical skinning with Triton X-100 to avoid contraction of the muscle that occurs using the procedures previously developed for isolation of skeletal muscle thick filaments. The negatively stained isolated filaments appear highly periodic, with a helical repeat every third cross-bridge level (43 nm). Computed Fourier transforms of the filaments show a strong set of layer lines corresponding to a 43-nm near-helical repeat out to the 6th layer line. Additional meridional reflections extend to at least the 12th layer line in averaged transforms of the filaments. The highly periodic structure of the filaments clearly suggests that the weakness of the layer lines in x-ray diffraction patterns of heart muscle is not due to an inherently more disordered cross-bridge arrangement. In addition, the isolated thick filaments are unusual in their strong tendency to remain bound to actin by anti-rigor oriented cross-bridges (state II or state III cross-bridges) under relaxing conditions.

3D Structure of fish muscle myosin filaments

Myosin filaments isolated from goldfish (Carassius auratus) muscle under relaxing conditions and viewed in negative stain by electron microscopy have been subjected to 3D helical reconstruction to provide details of the myosin head arrangement in relaxed muscle. Previous X-ray diffraction studies of fish muscle (plaice) myosin filaments have suggested that the heads project a long way from the filament surface rather than lying down flat and that heads in a single myosin molecule tend to interact with each other rather than with heads from adjacent molecules. Evidence has also been presented that the head tilt is away from the M-band. Here we seek to confirm these conclusions using a totally independent method. By using 3D helical reconstruction of isolated myosin filaments the known perturbation of the head array in vertebrate muscles was inevitably averaged out. The 3D reconstruction was therefore compared with the X-ray model after it too had been helically averaged. The resulting images showed the same characteristic features: heads projecting out from the filament backbone to high radius and the motor domains at higher radius and further away from the M-band than the light-chain-binding neck domains (lever arms) of the heads.

Structure and nucleotide-dependent changes of thick filaments in relaxed and rigor plaice fin muscle

The myosin crossbridge array, positions of non-crossbridge densities on the backbone, and the A-band "end filaments" have been compared in chemically skinned, unfixed, uncryoprotected relaxed, and rigor plaice fin muscles using the freeze-fracture, deep-etch, rotary-shadowing technique. The images provide a direct demonstration of the helical packing of the myosin heads in situ in relaxed muscle and show rearrangements of the myosin heads, and possibly of other myosin filament proteins, when the heads lose ATP on going into rigor. In the H-zone these changes are consistent with crossbridge changes previously shown by others using freeze-substitution. In addition, new evidence is presented of protein rearrangements in the M-region (bare zone), associated with the transition from the relaxed to the rigor state, including a 27-nm increase in the apparent width of the M-region. This is interpreted as being mostly due to loss or rearrangement of a nonmyosin (M9) protein component at the M-region edge. The structure and titin periodicity of the end-filaments are described, as are suggestions of titin structure on the myosin filament backbone.

A-band architecture in vertebrate skeletal muscle: polarity of the myosin head array

Despite extensive knowledge of many muscle A-band proteins (myosin molecules, titin, C-protein (MyBP-C)), details of the organization of these molecules to form myosin filaments remain unclear. Recently the myosin head (crossbridge) configuration in a relaxed vertebrate muscle was determined from low-angle X-ray diffraction (Hudson et al. (1997), J Mol Biol 273: 440-455). This showed that, even without C-protein, the myosin head array displays a characteristic polar pattern with every third 143 A-spaced crossbridge level particularly prominent. However, X-ray diffraction cannot determine the polarity of the crossbridge array relative to the neighbouring actin filaments; information crucial to a proper understanding of the contractile event. Here, electron micrographs of negatively-stained goldfish A-segments and of fast-frozen, freeze-fractured plaice A-bands have been used to determine the resting myosin head polarity relative to the M-band. In agreement with the X-ray data, the prominent 429 A-spaced striations are seen outside the C-zone, where no non-myosin proteins apart from titin are thought to be located. The head orientation is with the concave side of the curved myosin heads (containing the entrance to the ATP-binding site) facing towards the M-band and the convex surface (containing the actin-binding region at one end) facing away from the M-band.

A new model for the surface arrangement of myosin molecules in tarantula thick filaments

Three-dimensional reconstructions of the negatively stained thick filaments of tarantula muscle with a resolution of 50 A have previously suggested that the helical tracks of myosin heads are zigzagged, short diagonal ridges being connected by nearly axial links. However, surface views of lower contour levels reveal an additional J-shaped feature approximately the size and shape of a myosin head. We have modelled the surface array of myosin heads on the filaments using as a building block a model of a two-headed regulated myosin molecule in which the regulatory light chains of the two heads together form a compact head-tail junction. Four parameters defining the radius, orientation and rotation of each myosin molecule were varied. In addition, the heads were allowed independently to bend in a plane perpendicular to the coiled-coil tail at three sites, and to tilt with respect to the tail and to twist at one of these sites. After low-pass filtering, models were aligned with the reconstruction, scored by cross-correlation and refined by simulated annealing. Comparison of the geometry of the reconstruction and the distance between domains in the myosin molecule narrowed the choice of models to two main classes. A good match to the reconstruction was obtained with a model in which each ridge is formed from the motor domain of a head pointing to the bare zone together with the head-tail junction of a neighbouring molecule. The heads pointing to the Z-disc intermittently occupy the J-position. Each motor domain interacts with the essential and regulatory light chains of the neighbouring heads. A near-radial spoke in the reconstruction connecting the backbone to one end of the ridge can be identified as the start of the coiled-coil tail.

Developments in fiber diffraction

Improved specimen preparation methods, third generation synchrotron sources, new data processing algorithms and molecular dynamics refinement techniques are, together, allowing the high-resolution structure determination of larger and larger macromolecular complexes by fiber diffraction. New synchrotron sources are also making possible both time-resolved studies and studies of ordered fibers only a few microns in diameter.

Structure of the capsid of Pf3 filamentous phage determined from X-ray fibre diffraction data at 3.1 A resolution

We have recorded X-ray diffraction patterns at 3.1 A resolution from magnetically aligned fibres of the Pf3 strain of filamentous bacteriophage (Inovirus). The patterns are similar to patterns from the higher-temperature form of the Pf1 strain, indicating that the Pf3 and Pf1 virions have the same helix symmetry and similar protein subunit shape. This is of particular interest, given that the primary structures of the two protein subunits are quite different; and the nucleotide/protein subunit ratio in the Pf3 virion is more than twice that in Pf1, indicating important differences in DNA packaging. We have built a molecular model of the Pf3 protein capsid based on the model of Pf1, and refined it against the diffraction data using simulated annealing. The refinement confirms that the two structures are similar, which may reflect a fundamental motif of alpha-helix packing. However, there are some differences between the structures: the Pf3 subunit appears to be completely alpha-helical, beginning at the N terminus, whereas the first few residues of the Pf1 subunit are not helical; and the structure of the C-terminal region of the Pf3 subunit at the inner surface of the tubular capsid indicates that DNA/protein interactions in this virion may involve both aromatic side-chains and positively charged side-chains, whereas those in the Pf1 virion involve predominantly only the latter. In the course of this work, we have developed new approaches to refinement and validation of helical structures with respect to continuous transform fibre diffraction data.

Myosin rod-packing schemes in vertebrate muscle thick filaments

Muscle myosin filament backbones are known to be aggregates of long coiled-coil alpha-helical myosin rods, but the packing arrangement is not understood in detail. Here we present new data on fish muscle myosin filaments from low-angle X-ray diffraction and from freeze-fracture, deep-etch electron microscopy which put constraints on the kind of models that might explain all of the observations. In particular, it is known in the case of vertebrate striated muscle thick filaments that the myosin head array in resting muscle is not perfectly helical but contains periodic perturbations. We show by analysis of low-angle X-ray diffraction patterns from resting bony fish muscle that any radial, azimuthal, and axial perturbations of the myosin head origins on the filament surface (due to perturbed myosin rod packing) must all be rather small and that the main perturbations are in the myosin head configurations (i.e., tilts, slews, rotations) on those origins. We provide evidence that the likely arrangement of titin molecules on the myosin filament is with them aligned parallel to the filament long axis, rather than following helical tracks. We also show from freeze-fracture studies of fish muscle that the myosin filament backbone (including titin and other extra proteins) has a radius of about 65-75 A and appears to contain a small (approximately 15-20 A radius) hollow core. Together with previously published evidence showing that the myosin rods are nearly parallel to the thick filament long axis, these results are consistent with the curved crystalline layer model of Squire (J. M. Squire, 1973, J. Mol. Biol. 77, 291-323), and they suggest a general structure for the C-zone part of the thick filament