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

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.

Myosin Cross-Bridge Behaviour in Contracting Muscle-The T1 Curve of Huxley and Simmons (1971) Revisited

The stiffness of the myosin cross-bridges is a key factor in analysing possible scenarios to explain myosin head changes during force generation in active muscles. The seminal study of Huxley and Simmons (1971: Nature233: 533) suggested that most of the observed half-sarcomere instantaneous compliance (=1/stiffness) resides in the myosin heads. They showed with a so-called T₁ plot that, after a very fast release, the half-sarcomere tension reduced to zero after a step size of about 60Å (later with improved experiments reduced to 40Å). However, later X-ray diffraction studies showed that myosin and actin filaments themselves stretch slightly under tension, which means that most (at least two-thirds) of the half sarcomere compliance comes from the filaments and not from cross-bridges. Here we have used a different approach, namely to model the compliances in a virtual half sarcomere structure in silico. We confirm that the T₁ curve comes almost entirely from length changes in the myosin and actin filaments, because the calculated cross-bridge stiffness (probably greater than 0.4 pN/Å) is higher than previous studies have suggested. Our model demonstrates that the formulations produced by previous authors give very similar results to our model if the same starting parameters are used. However, we find that it is necessary to model the X-ray diffraction data as well as mechanics data to get a reliable estimate of the cross-bridge stiffness. In the light of the high cross-bridge stiffness found in the present study, we present a plausible modified scenario to describe aspects of the myosin cross-bridge cycle in active muscle. In particular, we suggest that, apart from the filament compliances, most of the cross-bridge contribution to the instantaneous T₁ response may come from weakly-bound myosin heads, not myosin heads in strongly attached states. The strongly attached heads would still contribute to the T₁ curve, but only in a very minor way, with a stiffness that we postulate could be around 0.1 pN/Å, a value which would generate a working stroke close to 100 Å from the hydrolysis of one ATP molecule. The new model can serve as a tool to calculate sarcomere elastic properties for any vertebrate striated muscle once various parameters have been determined (e.g., tension, T₁ intercept, temperature, X-ray diffraction spacing results).

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.

SAXS4COLL: an integrated software tool for analysing fibrous collagen-based tissues

SAXS4COLL is an interactive computer program for reduction and analysis of small-angle X-ray scattering data from fibrous collagen tissues, combining data reduction, bespoke background subtraction, semi-automated peak detection and calibration.

This article provides an overview of a new integrated software tool for reduction and analysis of small-angle X-ray scattering (SAXS) data from fibrous collagen tissues, with some wider applicability to other cylindrically symmetric scattering systems. SAXS4COLL combines interactive features for data pre-processing, bespoke background subtraction, semi-automated peak detection and calibration. Both equatorial and meridional SAXS peak parameters can be measured, and the former can be deconstructed into cylinder and lattice contributions. Finally, the software combines functionality for determination of collagen spatial order parameters with a rudimentary orientation plot capability.

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.

The myosin filament superlattice in the flight muscles of flies: A-band lattice optimisation for stretch-activation?

Low-angle X-ray diffraction patterns from relaxed fruitfly (Drosophila) flight muscle recorded on the BioCat beamline at the Argonne Advanced Photon Source (APS) show many features similar to such patterns from the "classic" insect flight muscle in Lethocerus, the giant water bug, but there is a characteristically different pattern of sampling of the myosin filament layer-lines, which indicates the presence of a superlattice of myosin filaments in the Drosophila A-band. We show from analysis of the structure factor for this lattice that the sampling pattern is exactly as expected if adjacent four-stranded myosin filaments, of repeat 116 nm, are axially shifted in the hexagonal A-band lattice by one-third of the 14.5 nm axial spacing between crowns of myosin heads. In addition, electron micrographs of Drosophila and other flies (e.g. the house fly (Musca) and the flesh fly (Sarcophaga)) combined with image processing confirm that the same A-band superlattice occurs in all of these flies; it may be a general property of the Diptera. The different A-band organisation in flies compared with Lethocerus, which operates at a much lower wing beat frequency (approximately 30 Hz) and requires a warm-up period, may be a way of optimising the myosin and actin filament geometry needed both for stretch activation at the higher wing beat frequencies (50 Hz to 1000 Hz) of flies and their need for a rapid escape response.

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.

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.