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.

Reprint of "Structural correlation between collagen VI microfibrils and collagen VI banded aggregates" [J. Struct. Biol. 154 (2006) 312-326]

Collagen VI is a component of the extracellular matrix that is able to form structural links with cells. Collagen VI monomers cross-link into tetramers that come together to form long molecular chains known as microfibrils. Collagen VI tetramers are also the most likely candidates for the formation of banded aggregates with an axial periodicity of about 105 nm that are seen in the retinas of people suffering from age-related macular degeneration and Sorsby's fundus dystrophy, in the vitreous of patients with full thickness macular holes and in the intervertebral discs of normal individuals. Here, a protocol is developed to carry out a structural comparison between the microfibrils, which are known to be made of collagen VI tetramers, and the banded aggregates. The comparison shows that the banded aggregates are easily explained as being a lateral assembly of microfibrils, thus supporting the hypothesis that they too are made of collagen VI. Understanding the role played by the collagen VI aggregates in normal and pathological conditions will help to throw light on the pathologies with which they are associated.

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.

Structural correlation between collagen VI microfibrils and collagen VI banded aggregates

Collagen VI is a component of the extracellular matrix that is able to form structural links with cells. Collagen VI monomers cross-link into tetramers that come together to form long molecular chains known as microfibrils. Collagen VI tetramers are also the most likely candidates for the formation of banded aggregates with an axial periodicity of about 105 nm that are seen in the retinas of people suffering from age-related macular degeneration and Sorsby's fundus dystrophy, in the vitreous of patients with full thickness macular holes and in the intervertebral discs of normal individuals. Here, a protocol is developed to carry out a structural comparison between the microfibrils, which are known to be made of collagen VI tetramers, and the banded aggregates. The comparison shows that the banded aggregates are easily explained as being a lateral assembly of microfibrils, thus supporting the hypothesis that they too are made of collagen VI. Understanding the role played by the collagen VI aggregates in normal and pathological conditions will help to throw light on the pathologies with which they are associated.

Molecular packing in network-forming collagens

Different collagen types can vary considerably in length, molecular weight, chemical composition, and the way they interact with each other to form molecular aggregates. Collagen Types IV, VI, VIII, X, and dogfish egg case collagen make linear and lateral associations to form open networks rather than fibers. The roles played by these network-forming collagens are diverse: they can act as support and anchorage for cells and tissues, serve as molecular filters, and even provide protective permeable barriers for developing embryos. Their functional properties are intimately linked to their molecular organization. This Chapter reviews what is known about the molecular structure of this group of collagens, describes the ways the molecules interact to form networks, and-despite the large variations in molecular size-identifies common aggregation themes.

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.

HELIX: a helical diffraction simulation program

The programHELIXhas been devised as a simple aid to understanding the origin and appearance of fibre diffraction patterns from helical structures. Helices are common as preferred conformations in both natural and synthetic macromolecules (e.g.DNA, α-helices, polysaccharides, synthetic polymers), and occur frequently in extended macromolecular aggregates (e.g.actin filaments, myosin filaments, microtubules, amyloid filamentsetc.). For this reason, a simple way of visualizing the kinds of diffraction patterns that these structures can give should have educational value and should also be useful as a quick means of testing possible symmetries in structural investigations before embarking on full helical diffraction analysis. Despite its simplicity, there is no other public program that provides these possibilities. TheHELIXprogram, running under Microsoft Windows, is freely available from the CCP13 website (http://www.ccp13.ac.uk).

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.

Modulation of Sub-RPE Deposits In Vitro: A Potential Model for Age-Related Macular Degeneration

PURPOSE

Sub-RPE deposits form in a variety of conditions most notably in age-related macular degeneration. The purpose of this study was to generate sub-RPE deposits in vitro and to test the hypotheses that high protein concentrations or retinal homogenate increase deposit formation and that a challenge with tumor necrosis factor (TNF)-alpha or metalloproteinase (MMP)-2 decreases such deposits.

METHODS

ARPE-19 cells were grown on plastic and on collagen type I-coated membrane inserts in media containing various concentrations of fetal calf serum (FCS), bovine serum albumin, or porcine retinal homogenate. In addition, cells grown on membrane inserts were treated with TNF-alpha or MMP-2. Sub-RPE deposits were assessed by electron microscopy and classified into fibrillar, condensed, banded, and membranous subtypes. The area of the micrograph occupied by each type was estimated with a point-counting technique. MMP-2 activity was assessed in tissue culture supernatants by zymography.

RESULTS

With increasing time in culture, total deposit formation did not change, but the amount of condensed material deposited by ARPE-19 cells increased while the fibrillar component decreased. Albumin challenge resulted in an increased amount of deposit, predominantly of the membranous type. Challenge with retinal homogenate led to a greater net deposit formation with significant increases in the condensed and banded forms. Cells treated with TNF-alpha or MMP-2 showed a dramatic reduction in all types of sub-RPE deposit. Zymography demonstrated that unchallenged cells produced predominantly MMP-2. Retinal homogenate challenge reduced the total amount of active MMP-2 produced, and TNF-alpha stimulated MMP-9 production.

CONCLUSIONS

Sub-RPE deposits formed in vitro share ultrastructural features with those seen in vivo. Deposit formation can be modulated by challenge with retinal homogenate, TNF-alpha, or MMP-2. Significantly, the results provide proof of the principle that sub-RPE deposits can be formed and modified in vitro.

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.

Molecular packing in network-forming collagens

Collagen is the most abundant protein among vertebrates and occurs in virtually all multicellular animals. Collagen molecules are classified into 21 different types and differ in their sequence, weight, structure, and function, but they can be broadly subdivided into families. Type IV, VI, VIII, X, and dogfish egg case collagens belong to the network-forming family. Here, we summarise what is known about the way these collagen molecules pack to form networks. In addition the main structural characteristics of the network-forming collagens are compared and discussed.

Modelling muscle motor conformations using low-angle X-ray diffraction

New results on myosin head organization using analysis of low-angle X-ray diffraction patterns from relaxed insect flight muscle (IFM) from a giant waterbug, building on previous studies of myosin filaments in bony fish skeletal muscle (BFM), show that the information content of such low-angle diffraction patterns is very high despite the 'crystallographically low' resolution limit (65 A) of the spacings of the Bragg diffraction peaks being used. This high information content and high structural sensitivity arises because: (i) the atomic structures of the domains of the myosin head are known from protein crystallography; and (ii) myosin head action appears to consist mainly of pivoting between domains which themselves stay rather constant in structure, thus (iii) the intensity distribution among diffraction peaks in even the low resolution diffraction pattern is highly determined by the high-resolution distribution of atomically modelled domain mass. A single model was selected among 5000+ computer-generated variations as giving the best fit for the 65 reflections recorded within the selected resolution limit of 65 A. Clear evidence for a change in shape of the insect flight muscle myosin motor between the resting (probably like the pre-powerstroke) state and the rigor state (considered to mimic the end-of-powerstroke conformation) has been obtained. This illustrates the power of the low-angle X-ray diffraction method. The implications of these new results about myosin motor action during muscle contraction are discussed.

Titin organisation and the 3D architecture of the vertebrate-striated muscle I-band

The giant muscle protein titin (connectin) is known to serve as a cytoskeletal element in muscle sarcomeres. It elastically restrains lengthening sarcomeres, it aids the integrity and central positioning of the A-band in the sarcomere and it may act as a template upon which some sarcomeric components are laid down during myogenesis. A puzzle has been how titin molecules, arranged systematically within the hexagonal A-band lattice of myosin filaments, can redistribute through the I-band to their anchoring sites in the tetragonal Z-band lattice. Recent work by Liversage and colleagues has suggested that there are six titin molecules per half myosin filament. Since there are two actin filaments per half myosin filament in a half sarcomere, this means that there are three titin molecules interacting with each Z-band unit cell containing one actin filament in the same sarcomere and one of opposite polarity from the next sarcomere. Liversage et al. suggested that the three titins might be distributed with two on an actin filament of one polarity and one on the filament of opposite polarity. Here, we build on this suggestion and discuss the transition of titin from the A-band to the Z-band. We show that there are good structural and mechanical reasons why titin might be organised as Liversage et al., suggested and we discuss the possible relationships between A-band arrangements in successive sarcomeres along a myofibril.

Collagen VI assemblies in age-related macular degeneration

Age-related macular degeneration (AMD) is the most common cause of incurable blindness in the developed world. Little is known about the pathogenesis of this condition, but deposits in Bruch's membrane and immediately beneath the retinal pigment epithelium are frequent findings associated with this disease. Within these deposits, molecular assemblies with an approximately 100-nm axial periodicity are seen. Two types of assembly are present: one exhibiting transverse double bands of protein density that are 30nm apart and repeat axially every approximately 100nm; the other with transverse double bands of protein density, 30nm apart and repeating axially every approximately 50nm. In this second type of assembly, more prominent pairs of bands alternate with less prominent ones. By comparison with analogous aggregates found in the vitreous of a patient with a full-thickness macular hole, collagen VI was singled out as the most probable protein constituent of the AMD aggregates. Possible models for the aggregation patterns of these assemblies are discussed in terms of collagen VI dimers and tetramers. Understanding the structure and chemical composition of the assemblies within the AMD basal deposits may prove of great help in understanding the pathophysiology of AMD itself.

Absence of clinically relevant drug interactions following simultaneous administration of didanosine-encapsulated, enteric-coated bead formulation with either itraconazole or fluconazole

This open-label, two-way crossover study was undertaken to determine whether the enteric formulation of didanosine influences the pharmacokinetics of itraconazole or fluconazole, two agents frequently used to treat fungal infections that occur with HIV infection, and whose bioavailability may be influenced by changes in gastric pH. Healthy subjects were randomized to Treatment A (200-mg itraconazole or 200-mg fluconazole) or Treatment B (same dose of itraconazole or fluconazole with 400 mg of didanosine as an encapsulated, enteric-coated bead formulation). In the itraconazole study, a lack of interaction was concluded if the 90% confidence interval (CI) of the ratio of the geometric means of log-transformed C(max) and AUC(0-T) values of itraconazole and hydroxyitraconazole, the active metabolite of itraconazole, were contained entirely between 0.75 and 1.33. In the fluconazole study, the equivalence interval for C(max) and AUC(0-T) was 0.80-1.25. The data showed that for itraconazole the point estimate and 90% CI of the ratios of C(max) and AUC(0-T) values were 0.98 (0.79, 1.20) and 0.88 (0.71, 1.09), respectively; for hydroxyitraconazole the respective values were 0.91 (0.76, 1.08) and 0.85 (0.68, 1.06). In the fluconazole study, the point estimate and 90% CI of the ratios of C(max) and AUC(0-T) values were 0.98 (0.93, 1.03) and 1.01 (0.99, 1.03), respectively. The T(max) for itraconazole, hydroxyitraconazole, and fluconazole were similar between treatments. Both studies indicated a lack of clinically significant interactions of the didanosine formulation with itraconazole or fluconazole. These results showed that the encapsulated, enteric-coated bead formulation of didanosine can be concomitantly administered with drugs, such as the azole antifungal agents, whose bioavailability may be influenced by interaction with antacids.

Analysis of the collagen VI assemblies associated with Sorsby's fundus dystrophy

Age-related macular degeneration is the leading cause of blindness in the Western world, and the pathophysiology of the condition is largely unknown. However, it shares many clinical and pathological features with Sorsby's fundus dystrophy (SFD), an autosomal dominant disease, known to be associated with mutations in the TIMP-3 gene. In Bruch's membrane of both conditions, there are molecular assemblies with distinct transverse bands occurring with a periodicity of about 100 nm. Similar assemblies were also found in the vitreous of a patient with full-thickness macular holes and were identified as being made of collagen VI. The assemblies found in the eye with SFD can be classified into two types, both with a 105-nm axial repeat, but one showing pairs of narrow bands about 30 nm apart and the other showing a single broad band in every repeat. By comparison with the assemblies in the vitreous, collagen VI is considered to be the most likely protein in these assemblies. Furthermore, both of the assemblies associated with SFD can be explained in terms of collagen VI tetramers, one in which the tetramers bind to the mutant tissue inhibitor of metalloproteinases-3 (the gene product of TIMP-3) and the other in which little or no binding occurs. TIMP-3 bound to collagen VI may be more resistant to degradation and create an imbalance between the normal amount of TIMP-3 and matrix metalloproteinases (the substrate of TIMPs) in Bruch's membrane with consequent disruption of the normal metabolic processes. Understanding the structure of these collagen VI/TIMP assemblies in Bruch's membrane may prove to be important for understanding the pathophysiology of age-related macular degeneration.

Review of the pharmacokinetics of cefepime in children

BACKGROUND

Because determining the pharmacokinetics of drugs used in pediatric patients allows for appropriate dosing and optimal clinical response, we have reviewed the pharmacokinetic data on the use of cefepime in the pediatric population.

METHODS

Three studies encompassing 88 patients ages 2 months to 16 years examined the pharmacokinetics of cefepime given as a single iv dose, as multiple iv doses and by im administration. In all studies serial blood and urine or cerebrospinal fluid (CSF) samples were collected after a single dose and/or at steady state, defined as after at least 2 days of dosing. Pharmacokinetic parameters were generated from concentration-vs.-time curves and were analyzed using noncompartmental methods.

RESULTS

In all studies cefepime exhibited a linear pharmacokinetic profile and concentrations declined proportionally over time. Minimal accumulation was observed after multiple dosing. Pharmacokinetic parameters were similar in all studies and appeared to be dose-independent. Mean (range) parameters observed in this review were: t 1/2 = 1.7 h (1.26 to 1.93); volume of distribution at steady state, 0.37 liter/kg (0.33 to 0.40); total body clearance, 3.1 ml/min/kg (1.43 to 4.01); renal total body clearance, 2.3 ml/min/kg (1.86 to 3.05); absolute bioavailability of cefepime after the im dose, 82.3%; and urinary recovery, 72% (57 to 85%). Penetration into CSF appeared to be good, with CSF concentrations averaging 3.3 to 5.7 microg/ml 0.5 and 8 h after administration of the dose, respectively.

CONCLUSION

Cefepime displayed a linear pharmacokinetic profile, was well-absorbed via im injection and had adequate penetration into the CSF of patients with bacterial meningitis, compared with other beta-lactams.

A new twist in the collagen story--the type VI segmented supercoil

Collagen occurs in two major forms: fibrillar and non-fibrillar. Non-fibrillar collagens are structurally more variable and relatively ill-understood. In this work we analysed the amino acid sequence of type VI collagen, a non-fibrillar collagen that forms antiparallel dimers. A sequence motif was discovered that gives rise to systematic molecular coiling. There is a common periodicity ( approximately 23 or 2 x 23 residues) in the charged amino acids, in the prolines and in the discontinuities in the Gly-X-Y triplets. In addition, there is a different periodicity ( approximately 21 amino acids) in the apolar groups. The two repeats mean that the only way to simultaneously maximize both the hydrophobic and polar interactions during dimer formation is with the molecules antiparallel, overlapped by 75 nm as observed, and supercoiled. The alternating proline-rich and charge-rich patches, often together with discontinuities in the Gly-X-Y sequences, coincide with each half-turn of the supercoil, thus breaking it into segments. We have termed this structure the collagen segmented supercoil. The segmented supercoil and variants may be common aggregation motifs for the non-fibrillar collagens.

Bioavailability of once- and twice-daily regimens of didanosine in human immunodeficiency virus-infected children

The bioavailability of didanosine at 180 mg/m(2) once daily was compared to that at 90 mg/m(2) twice daily in 24 children with advanced human immunodeficiency virus infection. Children were studied at steady state using optimal sampling and prior pharmacokinetic parameter estimates. Relative bioavailability was 0. 95 +/- 0.49, supporting the potential clinical adequacy of once-daily dosing.