Multi-wavelength anomalous diffraction using medium-angle X-ray solution scattering (MADMAX).

Proteins are dynamic molecules whose function in virtually all biological processes requires conformational motion. Direct experimental probes of protein structure in solution are needed to characterize these motions. Anomalous scattering from proteins in solution has the potential to act as a precise molecular ruler to determine the positions of specific chemical groups or atoms within proteins under conditions in which structural changes can take place free from the constraints of crystal contacts. In solution, anomalous diffraction has two components: a set of cross-terms that depend on the relative location of the anomalous centers and the rest of the protein, and a set of pure anomalous terms that depend on the distances between the anomalous centers. The cross-terms are demonstrated here to be observable and to provide direct information about the distance between the anomalous center and the center of mass of the protein. The second set of terms appears immeasurably small in the context of current experimental capabilities. Here, we outline the theory underlying anomalous scattering from proteins in solution, predict the anomalous differences expected on the basis of atomic coordinate sets, and demonstrate the measurement of anomalous differences at the iron edge for solutions of myoglobin and hemoglobin.

Characterisation of the learning curve of caesarean section.

INTRODUCTION: Caesarean section is one of the common operations in medicine. As almost all interventions, the quality of the operation depends on the training and skills of the surgeon. This study aims at characterising the learning curve of caesarean section. MATERIAL AND METHODS: All patients with a singleton pregnancy who underwent a caesarean section between 2000 and 2009 in our university hospital were identified. We analysed datasets from beginners (no experience at all) and experienced surgeons (>300 caesarean sections, consultant) comparing the parameter incision-suture time (I-S time), incision-delivery time (I-D time), maternal blood loss, umbilical artery pH (ua-pH), APGAR score after 1, 5 and 10 min, mean time in hospital and postoperative complications. In addition, the first 100 caesarean sections of each beginner surgeon were divided in groups of 10 (1-10, 11-20, etc.) and analysed using the above-mentioned parameters. The learning curves were calculated. RESULTS: 2,515 of 3,844 operations were carried out by 23 experienced surgeons versus 1,329 operations by 22 beginners. The I-S time and I-D time was significantly higher in the beginners group than in the experienced surgeon's group (45.9 vs. 41.3 min, p < 0.001). Furthermore, for the first ten caesarean sections, the mean I-S time (47.9 min, 95% CI 45.7-50.0 min vs. 31-40th caesarean section with 43.1 min, 95% CI 40.9-45.3 min, p < 0.0001) and I-D time (9.5 min, 95% CI 8.6-10.5 min vs. 71-80th caesarean section with 4.8 min, 95% CI 4.2-5.4 min, p < 0.0001) was significantly higher than of the subsequent datasets of ten operations, showing a typical learning curve. CONCLUSION: The learning curve for the total operation time and incision-delivery time reaches a flatter part after 10-15 caesarean sections. However, the learning process is highly individualised and difficult to predict, so that supervision and evaluation of the trainee by an experienced surgeon is important.

Sex related differences in therapy and outcome of patients with intermittent claudication in a real-world cohort.

BACKGROUND AND AIMS: The prevalence of lower extremity artery disease (LEAD) is increasing worldwide and sex-related differences are a current matter of debate. METHODS: We analysed claims data on unselected patients with in-patient treatment for LEAD with intermittent claudication (IC; Rutherford grade 1-3) from 01.01.2014 to 31.12.2015. Data files included diagnostic and procedural information from two years before index, and a five-year follow-up. RESULTS: Our analysis comprised 42,197 IC patients, thereof 28,520 (68%) male. Male patients were younger (median: 66.4 years vs. 72.6 years) but presented with higher frequency of cardiovascular risk factors such as diabetes (40% female vs. 46% male), atrial fibrillation (13% vs. 17%), chronic coronary syndrome (41% vs. 53%), chronic heart failure (23% vs. 27%), or chronic kidney disease (29% vs. 32%; all p < 0.001; age adjusted). Revascularisation applied in 80% of patients, thereof endovascular approach predominantly in female and surgery in male patients. Concomitant pharmacotherapy with statins (74% at 2 years) and platelet inhibitors (75% respectively) were long lasting below guideline recommendation, under-use being more pronounced in women. Two years after index, one-third of IC patients had subsequent revascularisation, one-quarter progressed to chronic limb threatening ischemia (CLTI), and 2% underwent amputation. Male sex was an independent risk factor for long-term mortality (female HR 0.75; 95%-CI 0.72-0.79; p < 0.001) and CLTI (female HR 0.89; 95%-CI 0.86-0.92; p < 0.001) during follow-up. CONCLUSIONS: The majority of in-patient treated patients for IC are male, presenting with worse cardiovascular risk profiles. In view of a general under-supply with statins and platelet inhibitors, women received somewhat less often preventive medication. Despite low LEAD stages at index, serious prognosis was observed in the long term. Particularly male patients were at high risk for all-cause mortality and the combined endpoint CLTI and death.

Gap junction structures. I. Correlated electron microscopy and x-ray diffraction.

X-ray crystallographic methods and electron microscope image analysis have been used to correlate the structure and the chemical composition of gap junction plaques isolated intact from mouse liver. The requirement that the interpretations of X-ray, electron microscope, and chemical measurements be consistent reduces the uncertainties inherent in the separate observations and leads to a unified picture of the gap junction structures. Gap junctions are built up of units called connexons that are hexagonally arrayed in the pair of connected cell membranes. X-ray diffraction and electron microscope measurements show that the lattice constant of this array varies from about 80 to 90 A. Analysis of electron micrographs of negatively stained gap junctions shows that there is significant short range disorder in the junction lattice. even though the long range order of the array is remarkably regular. Analysis of the disorder provides information about the nature of the intermolecular forces that hold the array together.

Gap junction structures. II. Analysis of the x-ray diffraction data.

Models for the spatial distribution of protein, lipid and water in gap junction structures have been constructed from the results of the analysis of X-ray diffraction data described here and the electron microscope and chemical data presented in the preceding paper (Caspar, D. L. D., D. A. Goodenough, L. Makowski, and W.C. Phillips. 1977. 74:605-628). The continuous intensity distribution on the meridian of the X-ray diffraction pattern was measured, and corrected for the effects of the partially ordered stacking and partial orientation of the junctions in the X-ray specimens. The electron density distribution in the direction perpendicular to the plane of the junction was calculated from the meridional intensity data. Determination of the interference function for the stacking of the junctions improved the accuracy of the electron density profile. The pair-correlation function, which provides information about the packing of junctions in the specimen, was calculated from the interference function. The intensities of the hexagonal lattice reflections on the equator of the X-ray pattern were used in coordination with the electron microscope data to calculate to the two-dimensional electron density projection onto the plane of the membrane. Differences in the structure of the connexons as seen in the meridional profile and equatorial projections were shown to be correlated to changes in lattice constant. The parts of the junction structure which are variable have been distinguished from the invariant parts by comparison of the X-ray data from different specimens. The combination of these results with electron microscope and chemical data provides low resolution three- dimensional representations of the structures of gap junctions.

Polymorphism of sickle cell hemoglobin aggregates: structural basis for limited radial growth.

Fibers composed of molecules of deoxygenated sickle cell hemoglobin are the basic cause of pathology in sickle cell disease. The hemoglobin molecules in these fibers are arranged in double strands that twist around one another with a long axial repeat. These fibrous aggregates exhibit a pattern of polymorphism in which the ratio of their helical pitch to their radius is approximately constant. The observed ratio agrees with an estimate of its value calculated from the geometric properties of helical assemblies and the degree of distortion that a protein-protein interface can undergo. This agreement indicates that the radius of an aggregate is limited by the maximum possible stretching of double strands. The geometric properties limiting the radial extent of sickle hemoglobin fibers are fundamental to all cables of protein filaments and could contribute to the control of diameter in other biological fibers such as collagen or fibrin.

X-ray diffraction from magnetically oriented solutions of macromolecular assemblies.

A simple system was developed for obtaining x-ray diffraction patterns from magnetically oriented solutions of macromolecular assemblies. A small permanent magnet was designed that produces a magnetic field of 16 kilogauss in a volume of 1 cubic millimeter and is mountable on most x-ray cameras. Many subcellular structures have sufficient diamagnetic anisotropy that they exhibit orientation in dilute solution when placed between the poles of the magnet. Diffraction from solutions oriented in this magnet can provide substantially more structural information than small-angle scattering from isotropic solutions. In favorable cases, such as dilute solutions of filamentous bacteriophages, it is possible to produce oriented fiber diffraction patterns from which intensities along layer lines can be measured to 7-angstrom resolution. The magnetically induced birefringence observed in solutions of other macromolecular assemblies suggests that this technique may have broad applicability to subcellular structures.

Membrane-mediated assembly of filamentous bacteriophage Pf1 coat protein.

Filamentous bacteriophage Pf1 assembles by a membrane-mediated process during which the viral DNA is secreted through the membrane while being encapsulated by the major coat protein. Neutron diffraction studies showed that in the virus most of the coat protein consists of two alpha-helical segments arranged end-to-end with an intervening mobile surface loop. Nuclear magnetic resonance studies of the coat protein in the membrane-bound form have shown that the secondary structure is essentially identical to that in the intact virus. A comparison indicates that during membrane-mediated viral assembly, while the secondary structure of the coat protein is largely conserved, its tertiary structure changes substantially.

Role of LKB1 in lung cancer development.

Three phenotypically related genetic syndromes and their lesions (LKB1, PTEN, and TSC1/2) are identified as frequently altered in lung cancer. LKB1, a kinase inactivated in 30% of lung cancers, is discussed in this review. Loss of LKB1 regulation often coincident with KRAS activation allows for unchecked growth and the metabolic capacity to accommodate the proliferation.

Altered insulin secretion associated with reduced lipolytic efficiency in aP2-/- mice.

Recent studies have shown that genetic deficiency of the adipocyte fatty acid-binding protein (aP2) results in minor alterations of plasma lipids and adipocyte development but provides significant protection from dietary obesity-induced hyperinsulinemia and insulin resistance. To identify potential mechanisms responsible for this phenotype, we examined lipolysis and insulin secretion in aP2-/- mice. Beta-adrenergic stimulation resulted in a blunted rise of blood glycerol levels in aP2-/- compared with aP2+/+ mice, suggesting diminished lipolysis in aP2-/- adipocytes. Confirming this, primary adipocytes isolated from aP2-/- mice showed attenuated glycerol and free fatty acid (FFA) release in response to dibutyryl cAMP. The decreased lipolytic response seen in the aP2-/- mice was not associated with altered expression levels of hormone-sensitive lipase or perilipin. The acute insulin secretory response to beta-adrenergic stimulation was also profoundly suppressed in aP2-/- mice despite comparable total concentrations and only minor changes in the composition of systemic FFAs. To address whether levels of specific fatty acids are different in aP2-/- mice, the plasma FFA profile after beta-adrenergic stimulation was determined. Significant reduction in both stearic and cis-11-eicoseneic acids and an increase in palmitoleic acid were observed. The response of aP2-/- mice to other insulin secretagogues such as arginine and glyburide was similar to that of aP2+/+ mice, arguing against generally impaired function of pancreatic beta-cells. Finally, no aP2 expression was detected in isolated pancreatic islet cells. These results provide support for the existence of an adipo-pancreatic axis, the proper action of which relies on the presence of aP2. Consequently, aP2's role in the pathogenesis of type 2 diabetes might involve regulation of both hyperinsulinemia and insulin resistance through its impact on both lipolysis and insulin secretion.

Terminating a macromolecular helix. Structural model for the minor proteins of bacteriophage M13.

Analysis of the results of X-ray diffraction, electron microscopy and s sequence studies of filamentous bacteriophage M13 are used to construct structural models for the minor proteins gp7 and gp9 at the end of the virus assembled first, and a portion of gp6 at the end of the virus that binds host. Comparison of the sequence of the major coat protein, gp8, with those of gp7, gp9 and gp6 indicates that significant portions of these three proteins have sequences similar to that of gp8. Assuming that sequence similarity is indicative of structural similarity, gp7, gp9 and portions of gp6 are modeled based on what is known about the structure of gp8. These molecular models are analyzed to predict the packing of the minor proteins with the terminal gp8 proteins (the last gp8 proteins at either end of the helix). This analysis indicates that the gp8 proteins integrated into the virus first may have a structure distinct from those in the body of the virus particle. The gp8 proteins at the end assembled last appear to have a conformation very similar to that of the integral coat proteins. These models place specific constraints on models for the process of viral assembly.

Helical structure of P pili from Escherichia coli. Evidence from X-ray fiber diffraction and scanning transmission electron microscopy.

The structure of the P pili from Escherichia coli has been studied using X-ray fiber diffraction and scanning transmission electron microscopy (STEM). Analysis of the fiber diffraction data indicates that the pili are constituted largely of structural subunits arranged helically with approximately 33 subunits in 10 turns in an axial repeat of 244.5 +/- 1.8 A. Radial electron density distributions calculated from equatorial diffraction data and STEM data indicate that the pili are about 65 A in diameter with a small central cavity roughly 15 A across. The principal protein component of the pili is PapA, which has a molecular weight of 16.5 kDa. Assuming that each subunit consists of a single PapA molecule, the mass-per-unit-length of the pili predicted from the X-ray data is 2.23 kDa/A. Measurements of mass-per-unit-length were also made through the analysis of STEM images. These measurements indicate a value of 2.13 +/- 0.14 kDa/A. STEM images demonstrated the presence of thin, thread-like structures emerging from the ends of pili and spanning breaks in the pili structure. These structures, which have been observed under other conditions, have been termed fibrillae. In the STEM images the fibrillae appear about 20 A in diameter. The mass-per-unit-length of the fibrillae was estimated using the STEM data to be 0.4 kDa/A. These data are consistent with the fibrillae representing an unwound or unraveled form of the pili proteins overstretched to about five times the length they would have in the intact pili.

Neutron diffraction studies of the structure of filamentous bacteriophage Pf1. Demonstration that the coat protein consists of a pair of alpha-helices with an intervening, non-helical surface loop.

The structure of filamentous bacteriophage Pf1 has been studied using neutron diffraction from magnetically oriented gels of native and specifically deuterated phage. These methods have been used to determine the positions of the two methionine, two tyrosine and six isoleucine residues of the coat protein. Combined with the positions of the five valine residues previously determined, they represent one third (15 of 46) of the residues of the coat protein. These 15 amino acid residue positions have been used as the basis for constructing a model for the protein consisting of two alpha-helices with an intervening surface loop. The first helix extends from near the amino terminus to Ile12. The second helix extends from Lys20 to at least Met42, and may contain a bend between Ile32 and Val35. The two helices are tilted by about 15 degrees relative to one another, and are positioned in such a way that they appear to be bound end-to-end by main-chain hydrogen bonds. The intervening, non-helical loop, made up of Thr13 to Met19, connects the two helices without disrupting the pattern of main-chain hydrogen bonding, but does not result in a bend in the otherwise continuous helical structure. This model is used to predict the approximate positions of all amino acid residues in the Pf1 protein coat, providing a basis for further understanding of a number of viral properties including the symmetry transitions, the non-isomorphism of heavy-atom derivatives, and the protein-protein and protein-DNA interactions in the virion.

Structure of a foreign peptide displayed on the surface of bacteriophage M13.

The use of filamentous bacteriophage M13 as a vehicle for display of foreign peptides and proteins provides a means for the construction of therapeutic, diagnostic and technological tools of broad utility. The usefulness of this technology is dependent on the ability of an inserted peptide to act as a ligand when fused to a structural protein. This, in turn, depends on the configuration in which the fused peptide is presented on the surface of the phage. X-ray diffraction from oriented fibers of three M13 strains with different sequences inserted near the amino terminus of the major coat protein (gp8) has been used to demonstrate that the inserts do not affect the helical symmetry of the phage particles. The structure of one insertion mutant (M13BOM2) was analyzed in detail. This strain contains the pentapeptide GQASG inserted between amino acids 4 and 5 of the major coat protein. Analysis of fiber diffraction from this strain was used to obtain its structure to 7 A resolution. Examination of the resulting electron density map indicated that the insert is presented in an extended conformation in a shallow groove between two alpha-helices on the surface of the virion. This arrangement is reminiscent of the presentation of peptides by major histocompatibility antigens. The extended conformation of the peptide provides substantial surface exposure and puts it in a favorable position to act as a ligand in a biochemical process. This form of presentation may contribute to the high immunogenicity observed for peptides inserted into the gene 8 product of M13. The length of the groove appears to correspond to the upper length limit observed when foreign peptides are fused to all copies of gp8.

Conformation of the coat protein of filamentous bacteriophage Pf1 determined by neutron diffraction from magnetically oriented gels of specifically deuterated virions.

The structure of filamentous bacteriophage Pf1 has been studied using neutron diffraction from magnetically oriented gels of native and valine-deuterated phage. Neutron diffraction intensities were measured to approximately 8 A resolution along the equator and first six layer-lines, and differences due to the deuterated valine residues were apparent. Analysis of equatorial data indicate that one valine residue is located at a radius of about 13 A, three are in the hydrophobic center of the protein coat at an average of about 22 A radius, and one is near the outer surface of the virion at about 28 A radius. Analysis of the three-dimensional data was initiated using the rod model for the alpha-helices of the coat protein derived from earlier X-ray diffraction studies. This model was refined against the neutron diffraction intensities from native phage to obtain a phase set that was used to calculate a difference map between the valine-deuterated and native phage. The difference map exhibits peaks that correspond to the positions of the five valine residues in the coat protein. From the amino acid sequence and the alpha-helical conformation of the coat protein, the five valine residues can be unambiguously assigned to the difference peaks. This assignment indicates that the two alpha-helices of the coat protein are parallel to one another, connected by a short stretch of non-helical peptide. The valine positions also indicate that the helical surface lattice of the phage particle is right-handed.

Three-dimensional structure of a cloning vector. X-ray diffraction studies of filamentous bacteriophage M13 at 7 A resolution.

Filamentous bacteriophage M13 is a single-stranded DNA phage about 65 A in diameter and 9300 A long. X-ray diffraction studies of magnetically oriented fibers of native, mercury and iodine-labeled phage particles have been used to determine the arrangement of the major coat protein, the gene 8 product, in the virion. The coat protein is made up of a single gently curving alpha-helix extending from approximately Pro6 to near the carboxyl terminus. The axis of the alpha-helix is tilted about 20 degrees from the viral axis and wraps around the axis in a right-handed helical sense. The surface of the virus is made up largely of polar residues in the amino-terminal half of the protein including the segment of alpha-helix extending from Pro6 to Tyr24. The interior surface of the protein coat faces the DNA and consists of an amphipathic helical segment extending from Thr36 to Ser50. The alpha-helices form a tightly packed 15 to 20 A thick cylindrical coat around the DNA. This structural model provides insight into the potential sites for incorporating foreign protein domains that may act as functional binding sites on the surface of M13.

Gap junction structures. V. Structural chemistry inferred from X-ray diffraction measurements on sucrose accessibility and trypsin susceptibility.

X-ray diffraction patterns have been recorded from partially oriented specimens of gap junctions isolated from mouse liver and suspended in sucrose solutions of different concentration and thus of different electron density. Analysis of these diffraction patterns has shown that sucrose is excluded from the 6-fold rotation axis of the junction lattice for a length of about 100 A. This indicates that the aqueous channel of the junctions is in the closed, high resistance state in these preparations. Mapping of the sucrose-accessible space in the junction indicates that the cross-sectional area of the channel entrance on the cytoplasmic side of the membrane could be up to five times larger than the area of the transmembrane channel. Sucrose does not penetrate more than 20 A into the membrane along the channel. Apparently the aqueous channel, 8 to 10 A in radius for most of its length, is narrowed or blocked by a small feature about 50 A from the center of the gap. Very close interactions exist between the gap junction protein and the lipid polar head groups on the cytoplasmic surface of the membrane. In this region, the protein intercalates between the polar head groups. These results suggest that the gap junction protein may have a functional two-domain structure. One domain, with a molecular weight of about 15,000, spans one bilayer and half of the gap and is contained largely within a radius of 25 A from the 6-fold axis. The second domain is smaller and occupies the cytoplasmic surface of the gap junction membrane. Trypsin digestion removes about 4000 Mr from the cytoplasmic surface domain of the junction protein. Most of the material susceptible to trypsin digestion is located more than 28 A from the 6-fold axis.

Construction of a microphage variant of filamentous bacteriophage.

The intergenic region in the genome of the Ff class of filamentous phage (comprising strains fl, fd and M13) genome constitutes 8% of the viral genome, and has essential functions in DNA replication and phage morphogenesis. The functional domains of this region may be inserted into separate sites of a plasmid to function independently. Here, we demonstrate the construction of a plasmid containing, sequentially, the origin of (+)-strand synthesis, the packaging signal and a terminator of (+)-strand synthesis. When host cells harboring this plasmid (pLS7) are infected with helper phage they produce a microphage particle containing all the structural elements of the mature, native phage. The microphage is 65 A in diameter and about 500 A long. It contains a 221-base single-stranded circle of DNA coated by about 95 copies of the major coat protein (gene 8 protein).

Screening of a library of phage-displayed peptides identifies human bcl-2 as a taxol-binding protein.

A random library of phage displayed peptides was screened for binding to a biotinylated derivative of paclitaxel (Taxol). Affinity-selected peptides were analyzed for similarity to human proteins. There was no significant similarity between the paclitaxel-selected peptides and tubulin. However, a subset of the peptides was identified that exhibits significant similarity to a non-conserved region of the anti-apoptotic human protein Bcl-2: ELISA assays confirmed binding of paclitaxel to Bcl-2, and circular dichroism spectroscopy demonstrated that a substantial conformational change accompanies this binding. In vivo, treatment with paclitaxel has been shown to lead to Bcl-2 inactivation with concomitant phosphorylation of residues in a disordered, regulatory loop region of the protein. Similarity between paclitaxel-selected peptides and this loop region implicate these residues in drug binding, and suggest that the apoptotic action of paclitaxel may involve the binding of paclitaxel to Bcl-2. These results demonstrate that peptides displayed on the surface of bacteriophage particles can mimic the ligand-binding properties of disordered regions of proteins.

Wide-angle X-ray solution scattering as a probe of ligand-induced conformational changes in proteins.

A chemical genetics approach to functional analysis of gene products utilizes high-throughput target-based screens of compound libraries to identify ligands that modulate the activity of proteins of interest. Candidates are further screened using functional assays designed specifically for the protein--and function--of interest, suffering from the need to customize the assay to each protein. An alternative strategy is to utilize a probe to detect the structural changes that usually accompany binding of a functional ligand. Wide-angle X-ray scattering from proteins provides a means to identify a broad range of ligand-induced changes in secondary, tertiary, and quaternary structure. The speed and accuracy of data acquisition, combined with the label-free targets and binding conditions achievable, indicate that WAXS is well suited as a moderate-throughput assay in the detection and analysis of protein-ligand interactions.