Structures of prokaryotic ribosomal proteins: implications for RNA binding and evolution

After a long hiatus, the pace of determination of the structures of ribosomal proteins has accelerated dramatically. We discuss here the structures of five ribosomal proteins from Bacillus stearothermophilus: S5, S17, L6, L9, and L14. These structures represent several new motifs. Each of these structures has revealed new insights, and we have developed criteria for recognizing RNA-binding regions of each protein and correlating the structures with such properties as antibiotic resistance. The information here should also prove invaluable in an eventual high-resolution picture of the intact ribosome.

X-ray crystallography shows that translational initiation factor IF3 consists of two compact alpha/beta domains linked by an alpha-helix

The structures of the two domains of translational initiation factor IF3 from Bacillus stearothermophilus have been solved by X-ray crystallography using single wavelength anomalous scattering and multiwavelength anomalous diffraction. Each of the two domains has an alpha/beta topology, with an exposed beta-sheet that is reminiscent of several ribosomal and other RNA binding proteins. An alpha-helix that protrudes out from the body of the N-terminal domain towards the C-terminal domain suggests that IF3 consists of two RNA binding domains connected by an alpha-helix and that it may bridge two regions of the ribosome. This represents the first high resolution structural information on a translational initiation factor.

Positive association between dietetics recommendations and achievement of enteral nutrition outcomes of care

OBJECTIVE

To identify planned dietetics outcomes of care, dietitians activities performed an recommendations made, and outcome achievement and its relationship to recommendations followed.

DESIGN

A multisite, single-group prospective pilot study was conducted to describe the care provided by dietitians to patients receiving enteral nutrition care.

SUBJECTS/SETTING

Participants were 172 patients (16 of whom died during hospitalization) receiving at least 75% of nutrient requirements from enteral nutrition products. Subjects were from six acute-care facilities and one rehabilitation facility in the Chicago metropolitan area.

MAIN OUTCOME MEASURES

Dietitians identified planned outcomes of care to be accomplished and documented activities performed during the provision of care. Data were collected to measure outcome achievement and to determine whether dietitians' recommendations were followed.

STATISTICAL ANALYSES PERFORMED

Descriptive data are reported as frequencies or means +/- standard error. Odds ratios were constructed to estimate the association between dietitians' enteral care recommendations and the achievement of planned outcomes of care.

RESULTS

Whether or not enteral nutrition outcomes of care were achieved was positively associated with dietitians' recommendations. The odds of patients' achieving the recommended energy intake goal (P < .001) or increasing (P < .01) or maintaining (P < .04) visceral protein stores were at least four times greater when dietitians' recommendations were followed than when they were not. In addition, dietetics activities performed at the local level were similar to established practices.

APPLICATIONS

Dietitians can identify and measure outcomes of dietetics-related care that demonstrate positive contributions to the interdisciplinary enteral nutrition care process.

Prokaryotic translation initiation factor IF3 is an elongated protein consisting of two crystallizable domains

We show that translation initiation factor IF3 can be split into two fragments of nearly equal size by the Escherichia coli outer membrane protease omptin. Circular dichroism and small-angle neutron scattering show that the two fragments are structured as domains. Each domain is relatively compact, and they are separated by about 45 A in intact IF3. Thus IF3 is an elongated protein that consists of two well-separated domains. We suggest that these two domains are involved in ribosome binding across the cleft of the 30S ribosome. We also report the crystallization of each domain of IF3.

Blood flow in colon anastomotic stricture formation

PURPOSE

The influence of both blood flow and anastomotic technique on the development of anastomotic stricture formation was studied using a dog model.

METHODS

Fifty-three dogs underwent distal colocolonic anastomosis with either an EEA (U.S. Surgical Corp., Norwalk, CT) circular stapler or a Czerny-Lembert two-layered, handsewn anastomosis. Blood flow was measured by Laser Doppler Velocimetry using the Laserflo BPM2 (Vasamedics Inc., St. Paul, MN). The animals were separated into three blood flow groups: greater than or equal to 62.5 percent of normal blood flow, between 37.5 percent and 62.5 percent of normal blood flow, and less than or equal to 37.5 percent of normal blood flow. Each blood flow group had an anastomosis performed by either stapling or by hand sewing techniques. At six weeks, the anastomoses were opened longitudinally and fixed to determine the anastomotic index (AI). AI is defined as two times the anastomotic circumference over the proximal circumference plus the distal circumference. Blood flow groups and anastomotic technique groups were compared with an interaction variable for the outcome, AI using a two-way analysis of variance.

RESULTS

The AI of the stapled anastomoses was found to be significantly higher than handsewn anastomoses (P < 0.006). There was no difference in AI between different blood flow groups and no correlation of observed histologic findings with AI.

CONCLUSION

Clinically relevant ischemia does not directly influence stricture formation in either handsewn or stapled distal colonic anastomoses.

Ultrasonographic detection of abnormal fetal growth with the gestational age-independent, transverse cerebellar diameter/abdominal circumference ratio

OBJECTIVES

We prospectively evaluated the accuracy of a gestational age-independent method of detecting abnormal growth, the transverse cerebellar diameter/abdominal circumference ratio, and compared this with standard ultrasonographic methods of growth assessment.

STUDY DESIGN

We prospectively studied 825 low-risk obstetric patients and 250 patients having risk factors for fetal macrosomia (n = 92) or growth retardation (n = 158). Measured fetal parameters included the biparietal diameter, head circumference, transverse cerebellar diameter, abdominal circumference, and femur length. The estimated fetal weight, head circumference/abdominal circumference, cerebellar diameter/abdominal circumference, and femur length/abdominal circumference ratios were calculated. Reference curves for these parameters were created from a cross-sectional analysis of the low-risk group. Univariate analysis was used to determine the sensitivity, specificity, predictive values, and odds ratios of each individual parameter in identifying a small- or large-for-gestational-age infant. A multivariate logistic regression model with a variable selection procedure was then used to determine whether significance remained when we controlled for other parameters.

RESULTS

Within the low-risk group, the transverse cerebellar/abdominal circumference ratio was gestational age independent between 14 and 42 weeks with a mean of 13.68 +/- 0.96. A value exceeding 2 SD of the mean was significantly associated with birth or a small-for-gestational-age infant, being abnormal in 98% and 71% of asymmetrically and symmetrically growth-retarded infants, respectively. Significance was maintained in the multivariate regression model. The ratio was not helpful in detecting the large-for-gestational-age infant.

CONCLUSION

The fetal transverse cerebellar diameter/abdominal circumference ratio is an accurate, gestational age-independent method of identifying the small-for-gestational-age but not the large-for-gestational-age infant.

Homo- and heteronuclear two-dimensional NMR studies of the globular domain of histone H1: full assignment, tertiary structure, and comparison with the globular domain of histone H5

The globular domain of chicken histone H1 (GH1) has been studied by 1H homonuclear and 1H-15N heteronuclear 2D NMR spectroscopy. After the full assignment of the proton and 15N resonances, the tertiary structure of GH1 was determined by an iterative procedure using distance geometry and restrained simulated annealing. The secondary structure elements of GH1, three helices (S5-A16, S24-A34, N42-K56) followed by a beta-hairpin (L59-L73), are folded in a manner very similar to the corresponding parts of the globular domain of chicken histone H5 (GH5) [Clore et al. (1987) EMBO J. 6, 1833-1842; Ramakrishnan et al. (1993) Nature 362, 219-223]. However, subtle differences are detected between the two structures and between the electrostatic potentials surrounding the molecules. The most important differences are located in the loop between the second and third helices, a region that could be responsible for the different affinity for DNA. The most positively charged regions are not found in exactly the same position in GH1 and GH5. Nevertheless, their location seems to agree with the model where nucleosome binding takes place through contact points located at one DNA terminus and close to the dyad axis of the nucleosome [Schwabe & Travers (1993) Curr. Biol. 3, 628-630].

Crystallization and preliminary X-ray diffraction studies of bacterial ribosomal protein L14

Based on amino-acid sequence homology, it is predicted that ribosomal protein L14 is a member of a recently identified family of structurally related RNA-binding proteins. To verify this, the gene for Bacillus stearothermophilus L14 has been cloned, and the protein has been purified and crystallized. The crystals are in space group C2 with cell dimensions a = 67.0, b = 32.7, c = 49.4 A, and beta = 101.8 degrees, and there is one molecule in the asymmetric unit (V(m) = 2.0 A(3) Da(-1)). They are of high quality, and a native data set has been collected to a resolution of 1.6 A, with an R(merge) of 5.3%.

Ultrasonographic growth and Doppler hemodynamic evaluation of fetuses of obese women

All fetuses benefit from ultrasonographic estimation of gestational age and evaluation of growth patterns. Monitoring the pregnancies of obese women is perceived as more difficult than monitoring those of nonobese women. The aim of this study was to determine if maternal obesity affects the growth and Doppler resistance indices (RI) of the fetus. Twenty-eight women with a preconception weight > 90.7 kg underwent obstetric ultrasonographic evaluations from the 20th week of gestation. Their ultrasonographic data were compared with those of controls. Ten of the obese women developed gestational diabetes and had lower umbilical artery RIs for a given gestational age (P < .0001) than did those obese women without other medical complications, those with medically controlled pregnancy-induced hypertension or those from the control population. The relation between fetal unit weight and umbilical artery RIs was established. The pattern of RI changes was similar in all groups when estimated fetal weight instead of gestational age was used as the covariant. Fetal growth and Doppler velocimetry can be monitored adequately in obese women. Gestational diabetes significantly influences the pattern of fetal growth and the impedance to flow in the umbilical artery.

Insomnia in Vietnam era veteran twins: influence of genes and combat experience

Genetic and environmental influences on insomnia were studied in 2,825 pairs of Vietnam era veteran male twins. The self-reported sleep problems studied included trouble falling asleep, trouble staying asleep, waking often, waking tired and a composite sleep scale. Twin correlations for each of the sleep problems were larger in monozygotic than in dizygotic pairs, with heritability estimates ranging from 0.21 to 0.42. There was no effect of common familial environment. Phenotypic correlations for combat experience and sleep problems were small, ranging from 0.00 to 0.09, with no differences seen in monozygotic and dizygotic twins. When the effects of genes and combat exposure were evaluated simultaneously, there was a significant genetic contribution to all sleep measures, but combat exposure was significantly associated only with overall sleep quality, waking often and having trouble staying asleep.

Expression of chicken linker histones in E. coli: sources of problems and methods for overcoming some of the difficulties

Expression of histones in Escherichia coli is important in structural studies on chromatin, because it allows isotopic labeling such as deuteration and replacement of methionines with selenomethionine as well as expression of specific domains of histones. We show that full-length H5 cannot be expressed in E. coli. We have determined that the problem is translational rather than transcriptional. Pulse-labeling studies show that protein turnover is not the reason for lack of accumulation. On dissecting the gene, we find that the problem lies in expressing the highly charged C-terminal tail of H5. We can make progressively increasing amounts of the tail, but at the point where over two-thirds of this region is transcribed, the protein ceases to be made. Surprisingly, full-length H1 is made. In vitro studies show that the H5 gene can be translated in a rabbit reticulocyte system but not in an E. coli system, suggesting that there may be a difference in the ability of eukaryotic and prokaryotic ribosomes to translate this message. The expression of the globular domains of H5 and H1 posed a different problem. There was little or no expression of some of the constructs, even though they were fragments of larger constructs that were well made. Replacement of the first five codons downstream of the initiating ATG codon with those optimized for E. coli, and which were AT rich, restored expression. This may have general implications for expression of eukaryotic proteins in E. coli.

Histone H1 is located in the interior of the chromatin 30-nm filament

The linker histone H1 binds to the nucleosome and is essential for the organization of nucleosomes into the 30-nm filament of chromatin. It has been implicated in the repression of transcription, and phosphorylation of H1 may be involved in cell-cycle-dependent chromatin condensation and decondensation. A long-standing issue concerns the location of H1 in the chromatin filament. The original solenoidal model proposes that H1 is inside the 30-nm filament, but other models, also helical, suggest a variable or more accessible location for H1. Investigations to determine the location of the linker histone based on its accessibility to antibodies or immobilized proteases under various ionic conditions have yielded conflicting results. Here we use neutron scattering in a direct structural determination to show that H1 is located in the interior of the filament.

The anion-binding exosite is critical for the high affinity binding of thrombin to the human thrombin receptor

The thrombin receptor has been shown to be a novel member of the family of G-protein coupled receptors (Vu, T.-K. H., Hung, D.T., Wheaton, V.I., and Coughlin, S.R. (1991) Cell 64, 1057-1068). This receptor appears to be activated through a thrombin-mediated proteolytic mechanism which exposes a "tethered ligand" responsible for receptor activation. In order to investigate the initial interactions of thrombin with this receptor, we have constructed cell lines which express high levels of the human thrombin receptor and studied the binding of various forms of thrombin to the cell surface. Analysis of transfected cells with thrombin receptor monoclonal antibodies identified a particular cell line (clone #5-18) which displayed > 150,000 thrombin receptors per cell. Clone #5-18 appeared to express functional receptors since treatment with thrombin resulted in both a 15-20 fold increase of cytoplasmic phosphoinositide levels and a comparable shift in the EC50 of thrombin-mediated calcium mobilization when compared to non-transfected CHO cells. Binding of 125I-alpha-thrombin to clone #5-18 did not reach equilibrium at 37 degrees C. However, direct binding studies of 125I-alpha-, 125I-diisopropylphospho (DIP)-alpha-, and 125I-beta-thrombin to clone #5-18 demonstrated that binding at 4 degrees C was saturable and reversible for each ligand. Analysis of the binding data revealed Kd's of 0.8 nM, 0.7 nM and 9.7 nM for 125I-alpha-, 125I-DIP-alpha- and 125I-beta-thrombin respectively. Association of 125I-alpha-, DIP-alpha, and beta-thrombin could be competed by unlabelled alpha- and DIP-alpha-thrombin. Unlabelled beta-thrombin, which has a modified anion-binding exosite, was a poor competitor for 125I-alpha- and 125I-DIP-alpha-thrombin, but did compete for 125I-beta-thrombin. In addition, the hirudin54-65 peptide competed at submicromolar concentrations for the binding of alpha- and DIP-alpha-thrombin, but not for beta-thrombin. This peptide binds specifically at the anion-binding exosite of alpha-thrombin and has been shown to have a lower affinity for beta-thrombin. These results demonstrate directly a high affinity interaction between thrombin and its receptor, and suggest that an important component is the high affinity association of the thrombin receptor with the anion-binding exosite of thrombin.

Crystal structure of prokaryotic ribosomal protein L9: a bi-lobed RNA-binding protein

The crystal structure of protein L9 from the Bacillus stearothermophilus ribosome has been determined at 2.8 A resolution using X-ray diffraction methods. This primary RNA-binding protein has a highly elongated and unusual structure consisting of two separated domains joined by a long exposed alpha-helix. Conserved, positively charged and aromatic amino acids on the surfaces of both domains probably represent the sites of specific interactions with 23S rRNA. Comparisons with other prokaryotic L9 sequences show that while the length of the connecting alpha-helix is invariant, the sequence within the exposed central region is not conserved. This suggests that the alpha-helix has an architectural role and serves to fix the relative separation and orientation of the N- and C-terminal domains within the ribosome. The N-terminal domain has structural homology to the smaller ribosomal proteins L7/L12 and L30, and the eukaryotic RNA recognition motif (RRM).

Ribosomal protein L6: structural evidence of gene duplication from a primitive RNA binding protein

In all cells, protein synthesis is coordinated by the ribosome, a large ribonucleoprotein particle that is composed of > 50 distinct protein molecules and several large RNA molecules. Here we present the crystal structure of ribosomal protein L6 from the thermophilic bacterium Bacillus stearothermophilus solved at 2.6 A resolution. L6 contains two domains with almost identical folds, implying that it was created by an ancient gene duplication event. The surface of the molecule displays several likely sites of interaction with other components of the ribosome. The RNA binding sites appear to be localized in the C-terminal domain whereas the N-terminal domain contains the potential sites for protein-protein interactions. The domain structure is homologous with several other ribosomal proteins and to a large family of eukaryotic RNA binding proteins.

Ribosomal protein S17: characterization of the three-dimensional structure by 1H and 15N NMR

The structure of ribosomal protein S17 from Bacillus stearothermophilus was investigated by two-dimensional homonuclear and heteronuclear magnetic resonance spectroscopy. The 1H and 15N chemical shift assignments are largely complete, and a preliminary structural characterization is presented. The protein consists of five beta-strands that form a single antiparallel beta-sheet with Greek-key topology. The beta-strands are connected by several extended loops, and two of these contain residue types that are frequently seen in the RNA-binding sites of proteins. Additionally, two point mutations that affect antibiotic resistance, translational fidelity, and ribosome assembly are located in these two regions of the protein. Since these potential RNA-binding sites are distributed over a large surface of the protein, it appears that the molecule may interact with several regions of 16S rRNA.

Homo- and heteronuclear two-dimensional NMR studies of the globular domain of histone H1: sequential assignment and secondary structure

A recombinant 75 amino acid polypeptide corresponding to the globular domain of the chicken histone H1 (GH1) has been studied by 1H homonuclear and 1H-15N heteronuclear 2D NMR spectroscopy. Sequential assignment of the backbone and beta-proton resonances has enabled us to determine the secondary structure of GH1. It was found to consist of three helical regions (T7-S17, L25-Y37, E40-K56) and probably a beta-hairpin (L59-L73). This structure is similar to the structure of the globular domain of histone H5 (GH5) obtained both by NMR spectroscopy [Zarbock et al. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 7628-7632; Clore et al. (1987) EMBO J. 6, 1833-1842] and by X-ray crystallography [Ramakrishnan et al. (1993) Nature 362, 219-223]. The beta-hairpin as suggested for GH1 is also present in the X-ray structure of GH5 but has not been reported for the NMR structure of GH5.

A strategy for assembling samples of adult twin pairs in the United States

In this paper we develop a methodology for the identification of large numbers of U.S. adult twin pairs. Data for this study derive from the U.S. Department of Defense and the Vietnam Era Twin (VET) Registry. The Department of Defense identified potential male twins (n = 10,002) using a computerized record linkage algorithm based on the same last name, same date of birth, and the same first five digits of the Social Security number. Twinship was confirmed by comparison with the Vietnam Era Twin Registry. We developed a logistic regression model that predicts the probability that a paired record identifies twins based on the absolute difference in the last four digits in the Social Security number, the age of issuance of the Social Security number, and the frequency of occurrence of the last name. We used the estimated coefficients derived from this regression model to assign predicted probabilities of being a twin to each matched record. There is a close correspondence between the observed and expected number of twins when evaluated across deciles of predicted probabilities of being a twin; the value of the Harrell's c index (c = 0.68 +/- 0.0004) indicates the overall predictive accuracy of the regression equation. The results from this study demonstrate the feasibility of identifying adult male-male twin pairs from any large computerized database that contains name, date of birth and Social Security number. However, the selection criteria used in the creation of the computer database must be clearly specified to avoid constructing a biased sample of twins.

Crystal structure of globular domain of histone H5 and its implications for nucleosome binding

The structure of GH5, the globular domain of the linker histone H5, has been solved to 2.5 A resolution by multiwavelength anomalous diffraction on crystals of the selenomethionyl protein. The structure shows a striking similarity to the DNA-binding domain of the catabolite gene activator protein CAP, thereby providing a possible model for the binding of GH5 to DNA.

Kinetics of CD11b expression on neutrophils isolated from subjects with healthy gingivae and patients with advanced periodontitis

The adhesion molecule, CD11b/CD18, plays a role in host defense against bacterial infections owing to its involvement in cell migration and phagocytosis. We examined the kinetics of CD11b expression on neutrophils isolated from peripheral blood (PB-PMNs) and gingival crevicular fluid (CF-PMNs) in subjects with healthy gingivae and in patients with advanced periodontitis in order to assess if CF-PMNs respond differently in regard to CD11b expression from PB-PMNs isolated from healthy or periodontitis subjects. CF-PMNs or formylmethionylleucylphenylalanine (fMLP)-stimulated PB-PMNs were incubated in buffer with or without divalent cations for 60, 90, or 110 minutes. Plasma membrane (surface) CD11b as measured by flow cytometry was found to be reduced with time when cells (PB-PMNs or CF-PMNs) from either controls or patients were treated with calcium- and magnesium-free buffer. However, when CF-PMNs were treated with buffer containing Ca++/Mg++, surface CD11b expression increased on cells from both controls and patients. The reduction in CD11b expression on PB-PMNs is significantly greater than that measured on CF-PMNs over time. Therefore, CF-PMNs respond differently from PB-PMNs which have been artificially stimulated with fMLP in regard to kinetics of CD11b expression on the plasma membrane.

A novel monoclonal antibody dependent on domain 5 of the platelet-derived growth factor beta receptor inhibits ligand binding and receptor activation

Platelet derived growth factor (PDGF) induces activation of the protein tyrosine kinase domain of the PDGF receptor, resulting in receptor dimerization and the initiation of mitogenesis in responsive cells. In order to identify domains of the receptor involved in these processes, a panel of monoclonal antibodies (MAbs) against the extracellular region of the human PDGF receptor was developed and screened to identify which of these specifically block PDGF binding. One of these, MAb 2A1E2, binds PDGF beta receptor with high affinity and blocks PDGF BB binding in a whole cell binding assay with an IC 50 of 0.1 nM. Inhibition of binding results in the inhibition of ligand-induced receptor phosphorylation, dimerization and mitogenesis in cells expressing the PDGF beta receptor. MAb 2A1E2 has been mapped to the fifth Ig domain of the PDGF beta receptor, implying that this domain is important for ligand binding, dimerization and/or activation. The potency of MAb 2A1E2 for inhibiting PDGF BB binding indicates that this antibody is ideally suited to identify and characterize PDGF BB-induced biological responses.

The menstrual cycle: relations of biophysical and hormonal determinations in normal women of reproductive age

Appropriate relationships between circulating levels of 17 beta-E2 and P are necessary for normal endometrial development and blastocyst implantation. The aim of this study was to relate biophysical and biochemical measurements obtained during the menstrual cycle of six healthy women in 25 menstrual cycles. One hundred eighteen vaginosonographic determinations of the endometrial thickness together with serum E2 and P assays were performed at 5-day intervals. The three parameters studied were standardized by the formula: observation minus mean determination for that parameter divided by the standard deviation of that parameter. Using this common unit, the physiological relations between ultrasonographically determined endometrial thickness, E2, and P were readily seen.

The structure of ribosomal protein S5 reveals sites of interaction with 16S rRNA

Understanding the process whereby the ribosome translates the genetic code into protein molecules will ultimately require high-resolution structural information, and we report here the first crystal structure of a protein from the small ribosomal subunit. This protein, S5, has a molecular mass of 17,500 and is highly conserved in all lifeforms. The molecule contains two distinct alpha/beta domains that have structural similarities to several other proteins that are components of ribonucleoprotein complexes. Mutations in S5 result in several phenotypes which suggest that S5 may have a role in translational fidelity and translocation. These include ribosome ambiguity or ram, reversion from streptomycin dependence and resistance to spectinomycin. Also, a cold-sensitive, spectinomycin-resistant mutant of S5 has been identified which is defective in initiation. Here we show that these mutations map to two distinct regions of the molecule which seem to be sites of interaction with ribosomal RNA. A structure/function analysis of the molecule reveals discrepancies with current models of the 30S subunit.

Elementary methods for the analysis of dichotomous outcomes in unselected samples of twins

This paper presents an elementary statistical method for analyzing dichotomous outcomes in unselected samples of twin pairs using stratified estimators of the odds ratio. The methodology begins by first randomly designating one member of each twin pair as an "index" twin and the other member as the "co-twin." Stratifying on zygosity, odds ratios are used to measure the association between disease in the index twin and disease in the co-twin. From these zygosity-specific tables we calculate the Woolf-Haldane estimator of the common odds ratio (psi F, the weighted average of the zygosity-specific odds ratios), the Mantel-Haenszel test statistic (chi 2M-H) for the common odds ratio, and a test (chi 2G) for the difference in the zygosity-specific odds ratios. In this application, psi F provides an estimate of the familial association for disease and the accompanying chi 2M-H provides a test of the null hypothesis, psi F = 1 (i.e., there is no evidence for a familial influence on disease). The chi 2G is a test of the null hypothesis that psi MZ = psi DZ; a significant value for chi 2G suggests a genetic influence on disease (assuming that the observed odds ratios follow a pattern where psi MZ greater than psi DZ). A new test statistic (chi 2c) is proposed that incorporates the expectation that psi MZ = psi 2DZ under a purely additive genetic model with no common environmental effects. A significant value of chi c2 indicates that the different odds ratios across zygosity are partly due to common environmental influences. Conversely, a nonsignificant value of chi 2c is an indication that the zygosity-specific odds ratios are due solely to additive genetic effects and not to common environment. This basic approach is extended to examine the effects of measured indicators of the specific environment and the assessment of certain forms of gene by environment interaction. All of the methods are easily understood, highly flexible, readily computed using a hand calculator, and incorporate the inherent genetic information contained within twin samples.

Conformation of one- and two-chain high molecular weight urokinase analyzed by small-angle neutron scattering and vacuum ultraviolet circular dichroism

The structures of one- and two-chain high molecular weight human urokinase were analyzed by small-angle neutron scattering and vacuum ultraviolet circular dichroism. Both one- and two-chain high molecular weight urokinases exhibited a radius of gyration of 31 A and a maximum dimension of 90 A. Neither parameter was affected by the presence of lysine sufficient to saturate all the lysine-binding sites in human plasminogen. These physical parameters are consistent with the sedimentation coefficient of high molecular weight urokinase and indicate that both proteins are highly asymmetric. Neither protein contained much alpha-helix or parallel beta-sheet. Most of the secondary structure was in the form of antiparallel beta-sheet and beta-turns, very similar to the secondary structure of plasminogen. The macroscopic kinetic constants, Km and kcat, for the hydrolysis of (pyroGlu-Gly-Arg-NH)2-rhodamine by two-chain high molecular weight urokinase and low molecular weight urokinase which lacks the epidermal growth factor and kringle domains were similar. These structural and kinetic data are consistent with the domains in both forms of urokinase being independent structural and functional units.

Conformation of Lys-plasminogen and the kringle 1-3 fragment of plasminogen analyzed by small-angle neutron scattering

Native human Glu-plasminogen (Glu1-Asn791) was previously shown to have a radius of gyration of 39 A and a shape best described by a prolate ellipsoid [Mangel, W. F., Lin, B., & Ramakrishnan, V. (1990) Science 248, 69-73]. Upon occupation of a weak lysine-binding site, the shape reversibly changes to that best described by a Debye random coil with a radius of gyration of 56 A. Conversion from the closed to the open form is not accompanied by any change in secondary structure, hence the closed conformation is formed by interaction between domains, the five kringles and the protease domain, and this is abolished upon conversion to the open form. Here we analyzed by small-angle neutron scattering the conformations of human Lys-plasminogen (Lys78-Asn791) and the fragment K1-3 that contains the first three kringles of plasminogen (Tyr80-Val338 or Tyr80-Val354). The shape of Lys-plasminogen was best described by a Debye random coil with a radius of gyration of 51 A, and occupation of its lysine-binding sites by 6-aminohexanoic acid did not dramatically alter its conformation. Thus Lys-plasminogen was in the open form, similar to that of Glu-plasminogen with its lysine-binding sites occupied. The fragment K1-3 in the absence or presence of 6-aminohexanoic acid had a shape best described equally either by an elongated prolate ellipsoid or by a Debye random coil, with a radius of gyration of 29 A. Our model for the two forms of plasminogen is that, in the closed form, domain interaction generates a compact, almost globular, structure.(ABSTRACT TRUNCATED AT 250 WORDS)

Iniencephaly with cyclopis (a case report)

Iniencephaly is a rare neural tube defect. We report a rare association of iniencephaly with cyclopia, probably the third such report in the literature.

Interaction of HMG14 with chromatin

Neutron scattering has been used to study the interaction of HMG14 with chromatin. Chromatin depleted of H1/H5 was reconstituted separately with histones H1 and H5, and complexed with HMG14. We have also studied the conformation of complexes formed by the binding of HMG14 to nucleosome dimers without linker DNA. Our data on the binding of HMG14 to linkerless nucleosome dimers argue against a significant change in the exit and entry angles of nucleosomal core DNA. Data on the condensation of chromatin into a higher-order structure suggest that there is no dramatic difference between the roles of H1 and H5 in their influence on HMG14 complex formation. However, there is a decrease of about 25% in the mass per unit length of chromatin fibers on HMG14 binding, which is not accompanied by a change in the fiber repeat distance. This is evidence that there are fewer nucleosomes per repeat in HMG14 containing chromatin fibers than in normal chromatin. Alteration of chromatin structure in this manner may be part of the role of HMG14 in actively transcribed chromatin.

Characterization of an extremely large, ligand-induced conformational change in plasminogen

Native human plasminogen has a radius of gyration of 39 angstroms. Upon occupation of a weak lysine binding site, the radius of gyration increases to 56 angstroms, an extremely large ligand-induced conformational change. There are no intermediate conformational states between the closed and open form. The conformational chang is not accompanied by a change in secondary structure, hence the closed conformation is formed by interaction between domains that is abolished upon conversion to the open form. This reversible change in conformation, in which the shape of the protein changes from that best described by a prolate ellipsoid to a flexible structure best described by a Debye random coil, is physiologically relevant because a weak lysine binding site regulates the activation of plasminogen.

Crystallization of the globular domain of histone H5

The globular domain of histone H1/H5 binds to the nucleosome and is crucial for the formation of chromatin higher order structure. We have expressed in Escherichia coli a gene that codes for the globular domain of H5. The protein produced in E. coli is functional in nucleosome binding assays. We have obtained crystals of the protein that diffract to beyond 2.5 A (1 A = 0.1 nm) resolution. The crystals are orthorhombic with unit cell dimensions of a = 80.1 A, b = 67.5 A and c = 38.0 A.

Interaction of wild-type and catalytically inactive mutant forms of tissue-type plasminogen activator with human umbilical vein endothelial cell monolayers

Several groups have demonstrated that radioiodinated tissue-type plasminogen activator (t-PA) binds to saturable sites on human umbilical vein endothelial cells (HUVECs) in culture (Hajjar, K. A., Hamel, N. M., Harpel, P. C., and Nachman, R. L. (1987) J. Clin. Invest. 80, 1712-1719; Beebe, D. P. (1987) Thromb. Res. 46, 241-254; Barnathan, E. S., Kuo, A., van der Keyl, H., McCrae, K. R., Larsen, G. L., and Cines, D. B. (1988) J. Biol. Chem. 263, 7792-7799). Here we report that most of the specific binding of 125I-t-PA to our HUVEC cultures is accounted for by binding to (i) plasminogen activator inhibitor type 1 (PAI-1), a t-PA inhibitor produced in abundance by HUVECs; and (ii) specific binding sites present on the plastic culture surface. The contribution of the sites on plastic can be eliminated by taking several precautions. Then, most or all of the specifically bound 125I-t-PA is present in a sodium dodecyl sulfate-stable 110-kDa 125I-t-PA.PAI-1 complex. Interestingly, a radioiodinated mutant form of t-PA, S478A, which is catalytically inactive and therefore unable to form the covalent complex with PAI-1, still binds to HUVECs. In fact, this ligand binds to HUVECs in 10-30-fold greater amounts than does wild-type 125I-t-PA (resulting in greater than 1 x 10(7) S478A 125I-t-PA molecules bound/cell at 12 nM ligand concentration). In contrast, diisopropyl fluorophosphate-treated t-PA binds to HUVECs in much smaller amounts than does wild-type t-PA. Several findings suggest that PAI-1 is a major binding site for S478A t-PA. The vast amount of binding observed with S478A t-PA, compared with wild-type t-PA, may be accounted for by an observed large scale release of wild-type 125I-t-PA.PAI-1 complexes from the solid phase (cells or extracellular matrix) into the culture medium. Immunoprecipitation experiments demonstrate that, in contrast to wild-type t-PA, S478A t-PA does not extract [35S]methionine-PAI antigen from metabolically labeled extracellular matrix. It is proposed that t-PA releases PAI-1 from the solid phase when it forms the irreversible covalent complex with the inhibitor, a process that does not occur with the catalytically inactive mutant form of t-PA.

Giant pigmented nevus with focal motor seizures

A 1-year old girl having a giant pigmented nevus over trunk and widespread smaller pigmented nevi presented with focal motor seizures. This combination of features is rate.