Solution structures of proteins from NMR data and modeling: alternative folds for neutrophil peptide 5

The structure of neutrophil peptide 5 in solution has recently been reported (Pardi et al., 1988). The structure determination was accomplished by using a distance geometry algorithm and 107 interproton distance constraints obtained from 2D NMR data. In each of the eight independent solutions to the distance geometry equations, the overall fold of the polypeptide backbone was identical and the root mean square (rms) deviation between backbone atoms of the superimposed structures was small (approximately 2.4 A). In this paper we report additional NP-5 structures obtained by using a new structure generation algorithm: a Monte Carlo search in torsion angle space. These structures have a large rms backbone deviation from the distance geometry structures (approximately 5.0 A). The backbone topologies differ in significant respects from the distance geometry structures and from each other. Structures are found that are pseudo mirror images of part or all of the fold corresponding to that first obtained with the distance geometry procedure. For small proteins, the problem of distinguishing the correct structure among pseudo mirror images is likely to be greater than previously recognized. When a set of test distance constraints constructed from a novel Monte Carlo structure is used as input in the distance geometry algorithm, the fold of the resulting structure does not correspond to that of the target. The results also demonstrate that the previously accepted criteria (the magnitude of the rms deviation between multiple solutions of the distance geometry equations) for defining the accuracy and precision of a peptide structure generated from NMR data are inadequate. An energetic analysis of structures corresponding to the different folding topologies has been carried out. The molecular mechanics energies obtained by minimization and molecular dynamics refinement provide sufficient information to eliminate certain alternative structures. On the basis of a careful comparison of the different trial structures with the experimental data, it is concluded that the NP-5 peptide fold which was originally reported is most consistent with the data. An alternative fold corresponding to structures with low energies and small total distance violations is ruled out because for this fold predicted NOEs are not observed experimentally.     

Solution structures of alpha-conotoxin G1 determined by two-dimensional NMR spectroscopy

Two-dimensional NMR data have been used to generate solution structures of alpha-conotoxin G1, a potent peptide antagonist of the acetylcholine receptor. Structural information was obtained in the form of proton-proton internuclear distance constraints, and initial structures were produced with a distance geometry algorithm. Energetically more favorable structures were generated by using the distance geometry structures as input for a constrained energy minimization program. The results of both of these calculations indicate that the overall backbone conformation of the molecule is well-defined by the NMR data whereas the side-chain conformations are generally less well-defined. The main structural features derived from the NMR data were the presence of tight turns centered on residues Pro5 and Arg9. The solution structures are compared with previous proposed models of conotoxin G1, and the NMR data are interpreted in conjunction with chemical modification studies and structural properties of other antagonists of the acetylcholine receptor to gain insight into structure-activity relationships in these peptide toxins.     

Recent coral facies of the Indian Ocean Coast of Somalia with an interim check list of corals

Summary From a study of two areas, Jesira and the Bajuni Archipelago, about 400 km apart, a general pattern can be established for the Recent facies, together with the morphological and taxonomic features of the corals. Present day coral development is characterized by true fringing reefs in the Bajuni Archipelago and by scattered patches and knolls in the Jesira area. The coral fauna, consisting of 27 genera and 63 species so far (including all uncertainties, but not sight records), is rather poor, though coral communities are locally well developed. These figures probably reflect incomplete study and sampling. Although comparison with other areas may therefore be premature, a preliminary biogeographical analysis suggests that this fauna is more closely related to that of the Red Sea than to East Africa and the Seychelles. This differs from other published biogeographical work on Indian Ocean coral faunas, but further study of the corals in this and neighbouring areas of the Indian Ocean is needed in order to resolve this apparent anomaly.     

Unambiguous through-bond sugar-to-base correlations for purines in 13C, 15N-labeled nucleic acids: The HsCsNb,HsCs(N)bCb,and HbNbCb experiments

Summary A set of three 3D (¹H, ¹³C, ¹⁵N) triple-resonance correlation experiments has been designed to provide H1-H8 intraresidue sugar-to-base correlations in purines in an unambiguous and efficient manner. Together, the H_sC_sN_b, H_sC_s(N)_bC_b, and H_bN_bC_b experiments correlate the H1 sugar proton to the H8 proton of the attached base by means of the {H1, C1, N9, C8, H8} heteronuclear scalar coupling network. The assignment strategy presented here allows for unambiguous H1-H8 intraresidue correlations, provided that no two purines have both the same H1 and C1 chemical shifts and the same C8 and N9 chemical shifts. These experiments have yielded H1-H8 intraresidue sugar-to-base correlations for all five guanosines in the [¹³C, ¹⁵N] isotopically labeled RNA duplex r(GGCGCUUGCGUC)₂.     

Ceramide composition of the psoriatic scale

This paper investigates the ceramide composition of the psoriatic scale compared with that of normal human SC. A method was optimalized, based on TLC separation followed by densitometry, allowing the provision of good resolution and quantification of ceramide fractions from both normal and pathological specimens. Seven ceramide fractions were isolated and submitted to compositional analysis. The obtained results suggested a revisitation of previous ceramide designation. Therefore a simple classification is suggested, based on grouping ceramides carrying structural similarities under common codes. According to these rules, ceramides were grouped into five classes designated as: (1) Cer[EOS], which contains ester-linked fatty acids, ω-OH fatty acids and sphingosines; (2) Cer[NS], which contains non-OH fatty acids and sphingosines; (3) Cer[NP], which contains non-OH fatty acids and phytosphingosines; (4) Cer[AS], which contains α-OH fatty acids and sphingosines; (5) Cer[AP], which contains α-OH fatty acids and phytosphingosines. Analysis of ceramides from the psoriatic scale, compared to those from normal human SC, resulted in an impairment of the Cer[EOS] content as well as of the ceramides containing phytosphingosine, with concurrent increase in ceramides containing sphingosine, being the total amount maintained identical. Since one of the suggested pathways for phytosphingosine biosynthesis involves the water addition to the corresponding sphingosine double bond, we can speculate that the observed alterarion is due to a deranged water bioavailability, associated with psoriaris.     

Neurological and electroencephalographic changes in newborns treated with prostaglandins E2 and E2

Six newborns with obstructive right heart lesions were examined neurologically and electroencephalographically during treatment with prostaglandin (PG) E₁ or E₂ given to maintain patency of the ductus arteriosus and to increase pulmonary blood flow. PG was administered intravenously or intraarterially in the aortic isthmus proximal to the ductus arteriosus. Besides a rise in arterial oxygen saturation, all patients had some sign of central nervous system involvement. The electroencephalogram showed minor changes suggestive of sedation. In addition, three patients in whom PG given intravenously presented various combinations of neurological abnormalities (“myoclonic jerks”, apnoeic spells, hiccup) of subcortical origin. Side-effects subsided after stopping the treatment anf posed no problem in the management of the patients. These findings confirm the usefulness and safety of the PG therapy and indicate that the intraaortic route of administration is preferable.     

Delayed hypersensitivity and Ig level in 210 patients with chronic myeloid leukemia

Summary Serum immunoglobulin concentration and skin reactivity to at least three recall antigens were determined in 210 patients with chronic myeloid leukemia (CML). Immunoglobulin concentration was normal in the great majority of the patients. Skin tests were negative in 50 of 210 cases (24%). No relationship could be demonstrated between skin reactivity, age, time since diagnosis, WBC, lymphocyte count, and splenectomy. Prior antileukemic therapy was a major factor in determining the response to skin tests.S. Tura (Chairman) and M. Baccarani (Secretary), Cattedra di Ematologia dell'Università e Servizio di Ematologia dell'Ospedale S. Orsola, Bologna; G. de Sandre, G. Perona, G. Cetto, G. Pizzolo, Istituto di Patologia Medica e Cattedra di Ematologia dell'Università, Verona; P. Rambotti, B. Falini, Clinica Medica dell'Università, Perugia; T. Chisesi, G. Capnist, Divisione di Ematologia, Ospedale Civile, Vicenza; A. Cajozzo, P. Citarella, Cattedra di Ematologia dell'Università, Palermo; G. Broccia, Sezione di Ematologia, Ospedale Armando Businco, Cagliari; V. Liso, G. Troccoli, Clinica Medica II dell'Università, Bari; L. Bruzzese, G. Nappi, A. Abbadessa, Clinica Medica (I Facoltà) dell'Università, Napoli; A. Porcellini, C. Delfini, Divisione di Ematologia, Ospedali Riuniti, Pesaro; E. Cacciola, R. Giustolisi, R. Musso, V. Raimondi, Cattedra di Ematologia dell'Università, Catania; G. Torlontano, L. Geraci, Cattedra di Ematologia dell'Università, Chieti, e Divisione di Ematologia, Ospedale Civile, Pescara; F. Mandelli, G. Mariani, B. Monarca, N. Petti, Cattedra di Ematologia dell'Università, Roma; R. di Guglielmo, A. Miliani, Clinica Medica dell'Università, Firenze; C. Bernasconi, M. Lazzarino, G. Castelli, Divisione di Ematologia, Ospedale S. Matteo, Pavia; A. Alberti, S. Magro, Servizio di Ematologia, Ospedale Generale Regionale, Catanzaro; A. Neri, P. Iacopino, Divisione di Ematologia, Ospedali Riuniti, Reggio Calabria; R. Delsignore, M. C. Baroni, Istituto di Patologia Medica dell'Universita, Parma; E. Bajetta, S. Monfardini, Istituto Nazionale per lo Studio e la Cura dei Tumori, Milano; S. Tognella, Istituto Scientifico di Medicina Interna, Cattedra di Clinica Medica 2R, Università, Genova.     

Chromosome constitution of in vitro segregated haploid and diploid cells of the mouse

The composition in segregated haploid sets of paternal and maternal chromosomes has been studied in order to verify whether their composition is uniparental of mixed, fixed or variable. Primary cultures where prepared using kidneys from hybrids of strains of Mus musculus in which the parental chromosomes are distinguishable; the maternal set consists of 20 teleocentric chromosomes, the paternal set of 9 metacentric chromosomes, derived by Robertsonian fusion and 2 telocentrics. Applying Seabright's banding technique, an analysis of segregated haploid and diploid cells, which have originated spontaneously through polyploidisation-segregation processes was carried out. It was concluded that the haploid sets have a variable composition of paternal and maternal chromosomes.