Complex Motifs Research Articles

New methods to predict MHC-binding sequences within protein antigens

The identification and analysis of MHC-binding sequences within protein antigens, and ultimately the ability to predict them, is central to immunology. Recent advances have revealed increasingly complex MHC-binding motifs and allow prediction of sequences that bind to both classes of MHC molecules. The systematic characterization of binding motifs for all human MHC alleles is now possible and will facilitate the design of peptides for therapeutic intervention.

Crystal and molecular structure of [formula omitted]: a novel packing of amphiphilic molecules

N-(n- Octyl)-6- deoxy- d- gluconamide crystallizes in the orthorhombic space group P2 12 12 1, with a = 5.4524(5), b = 16.662(3), and c = 36.897(5) Å. The structure was determined by X-ray diffraction and refined to R = 9.2%. The asymmetric crystal unit contains two molecules (A,B) with significantly different conformations. In contrast to the crystal structures of the N-(n- alkyl)- d- gluconamide family, in which the molecules were found arranged in head-to-tail monolayers, molecules A and B form a complex motif with pairwise alternating orientations and interdigitating antiparallel aliphatic chains. The two symmetry independent molecules form considerably different hydrogen bond patterns.

Parathyroid Hormone-Related Protein as a Prohormone: Posttranslational Processing and Receptor Interactions*

Since the elucidation of the structures of the three human PRHrP isoforms in 1987, information has rapidly accured which indicates that the role of PTHrP in normal physiology will prove to be crucial as well as exceedingly complex. The importance of the role of PTHrP in normal physiology is underscored by its broad tissue expression, by its intense evolutionary conservation, by its extremely early expression after fertilization of the ovum, and by the lethal consequences of PTHrP gene disruption. The complexity of the role of PTHrP in normal physiology increases almost monthly. This complexity is reflected in the broad tissue distribution of the peptide, its complex transcriptional regulation and mRNA instability motifs, and its multiple transcripts and isoforms. It is now clear that additional complexity exists at the level of posttranslational processing. Expression of the PTHrP gene leads to the tissue-specific processing and secretion of an increasingly complex family of derivative peptides, each with its own repertoire of cognate receptors, signal transduction pathways, and physiological consequences. Further elucidation of the posttranslational processing pathways and mechanisms can be anticipated in the coming years, coupled with a corresponding elucidation of multiple PTHrP receptors, their specific signal transduction pathways, and their unique physiological roles. The role of PTHrP in causing HHM is now clearly established. Work in the coming decade will focus on the normal physiological roles played by PTHrP.

Una nueva zona de arte rupestre al aire libre en el NW : la península de Barbanza

A new área with open air rock carvings in the Iberian NW; the península of Barbanza. Traditionally the research on Galician rock art had focused in the área around Campolameiro (Pontevedra) where the biggest number of sites was reported, whereas other zones to the North were almost unknown in that respect. In this paper we deal with the new finds of petroglyphs in the Barbanza, where intensive survey has multiplied the number of this tipe of sites. The usual motifs are abstract (mainly concentric circles and cupmarks) but also semischematic with representations of deer. The distribution of the art is more dense in the coastal lowlands, though a number of sites is reported in the passes leading into the high sierra and in this área itself. As to the relationship with the roughiy contemporary settiements (lllrd millenium BC), we have observed a definite pattern: cupmarks are sharing the same space with the more densely Inhabited áreas down to the coast and also they are found near to the mounds in the high plateau; animal representations and more complex abstract motifs (concentric circles with or without radius) are sited along small valleys or ridges that link the lowlands and the upper reaches of the Sierra. All this patterning would point out to the role of petrogliphs as a mechanism for defining the most resourceful or symbolic places and the paths leading into them.

The genomic structure of the human AP-2 transcription factor.

The transcription factor AP-2 is encoded by a gene located on chromosome 6 near the HLA locus. Here we describe the genomic organization of the AP-2 gene including an initial characterization of the promoter. We have mapped two mRNA initiation sites, the entire exon-intron structure and located two polyadenylation sites. The mature AP-2 mRNA is spliced from 7 exons distributed over a region of 18 kb genomic DNA. A recently cloned inhibitory AP-2 protein is generated by alternative usage of a C-terminal exon. The proline-rich transactivation motif is encoded by a single exon within the N-terminal region in contrast to the complex DNA binding and dimerization motif which involves amino acid residues located on four different exons. The sites of mRNA initiation are located 220 and 271 bases upstream from the ATG translation start site. Although the promoter contains no canonical sequence motifs for basal transcription factors, such as TATA-, CCAAT- or SP-1 boxes, it mediates cell-type-specific expression of a CAT reporter gene in PA-1 human teratocarcinoma cells and is inactive in murine F9 teratocarcinoma cells. We demonstrate that the promoter of the AP-2 gene is subject to positive autoregulation by its own gene product. A consensus AP-2 binding site is located at position -622 with respect to the ATG. This site binds specifically to bacterially expressed AP-2 as well as to multiple proteins, including AP-2, present in PA-1 and HeLa cell nuclear extracts. A partial AP-2 promoter fragment including the AP-2 consensus binding site is approximately 5-fold transactivated by cotransfection of an AP-2 expression plasmid.

The morphology of poly(vinylidene fluoride) crystallized from blends of poly(vinylidene fluoride) and poly(ethyl acrylate)

AbstractA combined optical and electron microscopical study has been carried out of the crystallization habits of poly(vinylidene fluoride) (PVF2) when it is crystallized from blends with noncrystallizable poly(ethyl acrylate) (PEA). The PVF2/PEA weight ratios were 0.5/99.5,5/95, and 15/85. Isothermal crystallization upon cooling the blends from the single‐phase liquid region was carried out in the range 135–155°C, in which the polymer crystallizes in the α‐orthorhombic unit cell form. The 0.5/99.5 blend yielded multilayered and planar lamellar crystals. The lamellae formed at low undercoolings were lozenge shaped and bounded laterally by {110} faces. This habit is prototypical of the dendritic lateral habits exhibited by the crystals grown from the same blend at high undercoolings as well as by the constituent lamellae in the incipient spherulitic aggregates and banded spherulites that formed from the 5/95 and the 15/85 blends, respectively. In contrast with the planar crystals grown from the 0.5/99.5 blend, the formation of the aggregates grown from the 5/95 blend is governed by a conformationally complex motif of dendritic lamellar growth and proliferation. The development of these aggregates is characterized by the twisting of the orientation of lamellae about their preferential b‐axis direction of growth, coupled with a fan‐like splaying or spreading of lamellae about that axis. The radial growth in the banded spherulites formed from the 15/85 blend is governed by a radially periodic repetition of a similar lamellar twisting/fan‐like spreading growth motif whose recurrence corresponds to the extinction band spacing. This motif differs in its fan‐like splaying component from banding due to just a helicoidal twisting of lamellae about the radial direction. © 1993 John Wiley & Sons, Inc.

Determination of the orientation of a DNA binding motif in a protein-DNA complex by photocrosslinking.

We have developed a straightforward biochemical method to determine the orientation of the DNA binding motif of a sequence-specific DNA binding protein relative to the DNA site in the protein-DNA complex. The method involves incorporation of a photoactivatable crosslinking agent at a single site within the DNA binding motif of the sequence-specific DNA binding protein, formation of the derivatized protein-DNA complex, UV-irradiation of the derivatized protein-DNA complex, and determination of the nucleotide(s) at which crosslinking occurs. We have applied the method to catabolite gene activator protein (CAP). We have constructed and analyzed two derivatives of CAP: one having a phenyl azide photoactivatable crosslinking agent at amino acid 2 of the helix-turn-helix motif of CAP, and one having a phenyl azide photoactivatable crosslinking agent at amino acid 10 of the helix-turn-helix motif of CAP. The results indicate that amino acid 2 of the helix-turn-helix motif is close to the top-strand nucleotides of base pairs 3 and 4 of the DNA half site in the CAP-DNA complex, and that amino acid 10 of the helix-turn-helix motif is close to the bottom-strand nucleotide of base pair 10 of the DNA half site in the CAP-DNA complex. The results define unambiguously the orientation of the helix-turn-helix motif relative to the DNA half site in the CAP-DNA complex. Comparison of the results to the crystallographic structure of the CAP-DNA complex [Schultz, S., Shields, S. & Steitz, T. (1991) Science 253, 1001-1007] indicates that the method provides accurate, high-resolution proximity and orientation information.

Structural motifs in dinuclear d8 metal complexes. Structural and spectroscopic characteristics of an alternative unsymmetrical 3:5 ligand distribution as compared to the symmetrical 4:4 or face-to-face arrangement

Addition of [Rh(CNCH 3 ) 4 ] (BPh 4 ) to an acetone solution of [Pt(dmp) 2 ]Cl 2 (dpm is bis(diphenylphosphino)methane) followed by addition of methanolic ammonium hexafluorophosphate yields ivory [(CH 3 NC)PtRh(CNCH 3 ) 3 (μ-dpm) 2 ](PF 6 ) 3 .

The Continental Affiliations of Two Palaeolithic Engraved Bones Found in England

The figurative and schematic designs on two pieces of decorated bone from Creswell, Derbyshire are related to motifs used in later Magdalenian portable art in south-western and northern France, and are assigned to a period between 11,000–12,000 years ago on grounds of design and environmental evidence. One piece, that from Robin Hood's Cave, which is carefully engraved with complex motifs on both sides, shows handling traces indicating carriage over a period of time by one or more individuals. As the late Glacial Hunters at Creswell are thought to be nomadic, and the cave to have been inhabited only in the Summer months, the piece may have been made elsewhere and carried to Derbyshire, possibly from the continent.

The Several Aspects of Fire in Achim von Arnim's der Tolle Invalide

In reading Achim von Arnim's Novelle, Der tolle Invalide, one is soon aware of the frequent occurrence of the word Feuer and related expressions. This seems at first to be merely clever word play, but a closer inspection shows that the various aspects of fire are so intimately connected with the events and characters of the story that they reflect the basic structure of the Novelle.' Fire is an unusually complex motif because it is so rich in connotative associations. From the earliest mention in primitive mythology, man has endowed fire with both natural and supernatural significance. He has sought it for its positive creative potentialities and has, at the same time, feared its destructive powers. Fire has thus come to represent symbolically things as various as home, love, heavenly grace, and on the other hand, war, hatred, and eternal damnation. Arnim's awareness of the basic complexity of his motif is evident in the opening scene of the narrative. Count Diirande, the elderly commander of disabled veterans at Marseilles, is shown complaining of two kinds of coldness. The penetrating dampness of the October air makes him shiver physically, while the thoughtless gaiety of people in the street on their way to a ball chills him psychologically with a sense of being left out of social affairs (einsam frierend, 317).2 To overcome his physical discomfort, the old commander shoves fuel onto the fire on his hearth, using his wooden leg as a poker. In addition to its warming effect, the fire also inspires his imagination by calling to mind his favorite hobby, fireworks. Diirande becomes so absorbed in daydreams that he forgets the danger inherent in the flames and