Topological Field Theory Interpretation of String Topology

The string bracket introduced by Chas and Sullivan is reinterpreted from the point of view of topological field theories in the Batalin-Vilkovisky or BRST formalisms. Namely, topological action functionals for gauge fields (generalizing Chern-Simons and BF theories) are considered together with generalized Wilson loops. The latter generate a (Poisson or Gerstenhaber) algebra of functionals with values in the S 1 -equivariant cohomology of the loop space of the manifold on which the theory is defined. It is proved that, in the case of GL(n,ℂ) with standard representation, the (Poisson or BV) bracket of two generalized Wilson loops applied to two cycles is the same as the generalized Wilson loop applied to the string bracket of the cycles. Generalizations to other groups are briefly describe

THE PROTEIN PHEROMONE FAMILY OF E. PETZI, A PSYCHROPHILIC AND EARLY BRANCHING EUPLOTES SPECIES

Euplotes species are valuable for the study of the structural and functional biology of water-borne protein pheromones that cells constitutively synthesize and use in intra-specific chemical communication. We have recently devoted particular attention to the pheromone family of the “cold loving” (psychrophilic) species E. petzi which dwells in the freezing Antarctic and Arctic coastal sea waters, and forms, together with E. sinicus, the earliest branch of the Euplotes phylogenetic tree. From cultures of genetically distinct strains, we have isolated and sequenced four E. petzi pheromones. With respect to the known pheromones from E. raikovi, E. octocarinatus, E. nobilii and E. crassus, the E. petzi pheromones are smaller (32 amino acids) and richer in Cys residues (eight) located in strictly conserved positions. These residues are predicted to form four intra-chain disulfide bridges, which suggests a compact globular fold of the molecules. However, the NMR solution structure determined for one of the E. petzi pheromones challenges this hypothesis. The structure consists of one more extended eight-residue alpha-helix and one smaller four-residue helix, and shows large polypeptide segments devoid of regular secondary structures. Pheromones from other Euplotes species which live in temperate waters and branch later than E. petzi in the Euplotes phylogenetic tree are known to be characterized by a three-helix fold and unstructured regions of comparatively limited dimensions. In the light of this knowledge, we can thus draw two distinct conclusions from our findings. The first, of phylogenetic nature, is that the structural evolution of the Euplotes pheromones involves an increase in size and complexity. This is in line with the smaller and simpler organization that also the macronuclear E. petzi pheromone genes show with respect to their homologues in other Euplotes species. The second conclusion is that the extended unstructured regions of E. petzi pheromones are likely correlated with an increased flexibility of the molecular backbone and, hence, reflect a common feature of protein cold-adaptation. In this regard, further insights will be obtained by ongoing experiments which aim to assess the unfolding and refolding properties of E. petzi pheromones when exposed to increased temperatures and variations of other environmental parameters

Topological Field Theory Interpretation of String Topology

The string bracket introduced by Chas and Sullivan [math.GT/9911159] is reinterpreted from the point of view of topological field theories in the Batalin-Vilkovisky or BRST formalisms. Namely, topological action functionals for gauge fields (generalizing Chern-Simons and BF theories) are considered together with generalized Wilson loops. The latter generate a (Poisson or Gerstenhaber) algebra of functionals with values in the $S^1$-equivariant cohomology of the loop space of the manifold on which the theory is defined. It is proved that, in the case of $GL_n$ with standard representation, the (Poisson or BV) bracket of two generalized Wilson loops applied to two cycles is the same as the generalized Wilson loop applied to the string bracket of the cycles. Generalizations to other groups are briefly described.Comment: 27 pages, 2 figure

Homo- and hetero-oligomeric protein–protein associations explain autocrine and heterologous pheromone-cell interactions in Euplotes

In Euplotes, protein pheromones regulate cell reproduction and mating by binding cells in autocrine or heterologous fashion, respectively. Pheromone binding sites (receptors) are identified with membrane-bound pheromone isoforms determined by the same genes specifying the soluble forms, establishing a structural equivalence in each cell type between the two twin proteins. Based on this equivalence, autocrine and heterologous pheromone/receptor interactions were investigated analyzing how native molecules of pheromones Er-1 and Er-13, distinctive of mating compatible E. raikovi cell types, associate into crystals. Er-1 and Er-13 crystals are equally ormed by molecules that associate cooperatively into oligomeric chains rigorously taking a mutually opposite orientation, and each burying two interfaces. A minor interface is pheromone-specific, while a major one is common in Er-1 and Er-13 crystals. A close structural inspection of this interface suggests that it may be used by Er-1 and Er-13 to associate into heterodimers, yet inapt to further associate into higher complexes. Pheromonemolecule homo-oligomerization into chains accounts for clustering and internalization of autocrine pheromone/receptor complexes in growing cells, while the heterodimer unsuitability to oligomerize may explain why heterologous pheromone/receptor complexes fail clustering and internalization. Remaining on the cell surface, they are credited with a key role in cell–cell mating adhesion

New maverick coset theories

We present new examples of maverick coset conformal field theories. They are closely related to conformal embeddings and exceptional modular invariants.Comment: 6 pages, LaTeX2

Molecular Structures and Coding Genes of the Water-Borne Protein Pheromones of Euplotes petzi, an Early Diverging Polar Species of Euplotes

Euplotes is diversified into dozens of widely distributed species that produce structurally homologous families of water-borne protein pheromones governing self-/nonself-recognition phenomena. Structures of pheromones and pheromone coding genes have so far been studied from species lying in different positions of the Euplotes phylogenetic tree. We have now cloned the coding genes and determined the NMR molecular structure of four pheromones isolated from Euplotes petzi, a polar species which is phylogenetically distant from previously studied species and forms the deepest branching clade in the tree. The E. petzi pheromone genes have significantly shorter sequences than in other congeners, lack introns, and encode products of only 32 amino acids. Likewise, the three-dimensional structure of the E. petzi pheromones is markedly simpler than the three-helix up-down-up architecture previously determined in another polar species, Euplotes nobilii, and in a temperate-water species, Euplotes raikovi. Although sharing the same up-down-up architecture, it includes only two short α-helices that find their topological counterparts with the second and third helices of the E. raikovi and E. nobilii pheromones. The overall picture that emerges is that the evolution of Euplotes pheromones involves progressive increases in the gene sequence length and in the complexity of the three-dimensional molecular structure

The J-UNIO protocol for automated protein structure determination by NMR in solution

The J-UNIO (JCSG protocol using the software UNIO) procedure for automated protein structure determination by NMR in solution is introduced. In the present implementation, J-UNIO makes use of APSY-NMR spectroscopy, 3D heteronuclear-resolved [1H,1H]-NOESY experiments, and the software UNIO. Applications with proteins from the JCSG target list with sizes up to 150 residues showed that the procedure is highly robust and efficient. In all instances the correct polypeptide fold was obtained in the first round of automated data analysis and structure calculation. After interactive validation of the data obtained from the automated routine, the quality of the final structures was comparable to results from interactive structure determination. Special advantages are that the NMR data have been recorded with 6-10days of instrument time per protein, that there is only a single step of chemical shift adjustments to relate the backbone signals in the APSY-NMR spectra with the corresponding backbone signals in the NOESY spectra, and that the NOE-based amino acid side chain chemical shift assignments are automatically focused on those residues that are heavily weighted in the structure calculation. The individual working steps of J-UNIO are illustrated with the structure determination of the protein YP_926445.1 from Shewanella amazonensis, and the results obtained with 17 JCSG targets are critically evaluate

Coding genes and molecular structures of the diffusible signalling proteins (pheromones) of the polar ciliate, Euplotes nobilii

In protozoan ciliates, diffusible signalling proteins (pheromones) regulate the vegetative growth and mating interactions. Here, the coding genes and the structures of the encoded pheromones were studied in genetically distinct wild-type strains representing interbreeding Antarctic and Arctic populations of the marine ciliate Euplotes nobilii. Determination of seven allelic pheromone-coding DNA sequences revealed that an unusual extension and high structural conservation of the 5′ non-coding region are peculiar traits of this gene family, implying that this region is directly involved in the mechanism of pheromone gene expression, possibly through phenomena of intron splicing and/or frame-shifting. For four pheromones, the three-dimensional structures were determined by nuclear magnetic resonance spectroscopy in solution. These structures show that the pheromones represent a protein family which adapts to its polar environment by combining a structurally stable core of a three-helix bundle with extended polypeptide segments that are devoid of regular secondary structures and concomitantly show enhanced structural flexibility

NMR structure of the protein NP_247299.1: comparison with the crystal structure

Comparison of the NMR and crystal structures of a protein determined using largely automated methods has enabled the interpretation of local differences in the highly similar structures. These differences are found in segments of higher B values in the crystal and correlate with dynamic processes on the NMR chemical shift timescale observed in solution