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

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

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

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

Comparison of NMR and crystal structures for the proteins TM1112 and TM1367

NMR structures of the proteins TM1112 and TM1367 solved by the JCSG in solution at 298 K could be superimposed with the corresponding crystal structures at 100 K with r.m.s.d. values of <1.0 Å for the backbone heavy atoms. For both proteins the structural differences between multiple molecules in the asymmetric unit of the crystals correlated with structural variations within the bundles of conformers used to represent the NMR solution structures. A recently introduced JCSG NMR structure-determination protocol, which makes use of the software package UNIO for extensive automation, was further evaluated by comparison of the TM1112 structure obtained using these automated methods with another NMR structure that was independently solved in another PSI center, where a largely interactive approach was applied