Structure-function relations in phosphorylcholine-binding mouse myeloma proteins

The binding site interactions between the phosphorylcholine (phosphocholine)-binding mouse myeloma proteins TEPC 15, W3207, McPC 603, MOPC 167, and MOPC 511 and the isotopically substituted hapten phosphoryl-[methyl-13C]choline have been investigated using 13C and 31P nuclear magnetic resonance (NMR) spectroscopy. Each protein exhibits a unique NMR pattern, but extensive similarities in chemical shift parameters upon binding of hapten to immunoglobulin suggest a significant degree of conservation of important hapten-binding site interactions. Moreover, independent binding studies, in conjunction with the NMR data, allow construction of a simple model of the binding sites of these antibodies, analyzed in terms of the relative strength of interaction between hapten and two main subsites. The NMR evidence supports the view that the heavy chains of these proteins dominate in interacting with bound phosphorylcholine; the various subspecificities of these proteins for phosphorylcholine analogues can be accounted for by amino acid changes in the hypervariable regions of the heavy chains

Comment on "Partial energies fluctuations and negative heat capacities" by X. Campi et al

Studying the energy partioning published in nucl-th/0406056v2 we show that the presented results do not fulfill the sum rule due to energy conservation. The observed fluctuations of the energy conservation test point to a numerical problem. Moreover, analysis of the binding energies show that the fragment recognition algorithm adopted by Campi et al. leads with a sizeable probability to fragments containing up to the total mass even for excitation energies as large as 3/4 of the total binding. This surprising result points to another problem since the published inter-fragment energy is not zero while a unique fragment is present. This problem may be due to either the fragment recognition algorithm or to the definition of the inter and intra-fragment energy. These numerical inconsistencies should be settled before any conclusion on the physics can be drawn

Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins

A method to detect DNA-binding sites on the surface of a protein structure is important for functional annotation. This work describes the analysis of residue patches on the surface of DNA-binding proteins and the development of a method of predicting DNA-binding sites using a single feature of these surface patches. Surface patches and the DNA-binding sites were initially analysed for accessibility, electrostatic potential, residue propensity, hydrophobicity and residue conservation. From this, it was observed that the DNA-binding sites were, in general, amongst the top 10% of patches with the largest positive electrostatic scores. This knowledge led to the development of a prediction method in which patches of surface residues were selected such that they excluded residues with negative electrostatic scores. This method was used to make predictions for a data set of 56 non-homologous DNA-binding proteins. Correct predictions made for 68% of the data set

Wide-Scale Analysis of Human Functional Transcription Factor Binding Reveals a Strong Bias towards the Transcription Start Site

We introduce a novel method to screen the promoters of a set of genes with shared biological function, against a precompiled library of motifs, and find those motifs which are statistically over-represented in the gene set. The gene sets were obtained from the functional Gene Ontology (GO) classification; for each set and motif we optimized the sequence similarity score threshold, independently for every location window (measured with respect to the TSS), taking into account the location dependent nucleotide heterogeneity along the promoters of the target genes. We performed a high throughput analysis, searching the promoters (from 200bp downstream to 1000bp upstream the TSS), of more than 8000 human and 23,000 mouse genes, for 134 functional Gene Ontology classes and for 412 known DNA motifs. When combined with binding site and location conservation between human and mouse, the method identifies with high probability functional binding sites that regulate groups of biologically related genes. We found many location-sensitive functional binding events and showed that they clustered close to the TSS. Our method and findings were put to several experimental tests. By allowing a "flexible" threshold and combining our functional class and location specific search method with conservation between human and mouse, we are able to identify reliably functional TF binding sites. This is an essential step towards constructing regulatory networks and elucidating the design principles that govern transcriptional regulation of expression. The promoter region proximal to the TSS appears to be of central importance for regulation of transcription in human and mouse, just as it is in bacteria and yeast.Comment: 31 pages, including Supplementary Information and figure

Resuscitation-promoting factors possess a lysozyme-like domain

The novel bacterial cytokine family – resuscitation-promoting factors (Rpfs) – share a conserved domain of uncharacterized function. Predicting the structure of this domain suggests that Rpfs possess a lysozyme-like domain. The model highlights the good conservation of residues involved in catalysis and substrate binding. A lysozyme-like function makes sense for this domain in the light of experimental characterization of the biological function of Rpfs

Security Trade-offs in Ancilla-Free Quantum Bit Commitment in the Presence of Superselection Rules

Security trade-offs have been established for one-way bit commitment in quant-ph/0106019. We study this trade-off in two superselection settings. We show that for an `abelian' superselection rule (exemplified by particle conservation) the standard trade-off between sealing and binding properties still holds. For the non-abelian case (exemplified by angular momentum conservation) the security trade-off can be more subtle, which we illustrate by showing that if the bit-commitment is forced to be ancilla-free an asymptotically secure quantum bit commitment is possible.Comment: 7 pages Latex; v2 has 8 pages and additional references and clarifications, this paper is to appear in the New Journal of Physic

String Network from M-theory

We study the three string junctions and string networks in Type IIB string theory by explicity constructing the holomorphic embeddings of the M-theory membrane that describe such configurations. The main feature of them such as supersymmetry, charge conservation and balance of tensions are derived in a more unified manner. We calculate the energy of the string junction and show that there is no binding energy associated with the junction.Comment: 16 pages, harvmac, 2 figures, references adde