Substitution Matrices of Residue Triplets Derived from Protein Blocks.

In protein sequence alignment, residue similarity is usually evaluated by substitution matrix, which scores all possible exchanges of one amino acid with another. Several matrices are widely used in sequence alignment, including PAM matrices derived from homologous sequence and BLOSUM matrices derived from aligned segments of BLOCKS. However, most matrices have not addressed the high-order residue-residue interactions that are vital to the bioproperties of protein.With consideration for the inherent correlation in residue triplet, we present a new scoring scheme for sequence alignment. Protein sequence is treated as overlapping and successive 3-residue segments. Two edge residues of a triplet are clustered into hydrophobic or polar categories, respectively. Protein sequence is then rewritten into triplet sequence with 2 · 20 · 2 = 80 alphabets. Using a traditional approach, we construct a new scoring scheme named TLESUMhp (TripLEt SUbstitution Matrices with hydropobic and polar information) for pairwise substitution of triplets, which characterizes the similarity of residue triplets. The applications of this matrix led to marked improvements in multiple sequence alignment and in searching structurally alike residue segments. The reason for the occurrence of the ‘‘twilight zone,’’ i.e., structure explosion of lowidentity sequences, is also discussed.

Decomposition of Noncommutative U(1) Gauge Potential

We investigate the decomposition of noncommutative gauge potential (A) over cap (i), and find that it has inner structure, namely, (A) over cap (i) can he decomposed in two parts, (b) over cap (i) and (a) over cap (i), where (b) over cap (i) satisfies gauge transformations while (a) over cap (i) satisfies adjoint transformations, so close the Seiberg-Witten mapping of noncommutative, U(1) gauge potential. By, means of Seiberg-Witten mapping, we construct a mapping of unit vector field between noncommutative space and ordinary space, and find the noncommutative U(1) gauge potential and its gauge field tensor can be expressed in terms of the unit vector field. When the unit vector field has no singularity point, noncommutative gauge potential and gauge field tensor will equal ordinary gauge potential and gauge field tensor

Structure analysis of the fulvic acids extracted from composted corn stalk residue

Chemical structure of fulvic acids extracted from composted corn stalk residue(CSR FA)was studied by Fourier transform infrared (FTIR) spectroscopy, H-1 and C-13 nuclear magnetic resonance(H-1-NMR, C-13-NMR) spectroscopy. The results show that CSR FA mainly consists of four types of carbon: carbonyl, aromatical, alkyl and carbohydrate, the carbohydrate is dominant. Its aromaticity is 15.42%, less than that of CSR HA. This indicates that the construction of CSR FA is simpler than that of CSR HA, FA can not be extracted from undecomposed corn stalk residue. CSR FA may be formed by cellulose or hemicellulosemorties combined with aromatic compound from decomposed lignin.

Substitution of pseudokinase domain residue Val-617 by large non-polar amino acids causes activation of JAK2

Explaining the uniqueness of the acquired somatic JAK2 V617F mutation, which is present in more than 95% of polycythemia vera patients, has been a challenge. The V617F mutation in the pseudokinase domain of JAK2 renders the unmutated kinase domain constitutively active. We have performed random mutagenesis at position 617 of JAK2 and tested each of the 20 possible amino acids for ability to induce constitutive signaling in Ba/F3 cells expressing the erythropoietin receptor. Four JAK2 mutants, V617W, V617M, V617I, and V617L, were able to induce cytokine independence and constitutive downstream signaling. Only V617W induced a level of constitutive activation comparable with V617F. Also, only V617W stabilized tyrosine-phosphorylated suppressor of cytokine signaling 3 ( SOCS3), a mechanism by which JAK2 V617F overcomes inhibition by SOCS3. The V617W mutant induced a myeloproliferative disease in mice, mainly characterized by erythrocytosis and megakaryocytic proliferation. Although JAK2 V617W would predictably be pathogenic in humans, the substitution of the Val codon, GTC, by TTG, the codon for Trp, would require three base pair changes, and thus it is unlikely to occur. We discuss how the predicted conformations of the activated JAK2 mutants can lead to better screening assays for novel small molecule inhibitors.

The human prion protein residue 129 polymorphism lies within a cluster of epitopes for T cell recognition.

T cell immune responses to central nervous system-derived and other self-antigens are commonly described in both healthy and autoimmune individuals. However, in the case of the human prion protein (PrP), it has been argued that immunologic tolerance is uncommonly robust. Although development of an effective vaccine for prion disease requires breaking of tolerance to PrP, the extent of immune tolerance to PrP and the identity of immunodominant regions of the protein have not previously been determined in humans. We analyzed PrP T cell epitopes both by using a predictive algorithm and by measuring functional immune responses from healthy donors. Interestingly, clusters of epitopes were focused around the area of the polymorphic residue 129, previously identified as an indicator of susceptibility to prion disease, and in the C-terminal region. Moreover, responses were seen to PrP peptide 121-134 containing methionine at position 129, whereas PrP 121-134 [129V] was not immunogenic. The residue 129 polymorphism was also associated with distinct patterns of cytokine response: PrP 128-141 [129M] inducing IL-4 and IL-6 production, which was not seen in response to PrP 128-141 [129V]. Our data suggest that the immunogenic regions of human PrP lie between residue 107 and the C-terminus and that, like with many other central nervous system antigens, healthy individuals carry responses to PrP within the T cell repertoire and yet do not experience deleterious autoimmune reactions.

Effects of seawater-neutralised bauxite refinery residue on properties of concrete

Various industrial by-products, such as fly ash, ground granulated blast-furnace slag and silica fume, have been used in concrete to improve its properties. This also enables any environmental issues associated with their disposal. Another material that is available in large quantities and requiring alternative methods of disposal is the Bauxite Refinery Reside (BRR) from the Bayer process used to extract alumina from bauxite. As this is highly caustic and causes many health hazards, Virotec International Ltd. developed a patented technology to convert this into a material that can be used commercially, known as Bauxsol™, for various environmental remediation applications. This use is limited to small quantities of seawater-neutralised BRR and hence an investigation was carried out to establish its potential utilisation as a sand replacement material in concrete. In addition to fresh properties of concrete containing seawater-neutralised BRR up to 20% by mass of Portland cement, mechanical and durability properties were determined. These properties indicated that seawater-neutralised BRR can be used to replace natural sand up to 10% by mass of cement to improve the durability properties of concrete without detrimentally affecting their physical properties. Combining these beneficial effects with environmental remediation applications, it can be concluded that there are specific applications where concretes containing seawater-neutralised BRR could be used.

On the function of the internal cavity of histone deacetylase protein 8: R37 is a crucial residue for catalysis

Biochemical studies reveal that a conserved arginine residue (R37) at the centre of the 14 angstrom internal cavity of histone deacetylase (HDAC) 8 is important for catalysis and acetate affinity. Computational studies indicate that R37 forms multiple hydrogen bonding interactions with the backbone carbonyl oxygen atoms of two conserved glycine residues, G303 and G305, resulting in a 'closed' form of the channel. One possible rationale for these data is that water or product (acetate) transit through the catalytically crucial internal channel of HDAC8 is regulated by a gating interaction between G139 and G303 tethered in position by the conserved R37. (C) 2011 Elsevier Ltd. All rights reserved.