Stochastic algorithm for kinase homology model construction.

A stochastic algorithm for constructing multiple loops in homology modeling of proteins is presented. The algorithm discards variable values in iterations based on a cost function and on statistical analysis of results. Values that remain are used for constructing an ensemble of best solutions. In test cases, the stochastic algorithm retains all the best solutions, compared to an exhaustive scan of the full set of conformations. Individual loops are constructed by adding dipeptide units. Dipeptide conformations are extracted from a database of proteins and their conformations include bond lengths and all angles. Single loops are constructed from both N- and C- terminals to the center, and loop closure is evaluated by a combination of penalties for the peptide closure and Miyazawa-Jernigan (MJ) [1]. residue-residue interactions with the rest of the protein. Large ensembles of each loop are clustered and re-evaluated with a refined [2]. energy term. The reduced, clustered set of each loop is then employed to construct simultaneously all the loops. The algorithm was applied to construct simultaneously six loops in c-Src kinase family proteins, incorporating a total of 37-40 residues. The best RMSD for reconstructing the loops is 1.45 A for Lck (structure 1QPE in the Protein Data Bank) and 2.54 A for human c-Src (structure 1FMK). The multiple loop conformations with lowest energy have higher RMSD values, of 2.06 A and 3.09 A, respectively. The average RMSD values for the first 1000 conformations are 3.00 A and 3.46 A, respectively. Models for the "open" structures of c-Src and of Jak-2 were constructed on the basis of 1QPE. The Jak-2 model is found to be more flexible in the loops region than its c-Src counterpart.

Epidermal surface antigen (MS17S1) is highly conserved between mouse and human.

A mouse monoclonal antibody ECS-1 raised to human keratinocytes detects a 35-kDa epidermal surface antigen (ESA) and causes keratinocyte dissociation in vitro. ECS-1 stains skin of 16-day mouse embryo and 8- to 9-week human fetus. Mouse Esa cDNA encodes a 379-amino-acid protein that is 99.2% identical to the human, differing at only 3 amino acids. The gene (M17S1) was mapped to mouse chromosome 11, high-lighting the conserved linkage synteny existing between human chromosome 17 and mouse chromosome 11. Although the nude locus has been mapped to the same region of chromosome 11, no abnormalities in protein, mRNA, or cDNA or genomic sequences were detected in nude mice. However, both nude and control mice were found to have a second Esa mRNA transcript that conserves amino acid sequence and molecular weight. The mouse and human 5' and 3' untranslated sequences are conserved. Similar RNA folding patterns of the 5' untranslated region are predicted despite a 91-bp insertion in the mouse. These data suggest that both the function and the regulation of ESA protein are of importance and that Esa (M17S1) is not the nude locus gene.

Type I keratinocyte transglutaminase: expression in human skin and psoriasis.

A 92-kD transglutaminase (TGase K), expressed in human cultured keratinocytes and stratum corneum, catalyzes a critical step in the formation of the cornified envelope of terminal differentiation. A rabbit polyclonal antibody to TGase K was used to isolate overlapping cDNA clones from a human keratinocyte cDNA expression library. The cDNA clones were sequenced and unequivocally identified as TGase K by comparison to the N-terminal amino acid sequences of two cyanogen bromide fragments from the purified enzyme. The mRNA for Tgase K is expressed in cultured keratinocytes but not in A431 squamous carcinoma cells, in fibroblasts, or in other non-epithelial tissues and cells. Although TGase K protein expression is limited to the upper layers of normal epidermis, the mRNA is generally present throughout the epidermis, suggesting the possibility of post-transcriptional regulation. Precocious expression of TGase K protein occurs in psoriasis, and quantitative Northern blot analysis of TGase K mRNA from normal and involved epidermal biopsies from psoriasis patients suggests that TGase K mRNA levels are increased in psoriatic lesions. By using quantitative laser scanning confocal microscopy (LSCM) and in situ hybridization, the increase of the TGase K mRNA was in the range of 3-7 times in the psoriatic epidermis and was significantly higher compared with normal skin and with paired adjacent skin. Quantitative LSCM provides a powerful and direct method for analysis of gene expression in skin.