An alternative method to amplify RNA without loss of signal conservation for expression analysis with a proteinase DNA microarray in the ArrayTube format.

Background: Recent developments in DNA microarray technology led to a variety of open and closed devices and systems including high and low density microarrays for high-throughput screening applications as well as microarrays of lower density for specific diagnostic purposes. Beside predefined microarrays for specific applications manufacturers offer the production of custom-designed microarrays adapted to customers' wishes. Array based assays demand complex procedures including several steps for sample preparation (RNA extraction, amplification and sample labelling), hybridization and detection, thus leading to a high variability between several approaches and resulting in the necessity of extensive standardization and normalization procedures.

Foldase function of the cathepsin S proregion is strictly based upon its domain structure.

Folding of cathepsin S, like other cathepsin L-like proteases, depends on its proregion. The major part of the proregion forms a small domain distal from the catalytic centre, suggesting function(s) beyond active-site shielding. Using an optimised in vitro trans-refolding assay, we compared reactivation of denatured cathepsin S by the genuine propeptide, wild-type and ten selected mutants.

Folding incompetence of cathepsin L-like cysteine proteases may be compensated by the highly conserved, domain-building N-terminal extension of the proregion.

Folding of cathepsins L and S depend upon their proregion which extends the enzyme part by about 100 amino acids. Only a minority of the prosequence follows the structural template provided by the enzyme part; the majority forms an autonomous minidomain fairly distant from the active site cleft. We suggest that this prodomain may be the structural correlate of a foldase function of the proregion within the cathepsin L-like subfamily of papain-type cysteine proteases and report on a functional approach supporting this hypothesis.

An evolutionarily conserved tripartite tryptophan motif stabilizes the prodomains of cathepsin L-like cysteine proteases.

Cathepsin L-like cysteine proteinases contain an evolutionarily highly conserved alpha-helical motif in the proregion. This is called the ER(F/W)N(I/V)N motif according to the conserved amino acids along one side of the helix. We studied the function of this motif using site-directed mutagenesis experiments of human procathepsin S.

The inhibition of cathepsin S by its propeptide--specificity and mechanism of action.

The interaction of human recombinant full-length cathepsin S propeptide (amino acids 16-114) with mature cysteine proteinases was studied with respect to selectivity and pH dependence. The inhibitory capacity was tested towards mature human recombinant cathepsin S, purified cathepsin L from rat and Paramecium tetraurelia, rat cathepsin B, human cathepsin H, and papain. The propeptide of cathepsin S strongly inhibited cathepsin S (Ki = 0.