Non-homology knowledge-based prediction of the papain prosegment folding pattern: a description of plausible folding...

A detailed knowledge of three-dimensional conformations is necessary in order to understand the close relationship between protein structure and function. Among current methodologies, homology modeling is an important tool for obtaining reliable geometries and it provides a direct alternative to X-ray or NMR techniques. In contrast, predictive methods with no three-dimensional template (non-homology) still require further validation and systematization.

Here, we present a non-homology knowledge-based strategy for the structural prediction of the proregion of a cysteine proteinase zymogen. This method analyzes individual sequences and multiple alignments of homologous sequences, making use of different published algorithms and incorporating all available structure-related information to obtain improved predictions. Our strategy yielded acceptable secondary structure and general three-dimensional assignments when compared with crystallographic data from homologous proteins.

We discuss our successes and failures as a contribution to non-homology prediction development. In addition, based on the information analyzed and generated in this work, we propose plausible folding and activation mechanisms for thiol-proteinase precursors that attempt to shed light on the molecular basis of prosegment functions.