Metal binding sites in plant soluble inorganic pyrophosphatases. An example of the use of ROSETTA design and hidden Markov models to guide the homology modeling of proteins

Abstract

In contrast to their counterparts in bacteria and animals the soluble inorganic pyrophosphatases from plant cells are active as monomers. The isoforms 1 and 4 from Arabidopsis thaliana have been characterized with more detail, but their three-dimensional structure is unavailable. Here, a recently published protocol (ROSETTA design-HMMer), is used to guide well-known techniques for homology-modeling, in the production of reliable models for the three-dimensional structure of these two arabidopsis isoforms. Their interaction with magnesium ions and pyrophosphate is analyzed in silico. © 2012, Sociedad Química de México.