Comparison of amino acid sequences and three-dimensional structures of aspartic proteases for use in their protein engineering

An approach was demonstrated to using amino acid sequence alignments of asp artic proteases for planning their protein engineering. The approach makes use of the basic elements of tertiary structure for the alignment. The simp lest description of the tertiary structures of the enzymes is presented, al lowing one to minimize the number of the basic structural elements by takin g into account the intramolecular symmetry. In order to analyze residue con servation and identify the key changes between different enzymes, it is ver y important to use a large array of proteins in the alignment, as done here . The use of internal coordinate systems allows one to define the conservat ion of the spatial location of amino acid residues and bound water molecule s. These data, forming a solid basis for planning protein engineering work, were used to design active HIV-1 protease with a large number of substitut ed residues.