Hydrogen bonding in molecular recognition by HIV-1 protease

Molecular recognition of the cleavage sites of the substrates by HIV-1 protease is analyzed in terms of hydrogen bonding. Crystal structures of an inactive enzyme complexed with six different substrates were used as reference structures. Applying molecular mechanics calculations it can be shown that the interaction energies between the real substrate and the enzyme are larger than with other peptides. From the analysis, it can be concluded that water molecules are essential in the recognition process. Moreover, the hydrogen bonds between the protease and various substrates are characterized in detail.