| Abstract
| - Structural water molecules within protein active sites are relevant for ligand−proteinrecognition because they modify the active site geometry and contribute to binding affinity. Inthis work an analysis of the interactions between 23 ligands and dimeric HIV-1 protease isreported. The X-ray structures of these complexes show the presence of four types of structuralwater molecules: water 301 (on the symmetry axis), water 313, water 313bis, and peripheralwaters. Except for water 301, these are generally complemented with a symmetry-related set.The GRID program was used both for checking water locations and for placing water moleculesthat appear to be missing from the complexes due to crystallographic uncertainty. Hydropathicanalysis of the energetic contributions using HINT indicates a significant improvement of thecorrelation between HINT scores and the experimentally determined binding constants whenthe appropriate bridging water molecules are taken into account. In the absence of water r2 =0.30 with a standard error of ± 1.30 kcal mol-1 and when the energetic contributions of theconstrained waters are included r2 = 0.61 with a standard error of ± 0.98 kcal mol-1. HINTwas shown to be able to map quantitatively the contribution of individual structural waters tobinding energy. The order of relevance for the various types of water is water 301 > water 313> water 313bis > peripheral waters. Thus, to obtain the most reliable free energy predictions,the contributions of structural water molecules should be included. However, care must betaken to include the effects of water molecules that add information value and not just noise.
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