Patterns for prediction of hydration around polar residues in proteins.
The atomic co-ordinates of seven very high resolution (< 1.4 A) proteins have been used to define a water-hydrogen bond template for five polar side-chains (arginine, aspartic acid, glutamic acid, asparagine and glutamine). The average water molecule positions determined were consistent with the hydrogen bonding stereochemistry expected for each side-chain. Hydrogen bonding geometry around nitrogen atoms was significantly better localized than around oxygen atoms, perhaps because of the proton on nitrogen. A prediction algorithm written to locate water molecule sites around these side-chains from the protein co-ordinates only was tested for crambin as well as for two high resolution protein structures not included in the hydrogen bond data base. The root-mean-square deviation of the predicted positions from the crystallographically determined ones for these structures was better than the resolution of these structures. The method also successfully predicted water positions for X-ray refinement of two proteins, indicating that predicted water molecules are within the radius of convergence of refinement. This method has utility for X-ray models as well as for analysis of enzyme hydration and function.
Department of Chemistry, Boston College, Chestnut Hill, MA 02167.
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Roe
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Teeter
D000465:Algorithms; D003574:Cytochrome c Group / Q000737:chemistry; D006860:Hydrogen Bonding; D009584:Nitrogen / Q000737:chemistry; D010100:Oxygen / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D012260:Ribonucleases / Q000737:chemistry; D014867:Water / Q000737:chemistry*; D014961:X-Ray Diffraction
D003574:Cytochrome c Group; D011506:Proteins; D014867:Water; D012260:Ribonucleases; D009584:Nitrogen; D010100:Oxygen