Dynamics of internal water in fatty acid binding protein: computer simulations and comparison with experiments

Multiple molecular dynamics (MD) simulations of fully solvated rat intestinal fatty acid binding protein (I-FABP) were conducted to investigate the dynamics of internal water molecules. Although the long time average of the number of internal water molecules in I-FABP is 22 as shown by the X-ray crystal structure, MD simulations predict large variations in the instantaneous number of internal water molecules on the nanosecond time scale. The computational model employed predicts that w135 (internal) and w217 (located on the protein surface) may be the water molecules with long residence times observed in previously reported magnetic relaxation dispersion studies. The average residence time of approximately 20 internal water molecules occupying the fatty acid binding cavity is estimated to be between 0.6 and 2.0 nanoseconds. Exchange of internal water in I-FABP appears to occur almost exclusively through the interface of beta-strands EF with the rest of the protein, which has significant implications for the pathways of the fatty acid entry and exit from the binding cavity. Proteins 2001;43:65-72.