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. Author manuscript; available in PMC: 2011 May 15.
Published in final edited form as: Proteins. 2010 May 15;78(7):1705–1723. doi: 10.1002/prot.22687

Figure 2.

Figure 2

Illustrating the construction of the explicit SCAAS simulation system on the crystal structure (PDB ID:1K1L) of bovine trypsin (flat ribbon) in complex with the cocrystallized inhibitor (stick) is solvated in water molecules (ball and stick) representing the model system used in the study. In PDLD/S-LRA/β, Region I is the ‘inhibitor’ or the group whose electrostatic energy is of interest, region II includes all protein residues within 18Å cutoff radius from the center of region I. Region III includes explicit water molecules in and around regions I and II and is completed by a 2Å surface which is subjected to polarization and radial constraints. This is surrounded by bulk solvent (region IV) with a high dielectric constant (ε =80). The electrostatic effects of regions I, II and III are treated explicitly while those of region IV are treated by a macroscopic continuum formulation.