PDLD model

The Protein Dipoles-Langevin Dipoles (PDLD) Model... 

FIGURE 4.7. A schematic description of the different contributions to the PDLD model. The figure considers the energetics of an ion pair inside a protein interior. The upper part describes the protein permanent dipoles, the middle part describes the induced dipoles of the protein, while the lower part describes the surrounding water molecules and the bulk region, which is represented by a macroscopic continuum model. 

Exercise 4.2. Use the PDLD Model to calculate the energy of a charged Asp 3 in the Protein BPTI, considering only UQy and A GQw. 

The PDLD model described above is quite useful for evaluating electrostatic free energies in proteins. However, with more computer power one can use... 

The simplest way to consider the energetics of this reaction is to use the EVB model for the reacting region and PDLD model for the protein. The EVB potential surface is formally identical to that used in Chapter 2, where the reaction is described in terms of two resonance structures,... 

Solution 8.5. First, use the LD model to calculate the Ag of w [the results should be -25, -220, and -190 kcal/mol for Ag , Ag2 and Ag, respectively]. Now you should repeat the calculations, modeling the protein-active site that includes the Zn2+ ion as well as the other protein residues by the PDLD model. 

The concept of electrostatic complimentarity is somewhat meaningless without the ability to estimate its contribution to AAg. Thus, it is quite significant that the electrostatic contribution to AAthat should be evaluated by rigorous FEP methods can be estimated with a given enzyme-substrate structure by rather simple electrostatic models (e.g., the PDLD model). It is also significant that calculated electrostatic contributions to A A g seem to account for its observed value (at least for the enzymes studied in this book). This indicates that simple calculations of electrostatic free energy can provide the correlation between structure and catalytic activity (Ref. 10). 

Page, M. I., and Jencks, W. P., entropic hypothesis of enzyme catalysis, 224-225 Papain, Cys-His proton transfer in, 140-143 Pauling, Linus, view of enzyme catalysis, 208 PDLD model, see Protein dipoles-Langevin dipoles model (PDLD)... 

Combining Equations (1) and (5) for the protein electronic polarizability and the solvent polarizability, respectively, with Eqn. (10) for the field Warshel and co-workers (Lee et al. 1993 Warshel and Aqvist 1991 Warshel and Russell 1984) developed the Protein Dipole Langevin Dipole (PDLD) model which was the first consistent model for treating protein/solvent polarizabilities in protein electrostatic applications. The electrostatic field distribution in this model is given by... 

---