Protein dipoles

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

FIGURE 7.7. The protein dipoles (hydrogen bonds) that stabilize the (- + -) transition state of jrypsin. 

The family of serine proteases has been subjected to intensive studies of site-directed mutagenesis. These experiments provide unique information about the contributions of individual amino acids to kcat and KM. Some of the clearest conclusions have emerged from studies in subtilisin (Ref. 9), where the oxyanion intermediate is stabilized by t>e main-chain hydrogen bond of Ser 221 and an hydrogen bond from Asn 155 (Ref. 2). Replacement of Asn 155 (e.g., the Asn 155— Ala 155 described in Fig. 7.9) allows for a quantitative assessment of the effect of the protein dipoles on Ag. ... 

Langevin dipoles, 52, 53, 125 Langevin dipoles model, 49-53, 50. See also Protein dipoles-Langevin dipole model for catalytic effect of carbonic anhydrase, 199... 

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)... 

Protein dipoles-Langevin dipoles model (PDLD), 123-125,124 Protein potential surfaces, see Enzyme potential surfaces... 

In addition, the pvalues of various residues within the surrounding protein environment were computed using the protein-dipoles Langevin-dipoles model, in a linear response approximation73 implementation (the PDLD/S-LRA method).84... 

Calculations of Electrostatic Properties in Proteins. Analysis of Contributions from Induced Protein Dipoles. 

Van Belle, D., Couplet, I., Prevost, M. and Wodak, S.J. (1987) Calculations of Electrostatic Properties of Proteins Analysis of Contributions from Induced Protein Dipoles, J. Mol. Biol. 198, 721-735. 

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... 

The results of an EVB/FEP for proton transfer from Cys to His were presented by Warshel (1991), based on a calibration of the protein reaction surface with solution results, which amount to 6 kcal/mol difference (in favor of SH relative to ImH+) due to the pKa values of the two conjugate acids. The protein is found to invert the stabilization of covalent and ionic state relative to their order in solution. This is a result of the stronger solvation in the enzyme, compared to water, and due to the orientation of protein dipoles. 

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