Protein ionization sites

In PB based methods, the pKa for a protein ionizable site i is given by [6],... 

The final system we consider in this tutorial is that of a spherical charged polyelectrolyte which serves as a model for a colloidal particle, micelle, or globular protein. The primary characteristic that differs between modeling a micelle and a protein at this level of representation is the much greater surface charge density associated with a micelle. A secondary, but still important, consideration, is the pK, values of the protein ionization sites, which might require use of boundary condition BC3 instead of BC2 as assumed below. °... 

To realize the reason for this result from a simple intuitive point of view it is important to recognize that the ionized form of Aspc is more stable in the protein-active site than in water, due to its stabilization by three hydrogen bonds (Fig. 7.7). This point is clear from the fact that the observed pKa of the acid is around 3 in chymotrypsin, while it is around 4 in solution. As the stability of the negative charge on Aspc increases, the propensity for a proton transfer from Hisc to Aspc decreases. 

Ficarro, S. B., Salomon, A. R., BriU, L. M., Mason, D. E., Stettler-GiU, M., Brock, A., and Peters, E. C., Automated immobilized metal affinity chromatography/nano-liquid chromatography/electrospray ionization mass spectrometry platform for profiling protein phosphorylation sites, Rapid Communications in Mass Spectrometry 19(1), 57-71, 2005. 

The ions obtained from large molecules carry a greater number of charges if several ionizable sites are present. Typically, a protein will carry one charge per thousand daltons... 

Electronspray ionization(ESI) MS Useful in quality control for recombinant proteins and site analysis of tryptic glycopeptides. Readily interfaced with HPLC or CE systems. It can differentiate between 0- and IV-linked glycans, and also between complex, hybrid or high mannose forms [275]... 

There are chemicals, especially biochetnicals, that have more than a single ionization state. Indeed, proteins, composed of many amino acids, have numerous ionization sites and therefore multiple ionization states with different net charges. As a simple introduction to species with multiple ionization sites, consider phthalic acid, a so-called dibasic acid that ionizes as follows ... 

A rule of thumb is that an amino acid or protein with multiple ionization sites will always include a primary carboxylic acid (—COOH) group that ionizes at low pH (usually 2 to 3), a primary amino (—NH2) group that ionizes in the pH range between 8 and 10, and other ionizable groups on side chains. 

The discussion that led to this equation is easily extended to amino acids, proteins, and other biomolecules with more than two ionizable sites (Problems 15.7 and 15.11). 

Derive the equation that replaces Eq. 15.3-3 for a protein that has six ionizable sites. 

Another modification in modeling the dielectric was described recently by Demchuk and Wade." They divided ionizable protein groups into two classes solvent-exposed residues for which the best results are obtained if the protein dielectric constant is set close to that of the aqueous solvent, and buried residues for which the best results are obtained using lower, site-specific protein dielectric constants. These two classes of ionizable sites can be distinguished using a criterion based on desolvation energy. 

Bezrukov, S. M. Kasianowicz, J. J. Current noise reveals protonation kinetics and number of ionizable sites in an open protein ion channel. Phys Rev Lett 1993, 70, 2352-2355. 

Gilson, M. K. Multiple-site titration and molecular modeling Two rapid methods for computing energies and forces for ionizable groups in proteins. Proteins Struct. Punct. Genet. 15 (1993) 266-282. 

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