Ph-Dependent Properties

This set of calculations results in an output file containing all of the energies required to solve for the pH-dependent properties of interest. The form and content of the file are as follows ... 

Antosiewicz J, McCammon JA, Gilson MK (1994) Prediction of pH-dependent properties of proteins. JMol Biol 238 415 136. 

James M. Briggs and Jan Antosiewicz, Simulation of pH-dependent Properties of Proteins Using Mesoscopic Models. 

Rostkowski M, Olsson MH, Sondergaard CR, Jensen JH (2011) Graphical analysis of pH-dependent properties of proteins predicted using PROPKA. BMC Struct Biol 11 6. doi 10.1186/1472-6807-11-6... 

The pH-dependent properties of the hydrophilic positively charged colloidal particles favor the adsorption of negatively charged nucleic acids at acidic pH and at low salt concentration. However, the desorption is favored at basic pH and at high ionic strength. The concentration process of adsorbed nucleic acid materials was performed via centrifugation [9], filtration, or magnetic separation [10] of the used colloidal particles. 

Two types of correlation have been investigated between a pH-dependent property of a certain material and the surface charging behavior of that material (based on authors own measurements with the same sample of material), and between a pH-independent property in a series of materials and the PZCs in that series of materials. The second type of correlation was studied using authors own experimental data, data from the literature, or a mixture of both. 

All the above structural and kinetic information obtained under a variety of conditions with different metal ions can be used to propose a catalytic cycle for carbonic anhydrase (Figure 2.21). As shown by studies on the pH-dependent properties of native and metal-substituted CAs, both type-I and type-II proteins have two acidic groups, the zinc-coordinated water and a free histidine. At... 

Nielsen, J.E. Analysing the pH-dependent properties of proteins using pKa calculations. J. Mol. Graph. 2006,25,691-9. 

In this section we will deal with pH-dependent properties of proteins and their building blocks, amino acids. We will also discuss in brief the pH-dependent properties of other biomolecules. 

D. B. Boyd, Eds., Wiley-VCH, New York, 1999, Vol. 13, pp. 249-311. Simulation of pH-Dependent Properties of Proteins Using Mesoscopic Models. 

This chapter provides an introductory overview of the approaches used to predict ionization states of titratable residues in proteins, based on the assumption that the difference in protonation behavior of a given group isolated in solution, for which the ionization constant is assumed to be known, and the protonation behavior in the protein environment is purely electrostatic in origin. Calculations of the relevant electrostatic free energies are based on the Poisson-Boltzmann (PB) model of the protein-solvent system and the finite difference solution to the corresponding Poisson-Boltzmaim equation. We also discuss some relevant pH-dependent properties that can be determined experimentally. The discussion is limited to models that treat the solvent and the solute as continuous dielectric media. Alternative approaches based on microscopic simulations, which can be useful for small molecules (e.g., see Refs. 19-24) are not covered here because they are, in general, too time intensive for proteins. The present treatment is intended to be simple and pedagogic. 

The data from these electrostatics calculations may be used in the computation of the electrostatic free energy of the protein in any of its 2 ionization states, using Eq. [10]. Basically, evaluation of the average pH-dependent properties of a protein would require computation of energies of all ionization states... 

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