Titratable residues

Prediction of pKaS of Titratable Residues in Proteins Using a Poisson-Boltzmann Model of the Solute-Solvent System... 

In order to summarize the procedures used for computing ionization constants of titratable residues in proteins, the steps used in our algorithm will be enumerated below ... 

The presented algorithm was applied to 4 proteins (lysozyme, ribonuclease A, ovomucid and bovine pancreatic trypsin inhibitor) containing 51 titratable residues with experimentally known pKaS [32, 33]. Fig. 2 shows the correlation between the experimental and calculated pKaS. The linear correlation coefficient is r = 0.952 the slope of the line is A = 1.028 and the intercept is B = -0.104. This shows that the overall agreement between the experimental and predicted pKaS is good. 

It can be seen from Table 2 that the intrinsic values of the pK s are close to the model compound value that we use for Cys(8.3), and that interactions with surrounding titratable residues are responsible for the final apparent values of the ionization constants. It can also be seen that the best agreement with the experimental value is obtained for the YPT structure suplemented with the 27 N-terminal amino acids, although both the original YPT structure and the one with the crystal water molecule give values close to the experimentally determined one. Minimization, however, makes the agreement worse, probably because it w s done without the presence of any solvent molecules, which are important for the residues on the surface of the protein. For the YTS structure, which refers to the protein crystallized with an SO4 ion, the results with and without the ion included in the calculations, arc far from the experimental value. This may indicate that con-... 

An alternative formalism to the acidostat method, continuous constant pH molecular dynamics (CPHMD), has been developed by Brooks and coworkers [42, 58] drawing on the flavor of the early work by Mertz and Pettitt [67], In CPHMD, each titration residue carries a titration coordinate, A j, which is a function of an unbounded variable 0j,... 

Another interesting application area of PHMD simulations is to investigate electrostatic interactions in the unfolded states of proteins. A traditional view that unfolded proteins adopt random conformational states that are devoid of electrostatic and hydrophobic interactions, are recently challenged by experimental data [20, 69], REX-CPHMD folding simulations of the 35 residue C-terminal subdomain of the villin headpiece domain revealed a significant deviation from the standard pKa values for several titratable residues. Additional simulations, in which a charged group is neutralized confirmed the existence of specific electrostatic interactions in the unfolded states (JK and CLB, manuscript in preparation). 

Shake flasks were inoculated with mixed liquor suspended solids from activated sludge units in a Houston area domestic waste sewage treatment plant. Initial surfactant concentrations were 20 mg/ . CO2 formed from biodegradation was trapped in aqueous Ba(OH)2. The amount of CO2 formed was determined by back-titrating residual Ba(OH)2 with HCl at the end of each test period. Glucose was included as a positive biodegradation standard. 

Finally, protonation states of all titratable residues should be determined before any atomic-level simulation. Several programs, such as WHATIF (16) and PROPKA (17-19) (see Notes 5 and 6), exist to predict protonation states of standard residues. 

There is a useful Web service at http //kryptonite.nbcr.net/ pdb2pqr (54) hosted by the National Biomedical Computation Resource (NBCR) for users who do not have local resources for PDB2PQR (55, 56) computations that use the PROPKA approach to predict protonation states of titratable residues. 

Black Pepper Oil, 47, 572, (S 1)5 Black Peppier Oleoresin, 391, 392 Blank Tests, 4 Blank Titration, Residual, 4 Bleached Starch, 159 Bleidner Apparatus, (S3)17 Blue Litmus Paper, 861 Bois de Rose Oil, 47, 576 Boric Acid-Potassium Chloride, 0.2 M, 848... 

Loss on drying Karl Fischer titration Residue on ignition Thermogravimetric analysis Differential scanning calorimetry High-performance... 

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. 

Ferrer S, Silla E, Tunon I, Oliva M, Moliner V, Williams IH (2005) Dependence of enzyme reaction mechanism on protonation state of titratable residues and QM level description lactate dehydrogenase. Chem Commun 47 5873-5875... 

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