Ionizable residues

Del Buono GS, Figueirido FE, Levy RM (1994) Intrinsic pKas of ionizable residues in proteins An explicit solvent calculation for lysozyme. Proteins 20 85-97. 

Sham YY, Chu ZT, Warshel A (1997) Consistent calculations of pKas of ionizable residues in proteins Semi-microscopic and microscopic approaches. J Phys ChemB 101 4458-4472. 

Sham, Y.Y. Chu, Z.T. Warshel, A., Consistent calculations of pKVs of ionizable residues in proteins semi-microscopic and microscopic approaches, J. Phys. Chem. B 1997,101, 4458-4472... 

Models of the nicotinic acetylcholine receptor consisting of the five M2 helices that form the pore have been investigated in a series of MD simulations [94]. The behavior of single helices in water and in lipid was compared, and the a-helical structure was again found to be stabilized by the membrane. Two simulations of bundles of five M2 helices forming a pore and differing in the ionization state of the ionizable amino acid residues were performed. When these residues were included in their ionized states, the bundle expanded over the 2 ns of the simulation, while it remained stable if calculated pit, values were used to determine the ionization states of ionizable residues. In these simulations structural fluctuations were also observed on a several hundred picosecond time scale that transiently closed the pore. 

A structure-function study of a proton pathway in the y-class carbonic anhydrase from Methanosarcina thermophila was conducted in the work of Tripp and Ferry (2000). Four enzyme glutamate residues were characterized by site-directed mutagenesis. It was shown that Glu 84 and an active site residue, Glu 89, are important for CO2 hydration activity, while external loop residues, Glu 88 and Glu 89 are less important. Glu 84 can be substituted for other ionizable residues with similar pKa values and, therefore, participates in the enzyme catalysis not as a chemical reagent but as a proton shuttle. 

S.4 Concentration of Buffers. A buffer concentration in the range of 10 to 50 mM is adequate for most re versed-phase applications. However, sometimes the concentration of the buffer does lead to improvement of peak shape, presumably because the cation of the buffer suppresses silanophilic interactions of the protonated base with accessible ionized residual silanols. 

Proteins, antibodies, and enzymes consist of long polypeptide sequences folded in ways that favor the positioning of hydrophobic residues at their interior, whereas more hydrophilic or easily ionizable residues are at the periphery. Water-exposed... 

E Tal hashi and CA Wraight (1992) Proton and electron transform the acceptor quinone complex of Rhodobacter sphaeroldes reaction centres characterization of site-directed mutants of the two ionizable residues, andAsp, in theQg binding site. Biochemistry 31 855-866... 

The potential problems of wafer contamination as a result of being exposed to the environment of the SEM chamber could adversely effect the performance of the devices on the wafer by introducing mobile ions or metallic contamination. Even though the vacuum in the SEM is typically down in the 10 Pa range, the electron beam can polymerize and/or ionize residual hydrocarbons in the chamber which can then be electrostatically attracted to the wafer surface. 

The formation of salt bridges in polyelectrolyte/protein complexes is widely accepted. Direct evidences for the release of counterions upon association of the macromolecular partners are however scarcely reported. Potentio-metric studies were found to reveal the ionization or neutralization of proteins in polymer complexes, i.e., a pKa shift of ionizable residues when an association took place [23,25,30], In the presence of neutral polyethylene glycol, pepsin was shown to take up protons from the solution [30], On the contrary, bovine serum albumin released protons from the addition of poly(diallyldimethylammonium chloride) (Figure 5). Despite the simplicity of both the method and the quantitative measurement of a number of ions released per protein, an interpretation in terms of a number of local bridges... 

TMADH showing ionizable residues and the aromatic bowl (Tyr-60, Trp-264 and Trp-355) that interacts with the three methyl groups of the substrate through amino-aromatic interactions. Residues His-172 and Tyr-60 play key roles in stabilising the trimethylamine... 

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