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Furthermore, in the folded protein, the aspartic acid will be closer to other titratable groups in the protein and will also interact with permanent charges (e.g. ions) and dipoles in the protein. All of these effects alter the p K a value of the amino acid side chain, and p K a calculation methods generally calculate the effect of the protein ...
The Wimley–White whole residue hydrophobicity scales are significant for two reasons. First, they include the contributions of the peptide bonds as well as the sidechains, providing absolute values. Second, they are based on direct, experimentally determined values for transfer free energies of polypeptides.
The pH at which the surface exhibits a neutral net electrical charge is the point of zero charge at the surface. Electrokinetic phenomena generally measure zeta potential, and a zero zeta potential is interpreted as the point of zero net charge at the shear plane. This is termed the isoelectric point. [28]
The net charge of the protein, determined by the sum charge of its constituents, results in electrophoretic migration in a physiologic electric field. These effects are short-range because of the high di-electric constant of water, however, once the protein is close to a charged surface, electrostatic coupling becomes the dominant force.
The peptide masses resulting from the digestion can be determined by mass spectrometry using peptide mass fingerprinting. If this information does not allow unequivocal identification of the protein, its peptides can be subject to tandem mass spectrometry for de novo sequencing. Small changes in mass and charge can be detected with 2D-PAGE.
The possible peptide that has the most similar spectrum will have the highest chance to be the right sequence. However, the number of possible peptides may be large. For example, a precursor peptide with a molecular weight of 774 has 21,909,046 possible peptides. Even though it is done in the computer, it takes a long time. [17] [18]
Charge transfer coefficient, and symmetry factor (symbols α and β, respectively) are two related parameters used in description of the kinetics of electrochemical reactions. They appear in the Butler–Volmer equation and related expressions.
This conformational flexibility is responsible for differences in the three-dimensional structure of proteins. The peptide bonds in the chain are polar, i.e. they have separated positive and negative charges (partial charges) in the carbonyl group, which can act as hydrogen bond acceptor and in the NH group, which can act as hydrogen bond donor ...