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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 ω angle at the peptide bond is normally 180°, since the partial-double-bond character keeps the peptide bond planar. [3] The figure in the top right shows the allowed φ,ψ backbone conformational regions from the Ramachandran et al. 1963 and 1968 hard-sphere calculations: full radius in solid outline, reduced radius in dashed, and ...
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. [29]
The adenylate energy charge is an index used to measure the energy status of biological cells. ATP or Mg-ATP is the principal molecule for storing and transferring energy in the cell : it is used for biosynthetic pathways, maintenance of transmembrane gradients, movement, cell division, etc...
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]
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 ...
Mulliken charges arise from the Mulliken population analysis [1] [2] and provide a means of estimating partial atomic charges from calculations carried out by the methods of computational chemistry, particularly those based on the linear combination of atomic orbitals molecular orbital method, and are routinely used as variables in linear regression (QSAR [3]) procedures. [4]