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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 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 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...
FDPB-based methods calculate the change in the pK a value of an amino acid side chain when that side chain is moved from a hypothetical fully solvated state to its position in the protein. To perform such a calculation, one needs theoretical methods that can calculate the effect of the protein interior on a p K a value, and knowledge of the pKa ...
The alpha helix is also commonly called a: Pauling–Corey–Branson α-helix (from the names of three scientists who described its structure); 3.6 13-helix because there are 3.6 amino acids in one ring, with 13 atoms being involved in the ring formed by the hydrogen bond (starting with amidic hydrogen and ending with carbonyl oxygen)
When Pauling and Corey first proposed the alpha sheet, they suggested that it agreed well with fiber diffraction results from beta-keratin fibers. [2] However, since the alpha sheet did not appear to be energetically favorable, they argued that beta sheets would occur more commonly among normal proteins, [3] and subsequent demonstration that beta-keratin is made of beta sheets consigned the ...
The overall net reaction is: Amino Acid + ATP + tRNA → Aminoacyl-tRNA + AMP + PP i. The net reaction is energetically favorable only because the pyrophosphate (PPi) is later hydrolyzed. The hydrolysis of pyrophosphate to two molecules of inorganic phosphate (Pi) reaction is highly energetically favorable and drives the other two reactions.
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.