Search results
Results from the WOW.Com Content Network
In computational biology, protein pK a calculations are used to estimate the pK a values of amino acids as they exist within proteins.These calculations complement the pK a values reported for amino acids in their free state, and are used frequently within the fields of molecular modeling, structural bioinformatics, and computational biology.
Aqueous and polymer phases were used in the development of a novel partitioning scale. [19] Partitioning methods have many drawbacks. First, it is difficult to mimic the protein interior. [20] [21] In addition, the role of self solvation makes using free amino acids very difficult. Moreover, hydrogen bonds that are lost in the transfer to ...
An example of an amino acid sequence plotted on a helical wheel. Aliphatic residues are shown as blue squares, polar or negatively charged residues as red diamonds, and positively charged residues as black octagons. A helical wheel is a type of plot or visual representation used to illustrate the properties of alpha helices in proteins.
In aqueous solution at pH close to neutrality, amino acids exist as zwitterions, i.e. as dipolar ions with both NH + 3 and CO − 2 in charged states, so the overall structure is NH + 3 −CHR−CO − 2. At physiological pH the so-called "neutral forms" −NH 2 −CHR−CO 2 H are not present to any measurable degree. [36]
An alpha-helix with hydrogen bonds (yellow dots) The α-helix is the most abundant type of secondary structure in proteins. The α-helix has 3.6 amino acids per turn with an H-bond formed between every fourth residue; the average length is 10 amino acids (3 turns) or 10 Å but varies from 5 to 40 (1.5 to 11 turns).
After protein folding in aqueous solution, hydrophobic amino acids usually form protected hydrophobic areas while hydrophilic amino acids interact with the molecules of solvation and allow proteins to form hydrogen bonds with the surrounding water molecules. If enough of the protein surface is hydrophilic, the protein can be dissolved in water.
This requires spectrophotometers capable of measuring in the UV range, which many cannot. Additionally, the absorption maxima at 280 nm requires that proteins contain aromatic amino acids such as tyrosine (Y), phenylalanine (F) and/or tryptophan (W). Not all proteins contain these amino acids, a fact which will skew the concentration measurements.
Ammonium sulfate is an inorganic salt with a high solubility that disassociates into ammonium (NH + 4) and sulfate (SO 2− 4) in aqueous solutions. [1] Ammonium sulfate is especially useful as a precipitant because it is highly soluble, stabilizes protein structure, has a relatively low density, is readily available, and is relatively inexpensive.