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In biochemistry, the molar absorption coefficient of a protein at 280 nm depends almost exclusively on the number of aromatic residues, particularly tryptophan, and can be predicted from the sequence of amino acids. [6] Similarly, the molar absorption coefficient of nucleic acids at 260 nm can be predicted given the nucleotide sequence.
Bovine serum albumin (BSA or "Fraction V") is a serum albumin protein derived from cows. It is often used as a protein concentration standard in lab experiments. The nickname "Fraction V" refers to albumin being the fifth fraction of the original Edwin Cohn purification methodology that made use of differential solubility characteristics of plasma proteins.
Then the following formula is used to calculate the first extinction coefficient: W*5500 + Y*1490 + cystines*125. This calculation assumes that all cysteines pair into cystines. The second version assumes that all cysteines are reduced and there are no cystines, thus it is calculated as W*5500 + Y*1490.
The Bradford protein assay (also known as the Coomassie protein assay) was developed by Marion M. Bradford in 1976. [1] It is a quick and accurate [ 2 ] spectroscopic analytical procedure used to measure the concentration of protein in a solution.
When consecutively measuring amino acids of a protein, changes in value indicate attraction of specific protein regions towards the hydrophobic region inside lipid bilayer. The hydrophobic or hydrophilic character of a compound or amino acid is its hydropathic character, [ 1 ] hydropathicity, or hydropathy.
The methodology involved in FFP based method starts by calculating the count of each possible k-mer (possible number of k-mers for nucleotide sequence: 4 k, while that for protein sequence: 20 k) in sequences. Each k-mer count in each sequence is then normalized by dividing it by total of all k-mers' count in that sequence. This leads to ...
The photophysical properties of the FbFPs are determined by the chromophore itself and its chemical surrounding in the protein. The extinction coefficient (ε) is around 14.200 M −1 cm −1 at 450 nm for all described FbFPs, which is slightly higher than that of free FMN (ε = 12.200 M −1 cm −1 [10]).
Often, it is more useful to calculate the information content with the background letter frequencies of the sequences you are studying rather than assuming equal probabilities of each letter (e.g., the GC-content of DNA of thermophilic bacteria range from 65.3 to 70.8, [3] thus a motif of ATAT would contain much more information than a motif of ...