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Because the Edman degradation proceeds from the N-terminus of the protein, it will not work if the N-terminus has been chemically modified (e.g. by acetylation or formation of pyroglutamic acid). Sequencing will stop if a non-α-amino acid is encountered (e.g. isoaspartic acid), since the favored five-membered ring intermediate is unable to be ...
Protein sequence interpretation: a scheme new protein to be engineered in a yeast. It is often desirable to know the unordered amino acid composition of a protein prior to attempting to find the ordered sequence, as this knowledge can be used to facilitate the discovery of errors in the sequencing process or to distinguish between ambiguous results.
Unsolved problems relating to the structure and function of non-human organs, processes and biomolecules include: Korarchaeota (archaea). The metabolic processes of this phylum of archaea are so far unclear. Glycogen body. The function of this structure in the spinal cord of birds is not known. Arthropod head problem. A long-standing zoological ...
In mass spectrometry, de novo peptide sequencing is the method in which a peptide amino acid sequence is determined from tandem mass spectrometry. Knowing the amino acid sequence of peptides from a protein digest is essential for studying the biological function of the protein. In the old days, this was accomplished by the Edman degradation ...
Examples of other questions that researchers use BLAST to answer are: Which bacterial species have a protein that is related in lineage to a certain protein with known amino-acid sequence; What other genes encode proteins that exhibit structures or motifs such as ones that have just been determined
For protein sequence spaces, each residue in the protein is represented by a dimension with 20 possible positions along that axis corresponding to the possible amino acids. [3] [4] Hence there are 400 possible dipeptides arranged in a 20x20 space but that expands to 10 130 for even a small protein of 100 amino acids arranged in a space with 100 ...
Protein sequence databases Swiss-Prot: Swiss Institute of Bioinformatics: protein knowledgebase Protein sequence databases Protein Data Bank: Protein DataBank in Europe (PDBe), [18] ProteinDatabank in Japan (PDBj), [19] Research Collaboratory for Structural Bioinformatics (RCSB) [20] (PDB) Protein structure databases Structural Classification ...
ChIP-sequencing, also known as ChIP-seq, is a method used to analyze protein interactions with DNA. ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. It can be used to map global binding sites precisely for any protein of interest.