PMC:7278709 / 31622-33789 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7278709","sourcedb":"PMC","sourceid":"7278709","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7278709","text":"Since for both reasons they be useful in deeper consideration of many results in the present paper, some comment may be useful to researchers less familiar with bioinformatics. See Ref. [4] for a further account. Note that the work of considering what is a conservative replacement is done automatically by the standard bioinformatics tools used. The replacements in Table 1 are consistent with the conservative replacement rules implied by the tables of weights implemented automatically in BLASTp and Clustal Omega mentioned above, which are discussed at those sites. However, the original intent as an application to peptide design means that in Table 1 there is a degree of asymmetry based on the author's experience in peptide design [4] because one is going from a natural protein state to less natural one without evolution making compensatory changes in the rest of the protein or system. For example, empirical studies show that serine (S) can be replaced by alanine (A) or threonine (T) but it is frequently important that a replacement to threonine should be isoleucine (I) in order to retain stability of a β-pleated sheet in which they occur. Strictly speaking, these are just fairly crude rules-of-thumb: the best replacements are dependent on more specific circumstances and detailed conformational and binding calculations. The assignment in Table 1 are not seen as controversial because apart from the asymmetry they relate to the “interchangability” or “alternative rule” of amino acid residues by many authors that are intended as universal, i.e. intended to apply to all proteins. This is because they relate to similarity of amino acid residues in terms of physicochemical, conformational, as well as biological properties of many sequences that are at least universal to, say, vertebrates. However, they are historically more directly empirically based on well-known studies probabilities of amino acid differences found by comparing amino acid residue sequences amongst fairly related proteins from a wide range of sets of different proteins, such that one is comparing sequences of hemoglobins, or of lysozymes, or of cytochromes C, and so 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