Dear All,
I want to study the role of an amino acid in a protein by mutating it to another amino acid. How will decide or select, the new amino acid? What are the parameters I need to consider?
I am afraid that a comprehensive anwer is not possible because the role of an amino acid does not depend only on the particular molecule but also on its chemical environment. As a first trial I would toggle on the polar character of your targetted amino acid. Could you give this target to give a more specific suggestion?. Good luck!
1a. Alanine (search: "alanine scanning mutagenesis").
1b. Glycine (search: "glycine scanning mutagenesis").
2. By similarity in physico-chemical properties (search: "Venn diagram and amino acids").
3. Based on the specific function of the amino acid in the given context.
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"1" is the default option and should be always included in the list of mutations: use "1b" for solvent-exposed loops, otherwise use "1a."
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A multiple sequence alignment of the protein with its homologs can tell you what is the natural amino-acid variability at the position of your interest . . .
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If you want to mutate using the free energy perturbation (FEP) approach, you might need to do it via one or more intermediates if the two amino acids differ too much; annihilating atoms is safer than creating atoms; when annihilating atoms, do it stepwise: first, gradually change the charges to zero; second, gradually change the van der Waals radii to zero.
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