Aminoacids incorporation into proteins

This is an important misconception that seriously complicates the efforts of students to understand the properties of proteins, but it is not as crazy as it may appear. If the free aminoacids are prepared in their pure forms they are indeed acids—aspartic acid and glutamic acid. However, when they are incorporated into proteins they lose two of their ionizable groups completely, and the third, the one that justifies calling these free forms acids, loses its proton in neutral solution it then no longer has a proton to donate, so it is no longer an acid but it can accept one, so it can act as a base. 

Relaxation-related work on proteins and polypeptides makes typically use of H, and NMR. A couple of papers have dealt with measurements on in fluorine-labelled aminoacids incorporated into peptide stuctures. Shi and co-workers introduced, at some specific sites, an unnatural fluorine-containing aminoacid and a nitroxide spin-label into a multidomain protein known to exist in different conformations. Measurements of F PRE allowed to determine the conformation under different conditions. Suzuki et used another fluorine-containing amino acid, inserted into different parts of a membrane-active peptide, as a local dynamics probe. They measured F transverse relaxation to examine changes in the mobility in different regions of the peptide upon binding to a lipid bilayer. 

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