GROUP FREQUENCIES amino acids

The non-polar amino acids glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine, and cysteine have lower exposure to the solvent environment than charged or polar residues. However, the frequency at which these groups are found to have an SEA of greater than 30 A2 is much higher than one would expect based solely upon consideration of their hydrophobicity. In fact, nearly 30-50 percent of the time non-polar amino acids in a protein can be found at the surface. 

In the local mechanical fluctuation model, the local motions of the amino acids on the proximal side of the heme are coupled to the heme through the side group of the proximal histidine. The side chain of the proximal histidine is covalently bonded to the Fe. This bond is the only covalent bond of the heme to the rest of the protein. Thus, motions of the a-helix that contains the proximal histidine are directly coupled the Fe. These motions can push and pull the Fe out of the plane of the heme. Since the CO is bound to the Fe, these motions may induce changes in the CO vibrational transition frequency causing pure dephasing. 

An interesting correlation between tripeptide sequences and genetic mutations has been made by compilation of the number of occurrences of the tripeptide sequence Asn—B—Ser and Asn—B—Thr in protein sequence-data at present available from the literature.134 A total of 18,251 tripeptide sequences from 264 proteins was grouped by computer into the 400 possible tripeptide combinations of the 20 amino acids in which the second position was ignored. The total number of Asn—B—(Ser/Thr) sequences actually present in these proteins was 61, whereas the total number theoretically expected, on the basis of a random distribution within the sequence, would have been 102. The observed data were thus lower than expected by 4 standard deviations. On the other hand, such chemically similar tripeptides as Gin—B—(Ser/Thr), Asp—B—(Ser/Thr), and (Ser/Thr)—B—Asn occurred the number of times expected for random distribution. It was suggested that this low frequency of incidence of the Asn—B—(Ser/Thr) sequence results from a restriction of its occurrence in proteins by a process of natural selection. Any protein that acquired this tripeptide as a result of a mutation would be soon rejected, because carbohydrate would be bound to the asparagine residue and its presence would interfere with the normal metabolic function of the protein. 

While empirical rules would fail to yield a correct conformational interpretation of the amide I spectrum, normal mode calculations using the SQM method clearly eliminate several possibilities and put forward a preferred structure for this peptide in water [70S], This approach can be extended to much larger peptides having stable secondary structures. We have collected spectra of several isotopomers of the 23-residue peptide magainin F. We observe in the difference spectra that the amide I bands corresponding to specific amino acids are much narrower than they are in the short peptides and clearly identify the amide I frequencies of these groups. 

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