Deamidation of human proteins

Abstract

Deamidation of asparaginyl and glutaminyl residues causes time-dependent changes in charge and conformation of peptides and proteins. Quantitative and experimentally verified predictive calculations of the deamidation rates of 1,371 asparaginyl residues in a representative collection of 126 human proteins have been performed. These rates suggest that deamidation is a biologically relevant phenomenon in a remarkably large percentage of human proteins.

Figure 1

Calculated single deamidation half-times for 10 individual Asn and 3 combinations of Asn residues in 10 different protein types vs. the corresponding experimentally observed deamidation half-times (, , , –35). Experiments were in vitro in Tris and phosphate buffers and in vivo in human blood. Buffer conditions in Tris and phosphate varied among these investigations but were comparable to pH 7.4, 37°C, 0.15 M. Some of the scatter in the figure is probably the result of these variations. If the calculated values and experimental values were identical, the points would lie on the solid black line, as do the values determined in Tris buffers. Catalysis of deamidation is higher by phosphate than by Tris and may be even higher in erythrocytes.

Figure 2

(a) Cumulative distribution function of the calculated first-order rate constants for deamidation of 1,371 Asn residues in 126 human proteins. As indicated, the Asn residues involved in the initial deamidation of these proteins comprise a relatively small part of the complete set. Computed percentages of the Asn residues that are 1/10 deamidated at 1 and 10 days in Tris are 1% and 4%, respectively, as shown. If this deamidation were not of positive biological value, more slowly deamidating sequences and 3D structures could easily have been used. (b) Differentiated values of the distribution function in a showing the special class of unstable Asn residues present in human proteins. Also shown is a Gaussian function that fits the distribution function except for that part arising from the especially unstable Asn residues. The shaded area contains those Asn residues computed to be one-tenth or more deamidated in 10 days in pH 7.4, 37°C, 0.15 M Tris⋅HCl. This shaded area for phosphate, physiological fluids, or longer time intervals would be a larger part of the illustrated deviation from Gaussian.