Protein deamidation

Abstract

A completely automatic computerized technique for the quantitative estimation of the deamidation rates of any protein for which the three-dimensional structure is known has been developed. Calculations of the specific deamidation rates of 170,014 asparaginyl residues in 13,335 proteins have been carried out. The calculated values have good quantitative reliability when compared with experimental measurements. These rates demonstrate that deamidation may be a biologically relevant phenomenon in a remarkably large percentage of proteins.

Figure 1

(a) Cumulative distribution function of the calculated first-order rate constants for deamidation of the 131,809 Asn residues in 10,369 proteins used in Table 1. Asn residues involved in the initial deamidation of these proteins are a relatively small part of the complete set. The computed percentage of the Asn residues that are 1/10 deamidated after 10 days in pH 7.4, 37°C, 0.15 M Tris⋅HCl is 4%, as shown. (b) Differentiated values of the distribution function in a showing the special class of unstable Asn residues present in these proteins. Also shown with a red line 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 1/10 or more deamidated in 10 days in pH 7.4, 37°C, 0.15 M Tris⋅HCl.

Figure 2

Percentage of deamidating amides of the 131,809 Asn residues in 10,369 proteins used in Table 1 vs. deamidation half-time for Asn-Gly sequences; Asn-His, Asn-Ser, and Asn-Ala sequences; all sequences other than Asn-Gly, Asn-His, Asn-Ser, Asn-Ala, Asn-Leu, Asn-Val, and Asn-Ile; and Asn-Leu, Asn-Val, and Asn-Ile sequences. As deamidation halftime increases, more sequences contribute to deamidation. Except for a small number of especially sterically unhindered Asn residues, these deamidation halftimes strongly depend upon primary and 3D structures. These values are estimated for pH 7.4, 37°C, 0.15 M Tris⋅HCl and would be faster in vivo at 37°C.

Figure 3

Deamidation resolving power, D_p vs. 3D structure coefficient C_m for 192 Asn residues in 22 proteins. The optimum value of C_m = 0.48 provides the most reliable estimated relative deamidation rates as compared with the experimental values for these proteins.