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.asparaginyl residue deamidation ͉ coefficient of deamidation ͉ deamidation index C hanges in peptide and protein structure through the spontaneous nonenzymatic deamidation of glutaminyl and asparaginyl residues have been observed in many in vitro and in vivo experiments. Rates of deamidation of individual amide residues depend upon primary sequence, three-dimensional (3D) structure, and solution properties such as pH, temperature, ionic strength, and buffer ions (1-8).Deamidation at neutral pH introduces a negative charge at the deamidation site and sometimes also leads to ␤ isomerization. These alterations in structure affect the properties of peptides and proteins in chemically and biologically important ways. It has been suggested that in vivo deamidation of proteins serves as a molecular timer of biological events and as a mechanism for postsynthetic production of unique proteins of biological significance (2,4,6,7,9,10). In the case of in vivo protein turnover, the use of deamidation as a molecular timer has been experimentally demonstrated (11-13).Progress in the understanding of deamidation and its potential biological importance has been impeded by the lack of reliable and useful experimental and theoretical information about the deamidation of most proteins. Experimental studies of the deamidation of individual proteins are laborious and time consuming. Until recently, there were no other means by which to estimate the deamidation rates of specific amides.The deamidation rates of individual Asn residues in a protein can now be reliably predicted as a result of two recent advances. First, the sequence-controlled Asn deamidation rates of most of the 400 possible near-neighbor combinations in pentapeptide models have been measured (10); the deamidation rates of a representative group of Gln pentapeptides have been determined (N.E.R. & A. B. Robinson, unpublished work); and the relevance of these rate libraries has been established (14). Second, these rates and the 3D structures of proteins with well characterized deamidations have been combined to produce a computation method that correctly predicts the deamidation rates of most Asn residues for which the 3D structure is known (15). This method has been shown to be Ϸ95% reliable in predicting relative deamidation rates of Asn residues within a single protein, and it is also useful for the prediction of absolute deamidation rates. It has been used to estimate the deamidation rates of 1,371 asparaginyl residues in 126 human pro...

Identification of amino acid substitutions in avian influenza virus (H5N1) matrix protein 1 by using nanoelectrospray MS and MS/MS

“…It was noticed that the neighboring residues next to the deamidated asparagines (N 85 and N 87 ) were glycines. The observed pattern of deamidation was consistent with the findings that glycine was observed as the most common (N ϩ 1) neighboring residue in proteins in which deamidation was established and characterized [24,25]. Accordingly, theoretical values of the deamidated peptide FVQNALNGNGDPNNMDR are m/z 631.93 and 947.41 for triply charged and doubly charged species, respectively, considering that the methionine is oxidized.…”

Chronoregulation by Asparagine Deamidation

“…The rate of Bcl-x L deamidation increases with increasing pH (24), and the two Bcl-x L asparagines that become deamidated are predicted to undergo nonenzymatic Bcl-x L deamidation rapidly at pH 7.4 (11,24). Additionally, a small change in pH between pH 7.0 and 8.0 can substantially increase the rate of deamidation of a protein (3).…”

“…Robinson and his son, Noah Robinson, devised a computational method for predicting the deamidation half-life of any asparagine in any protein for which the three-dimensional (3D) structure is known (11,12). Their formula combines the observed primary structure-determined deamidation rate with a modifying component that is computed on the basis of the 3D structure.…”

Accelerated removal of deamidated proteins and endogenous electric fields: possible implications

“…Deamidation of Asn and Gln residues is now recognized as one of the major pathways of spontaneous protein degradation, together with protein aggregation, oxidation, and glycation (Robinson 2002;Reissner and Aswad 2003;Li et al 2006).…”

“…A computation procedure for quantitatively combined primary-structure determined deamidation rate and the higher order structure modulation of that rate has been developed for 170,014 Asn residues in 13,335 proteins (Robinson 2002; http://www.deamidation.entrewave. com).…”