Deamidation and protein repair studies of bio-catalysts from different organisms

Abstract

Proteins undergo certain posttranslational modifications like acetylation, phosphorylation, methylation, deamidation etc as a step in protein biosynthesis. Protein post-translational modifications play a key role in many cellular processes such as cellular differentiation [G. Grotenbreg, H. Ploegh (2007)], protein degradation [R.Geiss-Friedlander, F.Melchior (2007)], signaling and regulatory processes [Morrison et al (2002)], regulation of gene expression, and protein-protein interactions. Deamidation is a type of posttranslational modification which changes the chemical nature of amide containing amino acids like asparagines (Asn). The reaction is initiated by the favorable nucleophilic attack on the side chain carbonyl by the peptide backbone nitrogen of the following amino acid residue. This leads to the formation of an unstable succinimidyl intermediate that non-enzymatically hydrolyzes into either L-aspartyl (normal) or L-isoaspartyl (abnormal) residue, resulting in a cumulative gain of net negative charge at their specific sites of chemical reaction [Q. Hasan et al (2005)] The metastable succinimide has a typical half life of 4 hours at pH-7.4, 37°C. The rapid hydrolysis of this intermediate mixture generates Asp (~30%) and predominantly isoAsp (~70%) residues. Each amide has a specific deamidation rate that is genetically determined by the sequence of residues immediately adjacent in the peptide chain and by secondary, tertiary and quarternary structure. The influence of local sequence and solution environment on the rates of deamidation has been extensively studied by researchers using synthetic /natual peptides. Isoaspartate forms most readily at sequences in which the side chain of the C flanking amino acid is relatively small and hydrophilic, and is less likely to be formed where bulky or hydrophobic residues are in this position. The most favorable C-flanking amino acids are Gly, Ser and His, leading to so called isoAsp hot spots at Asn-Gly, Asn-Ser, Asn-His and Asp-Gly sequences[A.Cimmino et al (2004)]. Protein deamidation occurs at flexible regions of proteins especially on those sites which are more exposed. Robinson and Robinson have recently designed a computational method which could estimate the probability of deamidation within a folded protein with known crystal structures [N. E.Robinson & A. B. Robinson (2001)]