Prediction of glycation sites: new insights from protein structural analysis

Abstract

Glycation of proteins is a nonenzymatic process in which proteins react with reducing sugar molecules. This process takes place at ε-amino (ε-NH +) groups of lysine or hydroxylysine residues as well as α-amino groups of N-terminal residues. In the present study glycation of ε-NH + groups of lysines was computationally analyzed for 26 proteins based on their 3D structures. We determined the spatial relationship with acidic or basic residues and correlated them with the glycation prediction algorithm Netglycate 1.0 software, which employed primary structure exclusively for glycation site prediction. Of the lysines from 19 of the 20 proteins employed to build the Netglycate 1.0 algorithm 87.80% depicted a spatial relationship with acidic or basic residues. For the remaining seven proteins that were not included in the algorithm, 95.23% of the lysines exhibited a spatial relationship with acidic or basic residues. For these seven proteins, Netglycate 1.0 predicted only 52.38% of the lysines with a previously reported experimental glycation as potential glycation sites. In all cases, distances between residues were less than or equal to 9.78 Å. These results suggest that it is the spatial relationship of lysines with acidic or basic residues in the 3D conformation of a protein that determines the glycation target site, rather than a specific sequence of the primary structure.

Global proteomic analysis of advanced glycation end products in the Arabidopsis proteome provides evidence for age-related glycation hot spots

“…The presence of glutamyl and aspartyl residues in close spatial proximity (typically less than 5.0 Å) from the corresponding AGE modification sites ( Fig. 10 supplemental Table S1-6) was in agreement with the kinetics of AGE formation and degradation obtained from model glycation experiments with synthetic peptides (4,18), as well as from observations done with the patterns of early glycation (45). Generally, the presence of negatively charged amino acid residues in close proximity to the glycation sites can be explained by the known AGE formation mechanisms.…”

“…serum albumin) (43) and recombinant antibodies (44). The existence of such hot spots can be explained not only by longer half-lives and different compartmentalization but also by different amino acids surrounding the polypep-tide chain and the three-dimensional structure of protein molecules (45).…”

Effects of Buffer Composition on Site-Specific Glycation of Lysine Residues in Monoclonal Antibodies

“…Proximity to acidic and basic residues has been previously suggested to positively influence the rate of glycation at specific lysines. 5,7,8,[10][11][12] We also compared the individual rate of glycation for each lysine in one buffer condition with the rate of glycation for the same lysine in media and all other buffers tested. An example plot comparing rates in HEPES versus media is shown in Figure 4a.…”

“…These proton transfer steps can be accelerated by nearby acidic and basic groups, either built into the protein structure or in solution. 5,7,8,[10][11][12] The final phase of the reaction is the formation of irreversible advanced glycation end products that are a hallmark of multiple human diseases and can result in cross-linking of the affected proteins. 3,13,14 Previous literature has uncovered a correlation between specific buffer components and the rate of glycation on model proteins at specific sites.…”

“…Numerous publications have proposed a catalytic effect from nearby acidic residues, 5,8,10,11 whereas others have suggested basic residues including histidine could play a role. 7,12,19,20 Given that abstraction and donation of protons are both required in the Amadori rearrangement, it is plausible that either, or both, of these residue types could accelerate the rate of reaction under the right circumstances. Other studies have simply cited solvent accessibility of the lysine side chain as a contributing factor to increased glycation rates, 21 although the vast majority of lysine residues in globular proteins are exposed to solvent.…”