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QM/MM Meta-Dynamics Study of Asparagine Deamidation in Proteins Universiteit Gent
DFT-based elucidation of asparagine deamidation in peptides Universiteit Gent
Asparagine (Asn) residues spontaneously – yet non-enzymatically – deamidate to form aspartate under physiological conditions, causing time-dependent changes in the conformation of proteins, limiting their lifetime [1]. Deamidation has been associated with aging, development and protein turnover. The ‘molecular clocks’ hypothesis [2], suggests that deamidation is a biological molecular timing mechanism that could be set to any desired time ...
QM metadynamics study on asparagine deamidation in proteins Universiteit Gent
Asparagine (Asn) residues spontaneously deamidate to form aspartate under physiological conditions, causing time-dependent changes in the conformation of proteins, limiting their lifetime. The 'molecular clocks' hypothesis [1], suggests that deamidation is a biological molecular timing mechanism that could be set to any desired time interval by genetic control of the protein structure. To date deamidation is believed to occur over a ...
Deamidation of asparagine residues: direct hydrolysis versus succinimide-mediated deamidation mechanisms Universiteit Gent
Quantum chemical calculations are reported to provide new insights on plausible mechanisms leading to the deamidation of asparagine residues in proteins and peptides. Direct hydrolysis to aspartic acid and several succinimide-mediated mechanisms have been described. The catalytic effect of water molecules has been explicitly analyzed. Calculations have been carried out at the density functional level (B3LYP/6-31+G**). Comparisons of free energy ...
The asparagine 533 residue in the outer pore loop region of the mouse PKD2L1 channel is essential for its voltage-dependent inactivation KU Leuven
Voltage-dependent inactivation of ion channels contributes to the regulation of the membrane potential of excitable cells. Mouse polycystic kidney disease 2-like 1 (PKD2L1) forms voltage-dependent nonselective cation channels, which are activated but subsequently inactivated in response to membrane depolarization. Here, we found that the mutation of an asparagine 533 residue (N533Q) in the outer pore loop region of PKD2L1 caused a marked ...
Role of glutamine and interlinked asparagine metabolism in vessel formation Vlaams Instituut voor Biotechnologie KU Leuven
Computational study on nonenzymatic peptide bond cleavage at asparagine and aspartic acid Universiteit Gent
Nonenzymatic peptide bond cleavage at asparagine (Asn) and glutamine (Gln) residues has been observed during peptide deamidation experiments; cleavage has also been reported at aspartic acid (Asp) and glutamic acid (Gin) residues. Although peptide backbone cleavage at Asn is known to be slower than deamidation, fragmentation products are often observed during peptide deamidation experiments. In this study, mechanisms leading to the cleavage of ...
Asparagine 42 of the conserved endo-inulinase INU2 motif WMNDPN from Aspergillus ficuum plays a role in activity specificity KU Leuven
Endo-inulinase INU2 from Aspergillus ficuum belongs to glycosidase hydrolase family 32 (GH32) that degrades inulin into fructo oligosaccharides consisting mainly of inulotriose and inulotetraose. The 3D structure of INU2 was recently obtained (Pouyez et al., 2012, Biochimie, 94, 2423-2430). An enlarged cavity compared to exo-inulinase formed by the conserved motif W-M(I)-N-D(E)-P-N-G, the so-called loop 1 and the loop 4, was identified. In the ...