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Reaction mechanism of deamidation of asparaginyl residues in peptides: effect of solvent molecules

Saron Catak UGent, Gerald Monard, Viktorya Aviyente and Manuel F Ruiz-Lopez (2006) JOURNAL OF PHYSICAL CHEMISTRY A. 110(27). p.8354-8365
abstract
Deamidation of proteins occurs spontaneously under physiological conditions. Asparaginyl (Asn) residues may deamidate into aspartyl (Asp) residues, causing a change in both the charge and the conformation of peptides. It has been previously proposed by Capasso et al. that deamidation of relatively unrestrained Asn residues proceeds through a succinimide intermediate. This mechanism has been modeled by Konuklar et al. and the rate determining step for the deamidation process in neutral media has been shown to be the cyclization step leading to the succinimide intermediate. In the present study, possible water-assisted mechanisms, for both concerted and stepwise succinimide formation, were computationally explored using the B3LYP method with 6-31+G** basis set. Single point solvent calculations were carried out in water, by means of integral equation formalism-polarizable continuum model (IEF-PCM) at the B3LYP/6-31++G** level of theory. A novel route leading to the succinimide intermediate via tautomerization of the Asn side chain amide functionality has been proposed. The energetics of these pathways have been subject to a comparative study to identify the most probable mechanism for the deamidation of peptides in solution.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
HYDROLYSIS, PROTEINS, TAUTOMERIZATION, GLUTAMINYL, RATES, SUCCINIMIDE, 3-DIMENSIONAL STRUCTURE, PREDICTION, DENSITY, ASPARTIC-ACID
journal title
JOURNAL OF PHYSICAL CHEMISTRY A
J. Phys. Chem. A
volume
110
issue
27
pages
8354 - 8365
publisher
AMER CHEMICAL SOC
place of publication
Washington, USA
Web of Science type
Article
Web of Science id
000238805600013
JCR category
PHYSICS, ATOMIC, MOLECULAR & CHEMICAL
JCR impact factor
3.047 (2006)
JCR rank
5/31 (2006)
JCR quartile
1 (2006)
ISSN
1089-5639
DOI
10.1021/jp056991q
language
English
UGent publication?
no
classification
A1
id
498153
handle
http://hdl.handle.net/1854/LU-498153
date created
2009-02-19 12:16:10
date last changed
2017-01-02 09:55:46
@article{498153,
  abstract     = {Deamidation of proteins occurs spontaneously under physiological conditions. Asparaginyl (Asn) residues may deamidate into aspartyl (Asp) residues, causing a change in both the charge and the conformation of peptides. It has been previously proposed by Capasso et al. that deamidation of relatively unrestrained Asn residues proceeds through a succinimide intermediate. This mechanism has been modeled by Konuklar et al. and the rate determining step for the deamidation process in neutral media has been shown to be the cyclization step leading to the succinimide intermediate. In the present study, possible water-assisted mechanisms, for both concerted and stepwise succinimide formation, were computationally explored using the B3LYP method with 6-31+G** basis set. Single point solvent calculations were carried out in water, by means of integral equation formalism-polarizable continuum model (IEF-PCM) at the B3LYP/6-31++G** level of theory. A novel route leading to the succinimide intermediate via tautomerization of the Asn side chain amide functionality has been proposed. The energetics of these pathways have been subject to a comparative study to identify the most probable mechanism for the deamidation of peptides in solution.},
  author       = {Catak, Saron and Monard, Gerald and Aviyente, Viktorya and Ruiz-Lopez, Manuel F},
  issn         = {1089-5639},
  journal      = {JOURNAL OF PHYSICAL CHEMISTRY A},
  keyword      = {HYDROLYSIS,PROTEINS,TAUTOMERIZATION,GLUTAMINYL,RATES,SUCCINIMIDE,3-DIMENSIONAL STRUCTURE,PREDICTION,DENSITY,ASPARTIC-ACID},
  language     = {eng},
  number       = {27},
  pages        = {8354--8365},
  publisher    = {AMER CHEMICAL SOC},
  title        = {Reaction mechanism of deamidation of asparaginyl residues in peptides: effect of solvent molecules},
  url          = {http://dx.doi.org/10.1021/jp056991q},
  volume       = {110},
  year         = {2006},
}

Chicago
Catak, Saron, Gerald Monard, Viktorya Aviyente, and Manuel F Ruiz-Lopez. 2006. “Reaction Mechanism of Deamidation of Asparaginyl Residues in Peptides: Effect of Solvent Molecules.” Journal of Physical Chemistry A 110 (27): 8354–8365.
APA
Catak, S., Monard, G., Aviyente, V., & Ruiz-Lopez, M. F. (2006). Reaction mechanism of deamidation of asparaginyl residues in peptides: effect of solvent molecules. JOURNAL OF PHYSICAL CHEMISTRY A, 110(27), 8354–8365.
Vancouver
1.
Catak S, Monard G, Aviyente V, Ruiz-Lopez MF. Reaction mechanism of deamidation of asparaginyl residues in peptides: effect of solvent molecules. JOURNAL OF PHYSICAL CHEMISTRY A. Washington, USA: AMER CHEMICAL SOC; 2006;110(27):8354–65.
MLA
Catak, Saron, Gerald Monard, Viktorya Aviyente, et al. “Reaction Mechanism of Deamidation of Asparaginyl Residues in Peptides: Effect of Solvent Molecules.” JOURNAL OF PHYSICAL CHEMISTRY A 110.27 (2006): 8354–8365. Print.