Ghent University Academic Bibliography

Advanced

Effect of the (n +1) residue on peptide deamidation

Saron Catak UGent, Jan Félix UGent, Veronique Van Speybroeck UGent, Michel Waroquier UGent and Ewald Pauwels UGent (2012) ACS National meeting, Abstracts. p.130-130
abstract
Deamidation occurs spontaneously in peptides and proteins [1]. Many reports show that deamidation has a substantial effect on protein structure, function and stability. An experimental study on pentapeptides [2] shows that Asn deamidation rates are directly related to primary structure near Asn, with a prominent effect from the carboxyl-side (Yyy). We explore the correlation between experimental deamidation rates and primary structure for two pentapeptides (Yyy=Gly, Ile), to identify the factors causing this dependence. A pentapeptide in a water box is subject to Replica-Exchange Molecular Dynamics (REMD) calculations performed with GROMACS 4 software. Furthermore, a succinimide-mediated reaction [3] is investigated with QM/MM calculations utilizing the CP2K code using Nudged-Elastic-Band (NEB) calculations.[p] [p] [p][1] Robinson, NE, Robinson, AB Proc. Natl. Acad. Sci. USA 2001 , 98, 944.[p][2] Robinson, NE J. Peptide Res. 2004 , 63, 426.[p][3] Catak, S., Monard, G., Aviyente, V., Ruiz-López, MF J. Phys. Chem. A 2009 , 113, 1111.
Please use this url to cite or link to this publication:
author
organization
year
type
conference
publication status
published
subject
in
ACS National meeting, Abstracts
pages
130 - 130
publisher
American Chemical Society (ACS)
conference name
ACS Spring 2012 National Meeting & Exposition
conference location
San Diego, CA, USA
conference start
2012-03-25
conference end
2012-03-29
project
HPC-UGent: the central High Performance Computing infrastructure of Ghent University
language
English
UGent publication?
yes
classification
C3
copyright statement
I have retained and own the full copyright for this publication
id
2974577
handle
http://hdl.handle.net/1854/LU-2974577
date created
2012-08-24 09:22:39
date last changed
2013-09-17 10:49:59
@inproceedings{2974577,
  abstract     = {Deamidation occurs spontaneously in peptides and proteins [1]. Many reports show that deamidation has a substantial effect on protein structure, function and stability. An experimental study on pentapeptides [2] shows that Asn deamidation rates are directly related to primary structure near Asn, with a prominent effect from the carboxyl-side (Yyy). We explore the correlation between experimental deamidation rates and primary structure for two pentapeptides (Yyy=Gly, Ile), to identify the factors causing this dependence. A pentapeptide in a water box is subject to Replica-Exchange Molecular Dynamics (REMD) calculations performed with GROMACS 4 software. Furthermore, a succinimide-mediated reaction [3] is investigated with QM/MM calculations utilizing the CP2K code using Nudged-Elastic-Band (NEB) calculations.[p] [p] [p][1] Robinson, NE, Robinson, AB Proc. Natl. Acad. Sci. USA 2001 , 98, 944.[p][2] Robinson, NE J. Peptide Res. 2004 , 63, 426.[p][3] Catak, S., Monard, G., Aviyente, V., Ruiz-L{\'o}pez, MF J. Phys. Chem. A 2009 , 113, 1111.},
  author       = {Catak, Saron and F{\'e}lix, Jan and Van Speybroeck, Veronique and Waroquier, Michel and Pauwels, Ewald},
  booktitle    = {ACS National meeting, Abstracts},
  language     = {eng},
  location     = {San Diego, CA, USA},
  pages        = {130--130},
  publisher    = {American Chemical Society (ACS)},
  title        = {Effect of the (n +1) residue on peptide deamidation},
  year         = {2012},
}

Chicago
Catak, Saron, Jan Félix, Veronique Van Speybroeck, Michel Waroquier, and Ewald Pauwels. 2012. “Effect of the (n +1) Residue on Peptide Deamidation.” In ACS National Meeting, Abstracts, 130–130. American Chemical Society (ACS).
APA
Catak, S., Félix, J., Van Speybroeck, V., Waroquier, M., & Pauwels, E. (2012). Effect of the (n +1) residue on peptide deamidation. ACS National meeting, Abstracts (pp. 130–130). Presented at the ACS Spring 2012 National Meeting & Exposition, American Chemical Society (ACS).
Vancouver
1.
Catak S, Félix J, Van Speybroeck V, Waroquier M, Pauwels E. Effect of the (n +1) residue on peptide deamidation. ACS National meeting, Abstracts. American Chemical Society (ACS); 2012. p. 130–130.
MLA
Catak, Saron, Jan Félix, Veronique Van Speybroeck, et al. “Effect of the (n +1) Residue on Peptide Deamidation.” ACS National Meeting, Abstracts. American Chemical Society (ACS), 2012. 130–130. Print.