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QM metadynamics study on asparagine deamidation in proteins

Saron Catak UGent, Bart De Sterck UGent, Michel Waroquier UGent and Veronique Van Speybroeck UGent (2010) ACS National Meeting, 239th, Abstracts.
abstract
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 succinimide-mediated pathway. Concerted and stepwise pathways leading to the succinimide intermediate were previously explored with the inclusion of explicit water molecules [2,3]. The current study introduces a new 'competing' route for the deamidation of asparagine residues. The aim is to comparatively analyze the feasibility of this new mechanism against the traditional succinimide route, taking into account the catalytic effect of the solvent environment via QM dynamics and meta-dynamics calculations on a model peptide placed in a periodic water box. These results will identify the lowest energy pathway for asparagine deamidation and will serve as a stepping stone for calculations of Asn deamidation in proteins.
Please use this url to cite or link to this publication:
author
organization
year
type
conference
publication status
published
subject
keyword
Quantum Chemistry
in
ACS National Meeting, 239th, Abstracts
article number
abstract 166
publisher
American Chemical Society (ACS)
conference name
239th ACS National Meeting
conference location
San Francisco, CA, USA
conference start
2010-03-21
conference end
2010-03-25
language
English
UGent publication?
yes
classification
C3
copyright statement
I have transferred the copyright for this publication to the publisher
id
1324270
handle
http://hdl.handle.net/1854/LU-1324270
date created
2011-06-23 11:25:05
date last changed
2016-12-21 15:41:00
@inproceedings{1324270,
  abstract     = {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 succinimide-mediated pathway. Concerted and stepwise pathways leading to the succinimide intermediate were previously explored with the inclusion of explicit water molecules [2,3]. The current study introduces a new 'competing' route for the deamidation of asparagine residues. The aim is to comparatively analyze the feasibility of this new mechanism against the traditional succinimide route, taking into account the catalytic effect of the solvent environment via QM dynamics and meta-dynamics calculations on a model peptide placed in a periodic water box. These results will identify the lowest energy pathway for asparagine deamidation and will serve as a stepping stone for calculations of Asn deamidation in proteins.},
  articleno    = {abstract 166},
  author       = {Catak, Saron and De Sterck, Bart and Waroquier, Michel and Van Speybroeck, Veronique},
  booktitle    = {ACS National Meeting, 239th, Abstracts},
  keyword      = {Quantum Chemistry},
  language     = {eng},
  location     = {San Francisco, CA, USA},
  publisher    = {American Chemical Society (ACS)},
  title        = {QM metadynamics study on asparagine deamidation in proteins},
  year         = {2010},
}

Chicago
Catak, Saron, Bart De Sterck, Michel Waroquier, and Veronique Van Speybroeck. 2010. “QM Metadynamics Study on Asparagine Deamidation in Proteins.” In ACS National Meeting, 239th, Abstracts. American Chemical Society (ACS).
APA
Catak, S., De Sterck, B., Waroquier, M., & Van Speybroeck, V. (2010). QM metadynamics study on asparagine deamidation in proteins. ACS National Meeting, 239th, Abstracts. Presented at the 239th ACS National Meeting, American Chemical Society (ACS).
Vancouver
1.
Catak S, De Sterck B, Waroquier M, Van Speybroeck V. QM metadynamics study on asparagine deamidation in proteins. ACS National Meeting, 239th, Abstracts. American Chemical Society (ACS); 2010.
MLA
Catak, Saron, Bart De Sterck, Michel Waroquier, et al. “QM Metadynamics Study on Asparagine Deamidation in Proteins.” ACS National Meeting, 239th, Abstracts. American Chemical Society (ACS), 2010. Print.