Molecular Biology, volume 44, issue 6, pages 958-967
Optimization of the methods for small peptide solution structure determination by NMR spectroscopy
Publication type: Journal Article
Publication date: 2010-12-03
Journal:
Molecular Biology
Quartile SCImago
Q4
Quartile WOS
Q4
Impact factor: 1.2
ISSN: 00268933, 16083245
Structural Biology
Biophysics
Abstract
NMR spectroscopy was recognized as a method of protein structure determination in solution. However, determination of the conformation of small peptides, which undergo fast molecular motions, remains a challenge. This is mainly caused by the impossibility to collect the required quantity of the distance and dihedral angle restraints from NMR spectra. At the same time, short charged peptides play an important role in a number of biological processes, in particular in pathogenesis of neurodegenerative diseases including Alzheimer’s disease. Therefore, development of a method for structure simulation of small peptides in aqueous environment using the most realistic force fields seems to be of current importance. Such algorithm has been developed using the Amber-03 force field and Gromacs program after modification of its code. Calculation algorithm has been verified on a model peptide with a known solution structure and a metal-binding fragment of rat β-amyloid, whose structure has been determined by alternative methods. The developed algorithm substantially increases structure quality, in particular Ramachandran plot statistics, and decreases RMSD of atomic coordinates inside the calculated family. The described protocol can be used for determination of conformation of short peptides, and also for optimization of structure of larger proteins containing poorly structured fragments.
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Pleiades Publishing
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Istrate A. N. et al. Optimization of the methods for small peptide solution structure determination by NMR spectroscopy // Molecular Biology. 2010. Vol. 44. No. 6. pp. 958-967.
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Istrate A. N., Mantsyzov A. B., Kozin S. A., Polshakov V. I. Optimization of the methods for small peptide solution structure determination by NMR spectroscopy // Molecular Biology. 2010. Vol. 44. No. 6. pp. 958-967.
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TY - JOUR
DO - 10.1134/S0026893310060130
UR - https://doi.org/10.1134%2FS0026893310060130
TI - Optimization of the methods for small peptide solution structure determination by NMR spectroscopy
T2 - Molecular Biology
AU - Istrate, A N
AU - Mantsyzov, A B
AU - Kozin, S A
AU - Polshakov, V I
PY - 2010
DA - 2010/12/03 00:00:00
PB - Pleiades Publishing
SP - 958-967
IS - 6
VL - 44
SN - 0026-8933
SN - 1608-3245
ER -
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@article{2010_Istrate
author = {A N Istrate and A B Mantsyzov and S A Kozin and V I Polshakov},
title = {Optimization of the methods for small peptide solution structure determination by NMR spectroscopy},
journal = {Molecular Biology},
year = {2010},
volume = {44},
publisher = {Pleiades Publishing},
month = {dec},
url = {https://doi.org/10.1134%2FS0026893310060130},
number = {6},
pages = {958--967},
doi = {10.1134/S0026893310060130}
}
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Istrate, A. N., et al. “Optimization of the methods for small peptide solution structure determination by NMR spectroscopy.” Molecular Biology, vol. 44, no. 6, Dec. 2010, pp. 958-967. https://doi.org/10.1134%2FS0026893310060130.
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