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Matematicheskaya Biologiya i Bioinformatika, 2017, Volume 12, Issue 2, Pages 446–456
DOI: https://doi.org/10.17537/2017.12.446
(Mi mbb305)
 

Bioinformatics

Time saving approach to design altered ligand structure

A. V. Danilkovichab, D. A. Tikhonovcd, V. I. Turobova, I. P. Udovichenkoab

a Branch of the M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Russia
b Pushchino State Institute of Natural Sciences, Pushchino, Russia
c Institute of Mathematical Problems of Biology – Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Russia
d Institute of Theoretical and Experimental Biophysics RAS, Pushchino, Russia
References:
Abstract: To find energetically advantageous variants of the structure of the peptide ligand complexing with the proteins of the major histocompatibility complex and the T-cell receptor (SwissProt ID: 2Z31), the binding energy of hexamers, which are fragments of the native ligand structure, was compared. To form a set of investigated hexamers, the Taguchi method was used. In total, 53 variants of the structure of the complex were constructed and investigated using molecular dynamics. Calculations were carried out both for complete complexes and for free structures - receptors and ligands. On the basis of the obtained molecular trajectories, using the generalized Born method, the free energy of the structures was calculated and averaged for each trajectory. Using the Taguchi method to analyze the peptide hexamer sequence, it was possible to determine prototypes of the ligand whose structures have a higher binding energy to the receptor than the fragment of the original SQYRPS ligand. The applied approach significantly reduces the time required for optimization of the peptide ligand structure.
Key words: Taguchi method, structure optimization, Gibbs energy, spatial model, molecular dynamics.
Funding agency Grant number
Ministry of Education and Science of the Russian Federation 14.607.21.0133 (RFMEFI60715X0133)
Received 20.11.2017, Published 01.12.2017
Document Type: Article
UDC: 51-76, 519.252
Language: Russian
Citation: A. V. Danilkovich, D. A. Tikhonov, V. I. Turobov, I. P. Udovichenko, “Time saving approach to design altered ligand structure”, Mat. Biolog. Bioinform., 12:2 (2017), 446–456
Citation in format AMSBIB
\Bibitem{DanTikTur17}
\by A.~V.~Danilkovich, D.~A.~Tikhonov, V.~I.~Turobov, I.~P.~Udovichenko
\paper Time saving approach to design altered ligand structure
\jour Mat. Biolog. Bioinform.
\yr 2017
\vol 12
\issue 2
\pages 446--456
\mathnet{http://mi.mathnet.ru/mbb305}
\crossref{https://doi.org/10.17537/2017.12.446}
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    References:22
     
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