A minimum set of stable blocks for rational design of polypeptide chains

Biochimie
Alexei N NekrasovAnastasia A Anashkina

Abstract

The aim of this work was to find a minimal set of structurally stable pentapeptides, which allows forming a polypeptide chain of a required 3D structure. To search for factors that ensure structural stability of the pentapeptide, we generated peptide sequences with no more than three functional groups, based on the alanine pentapeptide AAAAA. We analyzed 44,860 structures of peptides by the molecular dynamics method and found that 1,225 pentapeptides over 80% of the simulation time were in a stable conformation. Clustering of these conformations revealed 54 topological types of conformationally stable pentapeptides. These conformations relate to different combined elements of the protein secondary structure. So, we obtained a minimal set of amino acid structures of conformationally stable pentapeptides, creating a complete set of different topologies that ensure the formation of pre-folded conformation of protein structures.

References

Dec 1, 1994·International Journal of Peptide and Protein Research·G V Nikiforovich
Jul 30, 2002·Journal of Biomolecular Structure & Dynamics·Alexei N Nekrasov
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May 11, 2013·Journal of Biomolecular Structure & Dynamics·Sylvain LéonardAlexandre G de Brevern

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Citations

Aug 19, 2020·Briefings in Bioinformatics·Haitao YangJing Wu
Aug 8, 2021·International Journal of Molecular Sciences·Alexei N NekrasovAnastasia A Anashkina

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