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Updated: Jan 28, 2026

Using SecM Arrest Sequence as a Tool to Isolate Ribosome Bound Polypeptides
Published on: June 19, 2012
A minimum set of stable blocks for rational design of polypeptide chains
Alexei N Nekrasov1, Ludmila G Alekseeva1, Rudolf А Pogosyan1
1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997, Moscow, Russia.
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.
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