Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Hierarchical Structure of Protein Sequence

Version 1 : Received: 25 June 2021 / Approved: 28 June 2021 / Online: 28 June 2021 (14:11:39 CEST)

How to cite: Nekrasov, A.N.; Kozmin, Y.P.; Kozyrev, S.V.; Ziganshin, R.H.; de Brevern, A.G.; Anashkina, A.A. Hierarchical Structure of Protein Sequence. Preprints 2021, 2021060661 (doi: 10.20944/preprints202106.0661.v1). Nekrasov, A.N.; Kozmin, Y.P.; Kozyrev, S.V.; Ziganshin, R.H.; de Brevern, A.G.; Anashkina, A.A. Hierarchical Structure of Protein Sequence. Preprints 2021, 2021060661 (doi: 10.20944/preprints202106.0661.v1).

Abstract

Most non-infectious diseases are associated with dysfunction of proteins or protein complexes. Аssociation between sequence and structure is analyzed since a long time, and analysis of sequence organization in domains and motifs is actual research area. A mathematical method is proposed here to identify the hierarchical organization of protein sequences. The method is based on pentapeptide as a unit of protein sequences. This method was applied on a non-homologous dataset of protein sequences. The analysis revealed 11 hierarchical levels of protein sequence organization, showing the relationship of these multiple fragments of sequences. Using different examples, we illustrated how the fragments of the spatial structure of protein correspond to the elements of the hierarchical structure of the protein sequence. A hierarchical structure is observed in the protein sequence. This methodology is an interesting basis for mathematically based classification of elements of spatial organization of proteins. Elements of the hierarchical structure of different levels of the hierarchy can be used for biotechnological and medical problems.

Subject Areas

protein structure; hierarchy; protein sequence; ANIS method; supersecondary structure.

Comments (1)

Comment 1
Received: 3 July 2021
Commenter: R. Gonzalo Parra
The commenter has declared there is no conflict of interests.
Comment: Very interesting preprint! The authors may be interested to see some work we made some years ago about the hierarchical structure of proteins both at their structure and sequence levels.

"Detecting Repetitions and Periodicities in Proteins by Tiling the Structural Space"
https://pubs.acs.org/doi/abs/10.1021/jp402105j
"Protein Repeats from First Principles"
https://www.nature.com/articles/srep23959
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