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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
Published on: August 16, 2017
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Hierarchical Structure of Protein Sequence
Alexei N Nekrasov1, Yuri P Kozmin1, Sergey V Kozyrev2
1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997 Moscow, Russia.
International Journal of Molecular Sciences
|August 7, 2021
Summary
This study introduces a novel mathematical method to uncover the hierarchical organization within protein sequences using pentapeptides. This approach reveals structural relationships crucial for understanding protein function and disease.
Area of Science:
- Biophysics
- Computational Biology
- Structural Biology
Background:
- Non-communicable diseases often stem from protein or protein complex dysfunction.
- Understanding the relationship between protein sequence, structure, domains, and motifs is a key research area.
Purpose of the Study:
- To develop and present a novel mathematical method for identifying the hierarchical organization of protein sequences.
- To analyze the relationship between protein sequence elements and their spatial structure.
Main Methods:
- A mathematical method was developed utilizing pentapeptides as the fundamental unit of protein sequences.
- The frequency of pentapeptide occurrences in natural protein sequences was analyzed.
- The method was applied to a dataset of 24,647 non-homologous protein sequences (50-400 residues) from the NRDB90 database.
Main Results:
- A hierarchical structure within protein sequences was revealed using the proposed method.
- Statistical analysis identified 11 characteristic values related to the branching points of sequence graphs.
- Examples demonstrated correspondence between protein spatial structure fragments and hierarchical sequence elements.
Conclusions:
- The developed methodology offers a promising foundation for a mathematically-based classification of protein spatial organization.
- The identified hierarchical elements have potential applications in biotechnology and medicine, aiding in solving complex problems.
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