Mathematical Characterization of Protein Sequences Using Patterns as Chemical Group Combinations of Amino Acids.
Comparison of amino acid sequence similarity is the fundamental concept behind the protein phylogenetic tree formation. By virtue of this method, we can explain the evolutionary relationships, but further explanations are not possible unless sequences are studied through the chemical nature of indiv...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2016-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5145171?pdf=render |
| _version_ | 1828397522679234560 |
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| author | Jayanta Kumar Das Provas Das Korak Kumar Ray Pabitra Pal Choudhury Siddhartha Sankar Jana |
| author_facet | Jayanta Kumar Das Provas Das Korak Kumar Ray Pabitra Pal Choudhury Siddhartha Sankar Jana |
| author_sort | Jayanta Kumar Das |
| collection | DOAJ |
| description | Comparison of amino acid sequence similarity is the fundamental concept behind the protein phylogenetic tree formation. By virtue of this method, we can explain the evolutionary relationships, but further explanations are not possible unless sequences are studied through the chemical nature of individual amino acids. Here we develop a new methodology to characterize the protein sequences on the basis of the chemical nature of the amino acids. We design various algorithms for studying the variation of chemical group transitions and various chemical group combinations as patterns in the protein sequences. The amino acid sequence of conventional myosin II head domain of 14 family members are taken to illustrate this new approach. We find two blocks of maximum length 6 aa as 'FPKATD' and 'Y/FTNEKL' without repeating the same chemical nature and one block of maximum length 20 aa with the repetition of chemical nature which are common among all 14 members. We also check commonality with another motor protein sub-family kinesin, KIF1A. Based on our analysis we find a common block of length 8 aa both in myosin II and KIF1A. This motif is located in the neck linker region which could be responsible for the generation of mechanical force, enabling us to find the unique blocks which remain chemically conserved across the family. We also validate our methodology with different protein families such as MYOI, Myosin light chain kinase (MLCK) and Rho-associated protein kinase (ROCK), Na+/K+-ATPase and Ca2+-ATPase. Altogether, our studies provide a new methodology for investigating the conserved amino acids' pattern in different proteins. |
| first_indexed | 2024-12-10T08:48:16Z |
| format | Article |
| id | doaj.art-470b50cb432946bf9cbc5029ab9ed2f1 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-10T08:48:16Z |
| publishDate | 2016-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-470b50cb432946bf9cbc5029ab9ed2f12022-12-22T01:55:40ZengPublic Library of Science (PLoS)PLoS ONE1932-62032016-01-011112e016765110.1371/journal.pone.0167651Mathematical Characterization of Protein Sequences Using Patterns as Chemical Group Combinations of Amino Acids.Jayanta Kumar DasProvas DasKorak Kumar RayPabitra Pal ChoudhurySiddhartha Sankar JanaComparison of amino acid sequence similarity is the fundamental concept behind the protein phylogenetic tree formation. By virtue of this method, we can explain the evolutionary relationships, but further explanations are not possible unless sequences are studied through the chemical nature of individual amino acids. Here we develop a new methodology to characterize the protein sequences on the basis of the chemical nature of the amino acids. We design various algorithms for studying the variation of chemical group transitions and various chemical group combinations as patterns in the protein sequences. The amino acid sequence of conventional myosin II head domain of 14 family members are taken to illustrate this new approach. We find two blocks of maximum length 6 aa as 'FPKATD' and 'Y/FTNEKL' without repeating the same chemical nature and one block of maximum length 20 aa with the repetition of chemical nature which are common among all 14 members. We also check commonality with another motor protein sub-family kinesin, KIF1A. Based on our analysis we find a common block of length 8 aa both in myosin II and KIF1A. This motif is located in the neck linker region which could be responsible for the generation of mechanical force, enabling us to find the unique blocks which remain chemically conserved across the family. We also validate our methodology with different protein families such as MYOI, Myosin light chain kinase (MLCK) and Rho-associated protein kinase (ROCK), Na+/K+-ATPase and Ca2+-ATPase. Altogether, our studies provide a new methodology for investigating the conserved amino acids' pattern in different proteins.http://europepmc.org/articles/PMC5145171?pdf=render |
| spellingShingle | Jayanta Kumar Das Provas Das Korak Kumar Ray Pabitra Pal Choudhury Siddhartha Sankar Jana Mathematical Characterization of Protein Sequences Using Patterns as Chemical Group Combinations of Amino Acids. PLoS ONE |
| title | Mathematical Characterization of Protein Sequences Using Patterns as Chemical Group Combinations of Amino Acids. |
| title_full | Mathematical Characterization of Protein Sequences Using Patterns as Chemical Group Combinations of Amino Acids. |
| title_fullStr | Mathematical Characterization of Protein Sequences Using Patterns as Chemical Group Combinations of Amino Acids. |
| title_full_unstemmed | Mathematical Characterization of Protein Sequences Using Patterns as Chemical Group Combinations of Amino Acids. |
| title_short | Mathematical Characterization of Protein Sequences Using Patterns as Chemical Group Combinations of Amino Acids. |
| title_sort | mathematical characterization of protein sequences using patterns as chemical group combinations of amino acids |
| url | http://europepmc.org/articles/PMC5145171?pdf=render |
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