Is there an advantageous arrangement of aromatic residues in proteins? Statistical analysis of aromatic interactions in globular proteins
The aim of this study was to evaluate the favorability of different conformations of aromatic residues in proteins by analysing the occurrence of particular conformations. The clustering of protein structures from the Protein Data Bank (PDB) was performed. Conformations of interacting aromatic resid...
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| Format: | Article |
| Language: | English |
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Elsevier
2021-01-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S200103702100458X |
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| author | Mikhail Yu. Lobanov Leonid B. Pereyaslavets Ilya V. Likhachev Bakhyt T. Matkarimov Oxana V. Galzitskaya |
| author_facet | Mikhail Yu. Lobanov Leonid B. Pereyaslavets Ilya V. Likhachev Bakhyt T. Matkarimov Oxana V. Galzitskaya |
| author_sort | Mikhail Yu. Lobanov |
| collection | DOAJ |
| description | The aim of this study was to evaluate the favorability of different conformations of aromatic residues in proteins by analysing the occurrence of particular conformations. The clustering of protein structures from the Protein Data Bank (PDB) was performed. Conformations of interacting aromatic residues were analyzed for 511 282 pairs in 35 493 protein structures sharing less than 50% identity. Pairs with a parallel arrangement of aromatic residues made up 6.2% of all possible ones, which was twice as much as expected. Pairs with a perpendicular arrangement of aromatic residues made up 25%. We demonstrate that the most favorable arrangement was at an angle of 60° between the interacting aromatic residues. Among all possible aromatic pairs, the His-His pair was twice as frequent as expected, and the His-Phe pair was less frequent than expected. A server (CARP – Contacts of Aromatic Residues in Proteins) has been created for calculating essential structural features of interacting aromatic residues in proteins: http://bioproteom.protres.ru/arom_q_prog/. |
| first_indexed | 2024-12-20T17:01:10Z |
| format | Article |
| id | doaj.art-446e6f61aad0401e93e34ed10df033fd |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-12-20T17:01:10Z |
| publishDate | 2021-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-446e6f61aad0401e93e34ed10df033fd2022-12-21T19:32:31ZengElsevierComputational and Structural Biotechnology Journal2001-03702021-01-011959605968Is there an advantageous arrangement of aromatic residues in proteins? Statistical analysis of aromatic interactions in globular proteinsMikhail Yu. Lobanov0Leonid B. Pereyaslavets1Ilya V. Likhachev2Bakhyt T. Matkarimov3Oxana V. Galzitskaya4Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, RussiaInstitute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, RussiaInstitute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, RussiaNational Laboratory Astana, Nazarbayev University, Nur-Sultan, KazakhstanInstitute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; Corresponding author at: Laboratory of Bioinformatics and Proteomics, Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.The aim of this study was to evaluate the favorability of different conformations of aromatic residues in proteins by analysing the occurrence of particular conformations. The clustering of protein structures from the Protein Data Bank (PDB) was performed. Conformations of interacting aromatic residues were analyzed for 511 282 pairs in 35 493 protein structures sharing less than 50% identity. Pairs with a parallel arrangement of aromatic residues made up 6.2% of all possible ones, which was twice as much as expected. Pairs with a perpendicular arrangement of aromatic residues made up 25%. We demonstrate that the most favorable arrangement was at an angle of 60° between the interacting aromatic residues. Among all possible aromatic pairs, the His-His pair was twice as frequent as expected, and the His-Phe pair was less frequent than expected. A server (CARP – Contacts of Aromatic Residues in Proteins) has been created for calculating essential structural features of interacting aromatic residues in proteins: http://bioproteom.protres.ru/arom_q_prog/.http://www.sciencedirect.com/science/article/pii/S200103702100458XAromatic residuesConformationExhaustive enumerationStackingServerProtein Data Bank |
| spellingShingle | Mikhail Yu. Lobanov Leonid B. Pereyaslavets Ilya V. Likhachev Bakhyt T. Matkarimov Oxana V. Galzitskaya Is there an advantageous arrangement of aromatic residues in proteins? Statistical analysis of aromatic interactions in globular proteins Computational and Structural Biotechnology Journal Aromatic residues Conformation Exhaustive enumeration Stacking Server Protein Data Bank |
| title | Is there an advantageous arrangement of aromatic residues in proteins? Statistical analysis of aromatic interactions in globular proteins |
| title_full | Is there an advantageous arrangement of aromatic residues in proteins? Statistical analysis of aromatic interactions in globular proteins |
| title_fullStr | Is there an advantageous arrangement of aromatic residues in proteins? Statistical analysis of aromatic interactions in globular proteins |
| title_full_unstemmed | Is there an advantageous arrangement of aromatic residues in proteins? Statistical analysis of aromatic interactions in globular proteins |
| title_short | Is there an advantageous arrangement of aromatic residues in proteins? Statistical analysis of aromatic interactions in globular proteins |
| title_sort | is there an advantageous arrangement of aromatic residues in proteins statistical analysis of aromatic interactions in globular proteins |
| topic | Aromatic residues Conformation Exhaustive enumeration Stacking Server Protein Data Bank |
| url | http://www.sciencedirect.com/science/article/pii/S200103702100458X |
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