Engagement of intrinsic disordered proteins in protein–protein interaction
Proteins from the intrinsically disordered group (IDP) focus the attention of many researchers engaged in protein structure analysis. The main criteria used in their identification are lack of secondary structure and significant structural variability. This variability takes forms that cannot be ide...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-07-01
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| Series: | Frontiers in Molecular Biosciences |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmolb.2023.1230922/full |
| _version_ | 1797768793792970752 |
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| author | Irena Roterman Katarzyna Stapor Leszek Konieczny |
| author_facet | Irena Roterman Katarzyna Stapor Leszek Konieczny |
| author_sort | Irena Roterman |
| collection | DOAJ |
| description | Proteins from the intrinsically disordered group (IDP) focus the attention of many researchers engaged in protein structure analysis. The main criteria used in their identification are lack of secondary structure and significant structural variability. This variability takes forms that cannot be identified in the X-ray technique. In the present study, different criteria were used to assess the status of IDP proteins and their fragments recognized as intrinsically disordered regions (IDRs). The status of the hydrophobic core in proteins identified as IDPs and in their complexes was assessed. The status of IDRs as components of the ordering structure resulting from the construction of the hydrophobic core was also assessed. The hydrophobic core is understood as a structure encompassing the entire molecule in the form of a centrally located high concentration of hydrophobicity and a shell with a gradually decreasing level of hydrophobicity until it reaches a level close to zero on the protein surface. It is a model assuming that the protein folding process follows a micellization pattern aiming at exposing polar residues on the surface, with the simultaneous isolation of hydrophobic amino acids from the polar aquatic environment. The use of the model of hydrophobicity distribution in proteins in the form of the 3D Gaussian distribution described on the protein particle introduces the possibility of assessing the degree of similarity to the assumed micelle-like distribution and also enables the identification of deviations and mismatch between the actual distribution and the idealized distribution. The FOD (fuzzy oil drop) model and its modified FOD-M version allow for the quantitative assessment of these differences and the assessment of the relationship of these areas to the protein function. In the present work, the sections of IDRs in protein complexes classified as IDPs are analyzed. The classification “disordered” in the structural sense (lack of secondary structure or high flexibility) does not always entail a mismatch with the structure of the hydrophobic core. Particularly, the interface area, often consisting of IDRs, in many analyzed complexes shows the compliance of the hydrophobicity distribution with the idealized distribution, which proves that matching to the structure of the hydrophobic core does not require secondary structure ordering. |
| first_indexed | 2024-03-12T20:58:29Z |
| format | Article |
| id | doaj.art-d9e9f4798e364824b370d99f58874c1d |
| institution | Directory Open Access Journal |
| issn | 2296-889X |
| language | English |
| last_indexed | 2024-03-12T20:58:29Z |
| publishDate | 2023-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Molecular Biosciences |
| spelling | doaj.art-d9e9f4798e364824b370d99f58874c1d2023-07-31T11:31:28ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2023-07-011010.3389/fmolb.2023.12309221230922Engagement of intrinsic disordered proteins in protein–protein interactionIrena Roterman0Katarzyna Stapor1Leszek Konieczny2Department of Bioinformatics and Telemedicine, Jagiellonian University—Medical College, Kraków, PolandDepartment of Applied Informatics, Faculty of Automatic, Electronics and Computer Science, Silesian University of Technology, Gliwice, PolandChair of Medical Biochemistry, Medical College, Jagiellonian University, Kraków, PolandProteins from the intrinsically disordered group (IDP) focus the attention of many researchers engaged in protein structure analysis. The main criteria used in their identification are lack of secondary structure and significant structural variability. This variability takes forms that cannot be identified in the X-ray technique. In the present study, different criteria were used to assess the status of IDP proteins and their fragments recognized as intrinsically disordered regions (IDRs). The status of the hydrophobic core in proteins identified as IDPs and in their complexes was assessed. The status of IDRs as components of the ordering structure resulting from the construction of the hydrophobic core was also assessed. The hydrophobic core is understood as a structure encompassing the entire molecule in the form of a centrally located high concentration of hydrophobicity and a shell with a gradually decreasing level of hydrophobicity until it reaches a level close to zero on the protein surface. It is a model assuming that the protein folding process follows a micellization pattern aiming at exposing polar residues on the surface, with the simultaneous isolation of hydrophobic amino acids from the polar aquatic environment. The use of the model of hydrophobicity distribution in proteins in the form of the 3D Gaussian distribution described on the protein particle introduces the possibility of assessing the degree of similarity to the assumed micelle-like distribution and also enables the identification of deviations and mismatch between the actual distribution and the idealized distribution. The FOD (fuzzy oil drop) model and its modified FOD-M version allow for the quantitative assessment of these differences and the assessment of the relationship of these areas to the protein function. In the present work, the sections of IDRs in protein complexes classified as IDPs are analyzed. The classification “disordered” in the structural sense (lack of secondary structure or high flexibility) does not always entail a mismatch with the structure of the hydrophobic core. Particularly, the interface area, often consisting of IDRs, in many analyzed complexes shows the compliance of the hydrophobicity distribution with the idealized distribution, which proves that matching to the structure of the hydrophobic core does not require secondary structure ordering.https://www.frontiersin.org/articles/10.3389/fmolb.2023.1230922/fullintrinsically disordered proteinsdisporthydrophobicityprotein complexfunction-related structural changesorder-to-disorder |
| spellingShingle | Irena Roterman Katarzyna Stapor Leszek Konieczny Engagement of intrinsic disordered proteins in protein–protein interaction Frontiers in Molecular Biosciences intrinsically disordered proteins disport hydrophobicity protein complex function-related structural changes order-to-disorder |
| title | Engagement of intrinsic disordered proteins in protein–protein interaction |
| title_full | Engagement of intrinsic disordered proteins in protein–protein interaction |
| title_fullStr | Engagement of intrinsic disordered proteins in protein–protein interaction |
| title_full_unstemmed | Engagement of intrinsic disordered proteins in protein–protein interaction |
| title_short | Engagement of intrinsic disordered proteins in protein–protein interaction |
| title_sort | engagement of intrinsic disordered proteins in protein protein interaction |
| topic | intrinsically disordered proteins disport hydrophobicity protein complex function-related structural changes order-to-disorder |
| url | https://www.frontiersin.org/articles/10.3389/fmolb.2023.1230922/full |
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