Contribution to the Understanding of Protein–Protein Interface and Ligand Binding Site Based on Hydrophobicity Distribution—Application to Ferredoxin I and II Cases
Ferredoxin I and II are proteins carrying a specific ligand—an iron-sulfur cluster—which allows transport of electrons. These two classes of ferredoxin in their monomeric and dimeric forms are the object of this work. Characteristic of hydrophobic core in both molecules is analyzed via fuzzy oil dro...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-09-01
|
| Series: | Applied Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-3417/11/18/8514 |
| _version_ | 1797520355354476544 |
|---|---|
| author | Mateusz Banach Jacques Chomilier Irena Roterman |
| author_facet | Mateusz Banach Jacques Chomilier Irena Roterman |
| author_sort | Mateusz Banach |
| collection | DOAJ |
| description | Ferredoxin I and II are proteins carrying a specific ligand—an iron-sulfur cluster—which allows transport of electrons. These two classes of ferredoxin in their monomeric and dimeric forms are the object of this work. Characteristic of hydrophobic core in both molecules is analyzed via fuzzy oil drop model (FOD) to show the specificity of their structure enabling the binding of a relatively large ligand and formation of the complex. Structures of FdI and FdII are a promising example for the discussion of influence of hydrophobicity on biological activity but also for an explanation how FOD model can be used as an initial stage adviser (or a scoring function) in the search for locations of ligand binding pockets and protein–protein interaction areas. It is shown that observation of peculiarities in the hydrophobicity distribution present in the molecule (in this case—of a ferredoxin) may provide a promising starting location for computer simulations aimed at the prediction of quaternary structure of proteins. |
| first_indexed | 2024-03-10T07:55:36Z |
| format | Article |
| id | doaj.art-e43b94fd6bb94172a46af8759b9cacc9 |
| institution | Directory Open Access Journal |
| issn | 2076-3417 |
| language | English |
| last_indexed | 2024-03-10T07:55:36Z |
| publishDate | 2021-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Applied Sciences |
| spelling | doaj.art-e43b94fd6bb94172a46af8759b9cacc92023-11-22T11:53:57ZengMDPI AGApplied Sciences2076-34172021-09-011118851410.3390/app11188514Contribution to the Understanding of Protein–Protein Interface and Ligand Binding Site Based on Hydrophobicity Distribution—Application to Ferredoxin I and II CasesMateusz Banach0Jacques Chomilier1Irena Roterman2Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Medyczna 7, 30-688 Kraków, PolandInstitut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR CNRS 7590, Muséum National d’Histoire Naturelle, Sorbonne Université, 75 252 Paris, FranceDepartment of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Medyczna 7, 30-688 Kraków, PolandFerredoxin I and II are proteins carrying a specific ligand—an iron-sulfur cluster—which allows transport of electrons. These two classes of ferredoxin in their monomeric and dimeric forms are the object of this work. Characteristic of hydrophobic core in both molecules is analyzed via fuzzy oil drop model (FOD) to show the specificity of their structure enabling the binding of a relatively large ligand and formation of the complex. Structures of FdI and FdII are a promising example for the discussion of influence of hydrophobicity on biological activity but also for an explanation how FOD model can be used as an initial stage adviser (or a scoring function) in the search for locations of ligand binding pockets and protein–protein interaction areas. It is shown that observation of peculiarities in the hydrophobicity distribution present in the molecule (in this case—of a ferredoxin) may provide a promising starting location for computer simulations aimed at the prediction of quaternary structure of proteins.https://www.mdpi.com/2076-3417/11/18/8514antifreeze proteindivergence entropyferredoxinhydrophobic coreligand bindingmacromolecular docking |
| spellingShingle | Mateusz Banach Jacques Chomilier Irena Roterman Contribution to the Understanding of Protein–Protein Interface and Ligand Binding Site Based on Hydrophobicity Distribution—Application to Ferredoxin I and II Cases Applied Sciences antifreeze protein divergence entropy ferredoxin hydrophobic core ligand binding macromolecular docking |
| title | Contribution to the Understanding of Protein–Protein Interface and Ligand Binding Site Based on Hydrophobicity Distribution—Application to Ferredoxin I and II Cases |
| title_full | Contribution to the Understanding of Protein–Protein Interface and Ligand Binding Site Based on Hydrophobicity Distribution—Application to Ferredoxin I and II Cases |
| title_fullStr | Contribution to the Understanding of Protein–Protein Interface and Ligand Binding Site Based on Hydrophobicity Distribution—Application to Ferredoxin I and II Cases |
| title_full_unstemmed | Contribution to the Understanding of Protein–Protein Interface and Ligand Binding Site Based on Hydrophobicity Distribution—Application to Ferredoxin I and II Cases |
| title_short | Contribution to the Understanding of Protein–Protein Interface and Ligand Binding Site Based on Hydrophobicity Distribution—Application to Ferredoxin I and II Cases |
| title_sort | contribution to the understanding of protein protein interface and ligand binding site based on hydrophobicity distribution application to ferredoxin i and ii cases |
| topic | antifreeze protein divergence entropy ferredoxin hydrophobic core ligand binding macromolecular docking |
| url | https://www.mdpi.com/2076-3417/11/18/8514 |
| work_keys_str_mv | AT mateuszbanach contributiontotheunderstandingofproteinproteininterfaceandligandbindingsitebasedonhydrophobicitydistributionapplicationtoferredoxiniandiicases AT jacqueschomilier contributiontotheunderstandingofproteinproteininterfaceandligandbindingsitebasedonhydrophobicitydistributionapplicationtoferredoxiniandiicases AT irenaroterman contributiontotheunderstandingofproteinproteininterfaceandligandbindingsitebasedonhydrophobicitydistributionapplicationtoferredoxiniandiicases |