Modeling the Dynamics of Protein–Protein Interfaces, How and Why?
Protein–protein assemblies act as a key component in numerous cellular processes. Their accurate modeling at the atomic level remains a challenge for structural biology. To address this challenge, several docking and a handful of deep learning methodologies focus on modeling protein–protein interfac...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-03-01
|
| Series: | Molecules |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1420-3049/27/6/1841 |
| _version_ | 1797444353490157568 |
|---|---|
| author | Ezgi Karaca Chantal Prévost Sophie Sacquin-Mora |
| author_facet | Ezgi Karaca Chantal Prévost Sophie Sacquin-Mora |
| author_sort | Ezgi Karaca |
| collection | DOAJ |
| description | Protein–protein assemblies act as a key component in numerous cellular processes. Their accurate modeling at the atomic level remains a challenge for structural biology. To address this challenge, several docking and a handful of deep learning methodologies focus on modeling protein–protein interfaces. Although the outcome of these methods has been assessed using static reference structures, more and more data point to the fact that the interaction stability and specificity is encoded in the dynamics of these interfaces. Therefore, this dynamics information must be taken into account when modeling and assessing protein interactions at the atomistic scale. Expanding on this, our review initially focuses on the recent computational strategies aiming at investigating protein–protein interfaces in a dynamic fashion using enhanced sampling, multi-scale modeling, and experimental data integration. Then, we discuss how interface dynamics report on the function of protein assemblies in globular complexes, in fuzzy complexes containing intrinsically disordered proteins, as well as in active complexes, where chemical reactions take place across the protein–protein interface. |
| first_indexed | 2024-03-09T13:10:26Z |
| format | Article |
| id | doaj.art-3fcb87d98fc94b7f9c41530daf2ade14 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-09T13:10:26Z |
| publishDate | 2022-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-3fcb87d98fc94b7f9c41530daf2ade142023-11-30T21:42:02ZengMDPI AGMolecules1420-30492022-03-01276184110.3390/molecules27061841Modeling the Dynamics of Protein–Protein Interfaces, How and Why?Ezgi Karaca0Chantal Prévost1Sophie Sacquin-Mora2Izmir Biomedicine and Genome Center, Izmir 35340, TurkeyCNRS, Laboratoire de Biochimie Théorique, UPR9080, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, FranceCNRS, Laboratoire de Biochimie Théorique, UPR9080, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, FranceProtein–protein assemblies act as a key component in numerous cellular processes. Their accurate modeling at the atomic level remains a challenge for structural biology. To address this challenge, several docking and a handful of deep learning methodologies focus on modeling protein–protein interfaces. Although the outcome of these methods has been assessed using static reference structures, more and more data point to the fact that the interaction stability and specificity is encoded in the dynamics of these interfaces. Therefore, this dynamics information must be taken into account when modeling and assessing protein interactions at the atomistic scale. Expanding on this, our review initially focuses on the recent computational strategies aiming at investigating protein–protein interfaces in a dynamic fashion using enhanced sampling, multi-scale modeling, and experimental data integration. Then, we discuss how interface dynamics report on the function of protein assemblies in globular complexes, in fuzzy complexes containing intrinsically disordered proteins, as well as in active complexes, where chemical reactions take place across the protein–protein interface.https://www.mdpi.com/1420-3049/27/6/1841protein interactionsprotein interfacesprotein dynamicsmolecular modelingprotein docking |
| spellingShingle | Ezgi Karaca Chantal Prévost Sophie Sacquin-Mora Modeling the Dynamics of Protein–Protein Interfaces, How and Why? Molecules protein interactions protein interfaces protein dynamics molecular modeling protein docking |
| title | Modeling the Dynamics of Protein–Protein Interfaces, How and Why? |
| title_full | Modeling the Dynamics of Protein–Protein Interfaces, How and Why? |
| title_fullStr | Modeling the Dynamics of Protein–Protein Interfaces, How and Why? |
| title_full_unstemmed | Modeling the Dynamics of Protein–Protein Interfaces, How and Why? |
| title_short | Modeling the Dynamics of Protein–Protein Interfaces, How and Why? |
| title_sort | modeling the dynamics of protein protein interfaces how and why |
| topic | protein interactions protein interfaces protein dynamics molecular modeling protein docking |
| url | https://www.mdpi.com/1420-3049/27/6/1841 |
| work_keys_str_mv | AT ezgikaraca modelingthedynamicsofproteinproteininterfaceshowandwhy AT chantalprevost modelingthedynamicsofproteinproteininterfaceshowandwhy AT sophiesacquinmora modelingthedynamicsofproteinproteininterfaceshowandwhy |