Exploring the Dynamic Interplay of Deleterious Variants on the RAF1–RAP1A Binding in Cancer: Conformational Analysis, Binding Free Energy, and Essential Dynamics
<p dir="ltr">The RAF1–RAP1A interaction activates the MAPK/ERK pathway which is very crucial in the carcinogenesis process. This protein complex influences tumor formation, proliferation, and metastasis. Understanding aberrant interactions driven by clinical mutations is vital for ta...
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2024
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| _version_ | 1864513538000683008 |
|---|---|
| author | Abbas Khan (5141000) |
| author2 | Syed Shujait Ali (5159288) Muhammad Ammar Zahid (18123775) Shahenda Salah Abdelsalam (22330768) Noorah Albekairi (22330771) Raed M. Al‐Zoubi (21348629) Mohanad Shkoor (3768385) Dong‐Qing Wei (22330774) Abdelali Agouni (181926) |
| author2_role | author author author author author author author author |
| author_facet | Abbas Khan (5141000) Syed Shujait Ali (5159288) Muhammad Ammar Zahid (18123775) Shahenda Salah Abdelsalam (22330768) Noorah Albekairi (22330771) Raed M. Al‐Zoubi (21348629) Mohanad Shkoor (3768385) Dong‐Qing Wei (22330774) Abdelali Agouni (181926) |
| author_role | author |
| dc.creator.none.fl_str_mv | Abbas Khan (5141000) Syed Shujait Ali (5159288) Muhammad Ammar Zahid (18123775) Shahenda Salah Abdelsalam (22330768) Noorah Albekairi (22330771) Raed M. Al‐Zoubi (21348629) Mohanad Shkoor (3768385) Dong‐Qing Wei (22330774) Abdelali Agouni (181926) |
| dc.date.none.fl_str_mv | 2024-11-01T00:00:00Z |
| dc.identifier.none.fl_str_mv | 10.1002/prot.26759 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/journal_contribution/Exploring_the_Dynamic_Interplay_of_Deleterious_Variants_on_the_RAF1_RAP1A_Binding_in_Cancer_Conformational_Analysis_Binding_Free_Energy_and_Essential_Dynamics/30234403 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biological sciences Bioinformatics and computational biology Biomedical and clinical sciences Oncology and carcinogenesis binding free energy cancer docking MAPK mutations RAF1 simulation |
| dc.title.none.fl_str_mv | Exploring the Dynamic Interplay of Deleterious Variants on the RAF1–RAP1A Binding in Cancer: Conformational Analysis, Binding Free Energy, and Essential Dynamics |
| dc.type.none.fl_str_mv | Text Journal contribution info:eu-repo/semantics/publishedVersion text contribution to journal |
| description | <p dir="ltr">The RAF1–RAP1A interaction activates the MAPK/ERK pathway which is very crucial in the carcinogenesis process. This protein complex influences tumor formation, proliferation, and metastasis. Understanding aberrant interactions driven by clinical mutations is vital for targeted therapies. Hence, the current study focuses on the screening of clinically reported substitutions in the <i>RAF1</i> and <i>RAP1A</i> genes using predictive algorithms integrated with all‐atoms simulation, essential dynamics, and binding free energy methods. Survival analysis results revealed a strong association between <i>RAF1</i> and <i>RAP1A</i> expression levels and diminished survival rates in cancer patients across different cancer types. Integrated machine learning algorithms showed that among the 134 mutations reported for these 2 proteins, only 13 and 35 were classified as deleterious mutations in <i>RAF1</i> and <i>RAP1P</i>, respectively. Moreover, one mutation in RAF1 reported elevated levels of binding between <i>RAF1</i> and <i>RAP1P</i> while in <i>RAP1A</i>, 7 mutations were reported to increase the binding affinity. The high‐binding mutations, P34Q and V60F, were subjected to protein–protein coupling which confirmed the increase in the binding affinity. Wild‐type and mutant RAF1–RAP1P bound complexes were subjected to molecular simulation investigation, revealing enhanced structural stability, increased compactness, and stabilized residue fluctuations of the mutant systems in contrast to the wild‐type. In addition, hydrogen bonding analysis revealed a variation in the binding paradigm which further underscores the impact of these substitutions on the coupling of <i>RAF1</i> and <i>RAP1A</i>. Principal component analysis (PCA) and free energy landscape (FEL) evaluation further determined dynamical variations in the wild‐type and mutant complexes. Finally, the Gibbs free energy for each complex was estimated and found to be −71.94 ± 0.38 kcal/mol for the wild‐type, −95.57 ± 0.37 kcal/mol for the V60F, and −85.76 ± 0.72 kcal/mol for P34Q complex. These findings confirm the effect of these variants on increasing the binding affinity of RAF1 to RAP1P. These mutations can therefore be targeted for cancer therapy to modulate the activity of the MAPK/ERK signaling pathway.</p><h2>Other Information</h2><p dir="ltr">Published in: Proteins: Structure, Function, and Bioinformatics<br>License: <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">http://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1002/prot.26759" target="_blank">https://dx.doi.org/10.1002/prot.26759</a></p> |
| eu_rights_str_mv | openAccess |
| id | Manara2_c2a72f3161523d75e0201282c01e8aa9 |
| identifier_str_mv | 10.1002/prot.26759 |
| network_acronym_str | Manara2 |
| network_name_str | Manara2 |
| oai_identifier_str | oai:figshare.com:article/30234403 |
| publishDate | 2024 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Exploring the Dynamic Interplay of Deleterious Variants on the RAF1–RAP1A Binding in Cancer: Conformational Analysis, Binding Free Energy, and Essential DynamicsAbbas Khan (5141000)Syed Shujait Ali (5159288)Muhammad Ammar Zahid (18123775)Shahenda Salah Abdelsalam (22330768)Noorah Albekairi (22330771)Raed M. Al‐Zoubi (21348629)Mohanad Shkoor (3768385)Dong‐Qing Wei (22330774)Abdelali Agouni (181926)Biological sciencesBioinformatics and computational biologyBiomedical and clinical sciencesOncology and carcinogenesisbinding free energycancerdockingMAPKmutationsRAF1simulation<p dir="ltr">The RAF1–RAP1A interaction activates the MAPK/ERK pathway which is very crucial in the carcinogenesis process. This protein complex influences tumor formation, proliferation, and metastasis. Understanding aberrant interactions driven by clinical mutations is vital for targeted therapies. Hence, the current study focuses on the screening of clinically reported substitutions in the <i>RAF1</i> and <i>RAP1A</i> genes using predictive algorithms integrated with all‐atoms simulation, essential dynamics, and binding free energy methods. Survival analysis results revealed a strong association between <i>RAF1</i> and <i>RAP1A</i> expression levels and diminished survival rates in cancer patients across different cancer types. Integrated machine learning algorithms showed that among the 134 mutations reported for these 2 proteins, only 13 and 35 were classified as deleterious mutations in <i>RAF1</i> and <i>RAP1P</i>, respectively. Moreover, one mutation in RAF1 reported elevated levels of binding between <i>RAF1</i> and <i>RAP1P</i> while in <i>RAP1A</i>, 7 mutations were reported to increase the binding affinity. The high‐binding mutations, P34Q and V60F, were subjected to protein–protein coupling which confirmed the increase in the binding affinity. Wild‐type and mutant RAF1–RAP1P bound complexes were subjected to molecular simulation investigation, revealing enhanced structural stability, increased compactness, and stabilized residue fluctuations of the mutant systems in contrast to the wild‐type. In addition, hydrogen bonding analysis revealed a variation in the binding paradigm which further underscores the impact of these substitutions on the coupling of <i>RAF1</i> and <i>RAP1A</i>. Principal component analysis (PCA) and free energy landscape (FEL) evaluation further determined dynamical variations in the wild‐type and mutant complexes. Finally, the Gibbs free energy for each complex was estimated and found to be −71.94 ± 0.38 kcal/mol for the wild‐type, −95.57 ± 0.37 kcal/mol for the V60F, and −85.76 ± 0.72 kcal/mol for P34Q complex. These findings confirm the effect of these variants on increasing the binding affinity of RAF1 to RAP1P. These mutations can therefore be targeted for cancer therapy to modulate the activity of the MAPK/ERK signaling pathway.</p><h2>Other Information</h2><p dir="ltr">Published in: Proteins: Structure, Function, and Bioinformatics<br>License: <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">http://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1002/prot.26759" target="_blank">https://dx.doi.org/10.1002/prot.26759</a></p>2024-11-01T00:00:00ZTextJournal contributioninfo:eu-repo/semantics/publishedVersiontextcontribution to journal10.1002/prot.26759https://figshare.com/articles/journal_contribution/Exploring_the_Dynamic_Interplay_of_Deleterious_Variants_on_the_RAF1_RAP1A_Binding_in_Cancer_Conformational_Analysis_Binding_Free_Energy_and_Essential_Dynamics/30234403CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/302344032024-11-01T00:00:00Z |
| spellingShingle | Exploring the Dynamic Interplay of Deleterious Variants on the RAF1–RAP1A Binding in Cancer: Conformational Analysis, Binding Free Energy, and Essential Dynamics Abbas Khan (5141000) Biological sciences Bioinformatics and computational biology Biomedical and clinical sciences Oncology and carcinogenesis binding free energy cancer docking MAPK mutations RAF1 simulation |
| status_str | publishedVersion |
| title | Exploring the Dynamic Interplay of Deleterious Variants on the RAF1–RAP1A Binding in Cancer: Conformational Analysis, Binding Free Energy, and Essential Dynamics |
| title_full | Exploring the Dynamic Interplay of Deleterious Variants on the RAF1–RAP1A Binding in Cancer: Conformational Analysis, Binding Free Energy, and Essential Dynamics |
| title_fullStr | Exploring the Dynamic Interplay of Deleterious Variants on the RAF1–RAP1A Binding in Cancer: Conformational Analysis, Binding Free Energy, and Essential Dynamics |
| title_full_unstemmed | Exploring the Dynamic Interplay of Deleterious Variants on the RAF1–RAP1A Binding in Cancer: Conformational Analysis, Binding Free Energy, and Essential Dynamics |
| title_short | Exploring the Dynamic Interplay of Deleterious Variants on the RAF1–RAP1A Binding in Cancer: Conformational Analysis, Binding Free Energy, and Essential Dynamics |
| title_sort | Exploring the Dynamic Interplay of Deleterious Variants on the RAF1–RAP1A Binding in Cancer: Conformational Analysis, Binding Free Energy, and Essential Dynamics |
| topic | Biological sciences Bioinformatics and computational biology Biomedical and clinical sciences Oncology and carcinogenesis binding free energy cancer docking MAPK mutations RAF1 simulation |