Exploring the Dynamic Interplay of Deleterious Variants on the RAF1 - RAP1A Binding in Cancer - Research Article

Sep 21, 2026

RAF1–RAP1A interaction drives the MAPK/ERK signaling pathway that is central to carcinogenesis and strongly influences tumor formation, proliferation, and metastasis. Using predictive algorithms with all-atoms simulation, essential dynamics, and binding free energy methods, the study screens clinical substitutions in RAF1 and RAP1A and links expression levels with survival across cancer types. Among 134 reported mutations, only 13 (RAF1) and 35 (RAP1A) are classified as deleterious. Binding analyses, coupled protein–protein modeling, molecular simulations, hydrogen bonding, PCA, FEL evaluation, and Gibbs free energy estimates support increased binding affinity for specific high-binding variants including V60F and P34Q.

LanguageEnglish

CategoryResearch & Report

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Pages18

Reading Time45 min

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Abstract

Introduction

Proteins: Structure, Function, and Bioinformatics RESEARCH ARTICLE OPEN ACCESS Exploring the Dynamic Interplay of Deleterious Variantson the RAF1–RAP1A Binding in Cancer: Conformational Analysis, Binding Free Energy, and Essential Dynamics Abbas Khan1 | Syed Shujait Ali2 | Muhammad Ammar Zahid1 | Shahenda Salah Abdelsalam1 | Noorah Albekairi3 | Raed M. Al-Zoubi4,5,6 | Mohanad Shkoor7 | Dong-Qing Wei8 | Abdelali Agouni1 1Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha, Qatar | 2Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan | 3College of Pharmacy, King Saud University, Riyadh, Saudi Arabia | 4Surgical Research Section, Department of Surgery, Hamad Medical Corporation, Doha, Qatar | 5Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar | 6Department of Chemistry, Jordan University of Science and Technology, Irbid, Jordan | 7Department of Chemistry, College of Arts and Science, Qatar University, Doha, Qatar | 8Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China Correspondence: Dong-Qing Wei ([dqwei@sjtu.edu.cn](dqwei@sjtu.edu.cn)) | Abdelali Agouni ([aagouni@qu.edu.qa](aagouni@qu.edu.qa)) Received: 5 July 2024 | Revised: 17 September 2024 | Accepted: 18 October 2024 Funding: This study was supported by Qatar National Research Fund (Grant ARG01-0601-230451); Hamad Medical Corporation (Grant MRC-01-22-414); Qatar University (Grant QUPD-CPH-23/24-592); and Researchers Supporting Project (Grant RSPD2024R1035) from King Saud University. Open Access funding provided by the Qatar National Library. Keywords: binding free energy | cancer | docking | MAPK | mutations | RAF1 | simulation ABSTRACT 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 RAF1 and RAP1A genes using predictive algorithms integrated with all-atoms simulation, essential dynamics, and binding free energy methods. Survival analysis results revealed a strong association between RAF1 and RAP1A 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 RAF1 and RAP1P, respectively. Moreover, one mutation in RAF1 reported elevated levels of binding between RAF1 and RAP1P while in RAP1A, 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 RAF1 and RAP1A. 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 tobe −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 cance

FAQs

What biological pathway does the RAF1–RAP1A interaction regulate in cancer?

It activates the MAPK/ERK pathway, which plays a crucial role in carcinogenesis, including tumor formation, proliferation, and metastasis.

How were clinically reported mutations in RAF1 and RAP1A analyzed?

The study screened substitutions using predictive algorithms integrated with all-atom simulation, essential dynamics, and binding free energy methods.

Which mutations were highlighted as high-binding variants, and what was the evidence?

High-binding mutations such as P34Q and V60F were examined via protein–protein coupling and molecular simulations, with additional support from hydrogen bonding analysis, PCA/FEL evaluation, and Gibbs free energy estimates.

Sep 21, 2026

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