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Molecular Dynamics Simulations and Dynamic Network Analysis Reveal the Allosteric Unbinding of Monobody to H-Ras
Duan Ni1, Kun Song2, Jian Zhang3
1Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China. niduan11@sjtu.edu.cn.
Abstract:
Ras proteins, as small GTPases, mediate cell proliferation, survival and differentiation. Ras mutations have been associated with a broad spectrum of human cancers and thus targeting Ras represents a potential way forward for cancer therapy. A recently reported monobody NS1 allosterically disrupts the Ras-mediated signaling pathway, but its efficacy is reduced by R135K mutation in H-Ras. However, the detailed mechanism is unresolved. Here, using molecular dynamics (MD) simulations and dynamic network analysis, we explored the molecular mechanism for the unbinding of NS1 to H-Ras and shed light on the underlying allosteric network in H-Ras. MD simulations revealed that the overall structures of the two complexes did not change significantly, but the H-Ras-NS1 interface underwent significant conformational alteration in the mutant Binding free energy analysis showed that NS1 binding was unfavored after R135K mutation, which resulted in the unfavorable binding of NS1. Furthermore, the critical residues on H-Ras responsible for the loss of binding of NS1 were identified. Importantly, the allosteric networks for these important residues were revealed, which yielded a novel insight into the allosteric regulatory mechanism of H-Ras.
Insights
Monobody NS1 disrupts Ras signaling but R135K mutation reduces efficacy. Molecular dynamics revealed altered interfaces and identified key residues and allosteric networks in H-Ras, explaining reduced NS1 binding in cancer therapy research.
Area of Science:
- Biochemistry
- Molecular Biology
- Structural Biology
Background:
- Ras proteins are small GTPases crucial for cell signaling, proliferation, survival, and differentiation.
- Mutations in Ras are implicated in various human cancers, making Ras a key therapeutic target.
- Monobody NS1 allosterically inhibits Ras-mediated signaling, but its effectiveness is diminished by the R135K mutation in H-Ras.
Purpose of the Study:
- To elucidate the molecular mechanism behind the reduced efficacy of monobody NS1 due to the R135K mutation in H-Ras.
- To investigate the allosteric network within H-Ras that influences NS1 binding.
- To identify critical residues responsible for the loss of NS1 binding.
Main Methods:
- Molecular Dynamics (MD) simulations were employed to analyze the H-Ras-NS1 complex.
- Dynamic network analysis was used to explore allosteric pathways.
- Binding free energy calculations were performed to quantify the effect of the mutation.
Main Results:
- MD simulations showed significant conformational changes at the H-Ras-NS1 interface despite overall structural stability.
- Binding free energy analysis indicated that the R135K mutation unfavors NS1 binding.
- Critical residues on H-Ras contributing to the loss of NS1 binding were identified, along with their associated allosteric networks.
Conclusions:
- The R135K mutation in H-Ras alters the protein-monobody interface, leading to reduced binding affinity of NS1.
- Understanding the allosteric network provides novel insights into the regulatory mechanisms of H-Ras.
- This research contributes to the development of targeted cancer therapies by explaining resistance mechanisms.
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