Raf promotes dimerization of the Ras G-domain with increased allosteric connections

Ras dimerization is critical for Raf activation. Here we show that the Ras binding domain of Raf (Raf-RBD) induces robust Ras dimerization at low surface densities on supported lipid bilayers and, to a lesser extent, in solution as observed by size exclusion chromatography and confirmed by SAXS. Community network analysis based on molecular dynamics simulations shows robust allosteric connections linking the two Raf-RBD D113 residues located in the Galectin scaffold protein binding site of each Raf-RBD molecule and 85 Å apart on opposite ends of the dimer complex. Our results suggest that Raf-RBD binding and Ras dimerization are concerted events that lead to a high-affinity signaling complex at the membrane that we propose is an essential unit in the macromolecular assembly of higher order Ras/Raf/Galectin complexes important for signaling through the Ras/Raf/MEK/ERK pathway.

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Raf promotes dimerization of the Ras G-domain with increased allosteric connections

10.1101/2020.07.15.205070 ◽

2020 ◽

Author(s):

Morgan Packer ◽

Jillian A. Parker ◽

Jean K. Chung ◽

Zhenlu Li ◽

Young Kwang Lee ◽

...

Keyword(s):

Molecular Dynamics ◽

Lipid Bilayers ◽

Md Simulations ◽

Size Exclusion ◽

Supported Lipid Bilayers ◽

Erk Pathway ◽

Signaling Complex ◽

Macromolecular Assembly ◽

High Affinity ◽

Exclusion Chromatography

AbstractRas dimerization is critical for Raf activation, yet Ras alone does not dimerize. Here we show that the Ras binding domain of Raf (Raf-RBD) induces robust Ras dimerization at low surface densities on supported lipid bilayers and, to a lesser extent, in solution as observed by size exclusion chromatography and confirmed by SAXS. Community network analysis based on molecular dynamics (MD) simulations show robust allosteric connections linking the two Raf-RBD D113 residues, located in the Galectin scaffold protein binding site of each Raf-RBD molecule and 85 Å apart on opposite ends of the dimer complex. Our results suggest that Raf-RBD binding and Ras dimerization are concerted events that lead to a high-affinity signaling complex at the membrane that we propose is an essential unit in the macromolecular assembly of higher order Ras/Raf/Galectin complexes important for signaling through the Ras/Raf/MEK/ERK pathway.

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Phase behavior of supported lipid bilayers: A systematic study by coarse-grained molecular dynamics simulations

The Journal of Chemical Physics ◽

10.1063/1.4981008 ◽

2017 ◽

Vol 146 (15) ◽

pp. 154902 ◽

Cited By ~ 5

Author(s):

Asma Poursoroush ◽

Maria Maddalena Sperotto ◽

Mohamed Laradji

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Phase Behavior ◽

Lipid Bilayers ◽

Systematic Study ◽

Coarse Grained ◽

Supported Lipid Bilayers ◽

Dynamics Simulations ◽

Coarse Grained Molecular Dynamics

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Faculty Opinions recommendation of Understanding the Hofmeister effect in interactions between chaotropic anions and lipid bilayers: molecular dynamics simulations.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1014605.194151 ◽

2003 ◽

Author(s):

Bradley Smith

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Lipid Bilayers ◽

Hofmeister Effect ◽

Chaotropic Anions ◽

Dynamics Simulations

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Molecular Dynamics Simulations of Human Islet Amyloid Polypeptide (IAPP) Oligomers and their Interactions with Lipid Bilayers

Biophysical Journal ◽

10.1016/j.bpj.2010.12.1308 ◽

2011 ◽

Vol 100 (3) ◽

pp. 200a-201a ◽

Cited By ~ 2

Author(s):

Jun Zhao ◽

Xiang Yu ◽

Chao Zhao ◽

Qiuming Wang ◽

Jie Zheng

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Lipid Bilayers ◽

Islet Amyloid Polypeptide ◽

Human Islet ◽

Islet Amyloid ◽

Human Islet Amyloid Polypeptide ◽

Dynamics Simulations

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Computational Design of Macrocyclic Binders of S100B(ββ): Novel Peptide Theranostics

Molecules ◽

10.3390/molecules26030721 ◽

2021 ◽

Vol 26 (3) ◽

pp. 721

Author(s):

Srinivasaraghavan Kannan ◽

Pietro G. A. Aronica ◽

Thanh Binh Nguyen ◽

Jianguo Li ◽

Chandra S. Verma

Keyword(s):

Molecular Dynamics ◽

Computational Design ◽

Diagnostic Tools ◽

Stapled Peptides ◽

Altered Expression ◽

Cellular Processes ◽

High Affinity ◽

Limited Success ◽

Dynamics Simulations ◽

Partner Proteins

S100B(ββ) proteins are a family of multifunctional proteins that are present in several tissues and regulate a wide variety of cellular processes. Their altered expression levels have been associated with several human diseases, such as cancer, inflammatory disorders and neurodegenerative conditions, and hence are of interest as a therapeutic target and a biomarker. Small molecule inhibitors of S100B(ββ) have achieved limited success. Guided by the wealth of available experimental structures of S100B(ββ) in complex with diverse peptides from various protein interacting partners, we combine comparative structural analysis and molecular dynamics simulations to design a series of peptides and their analogues (stapled) as S100B(ββ) binders. The stapled peptides were subject to in silico mutagenesis experiments, resulting in optimized analogues that are predicted to bind to S100B(ββ) with high affinity, and were also modified with imaging agents to serve as diagnostic tools. These stapled peptides can serve as theranostics, which can be used to not only diagnose the levels of S100B(ββ) but also to disrupt the interactions of S100B(ββ) with partner proteins which drive disease progression, thus serving as novel therapeutics.

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