Molecular mechanism of regulation of RhoA GTPase by phosphorylation of RhoGDI

Krishnendu Sinha, Amit Kumawat, Hyunbum Jang, Ruth Nussinov*, Suman Chakrabarty*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Rho-specific guanine nucleotide dissociation inhibitors (RhoGDIs) play a crucial role in the regulation of Rho family GTPases. They act as negative regulators that prevent the activation of Rho GTPases by forming complexes with the inactive GDP-bound state of GTPase. Release of Rho GTPase from the RhoGDI-bound complex is necessary for Rho GTPase activation. Biochemical studies provide evidence of a “phosphorylation code,” where phosphorylation of some specific residues of RhoGDI selectively releases its GTPase partner (RhoA, Rac1, Cdc42, etc.). This work attempts to understand the molecular mechanism behind this specific phosphorylation-induced reduction in binding affinity. Using several microseconds long atomistic molecular dynamics simulations of the wild-type and phosphorylated states of the RhoA-RhoGDI complex, we propose a molecular-interaction-based mechanistic model for the dissociation of the complex. Phosphorylation induces major structural changes, particularly in the positively charged polybasic region (PBR) of RhoA and the negatively charged N-terminal region of RhoGDI that contribute most to the binding affinity. Molecular mechanics Poisson-Boltzmann surface area binding energy calculations show a significant weakening of interaction on phosphorylation at the RhoA-specific site of RhoGDI. In contrast, phosphorylation at a Rac1-specific site does not affect the overall binding affinity significantly, which confirms the presence of a phosphorylation code. RhoA-specific phosphorylation leads to a reduction in the number of contacts between the PBR of RhoA and the N-terminal region of RhoGDI, which manifests a reduction of the binding affinity. Using hydrogen bond occupancy analysis and energetic perturbation network, we propose a mechanistic model for the allosteric response, i.e., long-range signal propagation from the site of phosphorylation to the PBR and buried geranylgeranyl group in the form of rearrangement and rewiring of hydrogen bonds and salt bridges. Our results highlight the crucial role of specific electrostatic interactions in manifestation of the phosphorylation code.

Original languageEnglish
Pages (from-to)57-67
Number of pages11
JournalBiophysical Journal
Volume123
Issue number1
DOIs
StatePublished - 2 Jan 2024

Funding

FundersFunder number
Technical Research Centre
National Institutes of HealthHHSN261201500003I
U.S. Department of Health and Human Services
National Cancer Institute
Government of South Australia
Center for Cancer Research
Department of Science and Technology, Ministry of Science and Technology, India
Science and Engineering Research BoardECR/2018/002903

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