Unveiling the Dynamics of KRAS4b on Lipid Model Membranes

Cesar A López,Animesh Agarwal,Andrew G Stephen,Que N Van,S Gnanakaran

doi:10.1007/s00232-021-00176-z

Abstract

Small GTPase proteins are ubiquitous and responsible for regulating several processes related to cell growth and differentiation. Mutations that stabilize their active state can lead to uncontrolled cell proliferation and cancer. Although these proteins are well characterized at the cellular scale, the molecular mechanisms governing their functions are still poorly understood. In addition, there is limited information about the regulatory function of the cell membrane which supports their activity. Thus, we have studied the dynamics and conformations of the farnesylated KRAS4b in various membrane model systems, ranging from binary fluid mixtures to heterogeneous raft mimics. Our approach combines long time-scale coarse-grained (CG) simulations and Markov state models to dissect the membrane-supported dynamics of KRAS4b. Our simulations reveal that protein dynamics is mainly modulated by the presence of anionic lipids and to some extent by the nucleotide state (activation) of the protein. In addition, our results suggest that both the farnesyl and the polybasic hypervariable region (HVR) are responsible for its preferential partitioning within the liquid-disordered (Ld) domains in membranes, potentially enhancing the formation of membrane-driven signaling platforms.Graphic

Highlights

KRAS4b (Kirsten rat sarcoma viral oncogene homolog 4b) proteins are membrane-associated GTPases, responsible for regulating signaling pathways involved in cell growth and division (Hancock 2003; Hobbs et al 2016; Ntai et al 2018; Nussinov et al 2018)
Less is known about the conformational membranedependent orientations of KRAS4b and how its dynamics modulate the interaction with secondary effectors such as those involved in the Mitogen-activated protein kinase
Our initial studies focused on the effect of lipid membrane composition on the dynamics of KRAS4b

Summary

Introduction

KRAS4b (Kirsten rat sarcoma viral oncogene homolog 4b) proteins are membrane-associated GTPases, responsible for regulating signaling pathways involved in cell growth and division (Hancock 2003; Hobbs et al 2016; Ntai et al 2018; Nussinov et al 2018). Research has provided data that draws a mechanistic picture of KRAS4b function at the molecular level, including insights into its nucleotide exchange (Cromm et al 2015; Prakash and Gorfe 2014) coupled with conformational cycling between “active” and “inactive” states (Carvalho et al 2015) Such information has been relevant in understanding the phenotypic effects of oncogenic RAS gene mutations that lock the protein in the GTP-bound active state. Experimental data confirmed the presence of two main configurations; one parallel to the membrane in which helices 3, 4 and 5 enhance the association, and one orthogonal in which beta strands 1, 2 and 3 directly contact the membrane The latter occludes switch I of KRAS4b, potentially hiding the effector binding site (Fig. 1a right and left top panels)

Results

Discussion

Conclusion