Ras Isoforms Conformational Clustering and Community Networks Studies: Simulating Ras with Accelerated Molecular Dynamics

Abstract

Ras is a small GTPase that acts as a molecular switch and is involved in multiple cellular signaling pathways. The catalytic domains of the three major isoforms, H‐, K‐, and N‐Ras share an identical effector lobe, and 90% sequence identity in their allosteric lobe. Ras isoforms have been shown experimentally to exhibit functional specificity yet they display very similar three‐dimensional structures. In this study, we used accelerated Molecular Dynamics (aMD) to characterize the isoform‐dependent conformations of Ras. The aMD method enhances conformational sampling by reducing the energetic barriers between states of a system. Our results demonstrate a unique cluster of conformations between Ras isoforms. Additionally, we used community network analysis to probe the communication network between the effector and allosteric lobes across the three isoforms. We found that H‐ and K‐Ras share similar sets of community networks, whereas N‐Ras exhibits a unique set of community networks. These data on conformational clustering and community networks in Ras isoforms advance our understanding of the structural biology behind their functional specificity.