Conformational Dynamics of Lysine Methyltransferase Smyd2. Insights into the Different Substrate Crevice Characteristics of Symd2 and Symd3

Abstract: Smyd2, the SET and MYND domain containing proteinlysine methyltransferase, targets histone and nonhistone substrates.Methylation of nonhistone substrates has direct implications in cancerdevelopment and progression. Dynamic regulation of Smyd2 activityand the structural basis of broad substrate specificity still remain elusive.Herein, we report on extensive molecular dynamics simulations on a fulllength Smyd2 in the presence and absence of AdoMet cofactor(covering together 1.3 μs of sampling), and the accompanyingconformational transitions. Additionally, dynamics of the C-terminaldomain (CTD) and structural features of substrate crevices of Smyd2 and Smyd3 are compared. The CTD of Smyd2 exhibitsconformational flexibility in both states. In the holo form, however, it undergoes larger hinge motions resulting in more openedconfigurations than the apo form, which is confined around the partially open starting X-ray configuration. AdoMet bindingtriggers increased elasticity of the CTD leading Smyd2 to adopt fully opened configurations, which completely exposes thesubstrate binding crevice. These long-range concerted motions highlight Smyd2’s ability to target substrates of varying sizes.Substrate crevices of Smyd2 and Smyd3 show distinct features in terms of spatial, hydration, and electrostatic properties thatemphasize their characteristic modes of substrates interaction and entry pathways for inhibitor binding. On the whole, our studyshows how the elasticity and hinge motion of the CTD regulate its functional role and underpin the basis of broad substratespecificity of Smyd2. We also highlight the specific structural principles that guide substrate and inhibitor binding to Smyd2 andSmyd3