Conformational Dynamics of Lysine Methyltransferase Smyd2. Insights into the Different Substrate Crevice Characteristics of Smyd2 and Smyd3

Chandramouli, B; Chillemi, G (Cineca)

Smyd2, the SET and MYND domain containing protein lysine methyltransferase, targets histone and nonhistone substrates. Methylation of nonhistone substrates has direct implications in cancer development and progression. Dynamic regulation of Smyd2 activity and the structural basis of broad substrate specificity still remain elusive. Herein, we report on extensive molecular dynamics simulations on a full length Smyd2 in the presence and absence of AdoMet cofactor (covering together 1.3 mu s of sampling), and the accompanying conformational transitions. Additionally, dynamics of the C-terminal domain (CTD) and structural features of substrate crevices of Smyd2 and Smyd3 are compared. The CTD of Smyd2 exhibits conformational flexibility in both states. In the holo form, however, it undergoes larger hinge motions resulting in more opened configurations than the apo form, which is confined around the partially open starting X-ray configuration. AdoMet binding triggers increased elasticity of the CTD leading Smyd2 to adopt filmy opened configurations, which completely exposes the substrate 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 that emphasize their characteristic modes of substrates interaction and entry pathways for inhibitor binding. On the whole, our study shows how the elasticity and hinge motion of the CTD regulate its functional role and underpin the basis of broad substrate specificity of Smyd2. We also highlight the specific structural principles that guide substrate and inhibitor binding to Smyd2 and Smyd3.

JOURNAL OF CHEMICAL INFORMATION AND MODELING
Volume: 56
Issue: 12
Pages: 2467-2475
DOI: 10.1021/acs.jcim.6b00652
Published: DEC 2016