SUNY at Albany
June 19-23, 2001
Structure and Dynamics of the Sm Binding Site From Human U4 snRNA.
Our laboratory recently reported an analysis of a 3 ns molecular dynamics (MD) simulation of the Sm binding site from human U4 snRNA (Guo et al., J. Bio Struct. Dyn. 18: 335-344). The MD simulation was conducted using AMBER 5.1 with long-range electrostatic forces considered using the particle mesh Ewald (PME) summation method. The RNA was fully-solvated (>9,000 water molecules), and charge neutralized by inclusion of potassium ions. The initial model of the Sm binding site region had the central and 3Õ stem-loops that flanked the Sm site co-axial with one another, and with the single-stranded Sm binding site region ([I] conformation). During the course of the trajectory, the axes of the 3Õ stem-loop, and later the central stem-loop, became roughly orthogonal from their original anti-parallel orientation. As these conformational changes occurred, the snRNA adopted first an [L] conformation, and finally a [U] conformation. The [U] conformation was more stable than either the [I] or [L] conformations, and persisted for the final 1 ns of the trajectory. Analysis of the structure resulting from the MD simulations revealed the bulged nucleotide, U114, and the mismatched A91-G110 base pair provided distinctive structural features that may enhance Sm protein binding. We have initiated high resolution NMR studies to determine the three dimensional structures of the 3Õ stem-loop and central stem-loop, and thermodynamic studies using temperature-dependent UV spectroscopy and isothermal titration calorimetry to evaluate the stabilities of the component stem-loops and entire Sm binding site of U4 snRNA. An update of our structural and thermodynamics studies will be presented.
William H. Gmeiner (1)*,Cui Wei (1), Jian-xin Guo (2), Luis Commoli (3), Nikolai B. Ulyanov (3), Thomas L. James (3), Ana Maria Soto (4), Luis A. Marky (4)
Department of Biochemistry (1), Wake Forest University School of Medicine, Winston-Salem, NC 27157; Camitro Corporation (2), 4040 Campbell Ave, Menlo Park, CA 94025, Department of Pharmaceutical Chemistry (3), University of California at San Francisco, (4) Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE.