title: Native conformational dynamics of the spliceosomal U1A protein.
abstract: The complex of spliceosomal U1A protein and its cognate SL2 RNA is a prototype system for protein-RNA binding studies. A major question is whether U1A protein alone is capable of undergoing conformational dynamics similar to structural rearrangements upon RNA binding. Using a fast temperature jump and tryptophan fluorescence detection, we uncover a ∼20 μs conformational transition for the Lys22Gln/Phe56Trp-only mutant of U1A, yet a Phe56Trp-only control mutant does not show the transition. To explain this observation, we performed extensive molecular dynamics (MD) simulations. The simulations explain why only the Lys22Gln/Phe56Trp-only mutant shows a fluorescence signal: in the other mutant, the tryptophan probe is not quenched upon structural rearrangement. The simulations support helix C movement as the underlying structural rearrangement, although the simulated time scale is faster than experimentally detected. On the basis of our MD results, we propose a reversible two-pathway three-state transition for the helix C movement and assign T-jump kinetics to a closed to semi-closed transition of the helix. Our result provides a specific example of how alternative protein conformations on the native side of the folding barrier can be functionally important, for example in conformational selection by a binding partner.
authors: Department of Biochemistry, and ‡Department of Chemistry, Department of Physics, Center for the Physics of Living Cells, and Center for Biophysics and Quantitative Biology, University of Illinois , Urbana, Illinois 61801, United States.
authors: Irisbel
authors: I
authors: Guzman
authors: Zhaleh
authors: Z
authors: Ghaemi
authors: Anne
authors: A
authors: Baranger
authors: Zaida
authors: Z
authors: Luthey-Schulten
authors: Martin
authors: M
authors: Gruebele
mesh_terms: D000595:Amino Acid Sequence; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009154:Mutation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017412:Ribonucleoprotein, U1 Small Nuclear / Q000737:chemistry* / Q000235:genetics; D013696:Temperature
chemical_list: D017412:Ribonucleoprotein, U1 Small Nuclear; C075339:U1A protein