Native conformational dynamics of the spliceosomal U1A protein

Irisbel Guzman, Zhaleh Ghaemi, Anne Baranger, Zaida Luthey-Schulten, Martin Gruebele

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)3651-3661
Number of pages11
JournalJournal of Physical Chemistry B
Issue number9
StatePublished - Mar 5 2015

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry


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