Yi Xue Ph.D.

School of Life Sciences PI

Main Research Fields

Our primary research interests are focused on characterizing structure and dynamics

of non-coding RNAs and intrinsically disordered proteins using solution NMR

spectroscopy and computational approaches such as MD simulations. We aim to

develop novel NMR techniques, labeling methods, and computational tools to study

three-dimensional structure and conformational switch of large non-coding RNAs

and ribonucleoproteins, which pose a significant challenge to existing methods.

We are also interested in reconstructing conformational motion of highly flexible

biomolecules, as well as ensemble-based virtual drug screening.

Selected Publications

1. Xue Y, Gracia B, Herschlag D, Russell R, Al-Hashimi HM. (2016) Visualizing formation of an RNA folding intermediate through a fast highly modular secondary structure switch. Nature Communications, 7:11768.

2. Ren A, Xue Y, Peselis A, Serganov A, Al-Hashimi HM, Patel DJ. (2015) Structural and dynamic basis for low-affinity, high-selectivity binding of L-glutamine by the glutamine riboswitch. Cell Reports, 13(9):1800-13.

3. Ma P, Xue Y, Coquelle N, Haller JD, Yuwen T, Ayala I, Mikhailovskii O, Willbold D, Colletier JP, Skrynnikov NR, Schanda P. (2015) Observing the overall rocking motion of a protein in a crystal. Nature Communications, 6:8361.

4. Xue Y, Yuwen T, Zhu F, Skrynnikov NR. (2014) Role of electrostatic interactions in binding of peptides and intrinsically disordered proteins to their folded targets. 1. NMR and MD characterization of the complex between the c-Crk N-SH3 domain and the peptide Sos. Biochemistry, 53 (41): 6473–6495.

5. Xue Y, Ward JM, Yuwen T, Podkorytov IS, Skrynnikov NR. (2012) Microsecond time-scale conformational exchange in proteins: using long molecular dynamics trajectory to simulate NMR relaxation dispersion data. J Am Chem Soc, 134 (5):2555–2562.

6. Xue Y, Skrynnikov NR. (2011) Motion of a disordered polypeptide chain as studied by paramagnetic relaxation enhancements, 15N relaxation, and molecular dynamics simulations: how fast is segmental diffusion in denatured ubiquitin? J Am Chem Soc, 133 (37): 14614–14628.