Giulia Palermo


Giulia Palermo
Department of Bioengineering,
University of California, Riverside


The Palermo research group is focused on the development and applications of molecular dynamics simulations and mixed quantum mechanics/molecular mechanics (QM/MM) methods to study the molecular basis of gene regulation, chromatin structure and dynamics, enzymatic function and ribozyme catalysis. The lab expertise also includes emerging cryo-electron microscopy (cryo-EM) processing methods. Major accomplishments concern the study of the mechanism of action of the CRISPR-Cas9 system, allosteric pathways, catalytic mechanisms in DNA/RNA processing enzymes, membrane proteins and chromatin structures. The lab works in close collaboration with experimental scientists, providing validation to computations.

Giulia Palermo is a native of Italy where she earned her PhD in 2013 from the Italian Institute of Technology. She has been an early post-doctoral scientist in the group of Prof. Ursula Rothlisberger at the Swiss Federal Institute of Technology (EPFL), where she earned expertise in ab-initio Molecular Dynamics. In 2016, she has been awarded a Swiss National Science Foundation (NSF) post-doctoral fellowship to join the group of Prof. J. Andrew McCammon at the University of California San Diego, where she specialised in novel multiscale methods enabling the study of increasingly realistic biological systems.

Selected Publications:

1. C. G. Ricci, J. S. Chen, Y. Miao, M. Jinek, J. A. Doudna, J. A. McCammon and G. Palermo.† Deciphering Off-target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics. ACS Cent. Sci. 2019, in press

2. L. Casalino, G. Palermo, A. Spinello, U. Rothlisberger and A. Magistrato. All-Atom Simulations Disentangle the Functional Dynamics Underlying Gene Maturation in the Intron Lariat Spliceosome. Proc. Natl. Acad. Sci. USA 2018, 115, 6584-6589.

3. G. Palermo,† C. G. Ricci, A. Fernando, R. Basak, M. Jinek, I. Rivalta, V. S. Batista and J. A. McCammon PAM-induced allostery activates CRISPR-Cas9. J. Am. Chem. Soc. 2017, 139, 16028–16031. Journal Cover Art. Featured in the JACS 2018 Young Investigators Virtual Issue.

4. G. Palermo, Y. Miao, R. C. Walker, M. Jinek and J. A. McCammon. CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations. Proc. Natl. Acad. Sci. USA. 2017, 114, 7260–7265.

5. L. Casalino, G. Palermo, U. Rothlisberger and A. Magistrato. Who Activates the Nucleophile in Ribozyme Catalysis? An Answer from the Splicing Mechanism of Group II Introns. J. Am. Chem. Soc. 2016, 138, 10374–10377. Journal Cover Art.

6. G. Palermo, A. Cavalli, M. L. Klein, M. Alfonso Prieto, M. Dal Peraro and M. De Vivo. Catalytic metal ions and enzymatic processing of DNA and RNA. Acc. Chem. Res. 2015, 48, 220–228.