Dynamics and Mechanism of CRISPR systems


CRISPR-Cas9 is a revolutionary genome editing tool, which enables to easily manipulate nucleic acids. In 2016, we have published the first computational investigations of CRISPR-Cas9, starting large-scale simulations of these genome editing systems.

Our lab uses computational methods to unravel the function and improve biological applications of CRISPR genome editing machineries. So far, we described a mechanism for RNA binding and the association with the nucleic acids, and we delivered also molecular details on the off-target effects. We revealed an intriguing mechanism of allosteric regulation and the activation process of the HNH domain. We also established the atomic level details of the catalysis, a fundamental step for the editing of the genome. More research is yet to come! 


[1] Caslino et al. Accepted ACS Catal. 2020. [2] Saha et al. Accepted JCIM 2020. [3] Nierzwicki et al. WIREs Comp Mol Sci Accepted 2020. [4] East K. et al. J. Am. Chem. Soc. 2020. [5] Palermo G. J. Chem. Inf. Model. 2019. [6] Ricci C. G. et al. ACS Cent. Sci. 2019. [7] Palermo G. Chem 2019. [8] Palermo G. et al. Q. Rev. Biophys. 2018. [9] Palermo G. et al. J. Am. Chem. Soc. 2017. [10] Palermo G. et al. Proc. Natl. Acad. Sci. USA, 2017. [11] Palermo G. et al. ACS Cent. Sci. 2016.

Read about the invisible dance of CRISPR-Cas9 in Physics Today         

Nucleosome dynamics & chromatin drug development


The constituents of chromatin, chromosomal DNA and histone proteins, are key molecular targets for anticancer drugs. By integrating molecular dynamics with X-ray crystallography and biochemical assays, we have characterized the mechanism of action of promising metal-based anticancer agents at the level of the nucleosome core particle, the fundamental unit of chromatin. 


[1] Adhrikenesan Z. et al. Nat. Commun. 2017. [2] Ma Z. et al. Angew. Chem. Int. Ed. 2016 [3] Palermo G. et al. ChemMedChem 2016 

Non-coding RNA & splicing


RNA is a fundamental molecule that controls gene expression, playing a key regulation role in vital processes and diseases. We are interested in the molecular basis of non-coding RNA, which regulates gene expression via a variety of yet unknown mechanisms. We have suggested a mechanism for the splicing reaction in the bacterial groupII intron, and studied the functional dynamics of the human splicesome.


[1] Palermo G. et al. J. Struct. Biol. 2019. [2] Palermo G. et al. J. Chem. Theory Comput. 2013. [3] Casalino L. et al. Proc. Natl. Acad. Sci. USA 2018. [4] Casalino L. et al. J. Am. Chem. Soc. 2016. [5] Casalino L. et al. J. Chem. Theory Comput. 2017.

Catalytic Metals and Enzymatic Processing of DNA & RNA

As originally revealed by Steitz & Steitz (PNAS 1993, 90), DNA/RNA endonucleases perform phosphodiester bond cleavage via a two-metal-ion aided mechanism. We use computational methods to clarify the two-metal aided mechanism in several endonucleases. 


Read more: Acc. Chem. Res. 201548, pp 220–228
J. Chem. Theory Comput. 2013, 9, pp 857–862


Extraordinary developments of cryo-EM detectors are providing unprecedented description of biomolecules in their native environment.  While cryoEM is now reaching atomic level resolution,  the electron density maps often result not homogeneous, displaying regions of low density that hamper an ultimate characterization. We are developing a quantum-based method for cryo-EM refinement of metal centers in biomolecules, which will help the structural determination of metal centers. Our approach combines metadynamics and cryo-EM fitting approaches to define the energetics for the metal binding, as well as their position and nature. 


[1] Caslino et al. Accepted ACS Catal. 2020. [2] Palermo G. et al. Acc. Chem. Res. 2015