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Projects / Programmes source: ARIS

Atomistic Insights into the mechanism of the Spliceosome Machinery: Multiscale molecular dynamics simulations revealing the details of gene snip and stitch

Research activity

Code Science Field Subfield
1.04.00  Natural sciences and mathematics  Chemistry   

Code Science Field
P003  Natural sciences and mathematics  Chemistry 

Code Science Field
1.04  Natural Sciences  Chemical sciences 
Keywords
Spliceosome, molecular simulations, metadynamics, spliceosomal inhibitors
Evaluation (rules)
source: COBISS
Researchers (1)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  35380  PhD Jure Borišek  Chemistry  Head  2019 - 2021  58 
Organisations (1)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0104  National Institute of Chemistry  Ljubljana  5051592000  21,475 
Abstract
After decades of research efforts, the spliceosome (SPL) biology is undergoing a revolutionary phase due to increasing number of the cryo-electron microscopy (cryo-EM) structures at near-atomistic resolution from yeast and human SPL that have appeared in the last few years. The presence of non-coding sequences (introns) in nascent RNA transcripts is a hallmark of the genomes of all organisms. Introns have to be removed before protein translation occurs. The SPL, a macromolecular machinery composed of 5 small nuclear RNAs and hundreds of proteins, carries out intron removal (i.e. splicing) in eukaryotes. SPL catalyzes splicing in two subsequent reactions, mediated by two Mg2+ ions, undergoing a series of compositional and conformational changes. From the number of high impact factor papers appeared in the last few years it is strikingly clear that the structural biology of the SPL is undergoing a transformative phase and that the field of molecular simulation is mature enough to provide microscopic insights into the mechanism of such key biological machine. However, the main challenge remains to fully elucidate how introns of pre-mRNA are recognized and cleaved with single nucleotide precision, how the proteins interacting with snRNAs modulate splicing, and the mechanistic details of the two splicing reactions. The results of this project obtained by state-of-the-art molecular simulations will complement the current lack of knowledge in the SPL mechanism by: (i) refining the selected structures solved by cryo-EM at near atomic resolution; (ii) obtaining novel structural intermediates, (iii) elucidating the chemical mechanism of splicing, (iv) enlightening the mechanism of intron recognition at atomic-level, (v) rationalizing the impact of already mapped carcinogenic mutations on the structural and dynamical properties of the SPL, (vi) unveiling the molecular basis for the action of SPL small molecule modulators and predict their effects on SPL isoforms. To achieve aforementioned objectives, I will employ state-of-the-art molecular simulations methods ranging from molecular docking, to classical molecular dynamics simulations and quantum-classical (QM/MM) dynamics simulations, in combination with enhanced sampling methods. Mechanistic predictions obtained from molecular simulations will be validated with experimental data (binding assays and mutational studies). This knowledge can inspire future biochemical, biophysical, and genetic experiments aimed at unraveling the fundamental properties of this ancient regulator of gene expression. Besides understanding the SPL structural and functional biology, my study can provide information to be employed for implementing new biomedical strategies and treatments targeting RNA splicing, with the potential of impacting both basic and applied sciences.
Significance for science
Understanding the mechanism of splicing is of utmost microbiological, biotechnological, and pharmacological importance. Indeed, aberrant splicing is associated to numerous complex diseases (cancer and neurodegeneration). Besides contributing to the fundamental understanding of the SPL structural and functional biology, my study will also provide valuable information to harness splicing for revolutionary gene modulation tools and novel therapeutic approaches, with the potential of impacting both basic and applied sciences. This is highly interdisciplinary project as it is crossings the fields of medicinal chemistry, computational biology, molecular biology, cancer biology, and biotechnology, and can contribute to fundamentally impact the medicine and biotechnology fields.
Significance for the country
Understanding the mechanism of splicing is of utmost microbiological, biotechnological, and pharmacological importance. Indeed, aberrant splicing is associated to numerous complex diseases (cancer and neurodegeneration). Besides contributing to the fundamental understanding of the SPL structural and functional biology, my study will also provide valuable information to harness splicing for revolutionary gene modulation tools and novel therapeutic approaches, with the potential of impacting both basic and applied sciences. This is highly interdisciplinary project as it is crossings the fields of medicinal chemistry, computational biology, molecular biology, cancer biology, and biotechnology, and can contribute to fundamentally impact the medicine and biotechnology fields.
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