Ribosome Quality Control
Translation of mRNA by the ribosome results in the creation of greater than 99% of the proteins that make up all living organisms. Also there exist human ribosomal diseases called ribosomopathies that have deleterious effects on protein synthesis including protein misfolding, which have significant morbidity associated. This is an area of research Dr. Caulfield's lab is working on to better understand and help. Moreover, the unique differences in human and pathogenic microbes, such as bacteria, also may be exploited for differences in the ribosome structure allowing development of new antibiotics.
Additionally, Dr. Caulfield's lab will study ribosomes mechanisms and dynamics trajectories to better understand how diseases affected by frameshifting, mistranslation of protein and ribosome quality control (RQC) function. The lab uses advanced molecular-dynamics modeling in conjunction with cryogenic electron microscopy (cryo-EM) and experimentalists' labs to identify critical mechanisms that control the accuracy of protein translation by both prokaryotic (bacterial) and eukaryotic (human) ribosomes.
The Drug Discovery, Design, and Optimization for Novel Therapeutics Laboratory is using computational methods to generate novel trajectories that interconnect these hard-to-capture ribosomal substates from cryo-EM. Through a partnership with the protein engineering laboratory of Andrei A. Korostelev, Ph.D., at the RNA Therapeutics Institute in the Department of Biochemistry and Molecular Pharmacology at the University of Massachusetts Medical School, Dr. Caulfield's lab will be using computational toolkit items — MacroMolecularBuilder from the lab of Samuel Coulbourn Flores, Ph.D., at Stockholm University, Sweden, coupled with Maxwell's demon molecular dynamics and others — to determine putative pathways for human ribosomes captured during crucially important quality control steps of function.
But capturing all of these trajectories between substates is a challenge because this is among the largest macromolecular complexes with over 300,000 atoms not counting associated proteins and cofactors, which can easily exceed 3 million atoms in a solvate system. In addition, these ribosomes have a large therapeutic potential.
In other studies, Dr. Caulfield's team has used in silico docking screens coupled with high-throughput screening of large compound libraries to identify novel small-molecule inhibitors for pathogenic microbes such as malaria, which could be a new route for resistant strains of pathogens.
Further development of these small-molecule inhibitors for enhanced selectivity may generate therapeutics capable of suppressing pathogenic microbes in patients or serve a useful purpose in RQC-related diseases.
Related publications
Dr. Caulfield has published numerous scientific articles about his ribosome research, including:
- Caulfield T, Coban M, Tek A, Flores SC. Molecular dynamics simulations suggest a non-doublet decoding model of -1 frameshifting by tRNASer3. Biomolecules. 2019; doi:10.3390/biom9110745.
- Caulfield TR, Hayes KE, Qiu Y, Coban M, Seok Oh J, Lane AL, Yoshimitsu T, Hazlehurst L, Copland JA, Tun HW. A virtual screening platform identifies chloroethylagelastatin A as a potential ribosomal inhibitor. Biomolecules. 2020; doi:10.3390/biom10101407.
- Caulfield T, Devkota B. Motion of transfer RNA from the A/T state into the A-site using docking and simulations. Proteins. 2012; doi:10.1002/prot.24131.
- Caulfield TR, Devkota B, Rollins GC. Examinations of tRNA range of motion using simulations of cryo-EM microscopy and X-ray data. Journal of Biophysics. 2011; doi:10.1155/2011/219515.
- Mears JA, Sharma MR, Gutell RR, McCook AS, Richardson PE, Caulfield TR, Agrawal RK, Harvey SC. A structural model for the large subunit of the mammalian mitochondrial ribosome. Journal of Molecular Biology. 2006; doi:10.1016/j.jmb.2006.01.094.