Codon Adjacency Tunes Ribosome System H-Bonding

by

Faculty Sponsor: Michael Weir

Jane Doe
Luis Perez

Luis is a BA/MA student in the College of Integrative Sciences and a member of the Weir Laboratory. He is originally from NYC and his work as a part of the Weir lab focuses on molecular dynamics modeling of the ribosome and a proposed mechanism for differing codon translation rates. Outside of research he enjoys grappling, spending time with his family and buffets.

Abstract: The central dogma treats the ribosome as a molecular machine that reads one mRNA codon at a time as it adds each amino acid to its growing peptide chain. However, this and previous studies suggest that ribosomes actually perceive pairs of adjacent codons as they take three-nucleotide steps along the mRNA. 5′-NNN GNN adjacent codon pairs seem to induce a striking translation slowdown that is likely mediated, in part, by the ribosome’s CAR surface, which acts as an extension of the A-site tRNA anticodon during ribosome translocation and interacts through hydrogen bonding and pi stacking with the GNN codon. Using a systems “lens” for analyzing our 494 residue subsystem, this project seeks to highlight system-wide changes through the employment of hydrogen bonding adjacency matrices. By treating pairwise residue interactions of our system as a “network,” we hope to uncover new behaviors and confirm existing hypotheses.

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