Molecular Dynamics Studies of the Ribosome CAR Surface

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Live Poster Session: Zoom Link
Thursday, July 30th 1:15-2:30pm EDT

Abdelrahman Elsayed
Abdelrahman Elsayed

Abdelrahman Elsayed is a rising senior (’21) from Brooklyn, NY, where he graduated from NYC Lab Highschool for Collaborative Studies. Coming from an immigrant family, he has spent much of his life living in Cairo, Egypt and NYC. He studied abroad in Kyoto, Japan during the Spring 2020 semester. His interests are learning about different cultures, hanging out with friends, and engaging in cultural clubs such as the Middle Eastern Student Union. He is a computer science major and CEAS minor. He hopes to use his interdisciplinary studies at Wesleyan to pursue unique opportunities in the tech field.

Carol Dalgarno
Carol Dalgarno

Carol Dalgarno is a rising senior (’21) double majoring in Molecular Biology and Biochemistry and Science in Society. She grew up in Brookline, Massachusetts and graduated from Brookline High School. Outside of coursework, Carol enjoys working as a peer tutor, singing in the a cappella group Onomatopoeia, and hiking. After graduation she plans to apply to Biomedical Sciences PhD programs and pursue research with clinical applications.

Jack Kwon
Jack Kwon

Jack Kwon is a rising senior (’21), and he will be living in 76 Lawn Ave. He is from Suwanee, Georgia and graduated from Lambert High School in the spring of 2017. He loves to play Ultimate Frisbee and is part of the Wesleyan Men’s Ultimate Frisbee team: Nietzsch Factor. He also loves listening to music, learning new things in the field of molecular biology, and spending time with family and friends. He plans to double major in MB&B (Molecular Biology and Biochemistry) and CIS (College of Integrative Sciences) and then complete the BA/MA program at Wesleyan.

Abstract: mRNA codons with the sequence GCN are known to be overrepresented at the beginning of the open reading frame (ORF) of highly expressed yeast genes. This conserved periodicity suggests that these GCN repeats may play a role in regulating protein translation. The structural basis of this preference for GCN codons can be investigated using Molecular Dynamics (MD) simulations. Previous MD studies show at when the codon directly downstream of the A-site (the +1 codon) has the sequence GCU, the +1 codon interacts with the C1054-A1196-R146 (CAR) interaction surface of the ribosome through hydrogen bonding. Furthermore, the CAR surface is anchored to the wobble tRNA and the three CAR residues form a stable interaction surface through pi stacking of the nitrogenous bases of C1054 and A1196 and the guanidinium group of R146. This transient interaction between the ribosome and the mRNA likely plays a role in translation efficiency. To determine whether hydrogen bonding and stacking of the CAR surface is modulated by the mRNA sequence, we conducted MD simulations of the decoding center with different +1 codon substitutions. We created and simulated all 16 possible codon sequences with a uracil at position 3. These substitutions showed decreased hydrogen-bonding between the +1 codon and CAR and disruption of the stacking of the wobble tRNA to C1054 and the guanidinium group of R146 to A1196. Thus, the interaction of the CAR surface with mRNA is sequence dependent.

Summer_2020_MDPoster-Abdelrahman-Elsayed

Live Poster Session: Zoom Link
Thursday, July 30th 1:15-2:30pm EDT

1 thought on “Molecular Dynamics Studies of the Ribosome CAR Surface”

  1. Excellent poster! It has been a pleasure collaborating with you this summer! We have gotten so much done despite all the setbacks. The cream always rises to the top. I wish each of you a restful August and look forward to seeing you in the fall! Enjoy NOT having to wake up for our 8AM WeirLab Comp Group meetings!

    best,
    Prof. Thayer

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