TCBG Seminar

Probing Protein Motions for Sequence Fidelity Control and Information Detection along DNA

Professor Jin Yu
Department of Physics and Astronomy
University of California, Irvine
Irvine, CA

Monday, March 21, 2022
3:00 pm (CT)
Hybrid webinar recording


In template-based polymerization or transcription elongation, fidelity is mainly controlled by RNA polymerase (RNAP) selectivity on nucleotides. Although it is understood that RNAP operates in nonequilibrium for nucleotide addition or elongation to improve accuracy, it is not clear how it communicates with DNA template to assist cognate nucleotide incorporation. We have combined kinetic modeling with all-atom molecular dynamics (MD) simulation to show most critical residue motions supporting the nucleotide "recognition" and selectivity, from phage T7 to SARSCoV2 viral replication. The atomistic MD simulations are particularly useful in demonstrating hydrogen bonding (HB) interaction at the protein-DNA interface to detect DNA sequence information. The rate-limiting collective HB dynamics has been revealed in our recent work showing spontaneous stepping of a transcription factor (TF) protein along DNA. Modeled to coarse-grained level, protein-DNA electrostatics maintain significant impacts, for example, with the TF protein preferentially associating with one DNA strand in facilitated diffusion. Additionally, we have found that the protein-DNA associations can be notably impacted by protein rotation or re-orientation, which lead to a hierarchical free energy landscape of protein diffusion and dissociation along DNA for target search. pwd=bDV4a3ZJcHhrekFsS3pvK0RWbEtNZz09 Webinar ID: 876 3929 2770 Password: 627738

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