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Dynamics and recognition within a protein-DNA complex: a molecular dynamics study of the SKN-1/DNA interaction.

ABSTRACT: Molecular dynamics simulations of the Caenorhabditis elegans transcription factor SKN-1 bound to its cognate DNA site show that the protein-DNA interface undergoes significant dynamics on the microsecond timescale. A detailed analysis of the simulation shows that movements of two key arginine side chains between the major groove and the backbone of DNA generate distinct conformational sub-states that each recognize only part of the consensus binding sequence of SKN-1, while the experimentally observed binding specificity results from a time-averaged view of the dynamic recognition occurring within this complex.

SUBMITTER: Etheve L

PROVIDER: S-EPMC4756839 | biostudies-literature | 2016 Feb

REPOSITORIES: biostudies-literature

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Dynamics and recognition within a protein-DNA complex: a molecular dynamics study of the SKN-1/DNA interaction.

Etheve Loïc L Martin Juliette J Lavery Richard R

Nucleic acids research 20151231 3

Molecular dynamics simulations of the Caenorhabditis elegans transcription factor SKN-1 bound to its cognate DNA site show that the protein-DNA interface undergoes significant dynamics on the microsecond timescale. A detailed analysis of the simulation shows that movements of two key arginine side chains between the major groove and the backbone of DNA generate distinct conformational sub-states that each recognize only part of the consensus binding sequence of SKN-1, while the experimentally ob ...[more]

PMID: 26721385

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