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Do TN, Ippoliti E, Carloni P, et al. Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA. J Chem Theory Comput. 2012;8(2):688-94doi: 10.1021/ct2005769.
Do, T. N., Ippoliti, E., Carloni, P., Varani, G., & Parrinello, M. (2012). Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA. Journal of chemical theory and computation, 8(2), 688-94. https://doi.org/10.1021/ct2005769
Do, Trang N, et al. "Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA." Journal of chemical theory and computation vol. 8,2 (2012): 688-94. doi: https://doi.org/10.1021/ct2005769
Do TN, Ippoliti E, Carloni P, Varani G, Parrinello M. Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA. J Chem Theory Comput. 2012 Feb 14;8(2):688-94. doi: 10.1021/ct2005769. Epub 2012 Jan 20. PMID: 26596616.
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J Chem Theory Comput. 2012 Feb 14;8(2):688-94. doi: 10.1021/ct2005769. Epub 2012 Jan 20.

Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA.

Journal of chemical theory and computation

Trang N Do, Emiliano Ippoliti, Paolo Carloni, Gabriele Varani, Michele Parrinello

Affiliations

  1. SISSA/ISAS-International School for Advanced Studies, Trieste 34136, Italy.
  2. Department of Physics, University of Science, Hochiminh City 70000, Vietnam.
  3. German Research School for Simulation Sciences GmbH, Jülich 52425, Germany.
  4. Department of Chemistry and Department of Biochemistry, University of Washington, Seattle, Washington 98195-1700, United States.
  5. Department of Chemistry and Applied Biosciences, ETH Zurich, Lugano 6900, Switzerland.

PMID: 26596616 DOI: 10.1021/ct2005769

Abstract

Binding of proteins and small molecules to RNA involves many electrostatic interactions, which may alter the distribution of ions around the RNA molecule. Here, we use molecular dynamics simulations to investigate how binding of a cyclic peptide mimic of the HIV-1 Tat protein affects the ionic distribution around the HIV-1 TAR RNA element. The calculations reproduce the structural properties observed in NMR studies of TAR and its complex. They also provide insight into the rearrangement of counterions during the molecular recognition events leading to the formation of the protein/RNA complex.

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