title: Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA.
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.
authors.affiliation: SISSA/ISAS-International School for Advanced Studies, Trieste 34136, Italy.|Department of Physics, University of Science, Hochiminh City 70000, Vietnam.
authors.forename: Trang N
authors.initials: TN
authors.lastname: Do
authors.affiliation: German Research School for Simulation Sciences GmbH, Jülich 52425, Germany.
authors.forename: Emiliano
authors.initials: E
authors.lastname: Ippoliti
authors.affiliation: German Research School for Simulation Sciences GmbH, Jülich 52425, Germany.
authors.forename: Paolo
authors.initials: P
authors.lastname: Carloni
authors.affiliation: Department of Chemistry and Department of Biochemistry, University of Washington, Seattle, Washington 98195-1700, United States.
authors.forename: Gabriele
authors.initials: G
authors.lastname: Varani
authors.affiliation: Department of Chemistry and Applied Biosciences, ETH Zurich, Lugano 6900, Switzerland.
authors.forename: Michele
authors.initials: M
authors.lastname: Parrinello