Fig. 6: Structure/function analysis of HIV-1 dimerization.
From: Short- and long-range interactions in the HIV-1 5′ UTR regulate genome dimerization and packaging
a,c, Single nucleotide resolution functional profiling data pooled from six low salt samples mapped the dimer (a) and monomer (c) structures expressed as log2(Kdimer) values. Each individual mutant shown as one of three circle in the order A,C,G,U clockwise from upper position (excluding the WT base). Validation of structural models on 3G RNA by point mutagenesis followed by native agarose gel electrophoresis in two different buffer conditions. Experiments were performed at least twice, representative data shown. Red circles show mutations inhibiting dimerization, and blue circles show mutations enhancing dimerization. log2(Kdimer) values above 2 are capped. b, Functional profiling data mapped to different structural models of SL1 containing mutually exclusive internal loop configurations. The two-internal loop (2IL), 3IL and the 3WJ are mutually exclusive models of SL1 structure based on chemical probing or biophysical measurements. Green arrows show mutations that improve dimerization by closing or reducing the size of internal loops, providing evidence that SL1 is metastable and that alternative SL1 conformations can form and dimerize. Red arrows show mutations that have complex effects on dimerization because they affect the new PBS–SL1 interaction.
