Publication Date

Summer 2015

Degree Type


Degree Name

Master of Science (MS)




Brooke Lustig

Subject Areas

Chemistry; Physical chemistry


Interactions between viral encoded regulatory proteins and RNA target sequences control gene expression of Lentiviruses, including human immunodeficiency virus (HIV). Bovine immunodeficiency virus (BIV) provides a simpler model of interaction between the viral trans-activating protein (Tat) and trans-activation response RNA element (TAR), using Tat peptides binding to TAR RNA fragments. The resulting characterization of the hinge region of native BIV TAR-Tat complex was confirmed by more comprehensive calculations, involving an exhaustive generation of lattice chains. This modeled 2-residues per move of the native 11-mer Tat peptide and a 28-nucleotides TAR fragment. But these sorts of coarse-grained calculations, upon substitution of Gly at key hinge region positions, are not fully sensitive to the local flexibility of amino acid side chains optimized for packing and possible interaction with relevant all-atom RNA structure. An overall binding destabilization effect is indicated for the single substitution at 78 and double substitution of Gly at positions 75 and 78. Destabilization effects were further examined, and model data showed that it included both potential and flexibility effects. Future studies require 1-residue per move approach and building all-atom models to fully examine molecular interactions of TAR-Tat complexes.