BIV TAR RNA Binding Glycine Mutant Tat Peptides

Abstract

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. v ACKNOWLEDGEMENTS There are three main individuals whom I would like to offer my deep gratitude for helping m throughout my time at the Department of Chemistry at San Jose State University. First and foremost, I would like to thank Dr. Brooke Lustig, my research advisor, for mentoring me during my research projects and the writing of my Masters thesis. He provided me with his patience, knowledge, and expertise for the completion of this project. Most importantly, he gave me a chance to become a more scientific, logical, and critical thinker, which will definitely be helpful for my next career journey. I would also like to thank my committee members, Dr. Lionel Cheruzel and Dr. Elaine D. Collins, for taking the time to review my thesis. I especially would like to thank Dr. Cheruzel for putting up with me and giving me great advice. I would like to thank Savitha Srnivasan, a former graduate student at Dr. Lustig's lab for her help during my first time in the lab. I would also like to thank the undergraduate students, Reema Shalan, Lilley Tran, and Ashleen Kaur for assisting me throughout the project. For my family, I would like to thank my parents for their financial support. I am also extremely grateful to Hong Nguyen, my fiancée, who has been absolutely patient, encouraging, and my pillar of mental support throughout my academic years. With her unconditional love and unshakable support over the years, we manage to pull through the hard times and stay strong together. Last but not least, this thesis is dedicated to my loving and caring grandfather in heaven. To others who have been supporting me, I thank you very much.