Effect of Side Chain Length on Ion Pairing Interaction in β-Hairpin and Arginine Di-Methylation on RNA Recognition and Cellular Uptake

• Main Authors: Wen-Chieh Chiu, 邱玟潔
• Other Authors: 陳平
• Format: Others
• Language: en_US
• Published: 2013
• Online Access: http://ndltd.ncl.edu.tw/handle/06565281535238628465

碩士 === 國立臺灣大學 === 化學研究所 === 101 === Ion pairing interactions play important roles in protein stability and RNA recognition. Ion pairs are formed between a pair of oppositely charged amino acids. Interestingly, natural charged amino acids have different number of hydrophobic methylenes on their side chains. For negatively charged residues, Asp has one methylene and Glu has two methylenes. The analogous non-encoded negatively charged amino acid, Aad, contains three methylenes. To study the effect of negatively charged amino acid side chain length on cross strand ion pairs in β-sheets stability, a basic β-hairpin model HPTZbbArg was designed. Zbb denotes the negatively charged residues. The hairpin structure for peptides HPTAspArg, HPTGluArg, and HPTAadArg were confirmed by NMR methods. The fraction folded of the peptides was determined using chemical shift data involving the fully unfolded and the fully folded reference peptides. The interaction free energy followed the trend: Aad-Arg > Glu-Arg ≈ AspArg. Apparently, the longer the negatively charged residue side chain length, the stronger the ion pairing interaction. HIV-1 Tat protein contains an arginine-rich sequence (Tat49-57), which binds specifically to the trans-activating responsive (TAR) element and plays an important role in nuclear localization. The binding of HIV-1 Tat protein and TAR RNA is essential for HIV-1 virus genome replication. To study the effect of arginine dimethylation on RNA recognition and cellular uptake, each arginine residue in Tat49-57 was replaced with a dimethylated arginine including ADMA and SDMA, the asymmetric and symmetric dimethylated forms, respectively. The dissociation constant for the Tat derived peptide-TAR RNA complexes was determined by gel shift assay. The cellular uptake efficiency of these Tat derived peptides into Jurkat cells was assessed by flow cytometry.