在非氫鍵鍵結位置上離胺酸側鏈長度對β-Hairpin穩定度的影響及在Rev 胜肽N端利用氫鍵代替物對於核糖核酸辨認的影響

郭禮閎

doi:10.6342/NTU.2013.03111

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在非氫鍵鍵結位置上離胺酸側鏈長度對β-Hairpin穩定度的影響及在Rev 胜肽N端利用氫鍵代替物對於核糖核酸辨認的影響

Effect of Lysine Side Chain Length at Non-Hydrogen Bonded Strand Positions on β-Hairpin Stability and Toward Introducing a Hydrogen Bond Surrogate at the N-Terminus of Rev Peptide on RNA Recognition

郭禮閎 , Masters　　Advisor：陳平　　

繁體中文 DOI： 10.6342/NTU.2013.03111

離胺酸；摺板偏好； Rev ； RRE RNA ；氫鍵代替物； Lys ； sheet propensity ； β-hairpin ； Rev ； RRE RNA ； hydrogen bond surrogate.

Abstract │ Reference (214) │ Altmetrics

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There are many factors that contribute to protein folding and structure stability: intrinsic propensity of amino acids, side chain ion pairing interaction, hydrophobic effect, hydrogen bonding, van der Waals interaction. In this study, we focused on the effect of lysine side chain length on sheet propensity at a non-hydrogen bonded strand position in β-hairpin. The β-hairpin peptides HPTAlaXaa (Xaa= Dap, Dab, Orn, Lys) were designed with the side chain of Lys9 systematically shortened to investigate the effect of Lys side chain length on sheet propensity. The peptides were synthesized by solid phase peptide synthesis using Fmoc-based chemistry. All peptides were purified to 95% purity and were analyzed by 2D NMR experiments. Sequence specific assignment was performed. The hairpin structures were confirmed by chemical shift deviation, 3JHNα coupling  constants,and NOE signals.The fraction folded and ΔG of  peptides were  derived  by  comparing  the  chemical  shifts  with the fully folded  and  unfolded reference peptides. The percent folding of HPTAlaXaa peptides with Lys analogs at the guest   position   followed   the   trend:   HPTAlaDap   ~ HPTAlaDab < HPTAlaOrn ~ HPTAlaLys, showing that the longer the Lys analogue side chain, the more stable the β-haiprin structure.

The HIV Rev protein binds RRE RNA to regulate the transport of unspliced and spliced mRNA from the nucleus to the cytoplasm posttranscriptionally. The Rev peptide is a random-coil. However, the conformation of the Rev peptide changes to an α-helix while  binding  to  RRE  RNA.  Hydrogen  bond  surrogate  (HBS)  is  one  of  the  several 
cross-linking systems for stabilizing an α-helix, using the covalent bond C=C-C-N to substitute the C=O…H-N (i, i+4) hydrogen bond in a short helix. In order to synthesize 
an HBS peptide, strategy for synthesis of dipeptides that contained an allyl group on the amino group was designed and refined. Two wild type Rev peptides were synthesized by solid phase peptide synthesis using Fmoc-based chemistry. The secondary structure of the two peptides was random-coil analyzed by circular dichroism spectroscopy. The binding  specificity  of  the  Rev  peptides  was  determined  by  gel  shift  assay.  The dissociation constants of the Rev peptides were similar to previous studies.

Reference ( 214 ) 〈TOP〉

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