2KVJ

NMR and MD solution structure of a Gamma-Methylated PNA duplex

2KVJ の概要

• エントリーDOI: 10.2210/pdb2kvj/pdb
• 関連するPDBエントリー: 2k4g
• 分子名称: Gamma-Modified Peptide Nucleic Acid (1 entity in total)
• 機能のキーワード: pna, gamma-methylated pna, methyl modified pna, peptide nucleic acid
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 4676.70

構造登録者

He, W.,Crawford, M.J.,Rapireddy, S.,Madrid, M.,Gil, R.R.,Ly, D.H.,Achim, C. (登録日: 2010-03-15, 公開日: 2010-05-12, 最終更新日: 2023-11-15)

主引用文献

He, W.,Crawford, M.J.,Rapireddy, S.,Madrid, M.,Gil, R.R.,Ly, D.H.,Achim, C.
The structure of a gamma-modified peptide nucleic acid duplex.
Mol Biosyst, 6:1619-1629, 2010

PubMed Abstract: This paper presents the results of an NMR spectroscopy and distance-restrained molecular dynamics (MD) study of a gamma-methylated, palindromic, 8-base pair peptide nucleic acid (gamma-PNA) duplex. The goal of this study was to examine the impact of the gamma-backbone modification on the structure of the PNA duplex. The 2D NMR information involving the backbone methyl group, especially the NOEs between the methyl protons and those of the amide and methylene groups of the backbone, led to distance restraints useful in the elucidation of the structure of the backbone of gamma-PNA. Integration of the NOE peaks resulted in 138 inter-proton distance restraints, which were used in ten independent simulated annealing followed by 2 ns restrained MD runs. These simulations led to the conclusion that the gamma-PNA duplex adopts a general P-form helical structure similar to that observed for non-modified PNA but with a smaller base pair rise, which is an A-like helical feature, and a slight helical bending towards the major groove (PDB ID ). These properties of the gamma-PNA duplex may be induced by the gamma-methyl group. A similar effect of the methyl group was revealed by a previous NMR study of single stranded gamma-PNA [A. Dragulescu-Andrasi, S. Rapireddy, B. M. Frezza, C. Gayathri, R. R. Gil and D. H. Ly, J. Am. Chem. Soc., 2006, 128, 10258-10267]. It appears that the steric constraint exerted by the gamma-methyl on the backbone orientation is relatively independent of the base pairing and stacking and thus is likely to manifest when other substituents are introduced at the gamma-position of the PNA.

PubMed: 20386807
DOI: 10.1039/c002254c

実験手法

SOLUTION NMR