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| | ==NMR and MD solution structure of a Gamma-Methylated PNA duplex== | | ==NMR and MD solution structure of a Gamma-Methylated PNA duplex== |
| - | <StructureSection load='2kvj' size='340' side='right'caption='[[2kvj]], [[NMR_Ensembles_of_Models | 11 NMR models]]' scene=''> | + | <StructureSection load='2kvj' size='340' side='right'caption='[[2kvj]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2kvj]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KVJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2KVJ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2kvj]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KVJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KVJ FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=40A:N-[(2S)-2-AMINOPROPYL]-N-[(6-AMINO-9H-PURIN-9-YL)ACETYL]GLYCINE'>40A</scene>, <scene name='pdbligand=40C:N-[(4-AMINO-2-OXOPYRIMIDIN-1(2H)-YL)ACETYL]-N-[(2S)-2-AMINOPROPYL]GLYCINE'>40C</scene>, <scene name='pdbligand=40G:N-[(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)ACETYL]-N-[(2S)-2-AMINOPROPYL]GLYCINE'>40G</scene>, <scene name='pdbligand=40T:N-[(2S)-2-AMINOPROPYL]-N-[(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)ACETYL]GLYCINE'>40T</scene>, <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NME:METHYLAMINE'>NME</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2k4g|2k4g]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=40A:N-[(2S)-2-AMINOPROPYL]-N-[(6-AMINO-9H-PURIN-9-YL)ACETYL]GLYCINE'>40A</scene>, <scene name='pdbligand=40C:N-[(4-AMINO-2-OXOPYRIMIDIN-1(2H)-YL)ACETYL]-N-[(2S)-2-AMINOPROPYL]GLYCINE'>40C</scene>, <scene name='pdbligand=40G:N-[(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)ACETYL]-N-[(2S)-2-AMINOPROPYL]GLYCINE'>40G</scene>, <scene name='pdbligand=40T:N-[(2S)-2-AMINOPROPYL]-N-[(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)ACETYL]GLYCINE'>40T</scene>, <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NME:METHYLAMINE'>NME</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2kvj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kvj OCA], [http://pdbe.org/2kvj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2kvj RCSB], [http://www.ebi.ac.uk/pdbsum/2kvj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2kvj ProSAT]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2kvj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kvj OCA], [https://pdbe.org/2kvj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kvj RCSB], [https://www.ebi.ac.uk/pdbsum/2kvj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kvj ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Achim, C]] | + | [[Category: Achim C]] |
| - | [[Category: Crawford, M J]] | + | [[Category: Crawford MJ]] |
| - | [[Category: Gil, R R]] | + | [[Category: Gil RR]] |
| - | [[Category: He, W]] | + | [[Category: He W]] |
| - | [[Category: Ly, D H]] | + | [[Category: Ly DH]] |
| - | [[Category: Madrid, M]] | + | [[Category: Madrid M]] |
| - | [[Category: Rapireddy, S]] | + | [[Category: Rapireddy S]] |
| - | [[Category: Gamma-methylated pna]]
| + | |
| - | [[Category: Methyl modified pna]]
| + | |
| - | [[Category: Peptide nucleic acid]]
| + | |
| - | [[Category: Pna]]
| + | |
| Structural highlights
2kvj is a 2 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | Solution NMR |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Publication Abstract from PubMed
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.
The structure of a gamma-modified peptide nucleic acid duplex.,He W, Crawford MJ, Rapireddy S, Madrid M, Gil RR, Ly DH, Achim C Mol Biosyst. 2010 Apr 13. PMID:20386807[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ He W, Crawford MJ, Rapireddy S, Madrid M, Gil RR, Ly DH, Achim C. The structure of a gamma-modified peptide nucleic acid duplex. Mol Biosyst. 2010 Apr 13. PMID:20386807 doi:10.1039/c002254c
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