2kvj

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{{Seed}}
 
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[[Image:2kvj.png|left|200px]]
 
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==NMR and MD solution structure of a Gamma-Methylated PNA duplex==
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The line below this paragraph, containing "STRUCTURE_2kvj", creates the "Structure Box" on the page.
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<StructureSection load='2kvj' size='340' side='right'caption='[[2kvj]]' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<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>
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{{STRUCTURE_2kvj| PDB=2kvj | SCENE= }}
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<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>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===NMR and MD solution structure of a Gamma-Methylated PNA duplex===
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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<ref>PMID:20386807</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_20386807}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2kvj" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 20386807 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_20386807}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2KVJ is a 2 chains structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KVJ OCA].
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[[Category: Achim C]]
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[[Category: Crawford MJ]]
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==Reference==
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[[Category: Gil RR]]
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<ref group="xtra">PMID:20386807</ref><references group="xtra"/>
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[[Category: He W]]
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[[Category: Achim, C.]]
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[[Category: Ly DH]]
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[[Category: Crawford, M J.]]
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[[Category: Madrid M]]
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[[Category: Gil, R R.]]
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[[Category: Rapireddy S]]
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[[Category: He, W.]]
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[[Category: Ly, D H.]]
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[[Category: Madrid, M.]]
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[[Category: Rapireddy, S.]]
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[[Category: Gamma-methylated pna]]
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[[Category: Methyl modified pna]]
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[[Category: Peptide nucleic acid]]
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[[Category: Pna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu May 20 09:10:04 2010''
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Current revision

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

PDB ID 2kvj

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