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[[Image:1s4a.png|left|200px]]


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==NMR Structure of a D,L alternating decamer of norleucine: double antiparallel beta-helix==
The line below this paragraph, containing "STRUCTURE_1s4a", creates the "Structure Box" on the page.
<StructureSection load='1s4a' size='340' side='right'caption='[[1s4a]]' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1s4a]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S4A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S4A FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</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=DNE:D-NORLEUCINE'>DNE</scene>, <scene name='pdbligand=DNG:N-FORMYL-D-NORLEUCINE'>DNG</scene>, <scene name='pdbligand=DNM:N-METHYL-D-NORLEUCINE'>DNM</scene>, <scene name='pdbligand=NLE:NORLEUCINE'>NLE</scene>, <scene name='pdbligand=NLO:O-METHYL-L-NORLEUCINE'>NLO</scene>, <scene name='pdbligand=PRD_000108:HCO-(D-NLE-L-NLE)3-D-MENLE-L-NLE-D-NLE-L-NLE-OME'>PRD_000108</scene></td></tr>
{{STRUCTURE_1s4a|  PDB=1s4a  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1s4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s4a OCA], [https://pdbe.org/1s4a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s4a RCSB], [https://www.ebi.ac.uk/pdbsum/1s4a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s4a ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Alternating sequences of D and L residues in peptides are directly related to the formation of several kinds of regular helical conformations usually called beta-helices. The major feature of these structures is that they can be associated with the transmembrane ion-conducting channel activity in some natural antibacterial peptides. The study of alternating D,L synthetic peptides is critical to understand how factors such as surrounding media, main chain length, type of side chain and terminal groups, among others, can determine the adoption of a specific kind of beta-helix. Early studies pointed out that the peptides Boc-(D-NLeu-L-NLeu)(6)-D-MeNLe-L-Nl-D-Nl-L-Nl-OMe (Boc: tert-butyloxycarbonyl) and Boc-L-Nle-(D-Nle-L-Nle)(5)-D-MeNle-L-Nle-D-Nle-L-Nle-OMe adopt in chloroform a unique detectable conformation single beta(4.4)- and double beta(5.6) upward arrow downward arrow -helix, respectively. The influence of terminal groups on the final stable conformation of N-formylated peptides has been studied in this work. The initial basic NMR data analysis of a synthetic alternating D,L-oligopeptide with ten norleucines, N-methylated on the residue 7 and having HCO- and -OMe as terminal groups clearly indicates the coexistence of two different conformations in equilibrium. NMR data and molecular dynamics calculations point to a dimeric antiparallel beta-helix structure beta(5.6) upward arrow downward arrow for the main conformation. On the other hand, NMR data suggest a single beta-helix structure beta(4.4) for the second conformation. Finally, a thermodynamic analysis of the equilibrium between both conformations has been carried out by one-dimensional NMR measurements at ten different temperatures. The temperature at which 50% of dimer conformation is dissociated is 319 K. In addition, the dimer-monomer equilibrium curve obtained shows a DeltaG&gt;0 for the whole range of studied temperatures, and its behavior can be considered similar to the thermodynamic denaturation protein processes.


===NMR Structure of a D,L alternating decamer of norleucine: double antiparallel beta-helix===
Conformational and structural analysis of the equilibrium between single- and double-strand beta-helix of a D,L-alternating oligonorleucine.,Navarro E, Fenude E, Celda B Biopolymers. 2004 Feb 5;73(2):229-41. PMID:14755580<ref>PMID:14755580</ref>


 
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_14755580}}, adds the Publication Abstract to the page
<div class="pdbe-citations 1s4a" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 14755580 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_14755580}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S4A OCA].
[[Category: Celda B]]
 
[[Category: Fenude E]]
==Reference==
[[Category: Navarro E]]
Conformational and structural analysis of the equilibrium between single- and double-strand beta-helix of a D,L-alternating oligonorleucine., Navarro E, Fenude E, Celda B, Biopolymers. 2004 Feb 5;73(2):229-41. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14755580 14755580]
[[Category: Celda, B.]]
[[Category: Fenude, E.]]
[[Category: Navarro, E.]]
[[Category: Beta-helix]]
[[Category: D,l-alternating]]
[[Category: Gramicidin]]
[[Category: Norleucine]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 09:39:13 2008''

Latest revision as of 11:05, 15 November 2023

NMR Structure of a D,L alternating decamer of norleucine: double antiparallel beta-helixNMR Structure of a D,L alternating decamer of norleucine: double antiparallel beta-helix

Structural highlights

1s4a 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

Alternating sequences of D and L residues in peptides are directly related to the formation of several kinds of regular helical conformations usually called beta-helices. The major feature of these structures is that they can be associated with the transmembrane ion-conducting channel activity in some natural antibacterial peptides. The study of alternating D,L synthetic peptides is critical to understand how factors such as surrounding media, main chain length, type of side chain and terminal groups, among others, can determine the adoption of a specific kind of beta-helix. Early studies pointed out that the peptides Boc-(D-NLeu-L-NLeu)(6)-D-MeNLe-L-Nl-D-Nl-L-Nl-OMe (Boc: tert-butyloxycarbonyl) and Boc-L-Nle-(D-Nle-L-Nle)(5)-D-MeNle-L-Nle-D-Nle-L-Nle-OMe adopt in chloroform a unique detectable conformation single beta(4.4)- and double beta(5.6) upward arrow downward arrow -helix, respectively. The influence of terminal groups on the final stable conformation of N-formylated peptides has been studied in this work. The initial basic NMR data analysis of a synthetic alternating D,L-oligopeptide with ten norleucines, N-methylated on the residue 7 and having HCO- and -OMe as terminal groups clearly indicates the coexistence of two different conformations in equilibrium. NMR data and molecular dynamics calculations point to a dimeric antiparallel beta-helix structure beta(5.6) upward arrow downward arrow for the main conformation. On the other hand, NMR data suggest a single beta-helix structure beta(4.4) for the second conformation. Finally, a thermodynamic analysis of the equilibrium between both conformations has been carried out by one-dimensional NMR measurements at ten different temperatures. The temperature at which 50% of dimer conformation is dissociated is 319 K. In addition, the dimer-monomer equilibrium curve obtained shows a DeltaG>0 for the whole range of studied temperatures, and its behavior can be considered similar to the thermodynamic denaturation protein processes.

Conformational and structural analysis of the equilibrium between single- and double-strand beta-helix of a D,L-alternating oligonorleucine.,Navarro E, Fenude E, Celda B Biopolymers. 2004 Feb 5;73(2):229-41. PMID:14755580[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. Navarro E, Fenude E, Celda B. Conformational and structural analysis of the equilibrium between single- and double-strand beta-helix of a D,L-alternating oligonorleucine. Biopolymers. 2004 Feb 5;73(2):229-41. PMID:14755580 doi:http://dx.doi.org/10.1002/bip.10549
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