1s4a: Difference between revisions

Revision as of 15:57, 21 February 2008

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

OverviewOverview

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.

About this StructureAbout this Structure

1S4A is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

ReferenceReference

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

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 '''NMR Structure of a D,L alternating decamer of norleucine: double antiparallel beta-helix'''<br />
 ==Overview==
-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.
+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.
 ==About this Structure==
-S4A is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1S4A OCA].
+S4A is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S4A OCA].
 ==Reference==
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 [[Category: norleucine]]
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