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1dn3

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Revision as of 16:31, 13 December 2023

NMR STRUCTURE OF A MODEL HYDROPHILIC AMPHIPATHIC HELICAL BASIC PEPTIDE

Structural highlights

1dn3 is a 1 chain structure with sequence from Homo sapiens. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PLF4_HUMAN Released during platelet aggregation. Neutralizes the anticoagulant effect of heparin because it binds more strongly to heparin than to the chondroitin-4-sulfate chains of the carrier molecule. Chemotactic for neutrophils and monocytes. Inhibits endothelial cell proliferation, the short form is a more potent inhibitor than the longer form.^[1]

Publication Abstract from PubMed

Sodium dodecyl sulfate (SDS) has consistently been shown to induce secondary structure, particularly alpha-helices, in polypeptides, and is commonly used to model membrane and other hydrophobic environments. However, the precise mechanism by which SDS induces these conformational changes remains unclear. To examine the role of electrostatic interactions in this mechanism, we have designed two hydrophilic, charged amphipathic alpha-helical peptides, one basic (QAPAYKKAAKKLAES) and the other acidic (QAPAYEEAAEELAKS), and their structures were studied by CD and NMR. The design of the peptides is based on the sequence of the segment of residues 56-70 of human platelet factor 4 [PF4(56-70), QAPLYKKIIKKLLES]. Both peptides were unstructured in water, and in the presence of neutral, zwitterionic, or cationic detergents. However, in SDS at neutral pH, the basic peptide folded into an alpha-helix. By contrast, the pH needed to be lowered to 1.8 before alpha-helix formation was observed for the acidic peptide. Strong, attractive electrostatic interactions, between the anionic groups of SDS and the cationic groups of the lysines, appeared to be necessary to initiate the folding of the basic peptide. NMR analysis showed that the basic peptide was fully embedded in SDS-peptide micelles, and that its three-dimensional alpha-helical structure could be superimposed on that of the native structure of PF4(56-70). These results enabled us to propose a working model of the basic peptide-SDS complex, and a mechanism for SDS-induced alpha-helical folding. This study demonstrates that, while the folding of peptides is mostly driven by hydrophobic effects, electrostatic interactions play a significant role in the formation and the stabilization of SDS-induced structure.

Involvement of electrostatic interactions in the mechanism of peptide folding induced by sodium dodecyl sulfate binding.,Montserret R, McLeish MJ, Bockmann A, Geourjon C, Penin F Biochemistry. 2000 Jul 25;39(29):8362-73. PMID:10913242^[2]

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

References

↑ Gupta SK, Hassel T, Singh JP. A potent inhibitor of endothelial cell proliferation is generated by proteolytic cleavage of the chemokine platelet factor 4. Proc Natl Acad Sci U S A. 1995 Aug 15;92(17):7799-803. PMID:7644496
↑ Montserret R, McLeish MJ, Bockmann A, Geourjon C, Penin F. Involvement of electrostatic interactions in the mechanism of peptide folding induced by sodium dodecyl sulfate binding. Biochemistry. 2000 Jul 25;39(29):8362-73. PMID:10913242

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1dn3"

@@ Line 1: / Line 1: @@
 ==NMR STRUCTURE OF A MODEL HYDROPHILIC AMPHIPATHIC HELICAL BASIC PEPTIDE==
-<StructureSection load='1dn3' size='340' side='right'caption='[[1dn3]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>
+<StructureSection load='1dn3' size='340' side='right'caption='[[1dn3]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1dn3]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DN3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DN3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1dn3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DN3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DN3 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1rhp|1rhp]], [[1djf|1djf]]</div></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dn3 OCA], [https://pdbe.org/1dn3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dn3 RCSB], [https://www.ebi.ac.uk/pdbsum/1dn3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dn3 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/PLF4_HUMAN PLF4_HUMAN]] Released during platelet aggregation. Neutralizes the anticoagulant effect of heparin because it binds more strongly to heparin than to the chondroitin-4-sulfate chains of the carrier molecule. Chemotactic for neutrophils and monocytes. Inhibits endothelial cell proliferation, the short form is a more potent inhibitor than the longer form.<ref>PMID:7644496</ref>
+[https://www.uniprot.org/uniprot/PLF4_HUMAN PLF4_HUMAN] Released during platelet aggregation. Neutralizes the anticoagulant effect of heparin because it binds more strongly to heparin than to the chondroitin-4-sulfate chains of the carrier molecule. Chemotactic for neutrophils and monocytes. Inhibits endothelial cell proliferation, the short form is a more potent inhibitor than the longer form.<ref>PMID:7644496</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 22: @@
 __TOC__
 </StructureSection>
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Bockmann, A]]
+[[Category: Bockmann A]]
-[[Category: Geourjon, C]]
+[[Category: Geourjon C]]
-[[Category: McLeish, M J]]
+[[Category: McLeish MJ]]
-[[Category: Montserret, R]]
+[[Category: Montserret R]]
-[[Category: Penin, F]]
+[[Category: Penin F]]
-[[Category: De novo protein]]
-[[Category: Hydrophilic amphipathic basic helix model]]

1dn3

From Proteopedia

Revision as of 16:31, 13 December 2023

NMR STRUCTURE OF A MODEL HYDROPHILIC AMPHIPATHIC HELICAL BASIC PEPTIDE

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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