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| | ==Solution structure of gomesin at 298 K== | | ==Solution structure of gomesin at 298 K== |
| - | <StructureSection load='6my2' size='340' side='right'caption='[[6my2]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> | + | <StructureSection load='6my2' size='340' side='right'caption='[[6my2]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6my2]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MY2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MY2 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6my2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acanthoscurria_gomesiana Acanthoscurria gomesiana]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MY2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MY2 FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 20 models</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kfp|1kfp]], [[6myi|6myi]], [[6my3|6my3]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6my2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6my2 OCA], [http://pdbe.org/6my2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6my2 RCSB], [http://www.ebi.ac.uk/pdbsum/6my2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6my2 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=6my2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6my2 OCA], [https://pdbe.org/6my2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6my2 RCSB], [https://www.ebi.ac.uk/pdbsum/6my2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6my2 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Acanthoscurria gomesiana]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Chin, Y K.Y]] | + | [[Category: Chin YK-Y]] |
| - | [[Category: Deplazes, E]] | + | [[Category: Deplazes E]] |
| - | [[Category: Beta hairpin motif]]
| + | |
| - | [[Category: Spider venom peptide]]
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| - | [[Category: Toxin]]
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| Structural highlights
Publication Abstract from PubMed
The cross-strand disulfides (CSDs) found in beta-hairpin antimicrobial peptides (beta-AMPs) show a unique disulfide geometry that is characterized by unusual torsion angles and a short Calpha-Calpha distance. While the sequence and disulfide bond connectivity of disulfide-rich peptides is well studied, much less is known about the disulfide geometry found in CSDs and their role in the stability of beta-AMPs. To address this, we solved the nuclear magnetic resonance (NMR) structure of the beta-AMP gomesin (Gm) at 278, 298, and 310 K, examined the disulfide bond geometry of over 800 disulfide-rich peptides, and carried out extensive molecular dynamics (MD) simulation of the peptides Gm and protegrin. The NMR data suggests Calpha-Calpha distances characteristic for CSDs are independent of temperature. Analysis of disulfide-rich peptides from the Protein Data Bank revealed that right-handed and left-handed rotamers are equally likely in CSDs. The previously reported preference for right-handed rotamers was likely biased by restricting the analysis to peptides and proteins solved using X-ray crystallography. Furthermore, data from MD simulations showed that the short Calpha-Calpha distance is critical for the stability of these peptides. The unique disulfide geometry of CSDs poses a challenge to biomolecular force fields and to retain the stability of beta-hairpin fold over long simulation times, restraints on the torsion angles might be required.
The unusual conformation of cross-strand disulfide bonds is critical to the stability of beta-hairpin peptides.,Deplazes E, Chin YK, King GF, Mancera RL Proteins. 2019 Oct 7. doi: 10.1002/prot.25828. PMID:31589791[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Deplazes E, Chin YK, King GF, Mancera RL. The unusual conformation of cross-strand disulfide bonds is critical to the stability of beta-hairpin peptides. Proteins. 2019 Oct 7. doi: 10.1002/prot.25828. PMID:31589791 doi:http://dx.doi.org/10.1002/prot.25828
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