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| | ==Solution structure of gomesin at 278 K== | | ==Solution structure of gomesin at 278 K== |
| - | <StructureSection load='6my1' size='340' side='right'caption='[[6my1]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> | + | <StructureSection load='6my1' size='340' side='right'caption='[[6my1]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6my1]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MY1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MY1 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6my1]] 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=6MY1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MY1 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]], [[6my2|6my2]], [[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=6my1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6my1 OCA], [http://pdbe.org/6my1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6my1 RCSB], [http://www.ebi.ac.uk/pdbsum/6my1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6my1 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=6my1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6my1 OCA], [https://pdbe.org/6my1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6my1 RCSB], [https://www.ebi.ac.uk/pdbsum/6my1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6my1 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/GOME_ACAGO GOME_ACAGO] Active against several Gram-positive bacteria such as Bacillus spp, Staphylococcus spp and E.faecalis, several Gram-negative bacteria such as E.coli, K.pneumoniae, P.aeruginosa and Salmonella spp, filamentous fungi such as N.crassa, T.viridae and yeasts such as C.albicans. It is active against the parasite L.amazonensis as well. It shows hemolytic activity.<ref>PMID:10942757</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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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: Peptide]]
| + | |
| - | [[Category: Toxin]]
| + | |
| Structural highlights
Function
GOME_ACAGO Active against several Gram-positive bacteria such as Bacillus spp, Staphylococcus spp and E.faecalis, several Gram-negative bacteria such as E.coli, K.pneumoniae, P.aeruginosa and Salmonella spp, filamentous fungi such as N.crassa, T.viridae and yeasts such as C.albicans. It is active against the parasite L.amazonensis as well. It shows hemolytic activity.[1]
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[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Silva PI Jr, Daffre S, Bulet P. Isolation and characterization of gomesin, an 18-residue cysteine-rich defense peptide from the spider Acanthoscurria gomesiana hemocytes with sequence similarities to horseshoe crab antimicrobial peptides of the tachyplesin family. J Biol Chem. 2000 Oct 27;275(43):33464-70. PMID:10942757 doi:http://dx.doi.org/10.1074/jbc.M001491200
- ↑ 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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