2mdb: Difference between revisions

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'''Unreleased structure'''


The entry 2mdb is ON HOLD  until Paper Publication
==Tachyplesin I in the presence of lipopolysaccharide==
<StructureSection load='2mdb' size='340' side='right'caption='[[2mdb]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2mdb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Tachypleus_tridentatus Tachypleus tridentatus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MDB FirstGlance]. <br>
</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></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=2mdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mdb OCA], [https://pdbe.org/2mdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mdb RCSB], [https://www.ebi.ac.uk/pdbsum/2mdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mdb ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/TAC1_TACTR TAC1_TACTR] Significantly inhibits the growth of Gram-negative and Gram-positive bacteria.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Lipopolysaccharide (LPS) is a major constituent of the outer membrane of Gram-negative bacteria and is the very first site of interactions with antimicrobial peptides (AMPs). In order to gain better insight into the interaction between LPS and AMPs, we determined the structure of tachyplesin I (TP I), an antimicrobial peptide derived from horseshoe crab, in its bound state with LPS and proposed the complex structure of TP I and LPS using a docking program. CD and NMR measurements revealed that binding to LPS slightly extends the two beta-strands of TP I and stabilizes the whole structure of TP I. The fluorescence wavelength of an intrinsic tryptophan of TP I and fluorescence quenching in the presence or absence of LPS indicated that a tryptophan residue is incorporated into the hydrophobic environment of LPS. Finally, we succeeded in proposing a structural model for the complex of TP I and LPS by using a docking program. The calculated model structure suggested that the cationic residues of TP I interact with phosphate groups and saccharides of LPS, whereas hydrophobic residues interact with the acyl chains of LPS.


Authors: Kushibiki, T., Kamiya, M., Aizawa, T., Kumaki, Y., Kikukawa, T., Mizuguchi, M., Demura, M., Kawabata, S., Kawano, K.
Interaction between tachyplesin I, an antimicrobial peptide derived from horseshoe crab, and lipopolysaccharide.,Kushibiki T, Kamiya M, Aizawa T, Kumaki Y, Kikukawa T, Mizuguchi M, Demura M, Kawabata SI, Kawano K Biochim Biophys Acta. 2014 Jan 2;1844(3):527-534. doi:, 10.1016/j.bbapap.2013.12.017. PMID:24389234<ref>PMID:24389234</ref>


Description: Tachyplesin I in the presence of lipopolysaccharide
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2mdb" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Tachyplesin|Tachyplesin]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Tachypleus tridentatus]]
[[Category: Aizawa T]]
[[Category: Demura M]]
[[Category: Kamiya M]]
[[Category: Kawabata SI]]
[[Category: Kawano K]]
[[Category: Kikukawa T]]
[[Category: Kumaki Y]]
[[Category: Kushibiki T]]
[[Category: Mizuguchi M]]

Latest revision as of 08:21, 17 October 2024

Tachyplesin I in the presence of lipopolysaccharideTachyplesin I in the presence of lipopolysaccharide

Structural highlights

2mdb is a 1 chain structure with sequence from Tachypleus tridentatus. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR, 20 models
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TAC1_TACTR Significantly inhibits the growth of Gram-negative and Gram-positive bacteria.

Publication Abstract from PubMed

Lipopolysaccharide (LPS) is a major constituent of the outer membrane of Gram-negative bacteria and is the very first site of interactions with antimicrobial peptides (AMPs). In order to gain better insight into the interaction between LPS and AMPs, we determined the structure of tachyplesin I (TP I), an antimicrobial peptide derived from horseshoe crab, in its bound state with LPS and proposed the complex structure of TP I and LPS using a docking program. CD and NMR measurements revealed that binding to LPS slightly extends the two beta-strands of TP I and stabilizes the whole structure of TP I. The fluorescence wavelength of an intrinsic tryptophan of TP I and fluorescence quenching in the presence or absence of LPS indicated that a tryptophan residue is incorporated into the hydrophobic environment of LPS. Finally, we succeeded in proposing a structural model for the complex of TP I and LPS by using a docking program. The calculated model structure suggested that the cationic residues of TP I interact with phosphate groups and saccharides of LPS, whereas hydrophobic residues interact with the acyl chains of LPS.

Interaction between tachyplesin I, an antimicrobial peptide derived from horseshoe crab, and lipopolysaccharide.,Kushibiki T, Kamiya M, Aizawa T, Kumaki Y, Kikukawa T, Mizuguchi M, Demura M, Kawabata SI, Kawano K Biochim Biophys Acta. 2014 Jan 2;1844(3):527-534. doi:, 10.1016/j.bbapap.2013.12.017. PMID:24389234[1]

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

See Also

References

  1. Kushibiki T, Kamiya M, Aizawa T, Kumaki Y, Kikukawa T, Mizuguchi M, Demura M, Kawabata SI, Kawano K. Interaction between tachyplesin I, an antimicrobial peptide derived from horseshoe crab, and lipopolysaccharide. Biochim Biophys Acta. 2014 Jan 2;1844(3):527-534. doi:, 10.1016/j.bbapap.2013.12.017. PMID:24389234 doi:http://dx.doi.org/10.1016/j.bbapap.2013.12.017
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