2md4

From Proteopedia

(Difference between revisions)

Revision as of 09:33, 14 June 2023

Fragment based approach and binding behavior of LFampinB with Lipopolysaccharide: biophysical aspects

Structural highlights

2md4 is a 1 chain structure with sequence from Bos taurus. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TRFL_BOVIN Transferrins are iron binding transport proteins which can bind two Fe(3+) ions in association with the binding of an anion, usually bicarbonate.^[1] ^[2] Lactotransferrin has antimicrobial activity. The most effective inhibitory activity was seen against E.coli and P.aeruginosa.^[3] ^[4] Lactoferricin B is an antimicrobial peptide. Inhibits the growth of Gram-negative and Gram-positive bacteria.^[5] ^[6] The lactotransferrin transferrin-like domain 1 functions as a serine protease of the peptidase S60 family that cuts arginine rich regions. This function contributes to the antimicrobial activity.^[7] ^[8]

Publication Abstract from PubMed

Lactoferrampin (WR17, Trp 268-Arg 284), an antimicrobial peptide, is known to have significant antibacterial and candidacidal activities. However, there are no previous studies explaining how WR17 permeabilizes the outer membrane of Gram negative bacteria and neutralizes endotoxins. In this study we used a series of assays like antimicrobial activity, calcein leakage, NPN dye uptake and endotoxin neutralization assay to show that the sequence context of WR17 modulates its multi-faceted activities. We determined the high resolution NMR structure of WR17 in LPS and found that the N-ter region forms a helix (Trp1-Phe11) and orients itself at an angle of 45 degrees into the lipopolysaccharide (LPS) micelle, whereas the C-ter region (Lys13-Arg17) remains as a flexible extended random coil. We also verified this result through in silico molecular modeling simulation. Isothermal titration calorimetry showed that the interaction of WR17 and its analogues with LPS was primarily endothermic in nature. Using several fluorescence techniques such as anisotropy and red edge excitation shift assay we revealed motional restriction for Trp1 of WR17 in LPS. The distance between the indole ring of Trp1 of WR17 and the polar head group of LPS is around 7 A, as obtained from the depth of insertion assay. Additionally, MD simulation demonstrated that the incorporation of the peptide in LPS is achieved with the help of the K(13)xK(15)xR(17) motif at the C-terminus. This novel anchoring "K(13)NKSR(17)" motif is currently being utilized in our ongoing research to design novel anti-endotoxic molecules.

Sequence context induced antimicrobial activity: insight into lipopolysaccharide permeabilization.,Ghosh A, Datta A, Jana J, Kar RK, Chatterjee C, Chatterjee S, Bhunia A Mol Biosyst. 2014 Jun;10(6):1596-612. doi: 10.1039/c4mb00111g. Epub 2014 Apr 9. PMID:24714742^[9]

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

References

↑ Hoek KS, Milne JM, Grieve PA, Dionysius DA, Smith R. Antibacterial activity in bovine lactoferrin-derived peptides. Antimicrob Agents Chemother. 1997 Jan;41(1):54-9. PMID:8980754
↑ Massucci MT, Giansanti F, Di Nino G, Turacchio M, Giardi MF, Botti D, Ippoliti R, De Giulio B, Siciliano RA, Donnarumma G, Valenti P, Bocedi A, Polticelli F, Ascenzi P, Antonini G. Proteolytic activity of bovine lactoferrin. Biometals. 2004 Jun;17(3):249-55. PMID:15222473
↑ Hoek KS, Milne JM, Grieve PA, Dionysius DA, Smith R. Antibacterial activity in bovine lactoferrin-derived peptides. Antimicrob Agents Chemother. 1997 Jan;41(1):54-9. PMID:8980754
↑ Massucci MT, Giansanti F, Di Nino G, Turacchio M, Giardi MF, Botti D, Ippoliti R, De Giulio B, Siciliano RA, Donnarumma G, Valenti P, Bocedi A, Polticelli F, Ascenzi P, Antonini G. Proteolytic activity of bovine lactoferrin. Biometals. 2004 Jun;17(3):249-55. PMID:15222473
↑ Hoek KS, Milne JM, Grieve PA, Dionysius DA, Smith R. Antibacterial activity in bovine lactoferrin-derived peptides. Antimicrob Agents Chemother. 1997 Jan;41(1):54-9. PMID:8980754
↑ Massucci MT, Giansanti F, Di Nino G, Turacchio M, Giardi MF, Botti D, Ippoliti R, De Giulio B, Siciliano RA, Donnarumma G, Valenti P, Bocedi A, Polticelli F, Ascenzi P, Antonini G. Proteolytic activity of bovine lactoferrin. Biometals. 2004 Jun;17(3):249-55. PMID:15222473
↑ Hoek KS, Milne JM, Grieve PA, Dionysius DA, Smith R. Antibacterial activity in bovine lactoferrin-derived peptides. Antimicrob Agents Chemother. 1997 Jan;41(1):54-9. PMID:8980754
↑ Massucci MT, Giansanti F, Di Nino G, Turacchio M, Giardi MF, Botti D, Ippoliti R, De Giulio B, Siciliano RA, Donnarumma G, Valenti P, Bocedi A, Polticelli F, Ascenzi P, Antonini G. Proteolytic activity of bovine lactoferrin. Biometals. 2004 Jun;17(3):249-55. PMID:15222473
↑ Ghosh A, Datta A, Jana J, Kar RK, Chatterjee C, Chatterjee S, Bhunia A. Sequence context induced antimicrobial activity: insight into lipopolysaccharide permeabilization. Mol Biosyst. 2014 Jun;10(6):1596-612. doi: 10.1039/c4mb00111g. Epub 2014 Apr 9. PMID:24714742 doi:http://dx.doi.org/10.1039/c4mb00111g

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/2md4"

@@ Line 1: / Line 1: @@
 ==Fragment based approach and binding behavior of LFampinB with Lipopolysaccharide: biophysical aspects==
-<StructureSection load='2md4' size='340' side='right'caption='[[2md4]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
+<StructureSection load='2md4' size='340' side='right'caption='[[2md4]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2md4]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MD4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2md4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MD4 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;'>[[2md1|2md1]], [[2md2|2md2]], [[2md3|2md3]]</div></td></tr>
+</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=2md4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2md4 OCA], [https://pdbe.org/2md4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2md4 RCSB], [https://www.ebi.ac.uk/pdbsum/2md4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2md4 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=2md4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2md4 OCA], [https://pdbe.org/2md4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2md4 RCSB], [https://www.ebi.ac.uk/pdbsum/2md4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2md4 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/TRFL_BOVIN TRFL_BOVIN]] Transferrins are iron binding transport proteins which can bind two Fe(3+) ions in association with the binding of an anion, usually bicarbonate.<ref>PMID:8980754</ref> <ref>PMID:15222473</ref>   Lactotransferrin has antimicrobial activity. The most effective inhibitory activity was seen against E.coli and P.aeruginosa.<ref>PMID:8980754</ref> <ref>PMID:15222473</ref>   Lactoferricin B is an antimicrobial peptide. Inhibits the growth of Gram-negative and Gram-positive bacteria.<ref>PMID:8980754</ref> <ref>PMID:15222473</ref>   The lactotransferrin transferrin-like domain 1 functions as a serine protease of the peptidase S60 family that cuts arginine rich regions. This function contributes to the antimicrobial activity.<ref>PMID:8980754</ref> <ref>PMID:15222473</ref>
+[https://www.uniprot.org/uniprot/TRFL_BOVIN TRFL_BOVIN] Transferrins are iron binding transport proteins which can bind two Fe(3+) ions in association with the binding of an anion, usually bicarbonate.<ref>PMID:8980754</ref> <ref>PMID:15222473</ref>   Lactotransferrin has antimicrobial activity. The most effective inhibitory activity was seen against E.coli and P.aeruginosa.<ref>PMID:8980754</ref> <ref>PMID:15222473</ref>   Lactoferricin B is an antimicrobial peptide. Inhibits the growth of Gram-negative and Gram-positive bacteria.<ref>PMID:8980754</ref> <ref>PMID:15222473</ref>   The lactotransferrin transferrin-like domain 1 functions as a serine protease of the peptidase S60 family that cuts arginine rich regions. This function contributes to the antimicrobial activity.<ref>PMID:8980754</ref> <ref>PMID:15222473</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 21: @@
 __TOC__
 </StructureSection>
+[[Category: Bos taurus]]
 [[Category: Large Structures]]
-[[Category: Bhunia, A]]
+[[Category: Bhunia A]]
-[[Category: Chatterjee, S]]
+[[Category: Chatterjee S]]
-[[Category: Ghosh, A]]
+[[Category: Ghosh A]]
-[[Category: Jana, J]]
+[[Category: Jana J]]
-[[Category: Antimicrobial protein]]

2md4

From Proteopedia

Revision as of 09:33, 14 June 2023

Fragment based approach and binding behavior of LFampinB with Lipopolysaccharide: biophysical aspects

Structural highlights

Function

Publication Abstract from PubMed

References

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Proteopedia Page Contributors and Editors (what is this?)

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