5t8a - Revision history

OCA at 15:38, 6 March 2024

OCA — Wed, 06 Mar 2024 15:38:02 GMT

←Older revision		Revision as of 15:38, 6 March 2024
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	==Recombinant cytotoxin-I from the venom of cobra N. oxiana==		==Recombinant cytotoxin-I from the venom of cobra N. oxiana==
-	<StructureSection load='5t8a' size='340' side='right'caption='[[5t8a~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='5t8a' size='340' side='right'caption='[[5t8a]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5t8a]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Central_asian_cobra Central asian cobra~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T8A OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5T8A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5t8a]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Naja_oxiana Naja oxiana]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T8A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T8A FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[1rl5\|1rl5]], [[1zad\|1zad]]~~</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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5t8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t8a OCA], [~~http~~://pdbe.org/5t8a PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5t8a RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5t8a PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5t8a 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=5t8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t8a OCA], [https://pdbe.org/5t8a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t8a RCSB], [https://www.ebi.ac.uk/pdbsum/5t8a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t8a ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/3SA1_NAJOX 3SA1_NAJOX]] This three-finger cytotoxin is a basic protein that interacts and penetrates into the cell membrane, with the tips of all the three loops. Cytotoxins which have a 'Pro-30' (P-type) interacts with membrane stronger that those which have a Ser-28 (S-type). CTI interacts with membrane weaker than CTII.	+	[https://www.uniprot.org/uniprot/3SA1_NAJOX 3SA1_NAJOX] This three-finger cytotoxin is a basic protein that interacts and penetrates into the cell membrane, with the tips of all the three loops. Cytotoxins which have a 'Pro-30' (P-type) interacts with membrane stronger that those which have a Ser-28 (S-type). CTI interacts with membrane weaker than CTII.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Today, recombinant proteins are quite widely used in biomedical and biotechnological applications. At the same time, the question about their full equivalence to the native analogues remains unanswered. To gain additional insight into this problem, intimate atomistic details of a relatively simple protein, small and structurally rigid recombinant cardiotoxin I (CTI) from cobra Naja oxiana venom, were characterized using nuclear magnetic resonance (NMR) spectroscopy and atomistic molecular dynamics (MD) simulations in water. Compared to the natural protein, it contains an additional Met residue at the N-terminus. In this work, the NMR-derived spatial structure of uniformly 13C- and 15N-labeled CTI and its dynamic behavior were investigated and subjected to comparative analysis with the corresponding data for the native toxin. The differences were found in dihedral angles of only a single residue, adjacent to the N-terminal methionine. Microsecond-long MD traces of the toxins reveal an increased flexibility in the residues spatially close to the N-Met. As the detected structural and dynamic changes of the two CTI models do not result in substantial differences in their cytotoxicities, we assume that the recombinant protein can be used for many purposes as a reasonable surrogate of the native one. In addition, we discuss general features of the spatial organization of cytotoxins, implied by the results of the current combined NMR and MD study.	+
-		+
-	Structural and Dynamic "Portraits" of Recombinant and Native Cytotoxin I from Naja oxiana: How Close Are They?,Dubovskii PV, Dubinnyi MA, Konshina AG, Kazakova ED, Sorokoumova GM, Ilyasova TM, Shulepko MA, Chertkova RV, Lyukmanova EN, Dolgikh DA, Arseniev AS, Efremov RG Biochemistry. 2017 Aug 29;56(34):4468-4477. doi: 10.1021/acs.biochem.7b00453., Epub 2017 Aug 14. PMID:28749688<ref>PMID:28749688</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5t8a" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Central asian cobra]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dolgikh~~, D A~~]]	+	[[Category: Naja oxiana]]
-	[[Category: Dubinnyi~~, M A~~]]	+	[[Category: Dolgikh DA]]
-	[[Category: Dubovskii~~, P V~~]]	+	[[Category: Dubinnyi MA]]
-	[[Category: Efremov~~, R G~~]]	+	[[Category: Dubovskii PV]]
-	[[Category: Kirpichnikov~~, M P~~]]	+	[[Category: Efremov RG]]
-	[[Category: Lyukmanova~~, E N~~]]	+	[[Category: Kirpichnikov MP]]
-	[[Category: Shulepko~~, M A]]~~	+	[[Category: Lyukmanova EN]]
-	~~[[Category: All-beta sheet protein]]~~	+	[[Category: Shulepko MA]]
-	~~[[Category: Cytolytic peptide]]~~	+
-	~~[[Category: Recombinant production]]~~	+
-	~~[[Category: Structure from molmol]]~~	+
-	~~[[Category: Toxin~~]]	+

OCA at 13:19, 10 May 2019

OCA — Fri, 10 May 2019 13:19:56 GMT

←Older revision		Revision as of 13:19, 10 May 2019
Line 1:		Line 1:

	==Recombinant cytotoxin-I from the venom of cobra N. oxiana==		==Recombinant cytotoxin-I from the venom of cobra N. oxiana==
-	<StructureSection load='5t8a' size='340' side='right' caption='[[5t8a]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='5t8a' size='340' side='right'caption='[[5t8a]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5t8a]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Central_asian_cobra Central asian cobra]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T8A FirstGlance]. <br>		<table><tr><td colspan='2'>[[5t8a]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Central_asian_cobra Central asian cobra]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T8A FirstGlance]. <br>
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Central asian cobra]]		[[Category: Central asian cobra]]
		+	[[Category: Large Structures]]
	[[Category: Dolgikh, D A]]		[[Category: Dolgikh, D A]]
	[[Category: Dubinnyi, M A]]		[[Category: Dubinnyi, M A]]

OCA at 07:39, 8 November 2017

OCA — Wed, 08 Nov 2017 07:39:48 GMT

←Older revision		Revision as of 07:39, 8 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5t8a is ~~ON HOLD~~	+	==Recombinant cytotoxin-I from the venom of cobra N. oxiana==
		+	<StructureSection load='5t8a' size='340' side='right' caption='[[5t8a]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5t8a]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Central_asian_cobra Central asian cobra]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T8A FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rl5\|1rl5]], [[1zad\|1zad]]</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=5t8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t8a OCA], [http://pdbe.org/5t8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t8a RCSB], [http://www.ebi.ac.uk/pdbsum/5t8a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t8a ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/3SA1_NAJOX 3SA1_NAJOX]] This three-finger cytotoxin is a basic protein that interacts and penetrates into the cell membrane, with the tips of all the three loops. Cytotoxins which have a 'Pro-30' (P-type) interacts with membrane stronger that those which have a Ser-28 (S-type). CTI interacts with membrane weaker than CTII.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Today, recombinant proteins are quite widely used in biomedical and biotechnological applications. At the same time, the question about their full equivalence to the native analogues remains unanswered. To gain additional insight into this problem, intimate atomistic details of a relatively simple protein, small and structurally rigid recombinant cardiotoxin I (CTI) from cobra Naja oxiana venom, were characterized using nuclear magnetic resonance (NMR) spectroscopy and atomistic molecular dynamics (MD) simulations in water. Compared to the natural protein, it contains an additional Met residue at the N-terminus. In this work, the NMR-derived spatial structure of uniformly 13C- and 15N-labeled CTI and its dynamic behavior were investigated and subjected to comparative analysis with the corresponding data for the native toxin. The differences were found in dihedral angles of only a single residue, adjacent to the N-terminal methionine. Microsecond-long MD traces of the toxins reveal an increased flexibility in the residues spatially close to the N-Met. As the detected structural and dynamic changes of the two CTI models do not result in substantial differences in their cytotoxicities, we assume that the recombinant protein can be used for many purposes as a reasonable surrogate of the native one. In addition, we discuss general features of the spatial organization of cytotoxins, implied by the results of the current combined NMR and MD study.

-	~~Authors~~:	+	Structural and Dynamic "Portraits" of Recombinant and Native Cytotoxin I from Naja oxiana: How Close Are They?,Dubovskii PV, Dubinnyi MA, Konshina AG, Kazakova ED, Sorokoumova GM, Ilyasova TM, Shulepko MA, Chertkova RV, Lyukmanova EN, Dolgikh DA, Arseniev AS, Efremov RG Biochemistry. 2017 Aug 29;56(34):4468-4477. doi: 10.1021/acs.biochem.7b00453., Epub 2017 Aug 14. PMID:28749688<ref>PMID:28749688</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5t8a" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Central asian cobra]]
		+	[[Category: Dolgikh, D A]]
		+	[[Category: Dubinnyi, M A]]
		+	[[Category: Dubovskii, P V]]
		+	[[Category: Efremov, R G]]
		+	[[Category: Kirpichnikov, M P]]
		+	[[Category: Lyukmanova, E N]]
		+	[[Category: Shulepko, M A]]
		+	[[Category: All-beta sheet protein]]
		+	[[Category: Cytolytic peptide]]
		+	[[Category: Recombinant production]]
		+	[[Category: Structure from molmol]]
		+	[[Category: Toxin]]

OCA: Protected "5t8a" [edit=sysop:move=sysop]

OCA — Wed, 14 Sep 2016 14:08:13 GMT

Protected "5t8a" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:08, 14 September 2016

OCA: New page: '''Unreleased structure''' The entry 5t8a is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 14 Sep 2016 14:08:12 GMT

New page: '''Unreleased structure''' The entry 5t8a is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5t8a is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]