5npn - Revision history

OCA at 13:20, 15 November 2023

OCA — Wed, 15 Nov 2023 13:20:09 GMT

←Older revision		Revision as of 13:20, 15 November 2023
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	==Refined structure of cytotoxin I==		==Refined structure of cytotoxin I==
-	<StructureSection load='5npn' size='340' side='right'caption='[[5npn~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='5npn' size='340' side='right'caption='[[5npn]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5npn]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Naja_oxiana Naja oxiana]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NPN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5NPN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5npn]] 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=5NPN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NPN FirstGlance]. <br>
-	</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=5npn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5npn OCA], [~~http~~://pdbe.org/5npn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5npn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5npn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5npn ProSAT]</span></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'>[https://proteopedia.org/fgij/fg.htm?mol=5npn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5npn OCA], [https://pdbe.org/5npn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5npn RCSB], [https://www.ebi.ac.uk/pdbsum/5npn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5npn 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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Naja oxiana]]		[[Category: Naja oxiana]]
-	[[Category: Arseniev~~, A S~~]]	+	[[Category: Arseniev AS]]
-	[[Category: Dubinnyi~~, M A~~]]	+	[[Category: Dubinnyi MA]]
-	[[Category: Dubovskii~~, P V]]~~	+	[[Category: Dubovskii PV]]
-	~~[[Category: Cobra venom]]~~	+
-	~~[[Category: Cytolytic peptide]]~~	+
-	~~[[Category: Thre-finger folded protein]]~~	+
-	~~[[Category: Toxin~~]]	+

OCA at 13:14, 10 May 2019

OCA — Fri, 10 May 2019 13:14:15 GMT

←Older revision		Revision as of 13:14, 10 May 2019
Line 1:		Line 1:

	==Refined structure of cytotoxin I==		==Refined structure of cytotoxin I==
-	<StructureSection load='5npn' size='340' side='right' caption='[[5npn]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='5npn' size='340' side='right'caption='[[5npn]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5npn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Naja_oxiana Naja oxiana]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NPN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NPN FirstGlance]. <br>		<table><tr><td colspan='2'>[[5npn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Naja_oxiana Naja oxiana]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NPN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NPN FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Naja oxiana]]		[[Category: Naja oxiana]]
	[[Category: Arseniev, A S]]		[[Category: Arseniev, A S]]

OCA at 14:06, 11 April 2018

OCA — Wed, 11 Apr 2018 14:06:28 GMT

←Older revision		Revision as of 14:06, 11 April 2018
Line 8:		Line 8:
	== 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.		[[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.
		+
		+	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 5npn" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 05:51, 4 April 2018

OCA — Wed, 04 Apr 2018 05:51:29 GMT

←Older revision		Revision as of 05:51, 4 April 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5npn ~~is ON HOLD~~	+	==Refined structure of cytotoxin I==
-		+	<StructureSection load='5npn' size='340' side='right' caption='[[5npn]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
-	~~Authors~~: ~~Dubinnyi~~, M.A., ~~Dubovskii~~, P.V., ~~Arseniev~~, A.S.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5npn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Naja_oxiana Naja oxiana]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NPN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NPN FirstGlance]. <br>
-	~~Description~~: ~~Refined structure of~~ cytotoxin I	+	</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=5npn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5npn OCA], [http://pdbe.org/5npn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5npn RCSB], [http://www.ebi.ac.uk/pdbsum/5npn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5npn ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: Arseniev, A.S]]	+	== Function ==
-	[[Category: Dubovskii, P.V]]	+	[[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.
-	[[Category: ~~Dubinnyi, M.A~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Naja oxiana]]
		+	[[Category: Arseniev, A S]]
		+	[[Category: Dubinnyi, M A]]
		+	[[Category: Dubovskii, P V]]
		+	[[Category: Cobra venom]]
		+	[[Category: Cytolytic peptide]]
		+	[[Category: Thre-finger folded protein]]
		+	[[Category: Toxin]]

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

OCA — Thu, 27 Apr 2017 10:45:22 GMT

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

←Older revision

Revision as of 10:45, 27 April 2017

OCA: New page: '''Unreleased structure''' The entry 5npn is ON HOLD Authors: Dubinnyi, M.A., Dubovskii, P.V., Arseniev, A.S. Description: Refined structure of cytotoxin I [[Category: Unreleased Struc...

OCA — Thu, 27 Apr 2017 10:45:21 GMT

New page: '''Unreleased structure''' The entry 5npn is ON HOLD Authors: Dubinnyi, M.A., Dubovskii, P.V., Arseniev, A.S. Description: Refined structure of cytotoxin I [[Category: Unreleased Struc...

New page

'''Unreleased structure'''

The entry 5npn is ON HOLD

Authors: Dubinnyi, M.A., Dubovskii, P.V., Arseniev, A.S.

Description: Refined structure of cytotoxin I
[[Category: Unreleased Structures]]
[[Category: Arseniev, A.S]]
[[Category: Dubovskii, P.V]]
[[Category: Dubinnyi, M.A]]