7v5p - Revision history

OCA at 17:20, 29 November 2023

2023-11-29T17:20:36Z

←Older revision		Revision as of 17:20, 29 November 2023
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	==The dimeric structure of G80A/H81A myoglobin==		==The dimeric structure of G80A/H81A myoglobin==
-	<StructureSection load='7v5p' size='340' side='right'caption='[[7v5p]]' scene=''>	+	<StructureSection load='7v5p' size='340' side='right'caption='[[7v5p]], [[Resolution\|resolution]] 1.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7V5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V5P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7v5p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7V5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V5P FirstGlance]. <br>
-	</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=7v5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v5p OCA], [https://pdbe.org/7v5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v5p RCSB], [https://www.ebi.ac.uk/pdbsum/7v5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v5p ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.16Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=O:OXYGEN+ATOM'>O</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=7v5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v5p OCA], [https://pdbe.org/7v5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v5p RCSB], [https://www.ebi.ac.uk/pdbsum/7v5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v5p ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/MYG_HORSE MYG_HORSE] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Various factors, such as helical propensity and hydrogen bonds, control protein structures. A frequently used model protein, myoglobin (Mb), can perform 3D domain swapping, in which the loop at the hinge region is converted to a helical structure in the dimer. We have previously succeeded in obtaining monomer-dimer equilibrium in the native state by introducing a high alpha-helical propensity residue, Ala, to the hinge region. In this study, we focused on another factor that governs the protein structure, hydrogen bonding. X-ray crystal structures and thermodynamic studies showed that the myoglobin dimer was stabilized over the monomer when keeping His82 to interact with Lys79 and Asp141 through water moleclues and mutating Leu137, which was located close to the H-bond network at the dimer hinge region, to a hydrophilic amino acid (Glu or Asp). Molecular dynamics simulation studies confirmed that the number of H-bonds increased and the alpha-helices at the hinge region became more rigid for mutants with a tighter H-bond network, supporting the hypothesis that the myoglobin dimer is stabilized when the H-bond network at the hinge region is enhanced. This demonstrates the importance and utility of hydrogen bonds for designing a protein dimer from its monomer with 3D domain swapping.
		+
		+	Experimental and theoretical study on converting myoglobin into a stable domain-swapped dimer by utilizing a tight hydrogen bond network at the hinge region.,Xie C, Shimoyama H, Yamanaka M, Nagao S, Komori H, Shibata N, Higuchi Y, Shigeta Y, Hirota S RSC Adv. 2021 Nov 23;11(59):37604-37611. doi: 10.1039/d1ra06888a. eCollection , 2021 Nov 17. PMID:35496441<ref>PMID:35496441</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7v5p" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Myoglobin 3D structures\|Myoglobin 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Equus caballus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Xie, C, Nagao, S, Shibata, N,~~ Higuchi, Y, Hirota, S]]	+	[[Category: Higuchi Y]]
		+	[[Category: Hirota S]]
		+	[[Category: Nagao S]]
		+	[[Category: Shibata N]]
		+	[[Category: Xie C]]

OCA at 07:28, 29 June 2022

2022-06-29T07:28:15Z

←Older revision		Revision as of 07:28, 29 June 2022
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-	'''Unreleased structure'''

-	~~The entry 7v5p is ON HOLD until Paper Publication~~	+	==The dimeric structure of G80A/H81A myoglobin==
-		+	<StructureSection load='7v5p' size='340' side='right'caption='[[7v5p]]' scene=''>
-	~~Authors: Xie, C., Nagao, S., Shibata, N., Higuchi, Y., Hirota, S.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7V5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V5P FirstGlance]. <br>
-	~~Description:~~ The dimeric structure of G80A/H81A myoglobin	+	</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=7v5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v5p OCA], [https://pdbe.org/7v5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v5p RCSB], [https://www.ebi.ac.uk/pdbsum/7v5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v5p ProSAT]</span></td></tr>
-	[[~~Category: Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Hirota, S]~~]	+	__TOC__
-	[[~~Category~~: ~~Shibata~~, N]]	+	</StructureSection>
-	[[~~Category~~: ~~Higuchi~~, Y]]	+	[[Category: Large Structures]]
-	[[Category: ~~Xie, C~~]]	+	[[Category: Xie, C, Nagao, S, Shibata, N, Higuchi, Y, Hirota, S]]
-	[[Category: Nagao, S]]	+

OCA at 07:55, 8 September 2021

2021-09-08T07:55:46Z

←Older revision		Revision as of 07:55, 8 September 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7v5p is ON HOLD	+	The entry 7v5p is ON HOLD until Paper Publication

	Authors: Xie, C., Nagao, S., Shibata, N., Higuchi, Y., Hirota, S.		Authors: Xie, C., Nagao, S., Shibata, N., Higuchi, Y., Hirota, S.
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Hirota, S]]		[[Category: Hirota, S]]
-	[[Category: Xie, C]]
	[[Category: Shibata, N]]		[[Category: Shibata, N]]
	[[Category: Higuchi, Y]]		[[Category: Higuchi, Y]]
		+	[[Category: Xie, C]]
	[[Category: Nagao, S]]		[[Category: Nagao, S]]

OCA: Protected "7v5p" [edit=sysop:move=sysop]

2021-08-25T05:24:53Z

Protected "7v5p" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:24, 25 August 2021

OCA: New page: '''Unreleased structure''' The entry 7v5p is ON HOLD Authors: Xie, C., Nagao, S., Shibata, N., Higuchi, Y., Hirota, S. Description: The dimeric structure of G80A/H81A myoglobin [[Categ...

2021-08-25T05:24:52Z

New page: '''Unreleased structure''' The entry 7v5p is ON HOLD Authors: Xie, C., Nagao, S., Shibata, N., Higuchi, Y., Hirota, S. Description: The dimeric structure of G80A/H81A myoglobin [[Categ...

New page

'''Unreleased structure'''

The entry 7v5p is ON HOLD

Authors: Xie, C., Nagao, S., Shibata, N., Higuchi, Y., Hirota, S.

Description: The dimeric structure of G80A/H81A myoglobin
[[Category: Unreleased Structures]]
[[Category: Hirota, S]]
[[Category: Xie, C]]
[[Category: Shibata, N]]
[[Category: Higuchi, Y]]
[[Category: Nagao, S]]