5xx4 - Revision history

OCA at 08:16, 22 November 2023

OCA — Wed, 22 Nov 2023 08:16:57 GMT

←Older revision		Revision as of 08:16, 22 November 2023
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	<StructureSection load='5xx4' size='340' side='right'caption='[[5xx4]], [[Resolution\|resolution]] 1.67Å' scene=''>		<StructureSection load='5xx4' size='340' side='right'caption='[[5xx4]], [[Resolution\|resolution]] 1.67Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xx4]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bovin Bovin~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XX4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XX4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xx4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XX4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XX4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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]] 1.67Å</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=5xx4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xx4 OCA], [~~http~~://pdbe.org/5xx4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xx4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xx4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xx4 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5xx4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xx4 OCA], [https://pdbe.org/5xx4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xx4 RCSB], [https://www.ebi.ac.uk/pdbsum/5xx4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xx4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BPT1_BOVIN BPT1_BOVIN]] Inhibits trypsin, kallikrein, chymotrypsin, and plasmin.	+	[https://www.uniprot.org/uniprot/BPT1_BOVIN BPT1_BOVIN] Inhibits trypsin, kallikrein, chymotrypsin, and plasmin.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bovin~~]]	+	[[Category: Bos taurus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Islam~~, M M]]~~	+	[[Category: Islam MM]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase inhibitor~~]]	+

OCA at 12:27, 17 July 2019

OCA — Wed, 17 Jul 2019 12:27:49 GMT

←Older revision		Revision as of 12:27, 17 July 2019
Line 1:		Line 1:

	==A BPTI-[5,55] variant with C14GA38K mutations==		==A BPTI-[5,55] variant with C14GA38K mutations==
-	<StructureSection load='5xx4' size='340' side='right' caption='[[5xx4]], [[Resolution\|resolution]] 1.67Å' scene=''>	+	<StructureSection load='5xx4' size='340' side='right'caption='[[5xx4]], [[Resolution\|resolution]] 1.67Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xx4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XX4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XX4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xx4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XX4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XX4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5xx4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xx4 OCA], [http://pdbe.org/5xx4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xx4 RCSB], [http://www.ebi.ac.uk/pdbsum/5xx4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xx4 ProSAT]</span></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=5xx4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xx4 OCA], [http://pdbe.org/5xx4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xx4 RCSB], [http://www.ebi.ac.uk/pdbsum/5xx4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xx4 ProSAT]</span></td></tr>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/BPT1_BOVIN BPT1_BOVIN]] Inhibits trypsin, kallikrein, chymotrypsin, and plasmin.		[[http://www.uniprot.org/uniprot/BPT1_BOVIN BPT1_BOVIN]] Inhibits trypsin, kallikrein, chymotrypsin, and plasmin.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Protein stabilization is difficult to rationalize, but the detailed thermodynamic and structural analysis of a series of carefully designed mutants may provide experimental insights into the mechanisms underlying stabilization. Here, we report a systematic structural and thermodynamic analysis of bovine pancreatic trypsin inhibitor (BPTI) variants that are significantly stabilized through a single amino acid substitution at residue 38, which is located in a loop mostly exposed on the protein surface. Differential scanning calorimetry indicated that the BPTI-[5,55]Gly(14) variants with a single mutation at position 38 were stabilized in an enthalpy-driven manner and that the magnitude of the stabilization increased as the hydrophobicity of residue 38 increased. This increase in the thermal stability of BPTI was unexpected because a hydrophobic residue on a protein surface is usually destabilizing. To identify the structural determinants of this stabilization, we determined the crystal structures of six BPTI-[5,55]Gly(14) variants (Gly(14) Gly(38) , Gly(14) Ala(38) , Gly(14) Val(38) , Gly(14) Leu(38) , Gly(14) Ile(38) , and Gly(14) Lys(38) ) at high resolutions and showed that they retain essentially the same structure as the wild-type BPTI. A more detailed examination of their structures indicated that the extent of thermal stabilization correlated with both improved local packing and increased hydration around the substitution sites. In particular, the number of water molecules near residue 38 increased upon mutation to a hydrophobic residue suggesting that improved hydration contributed to the enthalpy-driven stabilization. Increasing a protein's thermal stability by the placement of a hydrophobic amino acid on the protein surface is a novel and unexpected phenomenon, and its exact nature is worth further examination, as it may provide a generic method for stabilizing proteins in an enthalpy-driven manner. DATABASE: The coordinates and structure factors of Gly(14) Gly(38) , Gly(14) Ile(38) , Gly(14) Leu(38) , and Gly(14) Lys(38) variants of BPTI-[5,55] are deposited in the Protein Data Bank under the PDB entry codes 5XX3, 5XX5, 5XX2, and 5XX4, respectively. We previously reported the structures of Gly(14) Ala(38) (2ZJX) and Gly(14) Val(38) (2ZVX).
		+
		+	Hydrophobic surface residues can stabilize a protein through improved water-protein interactions.,Islam MM, Kobayashi K, Kidokoro SI, Kuroda Y FEBS J. 2019 Jun 7. doi: 10.1111/febs.14941. PMID:31175706<ref>PMID:31175706</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5xx4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[BPTI 3D structures\|BPTI 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bovin]]
		+	[[Category: Large Structures]]
	[[Category: Islam, M M]]		[[Category: Islam, M M]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Hydrolase inhibitor]]		[[Category: Hydrolase inhibitor]]

OCA at 07:08, 4 July 2018

OCA — Wed, 04 Jul 2018 07:08:28 GMT

←Older revision		Revision as of 07:08, 4 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xx4 ~~is ON HOLD until Paper Publication~~	+	==A BPTI-[5,55] variant with C14GA38K mutations==
-		+	<StructureSection load='5xx4' size='340' side='right' caption='[[5xx4]], [[Resolution\|resolution]] 1.67Å' scene=''>
-	~~Authors~~: ~~Islam, M~~.M.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5xx4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XX4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XX4 FirstGlance]. <br>
-	~~Description~~: ~~A BPTI~~-[5,55] ~~variant with C14GA38K mutations~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=5xx4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xx4 OCA], [http://pdbe.org/5xx4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xx4 RCSB], [http://www.ebi.ac.uk/pdbsum/5xx4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xx4 ProSAT]</span></td></tr>
-	[[Category: Islam, M.M]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BPT1_BOVIN BPT1_BOVIN]] Inhibits trypsin, kallikrein, chymotrypsin, and plasmin.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Islam, M M]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolase inhibitor]]

OCA: Protected "5xx4" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 15:52:37 GMT

Protected "5xx4" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:52, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5xx4 is ON HOLD until Paper Publication Authors: Islam, M.M. Description: A BPTI-[5,55] variant with C14GA38K mutations [[Category: Unreleased Stru...

OCA — Wed, 27 Sep 2017 15:52:36 GMT

New page: '''Unreleased structure''' The entry 5xx4 is ON HOLD until Paper Publication Authors: Islam, M.M. Description: A BPTI-[5,55] variant with C14GA38K mutations [[Category: Unreleased Stru...

New page

'''Unreleased structure'''

The entry 5xx4 is ON HOLD until Paper Publication

Authors: Islam, M.M.

Description: A BPTI-[5,55] variant with C14GA38K mutations
[[Category: Unreleased Structures]]
[[Category: Islam, M.M]]