User:Eric Martz/5eon - Revision history

Eric Martz at 23:08, 19 June 2016

Eric Martz — Sun, 19 Jun 2016 23:08:14 GMT

←Older revision		Revision as of 23:08, 19 June 2016
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	[[Cation-pi interactions]] involving Phe cannot form since Phe is buried and Lys is on the surface. A few cation-pi interactions may form between Trp on the surface and Lys.		[[Cation-pi interactions]] involving Phe cannot form since Phe is buried and Lys is on the surface. A few cation-pi interactions may form between Trp on the surface and Lys.

-	==Sequence==	+	==Salt Bridges Between Hexamers==
		+	The arrangement of rows of alternating negative and positive charge on the surfaces of the hexamers suggests that salt bridges might form between hexamers, stabilizing the protein crystal. In fact, there is
		+
		+	only one salt bridge
		+
		+	between each pair of hexamers, as shown in the crystallographic unit cell.
		+
		+	==Sequence and Blocked Termini==
	The peptide sequence is constructed from 4 copies of heptad		The peptide sequence is constructed from 4 copies of heptad

Eric Martz at 23:04, 19 June 2016

Eric Martz — Sun, 19 Jun 2016 23:04:02 GMT

←Older revision		Revision as of 23:04, 19 June 2016
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	The <scene name='73/733958/Hexamer_of_5eon/5'>surface of the fiber</scene> is mostly charged <font color="blue">'''Lys+'''</font> and <font color="red">'''Glu-'''</font> sidechains, with an occasional Trp or Gln, interspersed with Ala (spheres).		The <scene name='73/733958/Hexamer_of_5eon/5'>surface of the fiber</scene> is mostly charged <font color="blue">'''Lys+'''</font> and <font color="red">'''Glu-'''</font> sidechains, with an occasional Trp or Gln, interspersed with Ala (spheres).
		+
		+	==Charges==
		+	The peptides were designed to form salt bridges between chains in the hexamer, assuming the peptides are parallel in the hexamer. Surprisingly, the peptides are anti-parallel in the hexmer that formed. This precluded salt bridges within the hexamer. The authors note that this shows that the energetics of the hydrophobic core are dominant, with the salt bridges being unnecessary.

	The charges form <scene name='73/733958/Hexamer_of_5eon/2'>helices of opposite charge</scene> on the surface, reminiscent of [[User:Ke Xiao/Geobacter pilus models\|Xiao's theoretical model of the ''Geobacter sulfurreducens'' pilus]]. Terminal charges on the chains were blocked (see below). Unlike Xiao's model, none of these form salt bridges (a few opposite charges are water-bridged).		The charges form <scene name='73/733958/Hexamer_of_5eon/2'>helices of opposite charge</scene> on the surface, reminiscent of [[User:Ke Xiao/Geobacter pilus models\|Xiao's theoretical model of the ''Geobacter sulfurreducens'' pilus]]. Terminal charges on the chains were blocked (see below). Unlike Xiao's model, none of these form salt bridges (a few opposite charges are water-bridged).

Eric Martz at 16:09, 17 June 2016

Eric Martz — Fri, 17 Jun 2016 16:09:50 GMT

←Older revision		Revision as of 16:09, 17 June 2016
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	The <scene name='73/733958/Hexamer_of_5eon/5'>surface of the fiber</scene> is mostly charged <font color="blue">'''Lys+'''</font> and <font color="red">'''Glu-'''</font> sidechains, with an occasional Trp or Gln, interspersed with Ala (spheres).		The <scene name='73/733958/Hexamer_of_5eon/5'>surface of the fiber</scene> is mostly charged <font color="blue">'''Lys+'''</font> and <font color="red">'''Glu-'''</font> sidechains, with an occasional Trp or Gln, interspersed with Ala (spheres).

-	The charges form <scene name='73/733958/Hexamer_of_5eon/2'>helices of opposite charge</scene> on the surface, reminiscent of [[User:Ke Xiao/Geobacter pilus models\|Xiao's theoretical model of the ''Geobacter sulfurreducens'' pilus]]. Unlike Xiao's model, none of these form salt bridges (a few opposite charges are water-bridged). [[Cation-pi interactions]] involving Phe cannot form since Phe is buried and Lys is on the surface. A few cation-pi interactions may form between Trp on the surface and Lys.	+	The charges form <scene name='73/733958/Hexamer_of_5eon/2'>helices of opposite charge</scene> on the surface, reminiscent of [[User:Ke Xiao/Geobacter pilus models\|Xiao's theoretical model of the ''Geobacter sulfurreducens'' pilus]]. Terminal charges on the chains were blocked (see below). Unlike Xiao's model, none of these form salt bridges (a few opposite charges are water-bridged).
		+
		+	[[Cation-pi interactions]] involving Phe cannot form since Phe is buried and Lys is on the surface. A few cation-pi interactions may form between Trp on the surface and Lys.

	==Sequence==		==Sequence==

Eric Martz at 01:21, 17 June 2016

Eric Martz — Fri, 17 Jun 2016 01:21:54 GMT

←Older revision		Revision as of 01:21, 17 June 2016
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	<StructureSection size='[300,400]' side='right' caption='Biological unit of [[5eon]].' scene='73/733958/Hexamer_of_5eon/1'>		<StructureSection size='[300,400]' side='right' caption='Biological unit of [[5eon]].' scene='73/733958/Hexamer_of_5eon/1'>

-	The [[biological unit]] of [[5eon]] (<scene name='73/733958/Hexamer_of_5eon/1'>restore initial scene</scene>) is a crystallographic structure of 6 alpha helices assembled into a fiber with a hydrophobic core<ref name="5eon">PMID: 27192036</ref>. The individual peptides are synthetic and were designed to assemble in this manner, with a ~~hydrophotic~~ core rich in phenylalanine. The crystal structure has a [[resolution]] of 1.7 Å (very good), and an [[Rfree]] of 0.22, which is average for this resolution, indicating that the model is reliable.	+	The [[biological unit]] of [[5eon]] (<scene name='73/733958/Hexamer_of_5eon/1'>restore initial scene</scene>) is a crystallographic structure of 6 alpha helices assembled into a fiber with a hydrophobic core<ref name="5eon">PMID: 27192036</ref>. The individual peptides are '''synthetic''' and were designed to assemble in this manner, with a hydrophobic core rich in phenylalanine. The crystal structure has a [[resolution]] of 1.7 Å (very good), and an [[Rfree]] of 0.22, which is average for this resolution, indicating that the model is reliable.

	The <scene name='73/733958/Hexamer_of_5eon/3'>aromatic rings of Phe pack in the core</scene>. The Phe rings (<font color="#686868">'''dark gray'''</font>) are surrounded by <scene name='73/733958/Hexamer_of_5eon/4'>hydrophobic sidechains of Ile</scene> (<font color="#909090">'''light gray'''</font>).		The <scene name='73/733958/Hexamer_of_5eon/3'>aromatic rings of Phe pack in the core</scene>. The Phe rings (<font color="#686868">'''dark gray'''</font>) are surrounded by <scene name='73/733958/Hexamer_of_5eon/4'>hydrophobic sidechains of Ile</scene> (<font color="#909090">'''light gray'''</font>).

Eric Martz at 19:21, 10 June 2016

Eric Martz — Fri, 10 Jun 2016 19:21:22 GMT

←Older revision		Revision as of 19:21, 10 June 2016
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	==View in FirstGlance==		==View in FirstGlance==
	*[http://firstglance.jmol.org/fg.htm?mol=5eon Asymmetric unit (trimer) of 5eon in FirstGlance]		*[http://firstglance.jmol.org/fg.htm?mol=5eon Asymmetric unit (trimer) of 5eon in FirstGlance]
-	*The biological unit is available from within FirstGlance (Resources tab), but for convenience:[http://firstglance.jmol.org/fg.htm?mol=http://proteopedia.org/wiki/images/a/a3/5eon_mm1.pdb Biological unit (hexamer) of 5eon in FirstGlance]	+	*The biological unit is available from within FirstGlance (Resources tab), but for convenience: [http://firstglance.jmol.org/fg.htm?mol=http://proteopedia.org/wiki/images/a/a3/5eon_mm1.pdb Biological unit (hexamer) of 5eon in FirstGlance]

	==References and Notes==		==References and Notes==
	<references />		<references />

Eric Martz at 19:20, 10 June 2016

Eric Martz — Fri, 10 Jun 2016 19:20:58 GMT

←Older revision		Revision as of 19:20, 10 June 2016
Line 22:		Line 22:
	==View in FirstGlance==		==View in FirstGlance==
	*[http://firstglance.jmol.org/fg.htm?mol=5eon Asymmetric unit (trimer) of 5eon in FirstGlance]		*[http://firstglance.jmol.org/fg.htm?mol=5eon Asymmetric unit (trimer) of 5eon in FirstGlance]
-	*The biological unit is available from within FirstGlance (Resources tab), but for convenience:	+	*The biological unit is available from within FirstGlance (Resources tab), but for convenience:[http://firstglance.jmol.org/fg.htm?mol=http://proteopedia.org/wiki/images/a/a3/5eon_mm1.pdb Biological unit (hexamer) of 5eon in FirstGlance]
-	[http://firstglance.jmol.org/fg.htm?mol=http://proteopedia.org/wiki/images/a/a3/5eon_mm1.pdb Biological unit (hexamer) of 5eon in FirstGlance]	+

	==References and Notes==		==References and Notes==
	<references />		<references />

Eric Martz at 19:20, 10 June 2016

Eric Martz — Fri, 10 Jun 2016 19:20:29 GMT

←Older revision		Revision as of 19:20, 10 June 2016
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	==View in FirstGlance==		==View in FirstGlance==
-	*[http://firstglance.jmol.org/fg.htm?mol=5eon Asymmetric unit of 5eon in FirstGlance]	+	*[http://firstglance.jmol.org/fg.htm?mol=5eon Asymmetric unit (trimer) of 5eon in FirstGlance]
-	*	+	*The biological unit is available from within FirstGlance (Resources tab), but for convenience:
		+	[http://firstglance.jmol.org/fg.htm?mol=http://proteopedia.org/wiki/images/a/a3/5eon_mm1.pdb Biological unit (hexamer) of 5eon in FirstGlance]

	==References and Notes==		==References and Notes==
	<references />		<references />

Eric Martz at 19:16, 10 June 2016

Eric Martz — Fri, 10 Jun 2016 19:16:38 GMT

←Older revision		Revision as of 19:16, 10 June 2016
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	</StructureSection>		</StructureSection>
		+
		+	==View in FirstGlance==
		+	*[http://firstglance.jmol.org/fg.htm?mol=5eon Asymmetric unit of 5eon in FirstGlance]
		+	*

	==References and Notes==		==References and Notes==
	<references />		<references />

Eric Martz at 20:00, 4 June 2016

Eric Martz — Sat, 04 Jun 2016 20:00:56 GMT

←Older revision		Revision as of 20:00, 4 June 2016
Line 7:		Line 7:
	The <scene name='73/733958/Hexamer_of_5eon/5'>surface of the fiber</scene> is mostly charged <font color="blue">'''Lys+'''</font> and <font color="red">'''Glu-'''</font> sidechains, with an occasional Trp or Gln, interspersed with Ala (spheres).		The <scene name='73/733958/Hexamer_of_5eon/5'>surface of the fiber</scene> is mostly charged <font color="blue">'''Lys+'''</font> and <font color="red">'''Glu-'''</font> sidechains, with an occasional Trp or Gln, interspersed with Ala (spheres).

-	The charges form <scene name='73/733958/Hexamer_of_5eon/2'>helices of opposite charge</scene> on the surface, reminiscent of [[User:Ke Xiao/Geobacter pilus models\|Xiao's theoretical model of the ''Geobacter sulfurreducens'' pilus]]. Unlike Xiao's model, none of these form salt bridges (a few opposite charges are water-bridged). ~~No cation~~-pi interactions ~~occur~~ since ~~the cations (~~Lys~~) are all~~ on the surface~~, and the~~ pi ~~(Phe) are all buried~~.	+	The charges form <scene name='73/733958/Hexamer_of_5eon/2'>helices of opposite charge</scene> on the surface, reminiscent of [[User:Ke Xiao/Geobacter pilus models\|Xiao's theoretical model of the ''Geobacter sulfurreducens'' pilus]]. Unlike Xiao's model, none of these form salt bridges (a few opposite charges are water-bridged). [[Cation-pi interactions]] involving Phe cannot form since Phe is buried and Lys is on the surface. A few cation-pi interactions may form between Trp on the surface and Lys.

	==Sequence==		==Sequence==

Eric Martz at 19:42, 4 June 2016

Eric Martz — Sat, 04 Jun 2016 19:42:57 GMT

←Older revision		Revision as of 19:42, 4 June 2016
Line 7:		Line 7:
	The <scene name='73/733958/Hexamer_of_5eon/5'>surface of the fiber</scene> is mostly charged <font color="blue">'''Lys+'''</font> and <font color="red">'''Glu-'''</font> sidechains, with an occasional Trp or Gln, interspersed with Ala (spheres).		The <scene name='73/733958/Hexamer_of_5eon/5'>surface of the fiber</scene> is mostly charged <font color="blue">'''Lys+'''</font> and <font color="red">'''Glu-'''</font> sidechains, with an occasional Trp or Gln, interspersed with Ala (spheres).

-	The charges form <scene name='73/733958/Hexamer_of_5eon/2'>helices of opposite charge</scene> on the surface, reminiscent of [[User:Ke Xiao/Geobacter pilus models\|Xiao's theoretical model of the ''Geobacter sulfurreducens'' pilus]].	+	The charges form <scene name='73/733958/Hexamer_of_5eon/2'>helices of opposite charge</scene> on the surface, reminiscent of [[User:Ke Xiao/Geobacter pilus models\|Xiao's theoretical model of the ''Geobacter sulfurreducens'' pilus]]. Unlike Xiao's model, none of these form salt bridges (a few opposite charges are water-bridged). No cation-pi interactions occur since the cations (Lys) are all on the surface, and the pi (Phe) are all buried.

	==Sequence==		==Sequence==