Chameleon peptide - Revision history

Michal Harel at 07:08, 1 February 2016

Michal Harel — Mon, 01 Feb 2016 07:08:31 GMT

←Older revision		Revision as of 07:08, 1 February 2016
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	==Does the amino acid sequence ''really'' determine the 3D structure of a peptide?==		==Does the amino acid sequence ''really'' determine the 3D structure of a peptide?==
-	<StructureSection load='2gb1' size='350' side='right' caption='2gb1' scene='61/611445/Rainbow_cartoon/1'>	+	<StructureSection load='2gb1' size='350' side='right' caption='Protein G immunoglobulin binding domain (PDB code [[2gb1]])' scene='61/611445/Rainbow_cartoon/1'>
	[[Image:Chameleon.jpg\|left\|170px\|thumb\|Chamelion]]		[[Image:Chameleon.jpg\|left\|170px\|thumb\|Chamelion]]
	==General question==		==General question==

Joel L. Sussman at 07:18, 4 December 2014

Joel L. Sussman — Thu, 04 Dec 2014 07:18:11 GMT

←Older revision		Revision as of 07:18, 4 December 2014
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	== Seeing is believing ==		== Seeing is believing ==
-	To simplify the figure, the entire IgG-Binding domain<ref>PMID:1871600 </ref> is colored <scene name='61/611445/Cartoon_beige/1'>beige</scene>. Now, if the amino acids residues, <scene name='61/611445/~~Cartoon_pink_23-33~~/1'>23-33</scene>, are changed to the ''Chameleon'' sequence i.e. <span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style>, virtually no change in structure is seen.	+	To simplify the figure, the entire IgG-Binding domain<ref>PMID:1871600 </ref> is colored <scene name='61/611445/Cartoon_beige/1'>beige</scene>. Now, if the amino acids residues, <<scene name='61/611445/Cartoon_blanche/2'>23-33</scene>>, are changed to the ''Chameleon'' sequence i.e. <span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style>, virtually no change in structure is seen.
	Specifically the WT sequence in yellow (residues 23-33) is changed to Chameleon sequence shown in pink, , n.b. only 5 AA's have been changed in this region<br />		Specifically the WT sequence in yellow (residues 23-33) is changed to Chameleon sequence shown in pink, , n.b. only 5 AA's have been changed in this region<br />

Joel L. Sussman at 14:48, 2 December 2014

Joel L. Sussman — Tue, 02 Dec 2014 14:48:30 GMT

←Older revision		Revision as of 14:48, 2 December 2014
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-	==Does the amino acid sequence ''really'' determine the 3D structure of a peptide?')==	+	==Does the amino acid sequence ''really'' determine the 3D structure of a peptide?==
	<StructureSection load='2gb1' size='350' side='right' caption='2gb1' scene='61/611445/Rainbow_cartoon/1'>		<StructureSection load='2gb1' size='350' side='right' caption='2gb1' scene='61/611445/Rainbow_cartoon/1'>
	[[Image:Chameleon.jpg\|left\|170px\|thumb\|Chamelion]]		[[Image:Chameleon.jpg\|left\|170px\|thumb\|Chamelion]]

Joel L. Sussman at 17:43, 1 December 2014

Joel L. Sussman — Mon, 01 Dec 2014 17:43:53 GMT

←Older revision		Revision as of 17:43, 1 December 2014
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	Mutated: TTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDG<span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style>TVTEK</font face>		Mutated: TTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDG<span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style>TVTEK</font face>

-	== 3D structure of sequence adopts to environment ==	+	== 3D structure of a sequence adopts to its environment ==
	The 3D structure of the ''Chameleon'' sequence, '''AWTVEKAFKTF''', appears to adopt to its environment.		The 3D structure of the ''Chameleon'' sequence, '''AWTVEKAFKTF''', appears to adopt to its environment.
	</StructureSection>		</StructureSection>
	== References ==		== References ==
	<references/>		<references/>

Joel L. Sussman at 17:43, 1 December 2014

Joel L. Sussman — Mon, 01 Dec 2014 17:43:04 GMT

←Older revision		Revision as of 17:43, 1 December 2014
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	Mutated: TTYKLILNGKTLKGETTTEAVD<span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style>ANDNGVDGEWTYDDATKTFTVTEK</font face>		Mutated: TTYKLILNGKTLKGETTTEAVD<span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style>ANDNGVDGEWTYDDATKTFTVTEK</font face>

-	If a similar change ~~from~~ the ~~Wild-Type~~ to ~~where 5 amino acids, in~~ the ~~region~~ <scene name='61/611445/Cartoon_pink_42-52/1'>42-52</scene> ~~are changed to~~ the ~~''Chameleon'' sequence, specifically from/to:~~<br />	+	If a similar change in the WT sequences is made to the Chameleon sequence for residues <scene name='61/611445/Cartoon_pink_42-52/1'>42-52</scene> again virtually no change in the 3D structure of this protein is seen.<br />
	<font face=Courier>		<font face=Courier>
-	TTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDG<span style="color:#000000; background:#FFFF00">EWTYDDATKTF</span style>TVTEK<br />	+	WT: &emsp;&emsp;&emsp;&emsp; TTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDG<span style="color:#000000; background:#FFFF00">EWTYDDATKTF</span style>TVTEK<br />
-	TTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDG<span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style>TVTEK</font face>	+	Mutated: TTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDG<span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style>TVTEK</font face>

	== 3D structure of sequence adopts to environment ==		== 3D structure of sequence adopts to environment ==

Joel L. Sussman at 17:39, 1 December 2014

Joel L. Sussman — Mon, 01 Dec 2014 17:39:42 GMT

←Older revision		Revision as of 17:39, 1 December 2014
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	<font face=Courier>		<font face=Courier>
-	WT: ~~{{spaces\|6}}~~ TTYKLILNGKTLKGETTTEAVD<span style="color:#000000; background:#FFFF00">AATAEKVFKQY</span style>ANDNGVDGEWTYDDATKTFTVTEK<br />	+	WT: &emsp;&emsp;&emsp;&emsp; TTYKLILNGKTLKGETTTEAVD<span style="color:#000000; background:#FFFF00">AATAEKVFKQY</span style>ANDNGVDGEWTYDDATKTFTVTEK<br />
	Mutated: TTYKLILNGKTLKGETTTEAVD<span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style>ANDNGVDGEWTYDDATKTFTVTEK</font face>		Mutated: TTYKLILNGKTLKGETTTEAVD<span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style>ANDNGVDGEWTYDDATKTFTVTEK</font face>

Joel L. Sussman at 17:34, 1 December 2014

Joel L. Sussman — Mon, 01 Dec 2014 17:34:38 GMT

←Older revision		Revision as of 17:34, 1 December 2014
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	== Seeing is believing ==		== Seeing is believing ==
-	To simplify the figure, the entire IgG-Binding domain<ref>PMID:1871600 </ref> is colored <scene name='61/611445/Cartoon_beige/1'>beige</scene>.	+	To simplify the figure, the entire IgG-Binding domain<ref>PMID:1871600 </ref> is colored <scene name='61/611445/Cartoon_beige/1'>beige</scene>. Now, if the amino acids residues, <scene name='61/611445/Cartoon_pink_23-33/1'>23-33</scene>, are changed to the ''Chameleon'' sequence i.e. <span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style>, virtually no change in structure is seen.
-	If residues <scene name='61/611445/Cartoon_pink_23-33/1'>23-33</scene> are changed to the ''Chameleon'' sequence i.e. <span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style>, virtually no change in structure is seen.	+
	Specifically the WT sequence in yellow (residues 23-33) is changed to Chameleon sequence shown in pink, , n.b. only 5 AA's have been changed in this region<br />		Specifically the WT sequence in yellow (residues 23-33) is changed to Chameleon sequence shown in pink, , n.b. only 5 AA's have been changed in this region<br />

	<font face=Courier>		<font face=Courier>
-	WT: TTYKLILNGKTLKGETTTEAVD<span style="color:#000000; background:#FFFF00">AATAEKVFKQY</span style>ANDNGVDGEWTYDDATKTFTVTEK<br />	+	WT: {{spaces\|6}} TTYKLILNGKTLKGETTTEAVD<span style="color:#000000; background:#FFFF00">AATAEKVFKQY</span style>ANDNGVDGEWTYDDATKTFTVTEK<br />
	Mutated: TTYKLILNGKTLKGETTTEAVD<span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style>ANDNGVDGEWTYDDATKTFTVTEK</font face>		Mutated: TTYKLILNGKTLKGETTTEAVD<span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style>ANDNGVDGEWTYDDATKTFTVTEK</font face>

Joel L. Sussman at 17:30, 1 December 2014

Joel L. Sussman — Mon, 01 Dec 2014 17:30:05 GMT

←Older revision		Revision as of 17:30, 1 December 2014
Line 9:		Line 9:

	== Seeing is believing ==		== Seeing is believing ==
-	To simplify the figure, the entire IgG-Binding domain<ref>PMID:1871600 </ref> is colored <scene name='61/611445/Cartoon_beige/1'>beige</scene>. ~~Now displaying, in pink, the amino acids in the region~~ <scene name='61/611445/Cartoon_pink_23-33/1'>23-33</scene>, are ~~change~~ to the ''Chameleon'' sequence, i.e. <span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style> (~~only 5 amino acids are mutated~~)~~, specifically from/~~to:<br />	+	To simplify the figure, the entire IgG-Binding domain<ref>PMID:1871600 </ref> is colored <scene name='61/611445/Cartoon_beige/1'>beige</scene>.
		+	If residues <scene name='61/611445/Cartoon_pink_23-33/1'>23-33</scene> are changed to the ''Chameleon'' sequence i.e. <span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style>, virtually no change in structure is seen.
		+	Specifically the WT sequence in yellow (residues 23-33) is changed to Chameleon sequence shown in pink, , n.b. only 5 AA's have been changed in this region<br />

-	<font face=Courier>	+	<font face=Courier>
-	TTYKLILNGKTLKGETTTEAVD<span style="color:#000000; background:#FFFF00">AATAEKVFKQY</span style>ANDNGVDGEWTYDDATKTFTVTEK<br />	+	WT: TTYKLILNGKTLKGETTTEAVD<span style="color:#000000; background:#FFFF00">AATAEKVFKQY</span style>ANDNGVDGEWTYDDATKTFTVTEK<br />
-	TTYKLILNGKTLKGETTTEAVD<span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style>ANDNGVDGEWTYDDATKTFTVTEK</font face>	+	Mutated: TTYKLILNGKTLKGETTTEAVD<span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style>ANDNGVDGEWTYDDATKTFTVTEK</font face>

	If a similar change from the Wild-Type to where 5 amino acids, in the region <scene name='61/611445/Cartoon_pink_42-52/1'>42-52</scene> are changed to the ''Chameleon'' sequence, specifically from/to:<br />		If a similar change from the Wild-Type to where 5 amino acids, in the region <scene name='61/611445/Cartoon_pink_42-52/1'>42-52</scene> are changed to the ''Chameleon'' sequence, specifically from/to:<br />

Joel L. Sussman at 17:24, 1 December 2014

Joel L. Sussman — Mon, 01 Dec 2014 17:24:03 GMT

←Older revision		Revision as of 17:24, 1 December 2014
Line 11:		Line 11:
	To simplify the figure, the entire IgG-Binding domain<ref>PMID:1871600 </ref> is colored <scene name='61/611445/Cartoon_beige/1'>beige</scene>. Now displaying, in pink, the amino acids in the region <scene name='61/611445/Cartoon_pink_23-33/1'>23-33</scene>, are change to the ''Chameleon'' sequence, i.e. <span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style> (only 5 amino acids are mutated), specifically from/to:<br />		To simplify the figure, the entire IgG-Binding domain<ref>PMID:1871600 </ref> is colored <scene name='61/611445/Cartoon_beige/1'>beige</scene>. Now displaying, in pink, the amino acids in the region <scene name='61/611445/Cartoon_pink_23-33/1'>23-33</scene>, are change to the ''Chameleon'' sequence, i.e. <span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style> (only 5 amino acids are mutated), specifically from/to:<br />

-	<font face=Courier>TTYKLILNGKTLKGETTTEAVD<span style="color:#000000; background:#FFFF00">AATAEKVFKQY</span style>ANDNGVDGEWTYDDATKTFTVTEK<br />	+	<font face=Courier>
		+	TTYKLILNGKTLKGETTTEAVD<span style="color:#000000; background:#FFFF00">AATAEKVFKQY</span style>ANDNGVDGEWTYDDATKTFTVTEK<br />
	TTYKLILNGKTLKGETTTEAVD<span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style>ANDNGVDGEWTYDDATKTFTVTEK</font face>		TTYKLILNGKTLKGETTTEAVD<span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style>ANDNGVDGEWTYDDATKTFTVTEK</font face>

	If a similar change from the Wild-Type to where 5 amino acids, in the region <scene name='61/611445/Cartoon_pink_42-52/1'>42-52</scene> are changed to the ''Chameleon'' sequence, specifically from/to:<br />		If a similar change from the Wild-Type to where 5 amino acids, in the region <scene name='61/611445/Cartoon_pink_42-52/1'>42-52</scene> are changed to the ''Chameleon'' sequence, specifically from/to:<br />
-	<font face=Courier>TTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDG<span style="color:#000000; background:#FFFF00">EWTYDDATKTF</span style>TVTEK<br />	+	<font face=Courier>
-	TTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDG<span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style>TVTEK</font face>	+	TTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDG<span style="color:#000000; background:#FFFF00">EWTYDDATKTF</span style>TVTEK<br />
		+	TTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDG<span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style>TVTEK</font face>

	== 3D structure of sequence adopts to environment ==		== 3D structure of sequence adopts to environment ==

Joel L. Sussman at 17:23, 1 December 2014

Joel L. Sussman — Mon, 01 Dec 2014 17:23:06 GMT

←Older revision		Revision as of 17:23, 1 December 2014
Line 12:		Line 12:

	<font face=Courier>TTYKLILNGKTLKGETTTEAVD<span style="color:#000000; background:#FFFF00">AATAEKVFKQY</span style>ANDNGVDGEWTYDDATKTFTVTEK<br />		<font face=Courier>TTYKLILNGKTLKGETTTEAVD<span style="color:#000000; background:#FFFF00">AATAEKVFKQY</span style>ANDNGVDGEWTYDDATKTFTVTEK<br />
-	TTYKLILNGKTLKGETTTEAVD<span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style>ANDNGVDGEWTYDDATKTFTVTEK</font face>	+	TTYKLILNGKTLKGETTTEAVD<span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style>ANDNGVDGEWTYDDATKTFTVTEK</font face>

	If a similar change from the Wild-Type to where 5 amino acids, in the region <scene name='61/611445/Cartoon_pink_42-52/1'>42-52</scene> are changed to the ''Chameleon'' sequence, specifically from/to:<br />		If a similar change from the Wild-Type to where 5 amino acids, in the region <scene name='61/611445/Cartoon_pink_42-52/1'>42-52</scene> are changed to the ''Chameleon'' sequence, specifically from/to:<br />
-	<font face=Courier>~~TTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEK~~<br />	+	<font face=Courier>TTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDG<span style="color:#000000; background:#FFFF00">EWTYDDATKTF</span style>TVTEK<br />
-	TTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDG~~'''~~AWTVEKAFKTF~~'''~~TVTEK</font face>	+	TTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDG<span style="color:#FFFFFF; background:#FF69B4">AWTVEKAFKTF</span style>TVTEK</font face>

	== 3D structure of sequence adopts to environment ==		== 3D structure of sequence adopts to environment ==