Homodimer Structure Calculation Using CYANA - Revision history

Ertekina at 12:36, 28 August 2012

2012-08-28T12:36:02Z

← Older revision		Revision as of 12:36, 28 August 2012
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	== '''Manual Calculation''' ==		== '''Manual Calculation''' ==

	*Manual ~~run~~		*Manual Run

	Similar to the automatic run, modify the <tt>seq</tt> file, <tt>prot</tt> list, <tt>init.cya</tt>, and run the CYANA manual CALC macro as usual.		Similar to the automatic run, modify the <tt>seq</tt> file, <tt>prot</tt> list, <tt>init.cya</tt>, and run the CYANA manual CALC macro as usual.

Jma at 21:56, 6 January 2010

2010-01-06T21:56:07Z

← Older revision		Revision as of 21:56, 6 January 2010
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	*Manual run		*Manual run

	Similar to the automatic run, modify the <tt>seq</tt> file, <tt>prot</tt> list, <tt>init.cya</tt>, and run the CYANA manual CALC macro as usual.		Similar to the automatic run, modify the <tt>seq</tt> file, <tt>prot</tt> list, <tt>init.cya</tt>, and run the CYANA manual CALC macro as usual.

	~~<br>~~

	~~<br> -- GaohuaLiu - 09 Nov 2007~~

	~~-- Edited by JimAramini - Nov 2009~~

Jma at 16:56, 13 November 2009

2009-11-13T16:56:53Z

← Older revision		Revision as of 16:56, 13 November 2009
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	= '''~~Symmetric Homodimer Structure Calculation by CYANA~~''' =		== '''Introduction''' ==

	CYANA versions 2.1 and up can perform structure calculation with automated NOE assignment for symmetric homodimers. The algorithm is slightly different from what is used to calculate monomers or asymmetric oligomers. Additional restraints are introduced to keep the molecule and the force field symmetric.  A tutorial for homodimer structure calculation is avaliable ~~in the~~ [http://www.cyana.org/wiki/index.php/Homodimer_structure_calculation_with_automated_NOESY_assignment ~~CYANA 3.0 wiki~~].		CYANA versions 2.1 and up can perform structure calculation with automated NOE assignment for symmetric homodimers. The algorithm is slightly different from what is used to calculate monomers or asymmetric oligomers. Additional restraints are introduced to keep the molecule and the force field symmetric.  A tutorial for homodimer structure calculation using CYANA 3.0 is avaliable [http://www.cyana.org/wiki/index.php/Homodimer_structure_calculation_with_automated_NOESY_assignment on-line].

	== '''Input Data''' ==		== '''Input Data''' ==

Jma at 16:38, 13 November 2009

2009-11-13T16:38:13Z

← Older revision		Revision as of 16:38, 13 November 2009
Line 1:		Line 1:
	= '''Symmetric Homodimer Structure Calculation by CYANA''' =		= '''Symmetric Homodimer Structure Calculation by CYANA''' =

	CYANA versions 2.1 and up can perform structure calculation with automated NOE assignment for symmetric homodimers. The algorithm is slightly different from what is used to calculate monomers or asymmetric oligomers. Additional restraints are introduced to keep the molecule and the force field symmetric.		CYANA versions 2.1 and up can perform structure calculation with automated NOE assignment for symmetric homodimers. The algorithm is slightly different from what is used to calculate monomers or asymmetric oligomers. Additional restraints are introduced to keep the molecule and the force field symmetric.  A tutorial for homodimer structure calculation is avaliable in the [http://www.cyana.org/wiki/index.php/Homodimer_structure_calculation_with_automated_NOESY_assignment CYANA 3.0 wiki].

	== '''Input Data''' ==		== '''Input Data''' ==

Jma: moved DimersByCYANA to Homodimer Structure Calculation Using CYANA

2009-11-05T22:20:49Z

moved DimersByCYANA to Homodimer Structure Calculation Using CYANA

← Older revision	Revision as of 22:20, 5 November 2009
(No difference)

Jma at 17:39, 4 November 2009

2009-11-04T17:39:48Z

← Older revision		Revision as of 17:39, 4 November 2009
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	<br>		<br>

	<br> -- ~~Main.~~GaohuaLiu - 09 Nov 2007		<br> -- GaohuaLiu - 09 Nov 2007

			-- Edited by JimAramini - Nov 2009

Jma at 18:59, 3 November 2009

2009-11-03T18:59:51Z

Jma at 00:02, 1 November 2009

2009-11-01T00:02:12Z

← Older revision		Revision as of 00:02, 1 November 2009
Line 36:		Line 36:
	The CYANA residue library provides the following linker pseudo-residues: <tt>PL</tt>, <tt>LP</tt>, <tt>LL</tt>, <tt>LL2</tt> and <tt>LL5</tt>. The first two are special transition "residues", which are required to start and terminate the linker, respectively. The last three are intermediate linker "residues" of differing sizes, with "bonds" of standard length, double length and quintuple length. The "atoms" of these linker "residues" have zero mass and zero Van-der-Vaals radii, thus the linker can freely pass through the structure during simulated annealing. The "bonds" of the linker cannot be stretched, however, and it is necessary to use a linker of sufficient length to avoid putting unnatural strain on the subunits.		The CYANA residue library provides the following linker pseudo-residues: <tt>PL</tt>, <tt>LP</tt>, <tt>LL</tt>, <tt>LL2</tt> and <tt>LL5</tt>. The first two are special transition "residues", which are required to start and terminate the linker, respectively. The last three are intermediate linker "residues" of differing sizes, with "bonds" of standard length, double length and quintuple length. The "atoms" of these linker "residues" have zero mass and zero Van-der-Vaals radii, thus the linker can freely pass through the structure during simulated annealing. The "bonds" of the linker cannot be stretched, however, and it is necessary to use a linker of sufficient length to avoid putting unnatural strain on the subunits.

	It is convenient to have the residue numbers of the second subunit shifted by 100 or 200 compared to the first subunit. The first subunit in this example protein has residue numbers 11 to 106, while the second subunit has residue numbers from 211 to 306. It is not necessary to insert a linker exactly 94 residues long - hops in the residue numbers, such as between <tt>LP 130</tt> and <tt>MET 211</tt>, are accepted.		It is convenient to have the residue numbers of the second subunit shifted by 100 or 200 compared to the first subunit. The first subunit in this example protein has residue numbers 11 to 106, while the second subunit has residue numbers from 211 to 306. It is not necessary to insert a linker exactly 94 residues long - hops in the residue numbers, such as between <tt>LP 130</tt> and <tt>MET 211</tt>, are accepted.

	~~ ~~

	==== '''Duplicated Atom List''' ====		==== '''Duplicated Atom List''' ====

Jma: moved NESG:DimerbyCYANA to DimersByCYANA

2009-10-31T23:58:19Z

moved NESG:DimerbyCYANA to DimersByCYANA

← Older revision	Revision as of 23:58, 31 October 2009
(No difference)

Jma at 23:57, 31 October 2009

2009-10-31T23:57:21Z

← Older revision		Revision as of 23:57, 31 October 2009
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	== '''Symmetric Homodimer Structure Calculation by CYANA''' ==		== '''Symmetric Homodimer Structure Calculation by CYANA''' ==

	~~CYANA2~~.1 can perform structure calculation with automated NOE assignment for symmetric homodimers. The algorithm is slightly different from what is used to calculate monomers or asymmetric oligomers. Additional restraints are introduced to keep the molecule and the force field symmetric.		CYANA versions 2.1 and up can perform structure calculation with automated NOE assignment for symmetric homodimers. The algorithm is slightly different from what is used to calculate monomers or asymmetric oligomers. Additional restraints are introduced to keep the molecule and the force field symmetric.

	=== '''Input Data''' ===		=== '''Input Data''' ===
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	It is convenient to have the residue numbers of the second subunit shifted by 100 or 200 compared to the first subunit. The first subunit in this example protein has residue numbers 11 to 106, while the second subunit has residue numbers from 211 to 306. It is not necessary to insert a linker exactly 94 residues long - hops in the residue numbers, such as between <tt>LP 130</tt> and <tt>MET 211</tt>, are accepted.		It is convenient to have the residue numbers of the second subunit shifted by 100 or 200 compared to the first subunit. The first subunit in this example protein has residue numbers 11 to 106, while the second subunit has residue numbers from 211 to 306. It is not necessary to insert a linker exactly 94 residues long - hops in the residue numbers, such as between <tt>LP 130</tt> and <tt>MET 211</tt>, are accepted.



	==== '''Duplicated Atom List''' ====		==== '''Duplicated Atom List''' ====
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	1822 31.426 0.000 CB 211		1822 31.426 0.000 CB 211
	1823 2.010 0.000 HB2 211		1823 2.010 0.000 HB2 211
	1824 2.137 0.000 HB3 211</pre>		1824 2.137 0.000 HB3 211</pre>

	==== '''Duplicated External Constraints''' ====		==== '''Duplicated External Constraints''' ====

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	read seq $name.seq		read seq $name.seq
	rmsdrange:=12..104,212..304		rmsdrange:=12..104,212..304
	molecules define 11..106 211..306 </pre>		molecules define 11..106 211..306 </pre>

	=== '''Automatic Calculation''' ===		=== '''Automatic Calculation''' ===

← Older revision		Revision as of 18:59, 3 November 2009
Line 1:		Line 1:
	== '''Symmetric Homodimer Structure Calculation by CYANA''' ==		= '''Symmetric Homodimer Structure Calculation by CYANA''' =

	CYANA versions 2.1 and up can perform structure calculation with automated NOE assignment for symmetric homodimers. The algorithm is slightly different from what is used to calculate monomers or asymmetric oligomers. Additional restraints are introduced to keep the molecule and the force field symmetric.		CYANA versions 2.1 and up can perform structure calculation with automated NOE assignment for symmetric homodimers. The algorithm is slightly different from what is used to calculate monomers or asymmetric oligomers. Additional restraints are introduced to keep the molecule and the force field symmetric.

	=== '''Input Data''' ===		== '''Input Data''' ==

	Chemical shift assignment is performed for a single protein chain. Thus, the input for a symmetric homodimer calculation must include:		Chemical shift assignment is performed for a single protein chain. Thus, the input for a symmetric homodimer calculation must include:
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	*duplicated external constraint files, if any		*duplicated external constraint files, if any

	==== '''Duplicated Sequence File''' ====		=== '''Duplicated Sequence File''' ===

	The protein sequence must be repeated twice with a linker between protein chains as in this example:<br>		The protein sequence must be repeated twice with a linker between protein chains as in this example:<br>
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	The CYANA residue library provides the following linker pseudo-residues: <tt>PL</tt>, <tt>LP</tt>, <tt>LL</tt>, <tt>LL2</tt> and <tt>LL5</tt>. The first two are special transition "residues", which are required to start and terminate the linker, respectively. The last three are intermediate linker "residues" of differing sizes, with "bonds" of standard length, double length and quintuple length. The "atoms" of these linker "residues" have zero mass and zero Van-der-Vaals radii, thus the linker can freely pass through the structure during simulated annealing. The "bonds" of the linker cannot be stretched, however, and it is necessary to use a linker of sufficient length to avoid putting unnatural strain on the subunits.		The CYANA residue library provides the following linker pseudo-residues: <tt>PL</tt>, <tt>LP</tt>, <tt>LL</tt>, <tt>LL2</tt> and <tt>LL5</tt>. The first two are special transition "residues", which are required to start and terminate the linker, respectively. The last three are intermediate linker "residues" of differing sizes, with "bonds" of standard length, double length and quintuple length. The "atoms" of these linker "residues" have zero mass and zero Van-der-Vaals radii, thus the linker can freely pass through the structure during simulated annealing. The "bonds" of the linker cannot be stretched, however, and it is necessary to use a linker of sufficient length to avoid putting unnatural strain on the subunits.

	It is convenient to have the residue numbers of the second subunit shifted by 100 or 200 compared to the first subunit. The first subunit in this example protein has residue numbers 11 to 106, while the second subunit has residue numbers from 211 to 306. It is not necessary to insert a linker exactly 94 residues long - hops in the residue numbers, such as between <tt>LP 130</tt> and <tt>MET 211</tt>, are accepted.		It is convenient to have the residue numbers of the second subunit shifted by 100 or 200 compared to the first subunit. The first subunit in this example protein has residue numbers 11 to 106, while the second subunit has residue numbers from 211 to 306. It is not necessary to insert a linker exactly 94 residues long - hops in the residue numbers, such as between <tt>LP 130</tt> and <tt>MET 211</tt>, are accepted.

	==== '''Duplicated Atom List''' ====		=== '''Duplicated Atom List''' ===

	Chemical shifts in the atom list (.prot file) should be duplicated to include assignments for the second chain.		Chemical shifts in the atom list (.prot file) should be duplicated to include assignments for the second chain.
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	1823 2.010 0.000 HB2 211		1823 2.010 0.000 HB2 211
	1824 2.137 0.000 HB3 211</pre>		1824 2.137 0.000 HB3 211</pre>
	==== '''Duplicated External Constraints''' ====		=== '''Duplicated External Constraints''' ===

	All external constraints, such as intramolecular UPLs, ACOs and hydrogen bond constraints, must be duplicated to include both chains, otherwise the symmetry of the model will be broken. Intermolecular UPLs should also be given as symmetric pairs.		All external constraints, such as intramolecular UPLs, ACOs and hydrogen bond constraints, must be duplicated to include both chains, otherwise the symmetry of the model will be broken. Intermolecular UPLs should also be given as symmetric pairs.

	==== '''Modified init.cya''' ====		=== '''Modified init.cya''' ===

	It is necessary to add a <tt>molecules define</tt> statement to the <tt>init.cya</tt> file. The statement tells CYANA to perform the symmetric homodimer calculation, and the residue ranges are used to maintain symmetry.<br>		It is necessary to add a <tt>molecules define</tt> statement to the <tt>init.cya</tt> file. The statement tells CYANA to perform the symmetric homodimer calculation, and the residue ranges are used to maintain symmetry.<br>
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	rmsdrange:=12..104,212..304		rmsdrange:=12..104,212..304
	molecules define 11..106 211..306 </pre>		molecules define 11..106 211..306 </pre>
	=== '''Automatic Calculation''' ===		== '''Automatic Calculation''' ==

	Run the same <tt>CALC.cya</tt> macro as usual.		Run the same <tt>CALC.cya</tt> macro as usual.
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	It is not necessary to generate constraints for every cross-peak in the X-filtered NOESY spectrum. Instead, one should focus on a few strong cross-peaks, which can be '''manually''' assigned with absolute certainty. For example, the structure calculation of StR106 converged to the correct dimer geometry after adding a single intermolecular UPL constraint between an aromatic ring proton and a methyl group.		It is not necessary to generate constraints for every cross-peak in the X-filtered NOESY spectrum. Instead, one should focus on a few strong cross-peaks, which can be '''manually''' assigned with absolute certainty. For example, the structure calculation of StR106 converged to the correct dimer geometry after adding a single intermolecular UPL constraint between an aromatic ring proton and a methyl group.

	=== '''Manual Calculation''' ===		== '''Manual Calculation''' ==

	*Manual run		*Manual run