Residual Dipolar Couplings in Structure Refinement - Revision history

Lmorris at 17:07, 11 May 2012

2012-05-11T17:07:35Z

← Older revision		Revision as of 17:07, 11 May 2012
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	( resid 500 and name Y )		( resid 500 and name Y )
	( resid 1 and name HN )		( resid 1 and name HN )
	( resid 1 and name N ) -8.1 0.6 0.5		( resid 1 and name N ) -8.1 0.5 0.5
	</pre>		</pre>
	<br>		<br>

Lmorris at 17:06, 11 May 2012

2012-05-11T17:06:51Z

← Older revision		Revision as of 17:06, 11 May 2012
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	Residual Dipolar Couplings (RDCs) originate from partial anisotropic averaging of the dipolar interaction which is dependent on the angle between an internuclear vector and the magnetic field. When a molecule sample orientations uniformly, as it does in normal solution NMR, RDCs average to zero and are not observable. However, if a molecule is dissolved in a dilute liquid crystalline medium it becomes partially aligned, and the dipolar couplings are not completely averaged to zero, leading to a small contribution to the splittings of NMR signals. The angular dependence of these contributions can provide valuable structural information. Protein structures can be validated using RDCs, and structures can be refined to improve quality.		Residual Dipolar Couplings (RDCs) originate from partial anisotropic averaging of the dipolar interaction which is dependent on the angle between an internuclear vector and the magnetic field. When a molecule sample orientations uniformly, as it does in normal solution NMR, RDCs average to zero and are not observable. However, if a molecule is dissolved in a dilute liquid crystalline medium it becomes partially aligned, and the dipolar couplings are not completely averaged to zero, leading to a small contribution to the splittings of NMR signals. The angular dependence of these contributions can provide valuable structural information. Protein structures can be validated using RDCs, and structures can be refined to improve quality.

	Another application of RDCs is identification of the correct monomer ~~orientations~~ in homodimers. This application requires RDCs from two or more alignment media that give different orientations of principal alignment axes.		Another application of RDCs is identification of the correct monomer orientation in homodimers. This application requires RDCs from two or more alignment media that give different orientations of principal alignment axes.

	Below are protocols for the refinement of protein structures with RDCs using XPLOR-NIH [1].		Below are protocols for the refinement of protein structures with RDCs using XPLOR-NIH [1].
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	*Obtain a good estimate of the magnitude of Da and R from the alignment tensors. The alignment tensors can be obtained either from the extremes of distribution of RDCs (which forms a histogram) or from ~~“REDCAT”~~. REDCAT gives values for Sxx, Syy and Szz. These values are relateive to the maxium RDC for that bond type. First, multiply these values from REDCAT by the associated maxium RDC value (for example 24350 for NH dipolar couplings). These ~~absolute~~ alignment ~~tensors~~ are related to Da and R as follows:		*Obtain a good estimate of the magnitude of Da and R from the alignment tensors. The alignment tensors can be obtained either from the extremes of distribution of RDCs (which forms a histogram) or from the program REDCAT. REDCAT gives values for Sxx, Syy and Szz. These values are relateive to the maxium RDC (RDCmax) for that bond type. First, multiply these values from REDCAT by the associated maxium RDC value (for example 24350 for NH dipolar couplings). These alignment parameters are related to Da and R as follows:
	<pre>Da = Szz/2		<pre>Da = RDCmax * Szz/2
	R=Dr/Da where Dr=0.5*(Sxx-Syy)		R = Dr/Da where Dr = 0.5 * (Sxx-Syy) * RDCmax
	</pre>		</pre>
	*Note that the sani constraint in XPLOR and or CNS requires three coefficients: DFS, Da and R. DFS is a fixed offset ~~(for example a scalar coupling)~~. For RDC data, DFS = 0.		*Note that the sani constraint in XPLOR and or CNS requires three coefficients: DFS, Da and R. DFS is a fixed offset. For RDC data, DFS = 0.
	*In XPLOR define the axis representing the alignment tensor coordinate system. The coordinate system is represented by four pseudo atoms: OO(origin), X ,Y and Z. The coordinate system has to be positioned far away to prevent any interaction with the protein. For more than one aligned media, define separate axes for each medium. These axes can either be defined at the end of the pdb file or as a separate .pdb file. Shown below is an example from the pdb:		*In XPLOR define the axis representing the alignment tensor coordinate system. The coordinate system is represented by four pseudo atoms: OO(origin), X ,Y and Z. The coordinate system has to be positioned far away to prevent any interaction with the protein. For more than one aligned media, define separate axes for each medium. These axes can either be defined at the end of the pdb file or as a separate .pdb file. Shown below is an example from the pdb:
	<pre>ATOM 608 X ANI 500 33.000 30.000 30.000 1.00 0.00		<pre>ATOM 608 X ANI 500 33.000 30.000 30.000 1.00 0.00
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	*Create an RDC constraint file. An example is shown below where -8.1 is the coupling value and ~~0.6~~ and 0.5 ~~are~~ the ~~errors~~ associated with it:		*Create an RDC constraint file. An example is shown below where -8.1 is the coupling value and plus and minus 0.5 is the error associated with it:
	<pre>assign ( resid 500 and name OO )		<pre>assign ( resid 500 and name OO )
	( resid 500 and name Z )		( resid 500 and name Z )
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	*The following perl script ('makeRdcAssign.pm') can be used to create RDC constraint file ('myprotRdc.tbl'). The input to the script is coupling values as one column text file (same as used in REDCAT to import rdcs). Usage for this script is <tt>makeRdcAssign.pm myprot.rdc myprotRdc.tbl startingResidue Err1 Err2</tt>. ~~Same~~ script can be used for CNS, the only change is to make a tbl file with only one error Err1.		*The following perl script ('makeRdcAssign.pm') can be used to create an RDC constraint file ('myprotRdc.tbl'). The input to the script is coupling values as one column text file (same as used in REDCAT to import rdcs). Usage for this script is: <tt>makeRdcAssign.pm myprot.rdc myprotRdc.tbl startingResidue Err1 Err2</tt>. The same script can be used for CNS, the only change is to make a tbl file with only one error Err1.
	<pre>#!/usr/bin/perl		<pre>#!/usr/bin/perl
	if($ARGC < 3 ) {		if($ARGC < 3 ) {

Lmorris at 17:01, 11 May 2012

2012-05-11T17:01:45Z

← Older revision		Revision as of 17:01, 11 May 2012
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	== '''Introduction''' ==		== '''Introduction''' ==

	Residual Dipolar Couplings (RDCs) originate from ~~the~~ anisotropic ~~component~~ of the dipolar interaction, which is dependent on the angle between an internuclear vector and the magnetic field. When a molecule sample orientations uniformly, as it does in normal solution NMR, RDCs average to zero and are not observable. However, if a molecule is dissolved in a dilute liquid crystalline medium it becomes partially aligned, and the dipolar couplings are not completely averaged to zero, leading to a small contribution to the splittings of NMR signals. The angular dependence of these contributions can provide valuable structural information. Protein structures can be validated using RDCs, and structures can be refined to improve quality.		Residual Dipolar Couplings (RDCs) originate from partial anisotropic averaging of the dipolar interaction which is dependent on the angle between an internuclear vector and the magnetic field. When a molecule sample orientations uniformly, as it does in normal solution NMR, RDCs average to zero and are not observable. However, if a molecule is dissolved in a dilute liquid crystalline medium it becomes partially aligned, and the dipolar couplings are not completely averaged to zero, leading to a small contribution to the splittings of NMR signals. The angular dependence of these contributions can provide valuable structural information. Protein structures can be validated using RDCs, and structures can be refined to improve quality.

	Another application of RDCs is identification of the correct monomer orientations in homodimers. This application requires RDCs from two or more alignment media that give different orientations of principal alignment axes.		Another application of RDCs is identification of the correct monomer orientations in homodimers. This application requires RDCs from two or more alignment media that give different orientations of principal alignment axes.

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2012-05-11T17:00:13Z

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Lmorris at 16:58, 11 May 2012

2012-05-11T16:58:31Z

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2012-02-21T17:21:27Z

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← Older revision		Revision as of 17:21, 21 February 2012
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	Another application of RDCs is identification of the correct monomer orientations in homodimers. This application requires RDCs from two or more alignment media that give different orientations of principal alignment axes.		Another application of RDCs is identification of the correct monomer orientations in homodimers. This application requires RDCs from two or more alignment media that give different orientations of principal alignment axes.

	Below are protocols for the refinement of protein structures with RDCs using XPLOR-NIH [1]. ~~2 3 4~~		Below are protocols for the refinement of protein structures with RDCs using XPLOR-NIH [1].

	<br>		<br>

Lmorris at 17:20, 21 February 2012

2012-02-21T17:20:49Z

← Older revision		Revision as of 17:20, 21 February 2012
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	Another application of RDCs is identification of the correct monomer orientations in homodimers. This application requires RDCs from two or more alignment media that give different orientations of principal alignment axes.		Another application of RDCs is identification of the correct monomer orientations in homodimers. This application requires RDCs from two or more alignment media that give different orientations of principal alignment axes.

	Below are protocols for the refinement of protein structures with RDCs using XPLOR-NIH [1].		Below are protocols for the refinement of protein structures with RDCs using XPLOR-NIH [1]. 2 3 4

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Jma at 20:51, 6 January 2010

2010-01-06T20:51:57Z

← Older revision		Revision as of 20:51, 6 January 2010
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	Another application of RDCs is identification of the correct monomer orientations in homodimers. This application requires RDCs from two or more alignment media that give different orientations of principal alignment axes.		Another application of RDCs is identification of the correct monomer orientations in homodimers. This application requires RDCs from two or more alignment media that give different orientations of principal alignment axes.

	Below are protocols for the refinement of protein structures with RDCs using XPLOR-NIH ~~(Ref.~~ 1).		Below are protocols for the refinement of protein structures with RDCs using XPLOR-NIH [1].

	<br>		<br>
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	== '''References''' ==		== '''References''' ==

	1.    Schwieters, C.D., Kuszewski, J.J., Tjandra, N. and Clore, G.M.  (2003) The Xplor-NIH NMR molecular structure determination package.  ''J. Magn. Res. 160'', 65-73.		[http://www.ncbi.nlm.nih.gov/pubmed/12565051?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=3 1.    Schwieters, C.D., Kuszewski, J.J., Tjandra, N. and Clore, G.M.  (2003) The Xplor-NIH NMR molecular structure determination package.  ''J. Magn. Res. 160'', 65-73.]

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Jma at 20:50, 6 January 2010

2010-01-06T20:50:49Z

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	*The refined structure can be validated with the RDCs that are not used in refinement. From the refined structure RDCs can be back calculated (using REDCAT) and plotted against the experimental RDCs.<br>		*The refined structure can be validated with the RDCs that are not used in refinement. From the refined structure RDCs can be back calculated (using REDCAT) and plotted against the experimental RDCs.<br>

			<br>

	=== Details for performing RDC refinement in XPLOR/NIH starting from CNS ===		=== Details for performing RDC refinement in XPLOR/NIH starting from CNS ===
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	*These refined structures may then be directly used in CNS if water bath refinement is desired.		*These refined structures may then be directly used in CNS if water bath refinement is desired.

			<br>

	=== Details for performing RDC refinement in XPLOR/NIH using Python Interface ===		=== Details for performing RDC refinement in XPLOR/NIH using Python Interface ===
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	<br>		<br>

	~~<br>~~

	~~<br>~~

	~~-- SonalBansal - 07 Sep 2007~~

	~~-- DavidParish - 09 Nov 2007~~

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

	<br>		<br>

Jma at 00:40, 14 November 2009

2009-11-14T00:40:57Z

← Older revision		Revision as of 00:40, 14 November 2009
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	*Set the Xplor-NIH input file for dipolar coupling refinement. The RDC restraint is known as sani (susceptibility anisotropy). Define the force constant, ksani for each media and for each type of couplings.<br>		*Set the Xplor-NIH input file for dipolar coupling refinement. The RDC restraint is known as sani (susceptibility anisotropy). Define the force constant, ksani for each media and for each type of couplings.<br>

	*The refined structure can be validated with the RDCs that are not used in refinement. From the refined structure RDCs can be back calculated (using REDCAT) and plotted against the experimental RDCs.		*The refined structure can be validated with the RDCs that are not used in refinement. From the refined structure RDCs can be back calculated (using REDCAT) and plotted against the experimental RDCs.<br>


	~~<br>~~

	=== Details for performing RDC refinement in XPLOR/NIH starting from CNS ===		=== Details for performing RDC refinement in XPLOR/NIH starting from CNS ===
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	*You must edit the script to provide the correct names for your noe, dihedral and rdc input files xxx.tbl, you must also edit the coefficients for the NH sani constraints to put in your Da and Rhombicity as calculated above.		*You must edit the script to provide the correct names for your noe, dihedral and rdc input files xxx.tbl, you must also edit the coefficients for the NH sani constraints to put in your Da and Rhombicity as calculated above.
	*The script "dos" will repeatedly run refine_rdc_myprot.inp, iterating over all of your input structures and creating refined structures.		*The script "dos" will repeatedly run refine_rdc_myprot.inp, iterating over all of your input structures and creating refined structures.
	*These refined structures may then be directly used in CNS if water bath refinement is desired.~~<br>~~		*These refined structures may then be directly used in CNS if water bath refinement is desired.


	~~=== ===~~

	=== Details for performing RDC refinement in XPLOR/NIH using Python Interface ===		=== Details for performing RDC refinement in XPLOR/NIH using Python Interface ===
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	== '''References''' ==		== '''References''' ==

	1.    Schwieters, C.D., Kuszewski, J.J., Tjandra, N. and Clore, G.M.  (2003) The Xplor-NIH NMR molecular structure determination package.  ''J. Magn. Res. 160'', 65-73.		1.    Schwieters, C.D., Kuszewski, J.J., Tjandra, N. and Clore, G.M.  (2003) The Xplor-NIH NMR molecular structure determination package.  ''J. Magn. Res. 160'', 65-73.

	<br>		<br>