Protein-Ligand Complexes - Revision history

Jma at 20:50, 6 January 2010

2010-01-06T20:50:00Z

← Older revision		Revision as of 20:50, 6 January 2010
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	HADDOCK can be used to calculate protein-ligand complex structures based only on chemical shift perturbation data alone. Optionally, distance restraints can be added. For this you need a structure of the ligand-free protein, then you dock the ligand to that structure assuming that the perturbed chemical shifts arise from proximity to the ligand. HADDOCK runs on top of CNS.<br>		HADDOCK can be used to calculate protein-ligand complex structures based only on chemical shift perturbation data alone. Optionally, distance restraints can be added. For this you need a structure of the ligand-free protein, then you dock the ligand to that structure assuming that the perturbed chemical shifts arise from proximity to the ligand. HADDOCK runs on top of CNS.<br>

	<br>		<br>

	~~- JohnCort - 26 Aug 2008~~

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

Jma at 19:45, 10 December 2009

2009-12-10T19:45:57Z

← Older revision		Revision as of 19:45, 10 December 2009
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	This topic addresses only the steps involved in determining the solution NMR structure of a protein with a bound ligand when the identity of the ligand is known.<br>		This topic addresses only the steps involved in determining the solution NMR structure of a protein with a bound ligand when the identity of the ligand is known.<br>

	<br>		<br>

	== '''Acquisition of NMR Data''' ==		== '''Acquisition of NMR Data''' ==
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	In the parameter and topology statements, read the ligand .par and .top files as well as those for the protein (e.g. parallhdg.pro, parallhdg.pro). When you write the .psf file, protein and ligand atoms will be there.<br>		In the parameter and topology statements, read the ligand .par and .top files as well as those for the protein (e.g. parallhdg.pro, parallhdg.pro). When you write the .psf file, protein and ligand atoms will be there.<br>

	===== .mtf file (~~[http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/~~CNS ~~CNS]~~) =====		===== .mtf file (CNS) =====

	The ~~[http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/~~CNS ~~CNS]~~ scripts have a line telling you where to put ligand parameter and topology files.		The CNS scripts have a line telling you where to put ligand parameter and topology files.

	<br>		<br>
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	=== '''HADDOCK''' ===		=== '''HADDOCK''' ===

	HADDOCK can be used to calculate protein-ligand complex structures based only on chemical shift perturbation data alone. Optionally, distance restraints can be added. For this you need a structure of the ligand-free protein, then you dock the ligand to that structure assuming that the perturbed chemical shifts arise from proximity to the ligand. HADDOCK runs on top of ~~[http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/~~CNS ~~CNS]~~.<br>		HADDOCK can be used to calculate protein-ligand complex structures based only on chemical shift perturbation data alone. Optionally, distance restraints can be added. For this you need a structure of the ligand-free protein, then you dock the ligand to that structure assuming that the perturbed chemical shifts arise from proximity to the ligand. HADDOCK runs on top of CNS.<br>

	<br>		<br>

	- ~~[http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/Main/~~JohnCort ~~JohnCort]~~ - 26 Aug 2008		- JohnCort - 26 Aug 2008

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

Jma: moved Protein-Ligand Structures to Protein-Ligand Complexes

2009-11-05T22:05:48Z

moved Protein-Ligand Structures to Protein-Ligand Complexes

← Older revision	Revision as of 22:05, 5 November 2009
(No difference)

Jma at 21:35, 5 November 2009

2009-11-05T21:35:07Z

← Older revision		Revision as of 21:35, 5 November 2009
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	== ~~'''<br>'''~~'''Introduction'''<br> ==		== '''Introduction'''<br> ==

	Many proteins bind small organic ligands. Such ligands are usually integral to the functions of their cognate proteins; therefore understanding the structural and dynamical aspects of their binding is an essential component of the overall structural picture.		Many proteins bind small organic ligands. Such ligands are usually integral to the functions of their cognate proteins; therefore understanding the structural and dynamical aspects of their binding is an essential component of the overall structural picture.
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	This topic addresses only the steps involved in determining the solution NMR structure of a protein with a bound ligand when the identity of the ligand is known.<br>		This topic addresses only the steps involved in determining the solution NMR structure of a protein with a bound ligand when the identity of the ligand is known.<br>

	<br>		<br>

	== '''Acquisition of NMR Data''' ==		== '''Acquisition of NMR Data''' ==

Jma at 21:34, 5 November 2009

2009-11-05T21:34:35Z

← Older revision		Revision as of 21:34, 5 November 2009
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	= '''~~Determining the Structure of a Protein with a Bound Ligand~~''' =		== '''<br>''''''Introduction'''<br> ==

	== '''Introduction'''<br> ==

	Many proteins bind small organic ligands. Such ligands are usually integral to the functions of their cognate proteins; therefore understanding the structural and dynamical aspects of their binding is an essential component of the overall structural picture.		Many proteins bind small organic ligands. Such ligands are usually integral to the functions of their cognate proteins; therefore understanding the structural and dynamical aspects of their binding is an essential component of the overall structural picture.
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	N.B.: if protein is purified from the expression culture with ligand already bound, then of course the ligand too is isotope labeled. Adding additional unlabled ligand can dilute the label as the bound and free ligand exchange over time.<br>		N.B.: if protein is purified from the expression culture with ligand already bound, then of course the ligand too is isotope labeled. Adding additional unlabled ligand can dilute the label as the bound and free ligand exchange over time.<br>

	<br>		<br>

	== '''Structure Calculation (XPLOR/CNS)''' ==		== '''Structure Calculation (XPLOR/CNS)''' ==
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	If not available from someone who as already constructed them for a particular ligand, they must be created. This can be done using the HICCUP server, which automatically generates them based on ligand coordinates in the PDB. Alternatively, the PRODRG server can be used to generate parameter and topology files.		If not available from someone who as already constructed them for a particular ligand, they must be created. This can be done using the HICCUP server, which automatically generates them based on ligand coordinates in the PDB. Alternatively, the PRODRG server can be used to generate parameter and topology files.

	Both sources must be used carefully, and the resulting files will require further editing--for example to add hydrogens and to allow free rotation about single bonds while planarity of aromatic rings and conjugated double bonds is maintained. It is essential that all atom names, atom types, atomic masses, charges, bond distances, bond angles, torsion angles, impropers, and stereochemistry be correct. Using some common sense organic chemistry, you often can borrow parameters from amino acids and nucleic acids in XPLOR parameter and topology files. Make sure the atom names are consistent between the pdb files and the parameter and topology files. Look up atom naming conventions for common ligands in the literature.<br>		Both sources must be used carefully, and the resulting files will require further editing--for example to add hydrogens and to allow free rotation about single bonds while planarity of aromatic rings and conjugated double bonds is maintained. It is essential that all atom names, atom types, atomic masses, charges, bond distances, bond angles, torsion angles, impropers, and stereochemistry be correct. Using some common sense organic chemistry, you often can borrow parameters from amino acids and nucleic acids in XPLOR parameter and topology files. Make sure the atom names are consistent between the pdb files and the parameter and topology files. Look up atom naming conventions for common ligands in the literature.<br>

	=== '''Example Parameter and Topology Files''' ===		=== '''Example Parameter and Topology Files''' ===

Jma: moved Small Ligands to Protein-Ligand Structures

2009-11-05T18:48:07Z

moved Small Ligands to Protein-Ligand Structures

← Older revision	Revision as of 18:48, 5 November 2009
(No difference)

Jma at 17:35, 4 November 2009

2009-11-04T17:35:26Z

← Older revision		Revision as of 17:35, 4 November 2009
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	<br>		<br>

	- [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/Main/JohnCort JohnCort] - 26 Aug 2008		- [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/Main/JohnCort JohnCort] - 26 Aug 2008

			-- Edited by JimAramini - Nov 2009

Jma at 18:38, 3 November 2009

2009-11-03T18:38:28Z

← Older revision		Revision as of 18:38, 3 November 2009
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	<br>		<br>

	=== '''Structure Calculation (XPLOR/CNS)''' ===		== '''Structure Calculation (XPLOR/CNS)''' ==

	In order to calculate the protein-ligand structure using restrained molecular dynamics and simulated annealing, it is necessary to have appropriate parameter and topology files for the ligand. You also need a .pdb file for the ligand.		In order to calculate the protein-ligand structure using restrained molecular dynamics and simulated annealing, it is necessary to have appropriate parameter and topology files for the ligand. You also need a .pdb file for the ligand.
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	If not available from someone who as already constructed them for a particular ligand, they must be created. This can be done using the HICCUP server, which automatically generates them based on ligand coordinates in the PDB. Alternatively, the PRODRG server can be used to generate parameter and topology files.		If not available from someone who as already constructed them for a particular ligand, they must be created. This can be done using the HICCUP server, which automatically generates them based on ligand coordinates in the PDB. Alternatively, the PRODRG server can be used to generate parameter and topology files.

	Both sources must be used carefully, and the resulting files will require further editing--for example to add hydrogens and to allow free rotation about single bonds while planarity of aromatic rings and conjugated double bonds is maintained. It is essential that all atom names, atom types, atomic masses, charges, bond distances, bond angles, torsion angles, impropers, and stereochemistry be correct. Using some common sense organic chemistry, you often can borrow parameters from amino acids and nucleic acids in XPLOR parameter and topology files. Make sure the atom names are consistent between the pdb files and the parameter and topology files. Look up atom naming conventions for common ligands in the literature.<br>		Both sources must be used carefully, and the resulting files will require further editing--for example to add hydrogens and to allow free rotation about single bonds while planarity of aromatic rings and conjugated double bonds is maintained. It is essential that all atom names, atom types, atomic masses, charges, bond distances, bond angles, torsion angles, impropers, and stereochemistry be correct. Using some common sense organic chemistry, you often can borrow parameters from amino acids and nucleic acids in XPLOR parameter and topology files. Make sure the atom names are consistent between the pdb files and the parameter and topology files. Look up atom naming conventions for common ligands in the literature.<br>

	=== '''Example Parameter and Topology Files''' ===		=== '''Example Parameter and Topology Files''' ===

Jma at 18:38, 3 November 2009

2009-11-03T18:38:10Z

← Older revision		Revision as of 18:38, 3 November 2009
Line 15:		Line 15:
	<br>		<br>

	=== '''Acquisition of NMR Data''' ===		== '''Acquisition of NMR Data''' ==

	Three types of data provide specific structural information about bound ligands:<br>		Three types of data provide specific structural information about bound ligands:<br>
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	N.B.: if protein is purified from the expression culture with ligand already bound, then of course the ligand too is isotope labeled. Adding additional unlabled ligand can dilute the label as the bound and free ligand exchange over time.<br>		N.B.: if protein is purified from the expression culture with ligand already bound, then of course the ligand too is isotope labeled. Adding additional unlabled ligand can dilute the label as the bound and free ligand exchange over time.<br>

	<br>		<br>

	=== '''Structure Calculation (XPLOR/CNS)''' ===		=== '''Structure Calculation (XPLOR/CNS)''' ===

Jma at 18:37, 3 November 2009

2009-11-03T18:37:40Z

← Older revision		Revision as of 18:37, 3 November 2009
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	= '''Determining the Structure of a Protein with a Bound Ligand''' =		= '''Determining the Structure of a Protein with a Bound Ligand''' =

	= '''Introduction'''<br> =		== '''Introduction'''<br> ==

	Many proteins bind small organic ligands. Such ligands are usually integral to the functions of their cognate proteins; therefore understanding the structural and dynamical aspects of their binding is an essential component of the overall structural picture.		Many proteins bind small organic ligands. Such ligands are usually integral to the functions of their cognate proteins; therefore understanding the structural and dynamical aspects of their binding is an essential component of the overall structural picture.
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	This topic addresses only the steps involved in determining the solution NMR structure of a protein with a bound ligand when the identity of the ligand is known.<br>		This topic addresses only the steps involved in determining the solution NMR structure of a protein with a bound ligand when the identity of the ligand is known.<br>

	<br>		<br>

	= '''Acquisition of NMR Data''' =		=== '''Acquisition of NMR Data''' ===

	Three types of data provide specific structural information about bound ligands:<br>		Three types of data provide specific structural information about bound ligands:<br>
Line 28:		Line 28:
	N.B.: if protein is purified from the expression culture with ligand already bound, then of course the ligand too is isotope labeled. Adding additional unlabled ligand can dilute the label as the bound and free ligand exchange over time.<br>		N.B.: if protein is purified from the expression culture with ligand already bound, then of course the ligand too is isotope labeled. Adding additional unlabled ligand can dilute the label as the bound and free ligand exchange over time.<br>

	<br>		<br>

	= '''Structure Calculation (XPLOR/CNS)''' =		=== '''Structure Calculation (XPLOR/CNS)''' ===

	In order to calculate the protein-ligand structure using restrained molecular dynamics and simulated annealing, it is necessary to have appropriate parameter and topology files for the ligand. You also need a .pdb file for the ligand.		In order to calculate the protein-ligand structure using restrained molecular dynamics and simulated annealing, it is necessary to have appropriate parameter and topology files for the ligand. You also need a .pdb file for the ligand.
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	Both sources must be used carefully, and the resulting files will require further editing--for example to add hydrogens and to allow free rotation about single bonds while planarity of aromatic rings and conjugated double bonds is maintained. It is essential that all atom names, atom types, atomic masses, charges, bond distances, bond angles, torsion angles, impropers, and stereochemistry be correct. Using some common sense organic chemistry, you often can borrow parameters from amino acids and nucleic acids in XPLOR parameter and topology files. Make sure the atom names are consistent between the pdb files and the parameter and topology files. Look up atom naming conventions for common ligands in the literature.<br>		Both sources must be used carefully, and the resulting files will require further editing--for example to add hydrogens and to allow free rotation about single bonds while planarity of aromatic rings and conjugated double bonds is maintained. It is essential that all atom names, atom types, atomic masses, charges, bond distances, bond angles, torsion angles, impropers, and stereochemistry be correct. Using some common sense organic chemistry, you often can borrow parameters from amino acids and nucleic acids in XPLOR parameter and topology files. Make sure the atom names are consistent between the pdb files and the parameter and topology files. Look up atom naming conventions for common ligands in the literature.<br>

	== '''Example Parameter and Topology Files''' ==		=== '''Example Parameter and Topology Files''' ===

	These were generated with the PRODRG server and extensively modified by John Cort<br>		These were generated with the PRODRG server and extensively modified by John Cort<br>
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	==== Coenzyme A ====		==== Coenzyme A ====

	[[~~media~~:~~coa~~.par.txt\|coa.par.txt]]: parameter file for coenzyme A<br>		[[Media:Coa.par.txt\|coa.par.txt]]: parameter file for coenzyme A<br>

	[[~~media~~:~~coa~~.top.txt\|coa.top.txt]]: topology file for coenzyme A<br>		[[Media:Coa.top.txt\|coa.top.txt]]: topology file for coenzyme A<br>

	[[~~media~~:~~coa~~.pdb\|coa.pdb]]: pdb file for coenzyme A with consistent atom names		[[Media:Coa.pdb\|coa.pdb]]: pdb file for coenzyme A with consistent atom names

	<br>		<br>

	==== Folinic Acid (5-formyltetrahydrofolate) ====		==== Folinic Acid (5-formyltetrahydrofolate) ====

	[[~~media~~:FON_top.txt\|FON_top.txt]]: topology file for folinic acid<br>		[[Media:FON_top.txt\|FON_top.txt]]: topology file for folinic acid<br>

	[[~~media~~:FON_par.txt\|FON_par.txt]]: parameter file for folinic acid<br>		[[Media:FON_par.txt\|FON_par.txt]]: parameter file for folinic acid<br>

	[[~~media~~:FON_6S_H.pdb\|FON_6S_H.pdb]]: pdb file for folinic acid with consistent atom names		[[Media:FON_6S_H.pdb\|FON_6S_H.pdb]]: pdb file for folinic acid with consistent atom names

	<br>		<br>

	Note that in the above examples, most dihedral parameters are commented out. Instead, improper angles are used to maintain planarity of sp2 hybridized carbons. As always, impropers are also used to maintain stereochemistry at all sp3 hybridized carbons.<br>		Note that in the above examples, most dihedral parameters are commented out. Instead, improper angles are used to maintain planarity of sp2 hybridized carbons. As always, impropers are also used to maintain stereochemistry at all sp3 hybridized carbons.<br>

	== '''Generating a .psf or .msf file''' ==		=== '''Generating a .psf or .msf file''' ===

	The next step is to generate a single .psf or .msf file for your protein and the ligand.<br>		The next step is to generate a single .psf or .msf file for your protein and the ligand.<br>
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	The [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/CNS CNS] scripts have a line telling you where to put ligand parameter and topology files.		The [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/CNS CNS] scripts have a line telling you where to put ligand parameter and topology files.

	<br>		<br>

	== '''Structure Calculation''' ==		=== '''Structure Calculation''' ===

	Once you have the .psf or .msf file, you need to make a starting structure. Concatentate the protein and ligand pdb files, giving the ligand a unique residue number like 999. Try both extended and folded protein structures. Then add intermolecular distance restraints to your table and calculate structures of your protein-ligand complex.		Once you have the .psf or .msf file, you need to make a starting structure. Concatentate the protein and ligand pdb files, giving the ligand a unique residue number like 999. Try both extended and folded protein structures. Then add intermolecular distance restraints to your table and calculate structures of your protein-ligand complex.
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	<br>		<br>

	== '''HADDOCK''' ==		=== '''HADDOCK''' ===

	HADDOCK can be used to calculate protein-ligand complex structures based only on chemical shift perturbation data alone. Optionally, distance restraints can be added. For this you need a structure of the ligand-free protein, then you dock the ligand to that structure assuming that the perturbed chemical shifts arise from proximity to the ligand. HADDOCK runs on top of [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/CNS CNS].<br>		HADDOCK can be used to calculate protein-ligand complex structures based only on chemical shift perturbation data alone. Optionally, distance restraints can be added. For this you need a structure of the ligand-free protein, then you dock the ligand to that structure assuming that the perturbed chemical shifts arise from proximity to the ligand. HADDOCK runs on top of [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/CNS CNS].<br>