CHECKSPMUTATE - Revision history

Adk44 at 09:53, 17 June 2020

2020-06-17T09:53:51Z

← Older revision		Revision as of 09:53, 17 June 2020
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	IT MUST ALSO BE NOTED that the pathway for the new system will not necessarily (and is indeed unlikely to be) the optimal one. Therefore, post CHECKSPMUTATE, an appropriate number of rounds of [[SHORTCUT]]/[[SHORTCUT 2 BARRIER]]/[[UNTRAP]] etc will need to be performed. It is not advised that CHECKSPMUTATE be used on proteins which are significantly different.		IT MUST ALSO BE NOTED that the pathway for the new system will not necessarily (and is indeed unlikely to be) the optimal one. Therefore, post CHECKSPMUTATE, an appropriate number of rounds of [[SHORTCUT]]/[[SHORTCUT 2 BARRIER]]/[[UNTRAP]] etc will need to be performed. It is not advised that CHECKSPMUTATE be used on proteins which are significantly different.

			Care must especially be taken when inserting residues within the chain. If possible to avoid, please do so. I have written the code so that a maximum of two such residues can be inserted at the same point along the chain. This is already likely to cause problematic steric clashes, and so adding more would not likely be feasible. Care must also be taken that these new residues, once added and optimised, have the correct cis-trans isomerism and chirality.

	=== Potential Uses ===		=== Potential Uses ===

Adk44: /* Potential Uses */

2020-06-11T19:26:30Z

Potential Uses

← Older revision		Revision as of 19:26, 11 June 2020
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	CHECKSPMUTATE could potentially be used to shed light on some of the following problems:		CHECKSPMUTATE could potentially be used to shed light on some of the following problems:

	* Comparing a wt protein against some mutations to determine how such mutations affect protein folding.		* Comparing a wt protein against some mutations to determine how such mutations affect protein folding. Care will need to be taken that sufficient sampling for alternative pathways is performed.
	* Comparing a wt protein against some mutations to determine how such mutations affect protein-cofactor interactions.		* Comparing a wt protein against some mutations to determine how such mutations affect protein-cofactor interactions.
	* Comparing a protein against a close homologue to see whether it engages in the same manner of protein folding.		* Comparing a protein against a close homologue to see whether it engages in the same manner of protein folding. Care will need to be taken that sufficient sampling for alternative pathways is performed.
	* Comparing a protein against a close homologue to see whether it engages in similar protein-cofactor interactions.		* Comparing a protein against a close homologue to see whether it engages in similar protein-cofactor interactions.
	* Transformation of a cofactor (for example from NADH to NADPH) to see whether this affects protein-cofactor interactions.		* Transformation of a cofactor (for example from NADH to NADPH) to see whether this affects protein-cofactor interactions.

Adk44: /* pathdata and odata.checksp files */

2020-06-04T09:10:47Z

pathdata and odata.checksp files

← Older revision		Revision as of 09:10, 4 June 2020
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	=== pathdata and odata.checksp files ===		=== pathdata and odata.checksp files ===

	Same as for the mutation example above. I would expect, for my example here with ChuS, an pathdata file like this:		Same as for the mutation example above. I would expect, for my example here with ChuS, a pathdata file like this:

	<pre>		<pre>

Adk44: /* Making auxiliary files */

2020-06-04T09:09:35Z

Making auxiliary files

← Older revision		Revision as of 09:09, 4 June 2020
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	GLY <font color="#ff0000 ">GLU</font> <font color="#ff0000 ">GLN</font> GLU GLN <font color="#ff0000 ">ALA</font> GLN TRP ARG <font color="#ff0000 ">LYS</font> GLN ILE ALA <font color="#ff0000 ">SER</font> LEU <font color="#ff0000 ">ILE</font> <font color="#ff0000 ">CPRO</font><font color="#33FF00 ">XXX</font> <font color="#FF00FF ">HEM</font> <font color="#FF00FF ">NAD</font>		GLY <font color="#ff0000 ">GLU</font> <font color="#ff0000 ">GLN</font> GLU GLN <font color="#ff0000 ">ALA</font> GLN TRP ARG <font color="#ff0000 ">LYS</font> GLN ILE ALA <font color="#ff0000 ">SER</font> LEU <font color="#ff0000 ">ILE</font> <font color="#ff0000 ">CPRO</font><font color="#33FF00 ">XXX</font> <font color="#FF00FF ">HEM</font> <font color="#FF00FF ">NAD</font>

	Here, <font color="#ff0000 ">red</font> font signifies a residue which has been mutated, <font color="#33FF00 ">green</font> represents a residue which has been deleted (given the code name XXX)~~, and its position in the original protein~~, and <font color="#FF00FF ">purple</font> represents the two cofactors.		Here, <font color="#ff0000 ">red</font> font signifies a residue which has been mutated, <font color="#33FF00 ">green</font> represents a residue which has been deleted (given the code name XXX), and <font color="#FF00FF ">purple</font> represents the two cofactors.

	We now need to prepare atomnumberlog, newreslog, nresidueslog, oldreslog and resnumberlog to define all the mutations/insertions/deletions we are making, and where in the chain they take place. In this example, we are making 113 mutations/insertions/deletions (to be precise, 111 mutations and 2 deletions) in total:		We now need to prepare atomnumberlog, newreslog, nresidueslog, oldreslog and resnumberlog to define all the mutations/insertions/deletions we are making, and where in the chain they take place. In this example, we are making 113 mutations/insertions/deletions (to be precise, 111 mutations and 2 deletions) in total:

Adk44: /* Preparation */

2020-06-04T09:04:42Z

Preparation

← Older revision		Revision as of 09:04, 4 June 2020
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	*'''odata.checksp''' list of conditions for optimisation carried out on each stationary point by [[OPTIM]].		*'''odata.checksp''' list of conditions for optimisation carried out on each stationary point by [[OPTIM]].
	*'''oldreslog''' list of codes for residues which we are CHANGING FROM.		*'''oldreslog''' list of codes for residues which we are CHANGING FROM.
	*'''original_protein.pdb''' pdb file for the system we are CHANGING FROM. All lines which do not dscribe an ATOM ~~are~~ (e.g. TITLE, TER and END) are removed, so that the number of lines of the file should correspond to the number of atoms in the system.		*'''original_protein.pdb''' pdb file for the system we are CHANGING FROM. All lines which do not dscribe an ATOM (e.g. TITLE, TER and END) are removed, so that the number of lines of the file should correspond to the number of atoms in the system.
	*'''pathdata''' organises [[OPTIM]] jobs. Certain keywords are required, described below.		*'''pathdata''' organises [[OPTIM]] jobs. Certain keywords are required, described below.
	*'''perm.allow''' full description of the groups of permutable atoms in the system we are CHANGING TO.		*'''perm.allow''' full description of the groups of permutable atoms in the system we are CHANGING TO.

Adk44: /* Potential Uses */

2020-06-04T09:03:21Z

Potential Uses

← Older revision		Revision as of 09:03, 4 June 2020
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	* Comparing a protein against a close homologue to see whether it engages in similar protein-cofactor interactions.		* Comparing a protein against a close homologue to see whether it engages in similar protein-cofactor interactions.
	* Transformation of a cofactor (for example from NADH to NADPH) to see whether this affects protein-cofactor interactions.		* Transformation of a cofactor (for example from NADH to NADPH) to see whether this affects protein-cofactor interactions.
			* Comparing a DNA strand against an RNA/XNA strand. Note that this would require some different python scripts, also found in '''/svn/SCRIPTS/AMBER/BHmutation_steps''', such as '''nucleic_acids.py'''.

	=== Acknowledgements ===		=== Acknowledgements ===

Adk44: /* Preparation */

2020-06-04T09:00:31Z

Preparation

← Older revision		Revision as of 09:00, 4 June 2020
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	== Preparation ==		== Preparation ==

	Before running the reoptimisations, we need to prepare a series of auxiliary files. In all, we should have the following files in our directory:		Before running the reoptimisations, we need to prepare a series of auxiliary files. In all, we should have the following files in our directory. Note that the python scripts can be found in '''/svn/SCRIPTS/AMBER/BHmutation_steps'''.

	*'''aa_ringdata.pyc''' list of parameters/definition of planes for residues with rings. Only required if we are mutating to a residue with a ring.		*'''aa_ringdata.pyc''' list of parameters/definition of planes for residues with rings. Only required if we are mutating to a residue with a ring.

Adk44 at 08:57, 4 June 2020

2020-06-04T08:57:10Z

← Older revision		Revision as of 08:57, 4 June 2020
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	== Purpose ==		== Purpose ==

	It can take an awfully long time to create a large database or to fully optimise a specific feature of it such as ~~afully~~ connected pathway showing complex protein folding. This is particularly acute when considering large proteins/protein+ligand systems.		It can take an awfully long time to create a large database or to fully optimise a specific feature of it such as a fully connected pathway showing complex protein folding. This is particularly acute when considering large proteins/protein+ligand systems.

	What if we are interested in examining how a Wild Type protein behaves with respect to some carefully selected mutants? Or in comparing one protein against a close homologue? It would seem like a colossal waste of time to create large databases for each of these similar cases, completely independently from each other. This is where CHECKSPMUTATE comes in.		What if we are interested in examining how a Wild Type protein behaves with respect to some carefully selected mutants? Or in comparing one protein against a close homologue? It would seem like a colossal waste of time to create large databases for each of these similar cases, completely independently from each other. This is where CHECKSPMUTATE comes in.

Adk44 at 10:10, 3 June 2020

2020-06-03T10:10:42Z

← Older revision		Revision as of 10:10, 3 June 2020
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	The advantage of this method is that time and computational resources can be significantly saved in transforming one database to a system of similar properties.		The advantage of this method is that time and computational resources can be significantly saved in transforming one database to a system of similar properties.

	It must be noted, however, that following the use of CHECKSPMUTATE, the new pathway might have gaps as not all of the stationary points necessarily will have converged. These gaps will need filled with the [[CONNECTPAIRS]] keyword.		It must be noted, however, that following the use of CHECKSPMUTATE, the new pathway might have gaps as not all of the stationary points necessarily will have converged. These gaps will need filled with the [[CONNECTPAIRS]] keyword. The full procedure that I used to fill such gaps is detailed in [[Pathway Gap Filling Post-CHECKSPMUTATE]]

	IT MUST ALSO BE NOTED that the pathway for the new system will not necessarily (and is indeed unlikely to be) the optimal one. Therefore, post CHECKSPMUTATE, an appropriate number of rounds of [[SHORTCUT]]/[[SHORTCUT 2 BARRIER]]/[[UNTRAP]] etc will need to be performed. It is not advised that CHECKSPMUTATE be used on proteins which are significantly different.		IT MUST ALSO BE NOTED that the pathway for the new system will not necessarily (and is indeed unlikely to be) the optimal one. Therefore, post CHECKSPMUTATE, an appropriate number of rounds of [[SHORTCUT]]/[[SHORTCUT 2 BARRIER]]/[[UNTRAP]] etc will need to be performed. It is not advised that CHECKSPMUTATE be used on proteins which are significantly different.

Adk44: /* Before and After Mutation */

2020-06-02T16:18:38Z

Before and After Mutation

← Older revision		Revision as of 16:18, 2 June 2020
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	Here is a rendering of [wt HemS + haem + NADH], alongside a rendering of the same minimum reoptimised after the F101A mutation was made.		Here is a rendering of [wt HemS + haem + NADH], alongside a rendering of the same minimum reoptimised after the F101A mutation was made.

	<gallery mode=packed widths="~~360px~~" heights="~~240px~~">		<gallery mode=packed widths="540px" heights="360px">
	File:wt_HemS_wiki.png\|wt HemS		File:wt_HemS_wiki.png\|wt HemS
	File:F101A_Hems_wiki.png\|F101A HemS		File:F101A_Hems_wiki.png\|F101A HemS