Lys modification with retinal isomers

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Hi John, after our email exchange, I'd like to submit this request for distinguishing the binding of retinal isomers to rhodopsin during visual transduction process. In PSI-MOD there is Retinylidene (MOD:00129), the conversion of an L-lysine residue by retinal.
In the visual transduction process, 11-cis-retinal first binds to rhodopsin then light causes isomerization of the cis form to all-trans-retinal. This causes a conformational change in rhodopsin which then tranduces the signal downstream via G-proteins.
For my work, it would be great if the PSI-MOD entry above can be resolved to two, one with 11cRAL modification and one with atRAL modification.
See PubMed:12177057 for reference.
Thanks

Reported by: beej160

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• assigned_to: nobody --> jsgaravelli

Original comment by: jsgaravelli

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Hi John

I think I found the appropriate mod for atRAL-L-lys (MOD:00317). Do you believe this to be the correct one? To update this request, please could a PSI-MOD be created for just 11cRAL-L-lys?

Regards

Bijay

Original comment by: beej160

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Sorry about this falling through the cracks. No, MOD:00317 (RESID:AA0312) is a modified form of the rentinal adduct (MOD:00129, RESID:AA0120) with two hydrogens removed to form a second double bond in the six member ring. to look at these, use the new RESID search page (to replace SRS) at
http://pir0.georgetown.edu/cgi-bin/resid
and those entries are at
http://pir0.georgetown.edu/cgi-bin/resid?id=AA0120
and
http://pir0.georgetown.edu/cgi-bin/resid?id=AA0312
What you are asking for is a geometric isomer of RESID:AA0120, which does not differ in molecular weight from it and is mentioned in the comment as the "11-cis (4Z) form". So it has the same molecular weight as MOD:00129; it could not be distinguished by mass-spec, and is not formed by direct enzymatic modification of the lysine residue in rhodopsin so cannot get its own entry in RESID. Technically, to create an entry for it in PSI-MOD, it would have to be derived from MOD:00129 with a mass difference of 0, and the mass-spec people do not like it when I make extra entries with identical masses.
I will go ahead and make an entry for it in the next PSI-MOD with a fictitious derivation from lysine so that it will duplicate the values in MOD:00129 but have different common ("11-cis") and systematic ("4Z") names. It will not be in the slim, so the mass-spec people will be able to ignore it. (But they will still complain.)

Original comment by: jsgaravelli

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Hi John

Good to hear from you!
Thanks for helping me with this.

I’m a little confused as to what PSI-MOD I should use for atRAL-L-lysine.
I know you say you’ll create a new PSI-MOD for 11cRAL-L-lysine.

Cheers

Bijay

On 20 Mar 2014, at 14:38, "John S. Garavelli" [email protected] wrote:

Sorry about this falling through the cracks. No, MOD:00317 (RESID:AA0312) is a modified form of the rentinal adduct (MOD:00129, RESID:AA0120) with two hydrogens removed to form a second double bond in the six member ring. to look at these, use the new RESID search page (to replace SRS) at
http://pir0.georgetown.edu/cgi-bin/resid
and those entries are at
http://pir0.georgetown.edu/cgi-bin/resid?id=AA0120
and
http://pir0.georgetown.edu/cgi-bin/resid?id=AA0312
What you are asking for is a geometric isomer of RESID:AA0120, which does not differ in molecular weight from it and is mentioned in the comment as the "11-cis (4Z) form". So it has the same molecular weight as MOD:00129; it could not be distinguished by mass-spec, and is not formed by direct enzymatic modification of the lysine residue in rhodopsin so cannot get its own entry in RESID. Technically, to create an entry for it in PSI-MOD, it would have to be derived from MOD:00129 with a mass difference of 0, and the mass-spec people do not like it when I make extra entries with identical masses.
I will go ahead and make an entry for it in the next PSI-MOD with a fictitious derivation from lysine so that it will duplicate the values in MOD:00129 but have different common ("11-cis") and systematic ("4Z") names. It will not be in the slim, so the mass-spec people will be able to ignore it. (But they will still complain.)

[mod-controlled-vocab-changes:#67] Lys modification with retinal isomers

Status: open
Group:
Created: Wed Aug 22, 2012 06:58 PM UTC by BijayJassal
Last Updated: Wed Mar 19, 2014 01:42 PM UTC
Owner: John S. Garavelli

Hi John, after our email exchange, I'd like to submit this request for distinguishing the binding of retinal isomers to rhodopsin during visual transduction process. In PSI-MOD there is Retinylidene (MOD:00129), the conversion of an L-lysine residue by retinal.
In the visual transduction process, 11-cis-retinal first binds to rhodopsin then light causes isomerization of the cis form to all-trans-retinal. This causes a conformational change in rhodopsin which then tranduces the signal downstream via G-proteins.
For my work, it would be great if the PSI-MOD entry above can be resolved to two, one with 11cRAL modification and one with atRAL modification.
See PubMed:12177057 for reference.
Thanks

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Original comment by: beej160

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If by "atRAL-L-lysine" you mean "all-trans-retinal-L-lysine", then that is the MOD:00129, RESID:AA0120. Look at the diagram, the configuration around all of the extended chain double bonds is "trans", now systematically designated as "E", aus deutsch "entgegen".

Original comment by: jsgaravelli

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Aha, OK, that’s good with me.

Thanks for clarifying.

When could you make the 11-cis form?
I only ask as it’s the only outstanding PSI-MOD we don’t have for our modifications in Reactome.

Cheers

Bijay

On 20 Mar 2014, at 15:44, "John S. Garavelli" [email protected] wrote:

If by "atRAL-L-lysine" you mean "all-trans-retinal-L-lysine", then that is the MOD:00129, RESID:AA0120. Look at the diagram, the configuration around all of the extended chain double bonds is "trans", now systematically designated as "E", aus deutsch "entgegen".

[mod-controlled-vocab-changes:#67] Lys modification with retinal isomers

Status: open
Group:
Created: Wed Aug 22, 2012 06:58 PM UTC by BijayJassal
Last Updated: Thu Mar 20, 2014 02:38 PM UTC
Owner: John S. Garavelli

Hi John, after our email exchange, I'd like to submit this request for distinguishing the binding of retinal isomers to rhodopsin during visual transduction process. In PSI-MOD there is Retinylidene (MOD:00129), the conversion of an L-lysine residue by retinal.
In the visual transduction process, 11-cis-retinal first binds to rhodopsin then light causes isomerization of the cis form to all-trans-retinal. This causes a conformational change in rhodopsin which then tranduces the signal downstream via G-proteins.
For my work, it would be great if the PSI-MOD entry above can be resolved to two, one with 11cRAL modification and one with atRAL modification.
See PubMed:12177057 for reference.
Thanks

Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/psidev/mod-controlled-vocab-changes/67/

To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

Original comment by: beej160

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Hi John

Please could you let me know a timescale for when this 11-cis form can be created.
Also, where to find it once created! I usually use OLS from EBI.

Cheers

Bijay

On 20 Mar 2014, at 16:18, BijayJassal [email protected] wrote:

Aha, OK, that’s good with me.

Thanks for clarifying.

When could you make the 11-cis form?
I only ask as it’s the only outstanding PSI-MOD we don’t have for our modifications in Reactome.

Cheers

Bijay

On 20 Mar 2014, at 15:44, "John S. Garavelli" [email protected] wrote:

If by "atRAL-L-lysine" you mean "all-trans-retinal-L-lysine", then that is the MOD:00129, RESID:AA0120. Look at the diagram, the configuration around all of the extended chain double bonds is "trans", now systematically designated as "E", aus deutsch "entgegen".

[mod-controlled-vocab-changes:#67] Lys modification with retinal isomers

Status: open
Group:
Created: Wed Aug 22, 2012 06:58 PM UTC by BijayJassal
Last Updated: Thu Mar 20, 2014 02:38 PM UTC
Owner: John S. Garavelli

Hi John, after our email exchange, I'd like to submit this request for distinguishing the binding of retinal isomers to rhodopsin during visual transduction process. In PSI-MOD there is Retinylidene (MOD:00129), the conversion of an L-lysine residue by retinal.
In the visual transduction process, 11-cis-retinal first binds to rhodopsin then light causes isomerization of the cis form to all-trans-retinal. This causes a conformational change in rhodopsin which then tranduces the signal downstream via G-proteins.
For my work, it would be great if the PSI-MOD entry above can be resolved to two, one with 11cRAL modification and one with atRAL modification.
See PubMed:12177057 for reference.
Thanks

Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/psidev/mod-controlled-vocab-changes/67/

To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

[mod-controlled-vocab-changes:#67] Lys modification with retinal isomers

Status: open
Group:
Created: Wed Aug 22, 2012 06:58 PM UTC by BijayJassal
Last Updated: Thu Mar 20, 2014 02:38 PM UTC
Owner: John S. Garavelli

Hi John, after our email exchange, I'd like to submit this request for distinguishing the binding of retinal isomers to rhodopsin during visual transduction process. In PSI-MOD there is Retinylidene (MOD:00129), the conversion of an L-lysine residue by retinal.
In the visual transduction process, 11-cis-retinal first binds to rhodopsin then light causes isomerization of the cis form to all-trans-retinal. This causes a conformational change in rhodopsin which then tranduces the signal downstream via G-proteins.
For my work, it would be great if the PSI-MOD entry above can be resolved to two, one with 11cRAL modification and one with atRAL modification.
See PubMed:12177057 for reference.
Thanks

Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/psidev/mod-controlled-vocab-changes/67/

To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

Original comment by: beej160

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Bijay, I have not been able to update RESID on 31 March as I had hoped. However, I will go ahead to make an interim release of PSI-MOD next week. I have reserved these identifiers for that relesae:
PSI-MOD:01999 N6-(11-cis)-retinylidene-L-lysine
PSI-MOD:02000 N6-retinylidene-L-lysine (unspecified geometric isomer)
The entry PSI-MOD:00129 N6-retinylidene-L-lysine will be given a synonym indicating that it is the "all trans isomer".

Original comment by: jsgaravelli