From emartz at microbio.umass.edu  Tue May 25 20:03:20 2021
From: emartz at microbio.umass.edu (Eric Martz)
Date: Tue, 25 May 2021 20:03:20 -0400
Subject: [Proteopedia] New kind of inter-chain bond involved in redox
	allostery
Message-ID: <09680462-68c9-0a2e-6895-ead90faadfda@microbio.umass.edu>

Earlier this month, a new kind of covalent linkage between the 
sidechains of Lys and Cys was reported in Nature, a 
Nitrogen-Oxygen-Sulfur (NOS) bond. In the initial case of the 
transaldolases studied, it serves as an allosteric redox switch for 
enzymatic activity. NOS appears likely to occur in proteins in all 
domains of life including /Homo sapiens/, apparently overlooked in 
earlier interpretations of electron density maps.

Have a look at this new page:

https://proteopedia.org/w/Lysine-cysteine_NOS_bonds

-Eric

P.S. Thanks to crystallographer Fadel Samatey for pointing out the 
original report to me.

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From karplus at soe.ucsc.edu  Tue May 25 21:39:30 2021
From: karplus at soe.ucsc.edu (Kevin Karplus)
Date: Tue, 25 May 2021 18:39:30 -0700
Subject: [Proteopedia] New kind of inter-chain bond involved in redox
	allostery
In-Reply-To: <09680462-68c9-0a2e-6895-ead90faadfda@microbio.umass.edu>
References: <09680462-68c9-0a2e-6895-ead90faadfda@microbio.umass.edu>
Message-ID: <CAJF5WLUHozvW8nXJ1Y7q342gK9haGwb_nmzDhmbi+xz0V-df7Q@mail.gmail.com>

Cool!  Is anyone planning to write a program or query to scan all of PDB
looking for places where this structure may have been missed?  Or has that
already been done?

Kevin Karplus   karplus at soe.ucsc.edu    http://www.soe.ucsc.edu/~karplus
Undergraduate Director for Biomolecular Engineering and Bioinformatics
Professor of Biomolecular Engineering, University of California, Santa Cruz
Author of *Applied Analog Electronics
<https://leanpub.com/applied_analog_electronics>*

*Affiliations for identification only.*


On Tue, May 25, 2021 at 5:03 PM Eric Martz <emartz at microbio.umass.edu>
wrote:

> Earlier this month, a new kind of covalent linkage between the
> sidechains of Lys and Cys was reported in Nature, a
> Nitrogen-Oxygen-Sulfur (NOS) bond. In the initial case of the
> transaldolases studied, it serves as an allosteric redox switch for
> enzymatic activity. NOS appears likely to occur in proteins in all
> domains of life including /Homo sapiens/, apparently overlooked in
> earlier interpretations of electron density maps.
>
> Have a look at this new page:
>
> https://proteopedia.org/w/Lysine-cysteine_NOS_bonds
>
> -Eric
>
> P.S. Thanks to crystallographer Fadel Samatey for pointing out the
> original report to me.
>
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> http://www.bioinformatics.org/pipermail/proteopedialist-for-users/attachments/20210525/13279180/attachment.html
> >
> _______________________________________________
> Proteopedialist-for-users mailing list
> Proteopedialist-for-users at bioinformatics.org
> http://www.bioinformatics.org/mm/listinfo/proteopedialist-for-users
>
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From amr_alhossary at hotmail.com  Wed May 26 05:03:35 2021
From: amr_alhossary at hotmail.com (Amr ALHOSSARY)
Date: Wed, 26 May 2021 09:03:35 +0000
Subject: [Proteopedia] New kind of inter-chain bond involved in
	redox	allostery
In-Reply-To: <CAJF5WLUHozvW8nXJ1Y7q342gK9haGwb_nmzDhmbi+xz0V-df7Q@mail.gmail.com>
References: <09680462-68c9-0a2e-6895-ead90faadfda@microbio.umass.edu>
	<CAJF5WLUHozvW8nXJ1Y7q342gK9haGwb_nmzDhmbi+xz0V-df7Q@mail.gmail.com>
Message-ID: <MWHPR19MB1357EF26F0D527F543B0A65D8E249@MWHPR19MB1357.namprd19.prod.outlook.com>

Good idea.
I had searched the PDB for occurrence of cation-pi interaction on both sides of aromatic rings, during my MSc.
I believe I still have that code. I can change and run it to search for NOS bonds.

Amr



Amr Ali Mokhtar ALHOSSARY?MBBS, PhD
Nanyang Technological University
11 Mandalay Road #14-03, Clinical Sciences Building, Singapore 308232.
T +65 6904-1355 M +65-9457-2816 
E aalhossary at ntu.edu.sg Web www.rris.ntu.edu.sg











-----Original Message-----
From: Proteopedialist-for-users <proteopedialist-for-users-bounces at bioinformatics.org> On Behalf Of Kevin Karplus
Sent: Wednesday, May 26, 2021 9:40 AM
To: Forum for the Proteopedia User Community <proteopedialist-for-users at bioinformatics.org>
Subject: Re: [Proteopedia] New kind of inter-chain bond involved in redox allostery

Cool!  Is anyone planning to write a program or query to scan all of PDB looking for places where this structure may have been missed?  Or has that already been done?

Kevin Karplus   karplus at soe.ucsc.edu    http://www.soe.ucsc.edu/~karplus
Undergraduate Director for Biomolecular Engineering and Bioinformatics Professor of Biomolecular Engineering, University of California, Santa Cruz Author of *Applied Analog Electronics
<https://leanpub.com/applied_analog_electronics>*

*Affiliations for identification only.*


On Tue, May 25, 2021 at 5:03 PM Eric Martz <emartz at microbio.umass.edu>
wrote:

> Earlier this month, a new kind of covalent linkage between the 
> sidechains of Lys and Cys was reported in Nature, a 
> Nitrogen-Oxygen-Sulfur (NOS) bond. In the initial case of the 
> transaldolases studied, it serves as an allosteric redox switch for 
> enzymatic activity. NOS appears likely to occur in proteins in all 
> domains of life including /Homo sapiens/, apparently overlooked in 
> earlier interpretations of electron density maps.
>
> Have a look at this new page:
>
> https://proteopedia.org/w/Lysine-cysteine_NOS_bonds
>
> -Eric
>
> P.S. Thanks to crystallographer Fadel Samatey for pointing out the 
> original report to me.
>
> -------------- next part -------------- An HTML attachment was 
> scrubbed...
> URL: <
> http://www.bioinformatics.org/pipermail/proteopedialist-for-users/atta
> chments/20210525/13279180/attachment.html
> >
> _______________________________________________
> Proteopedialist-for-users mailing list 
> Proteopedialist-for-users at bioinformatics.org
> http://www.bioinformatics.org/mm/listinfo/proteopedialist-for-users
>
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http://www.bioinformatics.org/mm/listinfo/proteopedialist-for-users

From emartz at microbio.umass.edu  Wed May 26 12:13:24 2021
From: emartz at microbio.umass.edu (Eric Martz)
Date: Wed, 26 May 2021 12:13:24 -0400
Subject: [Proteopedia] Scanning the entire PDB for NOS or isopeptide bonds
In-Reply-To: <MWHPR19MB1357EF26F0D527F543B0A65D8E249@MWHPR19MB1357.namprd19.prod.outlook.com>
References: <09680462-68c9-0a2e-6895-ead90faadfda@microbio.umass.edu>
	<CAJF5WLUHozvW8nXJ1Y7q342gK9haGwb_nmzDhmbi+xz0V-df7Q@mail.gmail.com>
	<MWHPR19MB1357EF26F0D527F543B0A65D8E249@MWHPR19MB1357.namprd19.prod.outlook.com>
Message-ID: <f78a077a-1f23-312e-d38e-0a6175cd561a@microbio.umass.edu>

As stated in the Proteopedia article

https://proteopedia.org/w/Lysine-cysteine_NOS_bonds

Wensien et al. have already scanned the PDB for putative NOS bonds. 
Their paper says they have a manuscript in publication.

Changing the subject to isopeptide bonds

https://proteopedia.org/w/Isopeptide_bond

I would like to know if the entire PDB has been scanned for those. I 
have an inquiry pending with the wwPDB about whether they offer a method 
to search for them, but have no reply yet. I will post an inquiry on the 
PDB email list. If this hasn't been done, Amr, perhaps you can do it? I 
will be in touch.

A forthcoming version of FirstGlance in Jmol 
(http://firstglance.jmol.org), still in preparation, will offer an alert 
when an isopeptide or NOS bond is present, and offer to zoom in to show 
details.

-Eric

On 5/26/21 5:03 AM, Amr ALHOSSARY wrote:
> Good idea.
> I had searched the PDB for occurrence of cation-pi interaction on both sides of aromatic rings, during my MSc.
> I believe I still have that code. I can change and run it to search for NOS bonds.
>
> Amr
>
>
>
> Amr Ali Mokhtar ALHOSSARY?MBBS, PhD
> Nanyang Technological University
> 11 Mandalay Road #14-03, Clinical Sciences Building, Singapore 308232.
> T +65 6904-1355 M +65-9457-2816
> E aalhossary at ntu.edu.sg Web www.rris.ntu.edu.sg
>
> -----Original Message-----
> From: Proteopedialist-for-users <proteopedialist-for-users-bounces at bioinformatics.org> On Behalf Of Kevin Karplus
> Sent: Wednesday, May 26, 2021 9:40 AM
> To: Forum for the Proteopedia User Community <proteopedialist-for-users at bioinformatics.org>
> Subject: Re: [Proteopedia] New kind of inter-chain bond involved in redox allostery
>
> Cool!  Is anyone planning to write a program or query to scan all of PDB looking for places where this structure may have been missed?  Or has that already been done?
>
> Kevin Karplus   karplus at soe.ucsc.edu    http://www.soe.ucsc.edu/~karplus
> Undergraduate Director for Biomolecular Engineering and Bioinformatics Professor of Biomolecular Engineering, University of California, Santa Cruz Author of *Applied Analog Electronics
> <https://leanpub.com/applied_analog_electronics>*
>
> *Affiliations for identification only.*
>
>
> On Tue, May 25, 2021 at 5:03 PM Eric Martz <emartz at microbio.umass.edu>
> wrote:
>
>> Earlier this month, a new kind of covalent linkage between the
>> sidechains of Lys and Cys was reported in Nature, a
>> Nitrogen-Oxygen-Sulfur (NOS) bond. In the initial case of the
>> transaldolases studied, it serves as an allosteric redox switch for
>> enzymatic activity. NOS appears likely to occur in proteins in all
>> domains of life including /Homo sapiens/, apparently overlooked in
>> earlier interpretations of electron density maps.
>>
>> Have a look at this new page:
>>
>> https://proteopedia.org/w/Lysine-cysteine_NOS_bonds
>>
>> -Eric
>>
>> P.S. Thanks to crystallographer Fadel Samatey for pointing out the
>> original report to me.
>>

From amr_alhossary at hotmail.com  Wed Jun  2 09:08:51 2021
From: amr_alhossary at hotmail.com (Amr ALHOSSARY)
Date: Wed, 2 Jun 2021 13:08:51 +0000
Subject: [Proteopedia] Scanning the entire PDB for NOS or isopeptide
	bonds
In-Reply-To: <f78a077a-1f23-312e-d38e-0a6175cd561a@microbio.umass.edu>
References: <09680462-68c9-0a2e-6895-ead90faadfda@microbio.umass.edu>
	<CAJF5WLUHozvW8nXJ1Y7q342gK9haGwb_nmzDhmbi+xz0V-df7Q@mail.gmail.com>
	<MWHPR19MB1357EF26F0D527F543B0A65D8E249@MWHPR19MB1357.namprd19.prod.outlook.com>
	<f78a077a-1f23-312e-d38e-0a6175cd561a@microbio.umass.edu>
Message-ID: <MWHPR19MB13573DF5338E0D5FD3A8D7688E3D9@MWHPR19MB1357.namprd19.prod.outlook.com>

Dear Dr Eric,

Checking the PDB mail list archive, I see no response to your question. Have you received any reply offline?
If you like to do it, I'd be happy to help you.

Regards

Amr

-----Original Message-----
From: Proteopedialist-for-users <proteopedialist-for-users-bounces at bioinformatics.org> On Behalf Of Eric Martz
Sent: Thursday, May 27, 2021 12:13 AM
To: proteopedialist-for-users at bioinformatics.org
Subject: [Proteopedia] Scanning the entire PDB for NOS or isopeptide bonds

As stated in the Proteopedia article

https://proteopedia.org/w/Lysine-cysteine_NOS_bonds

Wensien et al. have already scanned the PDB for putative NOS bonds. 
Their paper says they have a manuscript in publication.

Changing the subject to isopeptide bonds

https://proteopedia.org/w/Isopeptide_bond

I would like to know if the entire PDB has been scanned for those. I have an inquiry pending with the wwPDB about whether they offer a method to search for them, but have no reply yet. I will post an inquiry on the PDB email list. If this hasn't been done, Amr, perhaps you can do it? I will be in touch.

A forthcoming version of FirstGlance in Jmol (http://firstglance.jmol.org), still in preparation, will offer an alert when an isopeptide or NOS bond is present, and offer to zoom in to show details.

-Eric

On 5/26/21 5:03 AM, Amr ALHOSSARY wrote:
> Good idea.
> I had searched the PDB for occurrence of cation-pi interaction on both sides of aromatic rings, during my MSc.
> I believe I still have that code. I can change and run it to search for NOS bonds.
>
> Amr
>
>
>
> Amr Ali Mokhtar ALHOSSARY?MBBS, PhD
> Nanyang Technological University
> 11 Mandalay Road #14-03, Clinical Sciences Building, Singapore 308232.
> T +65 6904-1355 M +65-9457-2816
> E aalhossary at ntu.edu.sg Web www.rris.ntu.edu.sg
>
> -----Original Message-----
> From: Proteopedialist-for-users 
> <proteopedialist-for-users-bounces at bioinformatics.org> On Behalf Of 
> Kevin Karplus
> Sent: Wednesday, May 26, 2021 9:40 AM
> To: Forum for the Proteopedia User Community 
> <proteopedialist-for-users at bioinformatics.org>
> Subject: Re: [Proteopedia] New kind of inter-chain bond involved in 
> redox allostery
>
> Cool!  Is anyone planning to write a program or query to scan all of PDB looking for places where this structure may have been missed?  Or has that already been done?
>
> Kevin Karplus   karplus at soe.ucsc.edu    http://www.soe.ucsc.edu/~karplus
> Undergraduate Director for Biomolecular Engineering and Bioinformatics 
> Professor of Biomolecular Engineering, University of California, Santa 
> Cruz Author of *Applied Analog Electronics
> <https://leanpub.com/applied_analog_electronics>*
>
> *Affiliations for identification only.*
>
>
> On Tue, May 25, 2021 at 5:03 PM Eric Martz <emartz at microbio.umass.edu>
> wrote:
>
>> Earlier this month, a new kind of covalent linkage between the 
>> sidechains of Lys and Cys was reported in Nature, a 
>> Nitrogen-Oxygen-Sulfur (NOS) bond. In the initial case of the 
>> transaldolases studied, it serves as an allosteric redox switch for 
>> enzymatic activity. NOS appears likely to occur in proteins in all 
>> domains of life including /Homo sapiens/, apparently overlooked in 
>> earlier interpretations of electron density maps.
>>
>> Have a look at this new page:
>>
>> https://proteopedia.org/w/Lysine-cysteine_NOS_bonds
>>
>> -Eric
>>
>> P.S. Thanks to crystallographer Fadel Samatey for pointing out the 
>> original report to me.
>>
_______________________________________________
Proteopedialist-for-users mailing list
Proteopedialist-for-users at bioinformatics.org
http://www.bioinformatics.org/mm/listinfo/proteopedialist-for-users