[Proteopedia] Scanning the entire PDB for NOS or isopeptide bonds

[Eric Martz]

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.
>>