Re: [ccp4bb] About the A in AI

[Cowan, Richard H. (Dr.)]

The underlying model that drives Bing is ChatGPT, so perhaps not a surprise 
they produce the same output. Maybe giving Bard or Llama the same prompt might 
give different results.

Thanks,

Richard Cowan
Research Fellow

Leicester Institute of Structural and Chemical Biology
Department of Molecular and Cell Biology
University of Leicester | University Road | Leicester | LE1 7RH | UK

t: +44 (0)116 229 7077
e:  rc...@leicester.ac.uk
w: www.le.ac.uk
[vxWQrlsJKAEloASUgBJQAkpg+xJQQbp9+eroSkAJKAEloASUgBJQAg0QUEHaACB9rASUgBJQAkpACSgBJbB9Cagg3b58dXQloASUgBJQAkpACSiBBgioIG0AkD5WAkpACSgBJaAElIAS2L4EVJBuX746uhJQAkpACSgBJaAElEADBFSQNgBIHysBJaAElIASUAJKQAlsXwIqSLcvXx1dCSgBJaAElIASUAJKoAECKkgbAKSPlYASUAJKQAkoASWgBLYvARWk25evjq4ElIASUAJKQAkoASWgBJSAElACSkAJKAEloASUwI5M4P8AZ4taSLRHMpYASUVORK5CYII=]
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From: CCP4 bulletin board  on behalf of Bruno KLAHOLZ 

Date: Friday, 12 May 2023 at 16:36
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] About the A in AI
***CAUTION:*** This email was sent from an EXTERNAL source. Think before 
clicking links or opening attachments.

indeed, probably they are using the same databases and features.
Same happens in translations btw.

Cheers,

Bruno


From: CCP4 bulletin board  On Behalf Of Ian Tickle
Sent: 12 May 2023 17:33
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] About the A in AI


Hi Bernhard

Methinks there's some cribbing going on between Bing and ChatGPT - not only 
deja-vu but the reviews are identical word for word!  How is that possible?

Cheers

-- Ian


On Fri, 12 May 2023 at 16:15, Bernhard Rupp 
mailto:hofkristall...@gmail.com>> wrote:
For those who concern themselves with such matters, here the responses from 
Bing and ChatGPT to the prompt:

“Please write a critical review report rejecting a scientific paper reporting 
that the 1.0 angstrom crystal structure shows that psiX is a trimethylating 
enzyme”

Enjoy the frightening reading and then we can chat (LOL) about the creepy 
feeling of déjà-vu you might experience….

https://www.dropbox.com/s/2fo9u3d11dk8n0o/Bing.docx?dl=0
https://www.dropbox.com/s/9gr34grpcrf7yk7/ChatGPT.docx?dl=0

Cheers, BR

-
Bernhard Rupp
k.k. Hofkristallamt
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.hofkristallamt.org/
-
Hope is not a strategy - hope is a mistake.
-




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Re: [ccp4bb] Covalent Cysteine Aduct

[Cowan, Richard H. (Dr.)]

Hi to All,

Whilst this discussion has been going on, I've been carrying on with the work 
on this, and have now replaced the offending cysteine with CME. It seems to 
refine pretty well, fitting the density well, and the b-factors stay similar to 
those for nearby side chains, so I'm reasonably happy with it. Now to figure 
out where the BME came from.

Thanks to all who have offered suggestions and help. Now to check another 
structure with a related Fab with the same surface cysteine, this time heavily 
annisotropic, and in complex with the target, at 2.7A at best!

Thanks,

Dr Richard Cowan
Research Associate

HWLSB 1/05
Department of Biochemistry
University of Leicester
Lancaster Road
Leicester, LE1 9HN, U.K.

Phone +44 (0) 116 229 7077


From: Mark J van Raaij 
Sent: 27 March 2020 21:46
To: Cowan, Richard H. (Dr.) 
Subject: Re: [ccp4bb] Covalent Cysteine Aduct

I agree, but in my opinion the density is quite clear for a disulphide, so I 
would bet beta-mercaptoethanol *was* added at some step (perhaps even by 
accident). Even if it's not considered best practice, you seem to have "gotten 
away with it" and the Fab still crystallised ok.

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fjournals.iucr.org%2Ff%2F=02%7C01%7Crc273%40leicester.ac.uk%7C4d22be0719f0431dc69608d7d298414d%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C637209423675980222=QcQSKYwh%2BJ3a86IwEvh6J3UVOplgLRWdfSRvTL8j1sU%3D=0>


On 27 Mar 2020, at 22:38, Cowan, Richard H. (Dr.) 
mailto:rc...@leicester.ac.uk>> wrote:

Hi,

The Fab constructs have a c-terminal cysteines on both the heavy and light 
chains, which should form a disulphide. Adding reducing agent to the 
purification of the protein would potentially reduce this disulphide, possible 
causing issues the stability and heterogeneity? At least that's my 
understanding?

Thanks,

Dr Richard Cowan
Research Associate

HWLSB 1/05
Department of Biochemistry
University of Leicester
Lancaster Road
Leicester, LE1 9HN, U.K.

Phone +44 (0) 116 229 7077


From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Paul Emsley 
mailto:pems...@mrc-lmb.cam.ac.uk>>
Sent: 27 March 2020 21:33
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] Covalent Cysteine Aduct


On 27/03/2020 21:06, Cowan, Richard H. (Dr.) wrote:


  although [BME] seems unlikely, since the crystallized protein is a Fab.


I don't follow.



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Re: [ccp4bb] Covalent Cysteine Aduct

[Cowan, Richard H. (Dr.)]

Hi,

The Fab constructs have a c-terminal cysteines on both the heavy and light 
chains, which should form a disulphide. Adding reducing agent to the 
purification of the protein would potentially reduce this disulphide, possible 
causing issues the stability and heterogeneity? At least that's my 
understanding?

Thanks,

Dr Richard Cowan
Research Associate

HWLSB 1/05
Department of Biochemistry
University of Leicester
Lancaster Road
Leicester, LE1 9HN, U.K.

Phone +44 (0) 116 229 7077


From: CCP4 bulletin board  on behalf of Paul Emsley 

Sent: 27 March 2020 21:33
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Covalent Cysteine Aduct



On 27/03/2020 21:06, Cowan, Richard H. (Dr.) wrote:


  although [BME] seems unlikely, since the crystallized protein is a Fab.



I don't follow.




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Re: [ccp4bb] Covalent Cysteine Aduct

[Cowan, Richard H. (Dr.)]

Hi,

The gene was synthesized for the expression construct, so a sequence error 
seems unlikely, but I'll check. There should be mass spec data on the purified 
protein, but our collaborators, who are also shut down for the moment, will 
have to get that for me, as well as sequence data. I don't see a guanidino head 
group, which would match arginine (single base error), and the base changes to 
arrive at lysine or methionine seem unlikely to have passed even a cursory QC. 
I will admit that an surface cysteine in a Fab variable domain does seem to be 
unlikely, but I'm not sure how common it may actually be?

Thanks,

Dr Richard Cowan
Research Associate

HWLSB 1/05
Department of Biochemistry
University of Leicester
Lancaster Road
Leicester, LE1 9HN, U.K.

Phone +44 (0) 116 229 7077


From: Gulick, Andrew 
Sent: 27 March 2020 21:14
To: Cowan, Richard H. (Dr.) 
Subject: re: [ccp4bb] Covalent Cysteine Aduct


Also, are you sure of protein sequence. Density looked like a long side chain 
(Lys or Arg) so always worth considering.

Best,

Andrew







--

Andrew M. Gulick, 
Ph.D.<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmedicine.buffalo.edu%2Fcontent%2Fmedicine%2Ffaculty%2Fprofile.html%3Fubit%3Damgulick=02%7C01%7Crc273%40LEICESTER.AC.UK%7C9758cfe572d44a68177b08d7d293db66%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637209404794807376=%2F%2FLNQyUrw6ipa3B39U9Mb%2BEsoHRnoqApKMBcarsAtbA%3D=0>

Associate Professor

Department of Structural Biology

Jacobs School of Medicine and Biomedical Sciences

University at Buffalo

955 Main Street, Room 5152

Buffalo, New York 14203-1121

office: 716-829-3696

email: amgul...@buffalo.edu<mailto:amgul...@buffalo.edu>







From: CCP4 bulletin board  on behalf of "Cowan, Richard 
H. (Dr.)" 
Reply-To: "Cowan, Richard H. (Dr.)" 
Date: Friday, March 27, 2020 at 5:06 PM
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: [ccp4bb] Covalent Cysteine Aduct



Hi Robbie et al.,



I'm very sure on the crystallization conditions, but I'll check the 
purification for BME, although it seems unlikely, since the crystallized 
protein is a Fab.



What I would be less sure on is the age of the reagents used. Is anyone aware 
of significant breakdown products which might be more reactive, particularly 
the alcohols?



Thanks,



Dr Richard Cowan
Research Associate



HWLSB 1/05

Department of Biochemistry

University of Leicester

Lancaster Road

Leicester, LE1 9HN, U.K.



Phone +44 (0) 116 229 7077





From: robbie_joos...@hotmail.com 
Sent: 27 March 2020 20:57
To: Cowan, Richard H. (Dr.) 
Cc: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Covalent Cysteine Aduct



Are you absolutely sure about the conditions? The blob next to the sulfur looks 
pretty fat so I would guess BME.



Cheers,

Robbie



On 27 Mar 2020 21:32, "Cowan, Richard H. (Dr.)"  wrote:

Hi All,



During the current enforced shutdown, I've been going back over some older data 
and spotted this in one of my structures:



[cid:d2ff-a10c-4f19-9f47-4db92e7620ef]





It's what appears to be a covalent aduct onto a cysteine on the surface 
(originally modeled as 2 waters!). The condition was optimized from the 
Morpheus Screen condition D1, so MES/Imidazole pH 6.5, PEG 500MME, PEG20k and a 
mix of 1,6-Hexanediol, 1-Butanol, 1,2-Propanediol, 2-Propanol, 1,4-Butanediol 
and 1,3-Propanediol. The data has been cut at 1.7A, with good stats.




Has anyone seen anything like this before? what do you think my best bet for 
modeling this is? and aduct of 1,3-propanediol? It looks too short for 
1-butanol or 1,4-butandiol, and it's linear so 2-propanol and 1,2-propanediol 
seem unlikely.




Thanks,



Dr Richard Cowan
Research Associate



HWLSB 1/05

Department of Biochemistry

University of Leicester

Lancaster Road

Leicester, LE1 9HN, U.K.



Phone +44 (0) 116 229 7077







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###

Re: [ccp4bb] Covalent Cysteine Aduct

[Cowan, Richard H. (Dr.)]

Hi,

The density is very much a linear chain, without side branches. That would lead 
me to discount a DTT adduct, since I can't see anywhere for the hydroxls to go?

Thanks,

Dr Richard Cowan
Research Associate

HWLSB 1/05
Department of Biochemistry
University of Leicester
Lancaster Road
Leicester, LE1 9HN, U.K.

Phone +44 (0) 116 229 7077


From: Petri Kursula 
Sent: 27 March 2020 21:13
To: Cowan, Richard H. (Dr.) 
Cc: CCP4BB@jiscmail.ac.uk 
Subject: Re: [ccp4bb] Covalent Cysteine Aduct

Looks like DTT adduct to me; but then again, if you did not have it, it 
probably is not.
Petri

Petri Kursula
--
Professor
--
Department of Biomedicine
University of Bergen, Norway
http://www.uib.no/en/rg/petrikursula<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.uib.no%2Fen%2Frg%2Fpetrikursula=02%7C01%7Crc273%40leicester.ac.uk%7C5bd2d6eed27e46e7fa0908d7d293afd2%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C637209404081752652=XJzM3H1DJS4TGdmEMzAryNn2YQYpuxcoVkmp9u6sric%3D=0>
petri.kurs...@uib.no
--
Faculty of Biochemistry and Molecular Medicine
Biocenter Oulu
University of Oulu, Finland
--





On 27 Mar 2020, at 22:06, Cowan, Richard H. (Dr.) 
mailto:rc...@leicester.ac.uk>> wrote:

Hi Robbie et al.,

I'm very sure on the crystallization conditions, but I'll check the 
purification for BME, although it seems unlikely, since the crystallized 
protein is a Fab.

What I would be less sure on is the age of the reagents used. Is anyone aware 
of significant breakdown products which might be more reactive, particularly 
the alcohols?

Thanks,

Dr Richard Cowan
Research Associate

HWLSB 1/05
Department of Biochemistry
University of Leicester
Lancaster Road
Leicester, LE1 9HN, U.K.

Phone +44 (0) 116 229 7077


From: robbie_joos...@hotmail.com<mailto:robbie_joos...@hotmail.com> 
mailto:robbie_joos...@hotmail.com>>
Sent: 27 March 2020 20:57
To: Cowan, Richard H. (Dr.) 
mailto:rc...@leicester.ac.uk>>
Cc: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] Covalent Cysteine Aduct

Are you absolutely sure about the conditions? The blob next to the sulfur looks 
pretty fat so I would guess BME.

Cheers,
Robbie

On 27 Mar 2020 21:32, "Cowan, Richard H. (Dr.)" 
mailto:rc...@leicester.ac.uk>> wrote:
Hi All,

During the current enforced shutdown, I've been going back over some older data 
and spotted this in one of my structures:

[cid:d2ff-a10c-4f19-9f47-4db92e7620ef]


It's what appears to be a covalent aduct onto a cysteine on the surface 
(originally modeled as 2 waters!). The condition was optimized from the 
Morpheus Screen condition D1, so MES/Imidazole pH 6.5, PEG 500MME, PEG20k and a 
mix of 1,6-Hexanediol, 1-Butanol, 1,2-Propanediol, 2-Propanol, 1,4-Butanediol 
and 1,3-Propanediol. The data has been cut at 1.7A, with good stats.

Has anyone seen anything like this before? what do you think my best bet for 
modeling this is? and aduct of 1,3-propanediol? It looks too short for 
1-butanol or 1,4-butandiol, and it's linear so 2-propanol and 1,2-propanediol 
seem unlikely.

Thanks,

Dr Richard Cowan
Research Associate

HWLSB 1/05
Department of Biochemistry
University of Leicester
Lancaster Road
Leicester, LE1 9HN, U.K.

Phone +44 (0) 116 229 7077



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Re: [ccp4bb] Covalent Cysteine Aduct

[Cowan, Richard H. (Dr.)]

Hi Robbie et al.,

I'm very sure on the crystallization conditions, but I'll check the 
purification for BME, although it seems unlikely, since the crystallized 
protein is a Fab.

What I would be less sure on is the age of the reagents used. Is anyone aware 
of significant breakdown products which might be more reactive, particularly 
the alcohols?

Thanks,

Dr Richard Cowan
Research Associate

HWLSB 1/05
Department of Biochemistry
University of Leicester
Lancaster Road
Leicester, LE1 9HN, U.K.

Phone +44 (0) 116 229 7077


From: robbie_joos...@hotmail.com 
Sent: 27 March 2020 20:57
To: Cowan, Richard H. (Dr.) 
Cc: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Covalent Cysteine Aduct

Are you absolutely sure about the conditions? The blob next to the sulfur looks 
pretty fat so I would guess BME.

Cheers,
Robbie

On 27 Mar 2020 21:32, "Cowan, Richard H. (Dr.)"  wrote:
Hi All,

During the current enforced shutdown, I've been going back over some older data 
and spotted this in one of my structures:

[cid:d2ff-a10c-4f19-9f47-4db92e7620ef]


It's what appears to be a covalent aduct onto a cysteine on the surface 
(originally modeled as 2 waters!). The condition was optimized from the 
Morpheus Screen condition D1, so MES/Imidazole pH 6.5, PEG 500MME, PEG20k and a 
mix of 1,6-Hexanediol, 1-Butanol, 1,2-Propanediol, 2-Propanol, 1,4-Butanediol 
and 1,3-Propanediol. The data has been cut at 1.7A, with good stats.

Has anyone seen anything like this before? what do you think my best bet for 
modeling this is? and aduct of 1,3-propanediol? It looks too short for 
1-butanol or 1,4-butandiol, and it's linear so 2-propanol and 1,2-propanediol 
seem unlikely.

Thanks,

Dr Richard Cowan
Research Associate

HWLSB 1/05
Department of Biochemistry
University of Leicester
Lancaster Road
Leicester, LE1 9HN, U.K.

Phone +44 (0) 116 229 7077




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