Re: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide crystallization?

[David Briggs]

Hi Mark,

I also use dis.embl and IUPred in Jalview when trying to come up with construct 
boundaries.

In the specific case I was referring to, we had a secreted human protein with a 
long and atypical secretion tag, which made it difficult to place the 
N-terminus of the mature protein within the sequence.

My initial attempts didn't work at all, and after reviewing the AF2 model at 
the EBI database, I removed a further ~30 residues at the N-terminus, which 
yielded a well expressed, soluble, secreted product.

Speaking more generally, I think that AF2 is probably "just another tool" for 
helping to inform construct boundaries.
I have no empirical evidence that the AF2 pLDDT is more sensitive or accurate 
than other bespoke disorder prediction software.

Because it worked once for me, I'll run it/check the EBI database every time 
from now on, but you're absolutely right that I probably would have done that 
anyway!

Best,

Dave


--

Dr David C. Briggs CSci MRSB

Senior Laboratory Research Scientist

Signalling and Structural Biology Lab

The Francis Crick Institute

London, UK

==

about.me/david_briggs


From: Mark J. van Raaij 
Sent: 05 April 2022 14:47
To: CCP4BB@jiscmail.ac.uk 
Cc: David Briggs 
Subject: Re: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide 
crystallization?


External Sender: Use caution.

Hi David,

do you think that alphafold2 dis/order prediction is better than specific 
disorder predictors?

i.e.
http://dis.embl.de<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdis.embl.de%2F=04%7C01%7C%7C84f2f05bbd5a4598ff5908da170ae108%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637847632751920405%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000=2FjXOEwioG4hdIuef0nPFEM%2B4pV6V%2FB9kYa9phWu4Ds%3D=0>
 , which we've used for construct design
https://prdos.hgc.jp<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fprdos.hgc.jp%2F=04%7C01%7C%7C84f2f05bbd5a4598ff5908da170ae108%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637847632751920405%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000=ckpin7cUBV3sVYnc1Coxe72%2FQNMd1M%2ByXpoRaCbdRgE%3D=0>
 , which I haven't really tried yet
https://iupred2a.elte.hu<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fiupred2a.elte.hu%2F=04%7C01%7C%7C84f2f05bbd5a4598ff5908da170ae108%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637847632751920405%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000=5IVfLHj7g9Wq4BiQdoez1wB0mgsvQ608xAcw3LzY%2BnM%3D=0>
 (which a colleague here likes because it also tries to predict likelihood of 
protein interactions)

Or perhaps it's just because you were going to run alphafold2 anyway?

best wishes,

Mark

Mark J van Raaij
Dpto de Estructura de Macromoleculas, lab 20B
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. +34 91 585 4616 (internal 432092)


On 4 Apr 2022, at 21:30, David Briggs 
mailto:david.bri...@crick.ac.uk>> wrote:

Hi Scott,

I've used AF2 order/disorder prediction (based up pLDDT score) to decided upon 
construct boundaries. We turned a non-expressing construct into a reasonably 
well expressing construct based on the AF2 prediction.

It's part of my construct design process now.

HTH,

Dave

--
Dr David C. Briggs
Senior Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fabout.me%2Fdavid_briggs=04%7C01%7C%7C84f2f05bbd5a4598ff5908da170ae108%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637847632751920405%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000=RqGd8%2Fy%2FuaLk%2B9IjCfiagj%2BZiHQB%2BYwAu269u7C0HFs%3D=0>

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Scott Classen mailto:sclas...@lbl.gov>>
Sent: Monday, April 4, 2022 8:06:38 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide 
crystallization?


External Sender: Use caution.

Hello CCP4,

Has anyone successfully used the available ML/AI protein folding tools to guide 
crystallization construct design? Maybe you had a protein or domain that was 
resistant to crystallization efforts and the folding algorithms  predicted some 
loops or termini that were disordered? Then you trimmed or modified them in 
some way to aid in crystallization? Or if you haven’t done this yourself, are 
you aware of anyone who has?

Thanks,
Scott


~~
Scott Classen, Ph.D.
ALS-ENABLE
TomAlberTron Beamline 8.3.1
SIBYLS Beamline 12.3.1
Advanced Light Source
Lawrence Berkele

Re: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide crystallization?

[Mark J. van Raaij]

Hi David,

do you think that alphafold2 dis/order prediction is better than specific 
disorder predictors?

i.e.
http://dis.embl.de <http://dis.embl.de/> , which we've used for construct design
https://prdos.hgc.jp <https://prdos.hgc.jp/> , which I haven't really tried yet
https://iupred2a.elte.hu <http://iupred2a.elte.hu/> (which a colleague here 
likes because it also tries to predict likelihood of protein interactions)

Or perhaps it's just because you were going to run alphafold2 anyway?

best wishes,

Mark

Mark J van Raaij
Dpto de Estructura de Macromoleculas, lab 20B
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. +34 91 585 4616 (internal 432092)


> On 4 Apr 2022, at 21:30, David Briggs  wrote:
> 
> Hi Scott,
> 
> I've used AF2 order/disorder prediction (based up pLDDT score) to decided 
> upon construct boundaries. We turned a non-expressing construct into a 
> reasonably well expressing construct based on the AF2 prediction. 
> 
> It's part of my construct design process now.
> 
> HTH,
> 
> Dave
> 
> --
> Dr David C. Briggs
> Senior Laboratory Research Scientist
> Signalling and Structural Biology Lab
> The Francis Crick Institute
> London, UK
> ==
> about.me/david_briggs
> From: CCP4 bulletin board  on behalf of Scott Classen 
> 
> Sent: Monday, April 4, 2022 8:06:38 PM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide 
> crystallization?
>  
>  
> External Sender: Use caution.
>  
> Hello CCP4,
> 
> Has anyone successfully used the available ML/AI protein folding tools to 
> guide crystallization construct design? Maybe you had a protein or domain 
> that was resistant to crystallization efforts and the folding algorithms  
> predicted some loops or termini that were disordered? Then you trimmed or 
> modified them in some way to aid in crystallization? Or if you haven’t done 
> this yourself, are you aware of anyone who has?
> 
> Thanks,
> Scott 
> 
> 
> ~~
> Scott Classen, Ph.D.
> ALS-ENABLE
> TomAlberTron Beamline 8.3.1
> SIBYLS Beamline 12.3.1
> Advanced Light Source
> Lawrence Berkeley National Laboratory
> 1 Cyclotron Rd
> MS6R2100
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> ~~
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Re: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide crystallization?

[Diana Tomchick]

I would say that in a small survey (~5-6) of bacterial enzymes from our lab, 
AlphaFold2 predicted exactly the constructs that were discovered by limited 
proteolysis and/or sequence alignment for currently unpublished structures.

It’s a useful tool but I’ve also had two cases where it incorrectly predicted 
the sequences of helices in a helical bundle—frameshift errors in the sequence, 
which were confirmed by SeMet SAD data. Caveat emptor.

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)




On Apr 4, 2022, at 2:06 PM, Scott Classen 
mailto:sclas...@lbl.gov>> wrote:


EXTERNAL MAIL

Hello CCP4,

Has anyone successfully used the available ML/AI protein folding tools to guide 
crystallization construct design? Maybe you had a protein or domain that was 
resistant to crystallization efforts and the folding algorithms  predicted some 
loops or termini that were disordered? Then you trimmed or modified them in 
some way to aid in crystallization? Or if you haven’t done this yourself, are 
you aware of anyone who has?

Thanks,
Scott


~~
Scott Classen, Ph.D.
ALS-ENABLE
TomAlberTron Beamline 8.3.1
SIBYLS Beamline 12.3.1
Advanced Light Source
Lawrence Berkeley National Laboratory
1 Cyclotron Rd
MS6R2100
Berkeley, CA 94720
mobile 510.206.4418
desk 510.495.2697
beamline 510.495.2134
~~




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Re: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide crystallization?

[David Briggs]

Hi Scott,

I've used AF2 order/disorder prediction (based up pLDDT score) to decided upon 
construct boundaries. We turned a non-expressing construct into a reasonably 
well expressing construct based on the AF2 prediction.

It's part of my construct design process now.

HTH,

Dave

--
Dr David C. Briggs
Senior Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs

From: CCP4 bulletin board  on behalf of Scott Classen 

Sent: Monday, April 4, 2022 8:06:38 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide 
crystallization?


External Sender: Use caution.

Hello CCP4,

Has anyone successfully used the available ML/AI protein folding tools to guide 
crystallization construct design? Maybe you had a protein or domain that was 
resistant to crystallization efforts and the folding algorithms  predicted some 
loops or termini that were disordered? Then you trimmed or modified them in 
some way to aid in crystallization? Or if you haven’t done this yourself, are 
you aware of anyone who has?

Thanks,
Scott


~~
Scott Classen, Ph.D.
ALS-ENABLE
TomAlberTron Beamline 8.3.1
SIBYLS Beamline 12.3.1
Advanced Light Source
Lawrence Berkeley National Laboratory
1 Cyclotron Rd
MS6R2100
Berkeley, CA 94720
mobile 510.206.4418
desk 510.495.2697
beamline 510.495.2134
~~




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Re: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide crystallization?

[John R. Walker]

It may also be useful to look at homologues of the protein of interest, as
sometimes Alphafold shows very different domain arrangements despite close
sequence similarity.

John

On Mon, Apr 4, 2022 at 3:17 PM Andrew Lovering 
wrote:

> Hi Scott
> We have obtained a structure of a flexible clamshell like fold only after
> using a disulphide mutant to lock the domains based on a Rosetta Fold model.
> Interestingly, Alphafold put the very same residues further apart
> (probably a relevant "open" pose)
>
> Andy
>
> --
>
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Re: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide crystallization?

[Edward Snell]

Dear Scott,

Fabulous question. I think a lot of people are thinking about this quite deeply 
right now but our experience with single acylation and charge ladder work 
(unpublished) was that even a single amino acid charge change had a profound 
impact on crystallization outcome in the 1,536 conditions we probe. We use 
microbatch currently which is more static than vapor diffusion where the 
dynamics add another layer of complexity to the process. It could well be a 
beautiful application of ML/AI and there is a lot of interest in this here but 
even our database (~20 million images and a diverse chemical and protein 
landscape) may not be large enough for the learning process.

We had good experience in the ML/AI area automating image analysis and now 
routinely using this (with help from Google Brian - 
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0198883) but 
it required data from multiple generous sources in the community – both 
academic and industry.

(Unapologetic and shameless plug for the National Crystallization Center (get a 
crystal) at http://getacrystal.org where we use this).

I would love to add any good links in this area to our structural biology 
resources page - Structural Biology Resources | Hauptman-Woodward Medical 
Research Institute 
(buffalo.edu)<https://hwi.buffalo.edu/structural-biology-resources/>.
Best,

Eddie


Edward Snell Ph.D.

President and CEO | Hauptman-Woodward Medical Research Institute
Director | NSF BioXFEL Science and Technology Center
Professor, Materials Design and Innovation | University at Buffalo, SUNY

p: +1 716 898 8631 | f: +1 716 898 8660
e: esn...@hwi.buffalo.edu<mailto:esn...@hwi.buffalo.edu>
skype: eddie.snell

Hauptman-Woodward Medical Research Institute
700 Ellicott Street | Buffalo, NY 14203-1102
hwi.buffalo.edu<https://hwi.buffalo.edu/>


[hwi-logo-primary-horizontal]




From: CCP4 bulletin board  On Behalf Of Scott Classen
Sent: Monday, April 4, 2022 3:07 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide 
crystallization?

Hello CCP4, Has anyone successfully used the available ML/AI protein folding 
tools to guide crystallization construct design? Maybe you had a protein or 
domain that was resistant to crystallization ef
Warning! This message was sent from outside your organization and we were 
unable to verify the sender.

sophospsmartbannerend
Hello CCP4,

Has anyone successfully used the available ML/AI protein folding tools to guide 
crystallization construct design? Maybe you had a protein or domain that was 
resistant to crystallization efforts and the folding algorithms  predicted some 
loops or termini that were disordered? Then you trimmed or modified them in 
some way to aid in crystallization? Or if you haven’t done this yourself, are 
you aware of anyone who has?

Thanks,
Scott

~~
Scott Classen, Ph.D.
ALS-ENABLE
TomAlberTron Beamline 8.3.1
SIBYLS Beamline 12.3.1
Advanced Light Source
Lawrence Berkeley National Laboratory
1 Cyclotron Rd
MS6R2100
Berkeley, CA 94720
mobile 510.206.4418
desk 510.495.2697
beamline 510.495.2134
~~



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Re: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide crystallization?

[Joel Sussman]

The PROSS (Protein Repair One-Stop Shop) at: 
https://pross.weizmann.ac.il/step/pross-terms
was used to both express and be able to crystallize human acetylcholinesterase 
in E. coli, which prior to using PROSS had been impossible.

See paper:

Goldenzweig, A., Goldsmith, M., Hill, S. E., Gertman, O., Laurino, P., Ashani, 
Y., Dym, O., Unger, T., Albeck, S.,
Prilusky, J., Lieberman, R. L., Aharoni, A., Silman, I., Sussman, J. L., 
Tawfik, D. S., & Fleishman, S. J. (2016).
Automated structure- and sequence-based design of proteins for high bacterial 
expression and stability.
Molecular Cell, 63(2), 337–346. https://doi.org/10.1016/j.molcel.2016.06.012

and Proteopedia's Interactive 3D Complement (I3DC) page:

https://proteopedia.org/w/Journal:Molecular_Cell:1

Best regards
Joel

-
Prof. Joel L. Sussman   
joel.suss...@weizmann.ac.il
Dept. of Chemical and Structural Biologytel: +972  (8) 934 6309  
www.weizmann.ac.il/~joel
Weizmann Institute of Science   fax: +972  (8) 934 6312  
proteopedia.org
Rehovot 76100 ISRAELmob: +972 (50) 510 9600
-


On 4 Apr 2022, at 22:06, Scott Classen 
mailto:sclas...@lbl.gov>> wrote:

Hello CCP4,

Has anyone successfully used the available ML/AI protein folding tools to guide 
crystallization construct design? Maybe you had a protein or domain that was 
resistant to crystallization efforts and the folding algorithms  predicted some 
loops or termini that were disordered? Then you trimmed or modified them in 
some way to aid in crystallization? Or if you haven’t done this yourself, are 
you aware of anyone who has?

Thanks,
Scott


~~
Scott Classen, Ph.D.
ALS-ENABLE
TomAlberTron Beamline 8.3.1
SIBYLS Beamline 12.3.1
Advanced Light Source
Lawrence Berkeley National Laboratory
1 Cyclotron Rd
MS6R2100
Berkeley, CA 94720
mobile 510.206.4418
desk 510.495.2697
beamline 510.495.2134
~~




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[ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide crystallization?

[Andrew Lovering]

Hi Scott
We have obtained a structure of a flexible clamshell like fold only after using 
a disulphide mutant to lock the domains based on a Rosetta Fold model.
Interestingly, Alphafold put the very same residues further apart (probably a 
relevant "open" pose)

Andy



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[ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide crystallization?

[Scott Classen]

Hello CCP4,

Has anyone successfully used the available ML/AI protein folding tools to guide 
crystallization construct design? Maybe you had a protein or domain that was 
resistant to crystallization efforts and the folding algorithms  predicted some 
loops or termini that were disordered? Then you trimmed or modified them in 
some way to aid in crystallization? Or if you haven’t done this yourself, are 
you aware of anyone who has?

Thanks,
Scott 


~~
Scott Classen, Ph.D.
ALS-ENABLE
TomAlberTron Beamline 8.3.1
SIBYLS Beamline 12.3.1
Advanced Light Source
Lawrence Berkeley National Laboratory
1 Cyclotron Rd
MS6R2100
Berkeley, CA 94720
mobile 510.206.4418
desk 510.495.2697
beamline 510.495.2134
~~




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