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

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 predic

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

Hi David, do you think that alphafold2 dis/order prediction is better than specific disorder predictors? i.e. http://dis.embl.de , which we've used for construct design https://prdos.hgc.jp , which I haven't really tried yet https://iupred2a.elte.hu

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

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predicted exactly the constructs that were discovered by limited proteolysis and/or sequence alignment for currently unpublished structures.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

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

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.

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

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

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

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people are thinking about this quite deeply right now but our experience with single acylation and charge ladder work (unpublished) was that even a single amino acid charge change had a profound impact on crystallization outcome in the 1,536

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

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,