Hello Ethan,
Thank you for the suggestions. I should have mentioned in my initial post
that my intention is to first conduct a high throughput virtual screening
on these proteins, thus I would need high "resolution" of the structures
which SAXS could not provide, as far as I understand.
SAXS/SAS m
Hello, my numpty-level understanding is that being intrinsically disorder and
giving high-resolution structural data are mutually exclusive. I will re-read
your e-mails. Hope this helps. Cheers, Jon.C.
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Original Message
On 15 Aug 2021, 09:16, Sorin D
It is possible to get an ensemble for an intrinsically disordered segment from
NMR. We did this in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4008819/
Best wishes
James
On Aug 15, 2021, at 14:48, Jon Cooper
<488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
Hello, my numpty-level unders
Hello Jon,
Indeed - in the case of NMR, as far as I understand, we can't talk about
resolution (that is why I used quotes). What I need here is a structure (or
ensemble of structures) to which I could hope to dock ligands with some
level of accuracy - something that SAXS could not provide.
On S
Hi James,
Could you shed some light on the costs involved? This has been done also in
the case of the 2 proteins that I am interested in - however the data is
not publically available and the authors of the articles are reluctant to
share the data, which I could understand.
Many thanks!
On Sun,
I'm not really sure. I did this many years ago during my masters and applied it
to a much shorter segment (~20 amino acids), which we could chemically
synthesise and use for natural abundance HSQC experiments. The computational
cost was also much less as a consequence of the system size I imagin
Hello Sorin,
1. The cost of getting NMR data on the IDPs you propose depends upon the
expression levels of the protein/s as you will need to label with 15N and 13C -
and depending upon your overall yields per liter of E.coli culture, this can
add up. In addition you will need to run triple re
Stony Brook University/BNL has a Postdoc opening to work on the structural
mechanisms of plant stress signaling controlled by a family of conserved
cysteine proteases called metacaspase (MC). Structural, molecular and
genetic approaches will be deployed to dissect the mechanistic basis of MC
funct
Hi
Just my two ha’porth.
I’m currently involved in a project where my collaborators are investigating
the interactions between protein pairs (both hetero and homo) - they
specifically asked me _not_ to give them any models from ensembles (actually,
they said “no NMR structures because they are
Hi Sorin,
I hate to say it, but this is a really tough and expensive one. Solving a true
conformational ensemble of one IDP of decent size (~>70 residues) at something
like decent resolution is hard, and not that many labs actually do it (it's
usually a different set of NMR techniques than solv
As Joel has suggested before, alphafold on an IDP would be interesting and
would seem like a zero-cost starting point - perhaps one you have tried already.
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Original Message
On 15 Aug 2021, 15:53, Scott Horowitz wrote:
> Hi Sorin,
>
> I hate to say i
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