[3dem] About dynamics (Joey Davis)
Jay Rai
jrai at fsu.edu
Tue May 26 07:11:20 PDT 2020
Hi Joey,
Thank you for the reply and suggestion. I will certainly give a try. The problem from our structure is - the highly dynamic domain that we assumed contain around 255 amino acids. To be fair, I am a bit over-ambitious to see movement on those small regions. Needless to say that the small region is an ill-defined region (density is very poor). So I am shooting in the dark. Meaning- That small region might be degraded or fall off or high dynamics. The only supportive argument about that is in ugly dynamics is the region lies on the active site and our enzyme is more or less active. I am not neglecting the fact that the structure we solved might be after the enzyme activity (assuming the active is lightning fast).
Have you tried to see the movement in those small regions?
Thanks
Jay
________________________________
From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Joey Davis <jhdavis at mit.edu>
Sent: Monday, May 25, 2020 11:17 PM
To: 3dem at ncmir.ucsd.edu <3dem at ncmir.ucsd.edu>
Subject: Re: [3dem] About dynamics (Joey Davis)
Hi Jay,
In addition to cryoSPARC's 3DVA and Relion's multibody, I encourage you to try cryoDRGN, which we recently released. CryoDRGN's methods and underlying assumptions are quite different from those of cryoSPARC/Relion, and we've seen it work well with a variety of both discrete and continuously heterogeneous systems. You can find a preprint describing the approach here: https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2020.03.27.003871v1__;!!Mih3wA!VWuByf4rxt4ONyf9jlxyD7ESELKVXEoy-85is55hy6e4mK75hDBkKSgRePq_DEVPCQ$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2020.03.27.003871v1__;!!Mih3wA!WnEgFrgDg5fKSyjiE4f9IMamoJw2YDKQq2Q2O_hetUnwA2m35nlRYPWK61fc6FSoCg$>, and the source code/installation instructions/usage guide here: https://urldefense.com/v3/__https://github.com/zhonge/cryodrgn__;!!Mih3wA!VWuByf4rxt4ONyf9jlxyD7ESELKVXEoy-85is55hy6e4mK75hDBkKSgRePoapmWwKA$ <https://urldefense.com/v3/__https://github.com/zhonge/cryodrgn__;!!Mih3wA!WnEgFrgDg5fKSyjiE4f9IMamoJw2YDKQq2Q2O_hetUnwA2m35nlRYPWK61ctRUs-Fg$>.
Please let me know if you have any questions - happy to help.
Best of luck,
Joey
On Mon, May 25, 2020 at 9:34 PM <3dem-request at ncmir.ucsd.edu<mailto:3dem-request at ncmir.ucsd.edu>> wrote:
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Today's Topics:
1. About dynamics (Jay Rai)
2. Re: About dynamics (Jay Rai)
3. Re: About dynamics (Ali Punjani)
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Message: 1
Date: Mon, 25 May 2020 19:27:35 +0000
From: Jay Rai <jrai at fsu.edu<mailto:jrai at fsu.edu>>
To: "3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>" <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>
Subject: [3dem] About dynamics
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Dear Cryo-EM folks,
I am trying to solve the dynamics of 300 kD multi proteins complex. Any idea which software is the most useful? Any tips and suggestions. So, far I tried Relion and cryosprac. Both gave me different results.
Thanks
Jay
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Date: Tue, 26 May 2020 00:03:55 +0000
From: Jay Rai <jrai at fsu.edu<mailto:jrai at fsu.edu>>
To: "3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>" <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>
Subject: Re: [3dem] About dynamics
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Just to be add: Its work like a charm on big complexes like ribosome. In other words- which software is best for the multibody refinement/ protein dynamics?
Thanking you in advance,
jay
________________________________
From: 3dem <3dem-bounces at ncmir.ucsd.edu<mailto:3dem-bounces at ncmir.ucsd.edu>> on behalf of Jay Rai <jrai at fsu.edu<mailto:jrai at fsu.edu>>
Sent: Monday, May 25, 2020 3:27 PM
To: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu> <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>
Subject: [3dem] About dynamics
Dear Cryo-EM folks,
I am trying to solve the dynamics of 300 kD multi proteins complex. Any idea which software is the most useful? Any tips and suggestions. So, far I tried Relion and cryosprac. Both gave me different results.
Thanks
Jay
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Message: 3
Date: Mon, 25 May 2020 21:33:14 -0400
From: Ali Punjani <alipunjani at cs.toronto.edu<mailto:alipunjani at cs.toronto.edu>>
To: Jay Rai <jrai at fsu.edu<mailto:jrai at fsu.edu>>
Cc: "3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>" <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>
Subject: Re: [3dem] About dynamics
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Hi Jay,
In cryoSPARC, you can try the new 3D Variability Analysis (3DVA) algorithm
that can directly resolve continuous heterogeneity and flexibility from
single particle data. We've recently written a paper about the algorithm
and how to interpret results (preprint:
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2020.04.08.032466v1__;!!Mih3wA!TcYCUD_wBUr5IORGTt-uKmJtnjAN7is2w2qHfWKXW5ewtmxRcaG0CfJN6xQiqEm9CQ$ ) and there are
a couple of detailed tutorials online as well (
https://urldefense.com/v3/__https://cryosparc.com/docs/tutorials/3d-variability-analysis__;!!Mih3wA!TcYCUD_wBUr5IORGTt-uKmJtnjAN7is2w2qHfWKXW5ewtmxRcaG0CfJN6xQykYwUEg$ ). The
algorithm has been used in several published studies to date and can
resolve flexible dynamics even for smaller proteins eg. GPCR complexes.
You may also be interested in related discussions ongoing on the cryoSPARC
discussion forum (https://urldefense.com/v3/__https://discuss.cryosparc.com/__;!!Mih3wA!TcYCUD_wBUr5IORGTt-uKmJtnjAN7is2w2qHfWKXW5ewtmxRcaG0CfJN6xR2x7wM2Q$ ).
Thanks,
Ali Punjani
On Mon, May 25, 2020 at 8:04 PM Jay Rai <jrai at fsu.edu<mailto:jrai at fsu.edu>> wrote:
> Just to be add: Its work like a charm on big complexes like ribosome. In
> other words- which software is best for the multibody refinement/ protein
> dynamics?
> Thanking you in advance,
> jay
> ------------------------------
> *From:* 3dem <3dem-bounces at ncmir.ucsd.edu<mailto:3dem-bounces at ncmir.ucsd.edu>> on behalf of Jay Rai <
> jrai at fsu.edu<mailto:jrai at fsu.edu>>
> *Sent:* Monday, May 25, 2020 3:27 PM
> *To:* 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu> <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>
> *Subject:* [3dem] About dynamics
>
> Dear Cryo-EM folks,
> I am trying to solve the dynamics of 300 kD multi proteins complex. Any
> idea which software is the most useful? Any tips and suggestions. So, far I
> tried Relion and cryosprac. Both gave me different results.
> Thanks
> Jay
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem<https://urldefense.com/v3/__https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem__;!!PhOWcWs!iGCAsr2az0F9sRVWzx7GS-DviOAMWln4unQf9lNc2Son7ggbJgn2sVUGvROJ$>
>
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Joseph H. Davis
Whitehead Career Development Assistant Professor of Biology
Massachusetts Institute of Technology
77 Massachusetts Ave.
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