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Toni
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Message 44796 - Posted: 20 Oct 2016 | 18:29:45 UTC
Last modified: 22 Oct 2016 | 12:23:22 UTC

Dear all!

We added badges for two great papers which came out this year. Both appeared in Scientific Reports, a highly-regarded open-access journal.

I don't think I can do better justice to the works than the author's own words, so I am copying here their abstracts, which hopefully convey the gist of the respective impact:


  1. Noelia's study of ions binding to the myo-inositol monophosphatase enzyme:

    Molecular recognition is rarely a two-body protein-ligand problem, as it often involves the dynamic interplay of multiple molecules that together control the binding process. Myo-inositol monophosphatase (IMPase), a drug target for bipolar disorder, depends on 3 Mg2+ ions as cofactor for its catalytic activity. Although the crystallographic pose of the pre-catalytic complex is well characterized, the binding process by which substrate, cofactor and protein cooperate is essentially unknown. Here, we have characterized cofactor and substrate cooperative binding by means of large-scale molecular dynamics. Our study showed the first and second Mg2+ ions identify the binding pocket with fast kinetics whereas the third ion presents a much higher energy barrier. Substrate binding can occur in cooperation with cofactor, or alone to a binary or ternary cofactor-IMPase complex, although the last scenario occurs several orders of magnitude faster. Our atomic description of the three-body mechanism offers a particularly challenging example of pathway reconstruction, and may prove particularly useful in realistic contexts where water, ions, cofactors or other entities cooperate and modulate the binding process.


  2. Nathan's study of S1PR1 receptor:

    The binding process through the membrane bilayer of lipid-like ligands to a protein target is an important but poorly explored recognition process at the atomic level. In this work we succeeded in resolving the binding of the lipid inhibitor ML056 to the sphingosine-1-phosphate receptor 1 (S1P1R) using unbiased molecular dynamics simulations with an aggregate sampling of over 800 μs. The binding pathway is a multi-stage process consisting of the ligand diffusing in the bilayer leaflet to contact a “membrane vestibule” at the top of TM 7, subsequently moving from this lipid-facing vestibule to the orthosteric binding cavity through a channel formed by TMs 1 and 7 and the N-terminal of the receptor. Unfolding of the N-terminal alpha-helix increases the volume of the channel upon ligand entry, helping to reach the crystallographic pose that also corresponds to the predicted favorable pose. The relaxation timescales of the binding process show that the binding of the ligand to the “membrane vestibule” is the rate-limiting step in the multi microseconds timescale. We comment on the significance and parallels of the binding process in the context of other binding studies.




Edit: The Science page does not contain the new papars yet, but you will find them in your profile page. WU names were respectively like 1mgx1, 1mgx2, 3mgx1, 3mgx2, 5MG, 20MG, 20MG2, INSP, INS1P (Noelia's) and RPS1 (Nate's).

[CSF] Thomas H.V. Dupont
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Message 44797 - Posted: 20 Oct 2016 | 18:35:14 UTC

Very good news!
Thanks for the heads-up Toni :)
____________
[CSF] Thomas H.V. Dupont
Founder of the team CRUNCHERS SANS FRONTIERES
www.crunchersansfrontieres.org

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Message 44799 - Posted: 20 Oct 2016 | 19:12:30 UTC

Congratulations for the papers! good work!

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Message 44801 - Posted: 20 Oct 2016 | 19:24:43 UTC - in response to Message 44799.

Congratulations for the papers! good work!

+1!

Profile Logan Carr
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Message 44802 - Posted: 20 Oct 2016 | 19:25:34 UTC

Great to see progress being made. Congrats
____________
Cruncher/Learner in progress.

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Message 44803 - Posted: 21 Oct 2016 | 0:18:16 UTC

Great! First two badges after three years. :)

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Message 44804 - Posted: 21 Oct 2016 | 10:29:26 UTC

Great news! Thank you very much for your work :)

John C MacAlister
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Message 44805 - Posted: 21 Oct 2016 | 10:50:53 UTC - in response to Message 44796.
Last modified: 21 Oct 2016 | 11:07:41 UTC

Many thanks- after a long absence, I have returned to continue with this important research.

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Message 44806 - Posted: 21 Oct 2016 | 19:54:54 UTC

+1

Profile Retvari Zoltan
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Message 44813 - Posted: 22 Oct 2016 | 17:19:38 UTC
Last modified: 22 Oct 2016 | 17:33:05 UTC

Great news!
Could you make a list of the top contributors please (as for earlier badges)?

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Message 44822 - Posted: 23 Oct 2016 | 17:24:52 UTC - in response to Message 44796.

Noelia's study of ions binding to the myo-inositol monophosphatase enzyme:

1st RaymondFO
2nd Retvari Zoltan
3rd Stoneageman
4th HA-SOFT, s.r.o
5th Herb
6th Rick A. Sponholz
7th Roald
8th Beyond
9th Orange_1050
10th BruceR
11th ecafkid
12th Acey Pilot
13rd 5pot
14th Bedrich Hajek
15th petebe
16th TJ
17th Nikke
18th neilp62
19th Rion Family
20th Venec
21st IFRS
22nd Grumpy
23rd Bikermatt
24th Eagle07
25th Jozef J
26th Ken Florian
27th jjch
28th JugNut
29th s0m3wh4t
30th John

Nathan's study of S1PR1 receptor:

1st Stoneageman
2nd Retvari Zoltan
3rd Erik Postnieks
4th HA-SOFT, s.r.o
5th Venec
6th For the Universe ( Apaszko-Kaszkiety )
7th IFRS
8th 5pot
9th Ken Florian
10th Herb
11th Paul Raney
12th werwerdus
13rd GPUGRID Role account
14th Nikke
15th Bedrich Hajek
16th jlhal
17th comfortw
18th flashawk
19th eruda
20th Bikermatt
21st wdiz
22nd RaymondFO
23rd Profile PERPLEXER ~ Thomas Huettinger
24th John
25th Roald
26th Localizer
27th Snow Crash
28th Helmholdt
29th Alain Maes
30th Rayzor

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Message 44823 - Posted: 23 Oct 2016 | 18:02:34 UTC - in response to Message 44822.

Where did you find this?

Profile Retvari Zoltan
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Message 44825 - Posted: 23 Oct 2016 | 19:47:51 UTC - in response to Message 44823.

Where did you find this?

I did not find this. I've made this.

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Message 45070 - Posted: 31 Oct 2016 | 17:47:29 UTC

Did I not make the cut?

Profile Retvari Zoltan
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Message 45072 - Posted: 31 Oct 2016 | 18:31:53 UTC - in response to Message 45070.

Did I not make the cut?

You started crunching for GPUGrid in this March, but these badges have been awarded for a research done much earlier.
It could take years to get these results reviewed and published, everyone receives badges after that period, so will you.

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Message 45308 - Posted: 18 Nov 2016 | 1:00:00 UTC

Woohoo, my first badge!

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Message 46946 - Posted: 16 Apr 2017 | 2:44:03 UTC
Last modified: 16 Apr 2017 | 2:44:54 UTC

Something you may want to consider if you decide to create more badges:

There is an unusual amino acid called BMAA. Normally found only in blue-green algae, in cyanobacteria, in cycads, and in the brains of Alzheimer's victims. Not essential.

https://en.wikipedia.org/wiki/Beta-Methylamino-L-alanine

Toni
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Message 47168 - Posted: 5 May 2017 | 8:25:22 UTC - in response to Message 46946.

Fascinating, thanks.

John C MacAlister
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Message 47169 - Posted: 5 May 2017 | 13:47:16 UTC

thanks for the update
____________
John

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Message 47170 - Posted: 5 May 2017 | 20:49:33 UTC - in response to Message 46946.

Something you may want to consider if you decide to create more badges:

There is an unusual amino acid called BMAA. Normally found only in blue-green algae, in cyanobacteria, in cycads, and in the brains of Alzheimer's victims. Not essential.

https://en.wikipedia.org/wiki/Beta-Methylamino-L-alanine

Quote from the wikipedia article you've linked:
"BMAA is a neurotoxin and its potential role in various neurodegenerative disorders is the subject of scientific research."
Calling it "Not essential" is way too polite. :)

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