Free ligand binding success & continuation

Message boards : News : Free ligand binding success & continuation

Author	Message
ignasi Send message Joined: 10 Apr 08 Posts: 254 Credit: 16,836,000 RAC: 0 Level Scientific publications	Message 17932 - Posted: 12 Jul 2010 \| 12:49:18 UTC
	Dear crunchers, In the past months you crunched a set of WUs that aimed at observing a free ligand binding to a protein (IBUCH_esrever). At least 1 of the 750 simulations has reached destination! http://youtu.be/a3IsIQiEjeQ Congratulations for this amazing result. However, we lack a bit of statistics for this event and we need to get more of these. We are extending the experiment (IBUCH_freebind). They're sitting in the queue, get yours!
	ID: 17932 \| Rating: 0 \| rate: / Reply Quote

skgiven Volunteer moderator Volunteer tester Send message Joined: 23 Apr 09 Posts: 3968 Credit: 1,995,359,260 RAC: 0 Level Scientific publications	Message 17942 - Posted: 13 Jul 2010 \| 12:15:46 UTC - in response to Message 17932.
	What ligand was it?
	ID: 17942 \| Rating: 0 \| rate: / Reply Quote

ignasi Send message Joined: 10 Apr 08 Posts: 254 Credit: 16,836,000 RAC: 0 Level Scientific publications	Message 17948 - Posted: 14 Jul 2010 \| 10:31:47 UTC - in response to Message 17942. Last modified: 14 Jul 2010 \| 10:33:59 UTC
	The ligand is pYEEI (phosphorilated-Tyrosine, Glutamic Acid x2 and Isoleucine). It is the shortest to bind to and SH2 domain. We haven't performed any freeligand binding experiment of larger peptides. However we do have tryied to compute binding free energies for them: PQpYEEIPI,... cheers,
	ID: 17948 \| Rating: 0 \| rate: / Reply Quote

Retvari Zoltan Send message Joined: 20 Jan 09 Posts: 2353 Credit: 16,375,531,916 RAC: 5,811,976 Level Scientific publications	Message 17950 - Posted: 14 Jul 2010 \| 11:55:41 UTC - in response to Message 17932.
	So, these are those very long workunits. Give me more :) http://youtu.be/a3IsIQiEjeQ
	ID: 17950 \| Rating: 0 \| rate: / Reply Quote

skgiven Volunteer moderator Volunteer tester Send message Joined: 23 Apr 09 Posts: 3968 Credit: 1,995,359,260 RAC: 0 Level Scientific publications	Message 17953 - Posted: 14 Jul 2010 \| 13:12:41 UTC - in response to Message 17948.
	The pTyr seems to be behaving like an anchor, allowing for some serious changes in the rest of the peptide; at one stage it flips over (about 34sec). After being snapped into place it looks more at ease. Would be nice to see a big energy change at that point.
	ID: 17953 \| Rating: 0 \| rate: / Reply Quote

ignasi Send message Joined: 10 Apr 08 Posts: 254 Credit: 16,836,000 RAC: 0 Level Scientific publications	Message 17995 - Posted: 16 Jul 2010 \| 9:38:18 UTC - in response to Message 17950.
	So, these are those very long workunits. Give me more :) Nope, they are not. These are GCY not freebind.
	ID: 17995 \| Rating: 0 \| rate: / Reply Quote

ignasi Send message Joined: 10 Apr 08 Posts: 254 Credit: 16,836,000 RAC: 0 Level Scientific publications	Message 17996 - Posted: 16 Jul 2010 \| 9:43:29 UTC - in response to Message 17953.
	The pTyr seems to be behaving like an anchor, allowing for some serious changes in the rest of the peptide; at one stage it flips over (about 34sec). After being snapped into place it looks more at ease. Would be nice to see a big energy change at that point. Exactly. pTyr is the principal residue establishing the first contacts with the SH2 domain. Once it does, it doesn't detach (at the timescale we're looking at) and reduces the number of conformations that it needs to explore before binding. It is falling down to an energetic well--it likes to be there. cheers
	ID: 17996 \| Rating: 0 \| rate: / Reply Quote

Retvari Zoltan Send message Joined: 20 Jan 09 Posts: 2353 Credit: 16,375,531,916 RAC: 5,811,976 Level Scientific publications	Message 18001 - Posted: 16 Jul 2010 \| 15:58:15 UTC - in response to Message 17995.
	Nope, they are not. These are GCY not freebind. Thank you for pointing out my mistake.... I got a lot of freebind too. But I like the GCY more, because these are more gainful in a view of the credit/time ratio :)
	ID: 18001 \| Rating: 0 \| rate: / Reply Quote

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Message boards : News : Free ligand binding success & continuation

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Author	Message
ignasi Send message Joined: 10 Apr 08 Posts: 254 Credit: 16,836,000 RAC: 0 Level Scientific publications	Message 17932 - Posted: 12 Jul 2010 \| 12:49:18 UTC
	Dear crunchers, In the past months you crunched a set of WUs that aimed at observing a free ligand binding to a protein (IBUCH_esrever). At least 1 of the 750 simulations has reached destination! http://youtu.be/a3IsIQiEjeQ Congratulations for this amazing result. However, we lack a bit of statistics for this event and we need to get more of these. We are extending the experiment (IBUCH_freebind). They're sitting in the queue, get yours!
	ID: 17932 \| Rating: 0 \| rate: / Reply Quote

skgiven Volunteer moderator Volunteer tester Send message Joined: 23 Apr 09 Posts: 3968 Credit: 1,995,359,260 RAC: 0 Level Scientific publications	Message 17942 - Posted: 13 Jul 2010 \| 12:15:46 UTC - in response to Message 17932.
	What ligand was it?
	ID: 17942 \| Rating: 0 \| rate: / Reply Quote

ignasi Send message Joined: 10 Apr 08 Posts: 254 Credit: 16,836,000 RAC: 0 Level Scientific publications	Message 17948 - Posted: 14 Jul 2010 \| 10:31:47 UTC - in response to Message 17942. Last modified: 14 Jul 2010 \| 10:33:59 UTC
	The ligand is pYEEI (phosphorilated-Tyrosine, Glutamic Acid x2 and Isoleucine). It is the shortest to bind to and SH2 domain. We haven't performed any freeligand binding experiment of larger peptides. However we do have tryied to compute binding free energies for them: PQpYEEIPI,... cheers,
	ID: 17948 \| Rating: 0 \| rate: / Reply Quote

Retvari Zoltan Send message Joined: 20 Jan 09 Posts: 2353 Credit: 16,375,531,916 RAC: 5,811,976 Level Scientific publications	Message 17950 - Posted: 14 Jul 2010 \| 11:55:41 UTC - in response to Message 17932.
	So, these are those very long workunits. Give me more :) http://youtu.be/a3IsIQiEjeQ
	ID: 17950 \| Rating: 0 \| rate: / Reply Quote

skgiven Volunteer moderator Volunteer tester Send message Joined: 23 Apr 09 Posts: 3968 Credit: 1,995,359,260 RAC: 0 Level Scientific publications	Message 17953 - Posted: 14 Jul 2010 \| 13:12:41 UTC - in response to Message 17948.
	The pTyr seems to be behaving like an anchor, allowing for some serious changes in the rest of the peptide; at one stage it flips over (about 34sec). After being snapped into place it looks more at ease. Would be nice to see a big energy change at that point.
	ID: 17953 \| Rating: 0 \| rate: / Reply Quote

ignasi Send message Joined: 10 Apr 08 Posts: 254 Credit: 16,836,000 RAC: 0 Level Scientific publications	Message 17995 - Posted: 16 Jul 2010 \| 9:38:18 UTC - in response to Message 17950.
	So, these are those very long workunits. Give me more :) Nope, they are not. These are GCY not freebind.
	ID: 17995 \| Rating: 0 \| rate: / Reply Quote

ignasi Send message Joined: 10 Apr 08 Posts: 254 Credit: 16,836,000 RAC: 0 Level Scientific publications	Message 17996 - Posted: 16 Jul 2010 \| 9:43:29 UTC - in response to Message 17953.
	The pTyr seems to be behaving like an anchor, allowing for some serious changes in the rest of the peptide; at one stage it flips over (about 34sec). After being snapped into place it looks more at ease. Would be nice to see a big energy change at that point. Exactly. pTyr is the principal residue establishing the first contacts with the SH2 domain. Once it does, it doesn't detach (at the timescale we're looking at) and reduces the number of conformations that it needs to explore before binding. It is falling down to an energetic well--it likes to be there. cheers
	ID: 17996 \| Rating: 0 \| rate: / Reply Quote

Retvari Zoltan Send message Joined: 20 Jan 09 Posts: 2353 Credit: 16,375,531,916 RAC: 5,811,976 Level Scientific publications	Message 18001 - Posted: 16 Jul 2010 \| 15:58:15 UTC - in response to Message 17995.
	Nope, they are not. These are GCY not freebind. Thank you for pointing out my mistake.... I got a lot of freebind too. But I like the GCY more, because these are more gainful in a view of the credit/time ratio :)
	ID: 18001 \| Rating: 0 \| rate: / Reply Quote