Active | A molecular switch strips transcription factor from DNA3729| In this video, Rice University scientists used molecular modeling with a mathematical algorithm called AWSEM (for associative memory, water-mediated, structure and energy model) and structural data to analyze how a transcription factor called nuclear factor kappa B (NFkB) is removed from DNA to stop gene activation. AWSEM uses the interacting energies of their components to predict how proteins fold. At the start, the NFkB dimer (green and yellow, in the center) grips DNA (red, to the left), which activates the transcription of genes. IkB (blue, to the right), an inhibitor protein, stops transcription when it binds to NFkB and forces the dimer to twist and release its hold on DNA. The yellow domain at the bottom of IkB is the PEST domain, which binds first to NFkB. For more details about this mechanism called molecular stripping, see here. | | Public Note | | | | | Internal Note | | Researchers gave permission for public use:
David Potoyan [david.potoyan@gmail.com]
Tuesday, January 26, 2016 6:41 PM
Dear Martin,
Thank you for taking interest in our research. I am a postdoctoral associate in Peter's lab who made the animation. Please find the video file attached to this email. Also feel free to ask any questions that you might have or if you would like other media files.
Best,
-Davit
Peter Wolynes [pwolynes@rice.edu]
To:
Spiering, Martin (NIH/NIGMS) [C]?; David Potoyan ?[potoyan@rice.edu]??; pwolynes@rice.edu
Monday, January 25, 2016 2:04 PM
Thanks for your kind words ! Putting it together was quite interesting
because it is not just a straight "morph" but uses structures sampled
properly by WHAM.It would be great if you could use our animation. My
postdoc Davit Potoyan has the files. I am connecting him with you so he
can send the animation.
Best regards, Peter
On 1/25/16 11:41 AM, Spiering, Martin (NIH/NIGMS) [C] wrote:
Dear Dr. Wolynes,
I am a writer and editor with the Office of Communication and Public Liaison at the National Institute of General Medical Sciences. I am reaching out to you because we would like to include your striking and insightful animation of the NFkappaB-DNA-IkappaB switch (https://www.youtube.com/watch?v=_ADwUClCzMA) on the NIGMS website (at https://images.nigms.nih.gov/).
Images and videos in the NIGMS Image Gallery highlight NIGMS-funded work and are made available to the public for educational uses, provided that users credit the creator, i.e., you, for this work. Would let us feature your video on the NIGMS Image Gallery in this way? If so, could you please send me a file containing this animation?
Thank you,
Martin J Spiering, PhD, ELS
Science Writer& Editor (contractor)
OCPL, National Institutes of Health/NIGMS | | | Keywords | | | | | Source | | Davit Potoyan and Peter Wolynes | | | Date | | 2016-01-27 00:00:00 | | | Credit Line | | Davit Potoyan and Peter Wolynes | | | Investigator | | Peter Wolynes | | | Record Type | | Video | | | Topic Area(s) | | ;#Molecular Structures;#Tools and Techniques;# | | | Previous Uses | | | | | Status | | Active | |
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