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Susume's picture
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The team of 2017 Nobel laureate Joachim Frank at Columbia, along with several collaborators, have found a way to extract still image data from cryo-EM images of proteins and combine it with machine learning and molecular dynamics modeling to produce videos of those proteins in motion, such as opening and closing:

https://www.cuimc.columbia.edu/news/new-technique-biologists-capture-molecules-motion

Joined: 09/24/2012
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Question

Personally, I don't understand what happens in this movie. Do anybody understand why the extremities move from small distance (blue) to high distance (red)? Distance of what ? (I don't see distance moving, only colour of the distance).

jeff101's picture
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Video(s)
https://youtu.be/H4j2-pgdelQ shows a video.
Comparing it with Fig.6 in the Results section
of https://www.nature.com/articles/s41467-020-18403-x
it looks like the image begins all blue, where blue
parts have moved 0 Angstroms from their starting
positions. The motions are small (up to 10 Angstroms), 
so the color-coding helps to see them. As you watch
the video, parts that have moved the most turn red
while parts that have moved very little stay blue.

The paper's Supplementary Information at
https://www.nature.com/articles/s41467-020-18403-x#Sec27
contains 13 Supplementary Movies.
jeff101's picture
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10 Angstroms isn't so small
The motions in the video above look small compared to 
the size of the protein complex shown, but these motions 
are up to 10 Angstroms. For comparison, the diameter of 
an alpha-helix is about 12 Angstroms according to
https://en.wikipedia.org/wiki/Alpha_helix#Functional_roles
jeff101's picture
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10 Angstroms isn't so small
Fig.1 at http://book.bionumbers.org/how-big-are-biochemical-nuts-and-bolts/
shows many molecules with sizes up to 10 Angstroms (1 nm). This web page 
also says that the naturally occurring amino acids range in length from 
4 Angstroms for glycine to 10 Angstroms for tryptophan. It also says that 
"In summary, if one has to carry one round number to utilize for thinking 
about sizes of small building blocks such as amino acids, nucleotides, 
energy carriers etc., 1 nm is an excellent rule of thumb."

The above web page is full of links to BNID like "BNID 106983" below:
https://bionumbers.hms.harvard.edu/bionumber.aspx?&id=106983
The BNID pages in turn link to useful charts. BNID 106983, for example,
links to a chart of lengths and widths for the amino acids.
Sitemap

Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons