Protein Packing
April 10, 2014 9:21 AM   Subscribe

Harvard University and XVIVO have come together again (Previouslyw/ a commercial focus, Previouslierw/an Academic focus) to add to the growing series of scientific animations for BioVisions -- Harvard's multimedia lab in the department of Molecular and Cellular Biology. 'Protein Packing' strives to more accurately depict the molecular chaos in each and every cell, with proteins jittering around in what may seem like random motion. Proteins occupy roughly 40% of the cytoplasm, creating an environment that risks unintentional interaction and aggregation. Via diffusion and motor protein transport, these molecules are directed to sites where they are needed.
Much of this is no doubt inspired by the beautiful art and explained illustrations of David Goodsell, a biologist at Scripps who has been accurately portraying the crowdedness of the cellular landscape for a long time now.

Having watched the animation, you will be in a much better place to understand one of the most mind-blowingly weird yet powerful papers in molecular biology to have come out yet this year. Where it turns out that the crowdedness of the cellular cytoplasm, as well as the nature of the particles within it, cause the insides of cells to resemble a glass forming liquid when starved of energy and return to fluidity when energy is restored.
The Bacterial Cytoplasm Has Glass-like Properties and Is Fluidized by Metabolic Activity
The physical nature of the bacterial cytoplasm is poorly understood even though it determines cytoplasmic dynamics and hence cellular physiology and behavior. Through single-particle tracking of protein filaments, plasmids, storage granules, and foreign particles of different sizes, we find that the bacterial cytoplasm displays properties that are characteristic of glass-forming liquids and changes from liquid-like to solid-like in a component size-dependent fashion. As a result, the motion of cytoplasmic components becomes disproportionally constrained with increasing size. Remarkably, cellular metabolism fluidizes the cytoplasm, allowing larger components to escape their local environment and explore larger regions of the cytoplasm. Consequently, cytoplasmic fluidity and dynamics dramatically change as cells shift between metabolically active and dormant states in response to fluctuating environments. Our findings provide insight into bacterial dormancy and have broad implications to our understanding of bacterial physiology, as the glassy behavior of the cytoplasm impacts all intracellular processes involving large components.
This video also stands in contrast to the largely emptied cell portrayed in their other magnum opus The Inner Life of the Cell as well as Powering the Cell: Mitochondria, which allowed them to focus more on specific functions.
posted by Blasdelb (9 comments total) 33 users marked this as a favorite

I can never get enough of this high-end animation type of molecular biology exploration. As an undergrad and grad student, I spent so, so many hours trying to form these images in my mind to understand the mechanics of things I was working on (and I spy at least two proteins in this video that I spent years working on in various labs). It's almost like having an expert come back and make an amazing movie out of a book you loved when you were growing up.
posted by late afternoon dreaming hotel at 9:48 AM on April 10 [3 favorites]

Love the Goodsell images.
posted by benito.strauss at 9:54 AM on April 10

Why does everything shake?
posted by Reverend John at 10:14 AM on April 10

I'm guessing that's Brownian motion. So actually pretty realistic.
posted by echo target at 10:37 AM on April 10 [1 favorite]

I would have loved to have videos like this when I was getting my degree in cell bio. Kids today are spoiled and should get off my lawn, etc.
posted by Thoughtcrime at 11:02 AM on April 10

Holy shit do I need smaller coffee mugs, thank you Kabanos, that is awesome.
posted by Blasdelb at 11:21 AM on April 10

Those little motor protein dudes delivering cellular cargo along the microtubules are unforgettable. Who wouldn't shake?
posted by de at 11:33 AM on April 10

I was at a conference last year where Andy Ellington criticized Gael McGill for these animations because they are so unrealistic; so lacking in crowding, so lacking in stochasticity, amongst other things.

Look at the old inner life of the cell with the kinesin dragging a vesicle in a very deterministic and planned and robotic and machine-like way.

Compare this to the new animation ..... kinesin dragging a vesicle and its stochastic search or a microtubule, along with the jerky biased random walk-like action, as well as the crowdedness, for each step. I think this kind of model is a 'step' in the right direction. I hope Andy likes these more.....

I'm a fan of these representations , as long as we remember that i) The map/model is not the territory* and ii) that if you use ANY map/model too much in your thoughts uncritically it will cloud your view and make you rule out hypotheses/insights.

I think that this is the danger, that if we wean undergrads or grad students on these** animations, they will lose sight of the fact that these are IMMENSE simplifcations. Always look at the problem from as many angles as possble, not just the pretty-picture one!

* And often all we can deal with are maps/models!
** In pretty much any discipline
posted by lalochezia at 2:07 PM on April 10 [6 favorites]

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