More “Inner Life of the Cell” Explanations

I’ve already posted twice on this widely seen video, but I haven’t really had a chance to go into explaining it in depth.  The makers of the video already provided an explanation video, and Wayne at the Niches blog did some frame-by-frame analysis, but, judging from the google searches to my blog, people are hoping for a more detailed explanation.  I’ve produced a transcript of the explanation video which I’ll take section by section in the next series of posts.  I’ve transcribed this myself so I can’t attest that it’s 100% accurate – if you notice any errors, let me know.  The basic summary is that this video provides a glimpse of one specific cellular process: the activation of a white blood cell in an inflammation response.  The not-so-basic summary will start with the next post.

Update 11/29/08: Part I- Rolling is up

Update 05/25/09: Part II – “Adhesion” & the Organization of the Cell is up.

While red blood cells are carried away at high velocity by strong blood flow , leukocytes roll slowly on endothelial cells.  P-selectins on endothelial cells interact with PSGL1 a glycoprotein on leukocyte microvillae.  Leukocytes pushed by the blood flow adhere and roll on endothelial cells because existing interactions are broken while new ones are formed.

These interactions are possible because the extended extracellular domains of both proteins emerge from the extracellular matrix which covers the surface of both cell types.The outer leaflet of the lipid bilayer is enriched in sphingolipids and phosphatidylcholine.  Sphingolipid-rich rafts raised above the rest of the leaflet recruit specific membrane proteins. Rafts rigidity is caused by the tight packing of cholesterol molecules against the straight sphingolipids hydrocarbon chains.  Outside the rafts, kinks in unsaturated hydrocarbon chains and lower cholesterol concentration result in increased fluidity. At sites of inflammation, secreted chemokines, bound to heparin-sulfate proteoglycan on endothelial cells are presented to leukocyte 7 transmembrane receptors.  The binding stimulates leukocytes and triggers an intracellular cascade of signaling reactions.

The inner leaflet of the bilayer has a very different composition than that of the outer leaflet. While some proteins traverse the membrane, others are either anchored into the inner leaflet by covalently attached fatty acid chains, or are recruited through non covalent interactions with membrane proteins. The membrane bound protein complexes are critical for transmission of signals across the plasma membrane.

Beneath the lipid bilayer, spectrin tetramers arranged into a hexagonal network are anchored by membrane proteins.  This network forms the membrane skeleton that contributes to membrane stability and membrane protein distribution.  The cytoskeleton is comprised of networks of filamentous proteins that are responsible for the special organization of cytosolic components.   Inside microvillae, actin filaments form tight parallel  bundles which are stabilized by cross-linking proteins.  While (deeper?) in the cystol the actin network adopts a gel-like structure, stabilized by a variety of actin binding proteins.  Filaments, capped at their minus ends by a protein complex, grow away from the plasma membrane by the addition of actin monomers to their plus end. The actin network is a very dynamic structure with a continuous directional polymerization and disassembly.  Severing proteins induce kinks in the filament and lead to short fragments that rapidly depolymerize or give rise to new filaments.

The cytoskeleton includes a network of microtubules created by the lateral association of protofilaments formed by the polymerization of tubulin dimers.  While the plus ends of some microtubules extend toward the plasma membrane, proteins stabilize the curved conformation of protofilaments from other microtubules, causing their rapid plus end depolymerization.  Microtubules provide tracks along which membrane bound vesicles travel to and from the plasma membrane.  The directional movement of these cargo vesicles is due to a family of motor proteins linking vesicles and microtubules.   Membrane bound organelles like mitochondria are loosely trapped by the cytoskeleton.  Mitochondria change shape continuously and their orientation is partly dictated by their interaction with microtubules.  All the microtubules originate from the centrosome, a discrete fibrous structure containing two orthogonal centrioles and located near the cell nucleus.

Pores in the nuclear envelope allow the import of particles containing mRNA and proteins into the cytosol. Here free ribosomes translate the mRNA molecules into proteins.  Some of these proteins will reside in the cytosol.  Others will associate with specialized cytosolic proteins and be imported into mitochondria or other organelles.  The synthesis of cell secreted and integral membrane proteins is initiated by free ribosomes which then dock to protein translocators at the surface of the endoplasmic reticulum.  Nascent proteins pass through an aqueous pore in the translocator.  Cell secreted proteins accumulate in the lumen of the endoplasmic reticulum, while integral membrane proteins become embedded in the endoplasmic reticulum membrane.

Proteins are transported from the endoplasmic reticulum to the Golgi apparatus by vesicles traveling along the microtubules.  Protein glycosylation initiated in the endoplasmic reticulum is completed inside the lumen of the Golgi apparatus.  Fully glycoslated proteins are transported from the Golgi apparatus to the plasma membrane.  When a vesicle fuses with the plasma membrane, proteins contained in the vesicle’s lumen are secreted and proteins embedded in the vesicle’s membrane diffuse in the cell membrane.

At sites of inflammation, chemokines secreted by endothelial cells bind to the extracellular domains of G protein coupled membrane receptors.  This binding causes a conformational change in the cytosolic portion of the receptor and the consequent activation of a subunit of the G protein.  The activation of the G protein subunit triggers a cascade of protein activation, which in turn leads to the activation and clustering of integrins inside lipid rafts.  A dramatic conformational change occurs in the extracellular domain of the activated integrins.  This now allows for their interactions with I-cam proteins, displayed at the surface of endothelial cells.  These strong interactions immobilize the rolling leukocyte at the site of inflammation.  Additional signaling events cause a profound reorganization of the cytoskeleton, resulting in the spreading of one edge of the leukocyte.  The leading edge of the leukocyte inserts itself between endothelial cells and the leukocyte migrates through the blood vessel wall into the inflamed tissue.  Rolling, activation, adhesion, and transendothelial migration are the four steps of a process called leukocyte extravasation

Making “The Inner Life of the Cell”

Even while I’ve neglected this blog, my previous post on The Inner Life of the Cell remains quite popular. David Bolinksy, one of the creators of the video, gave a TED talk on making the movie. His talk is not particularly interesting from a scientific perspective, but one thing that he emphasizes that deserves restatement is the view of the cell as a series of micromachines.  A lot of current biologocial research focuses on understanding how proteins, nucleic acids, small molecules, and all the other contents of a cell,  assemble together to form higher order structures that perform complex reactions.  One of the challenges that has arisen in modern biology is taking large scale datasets that we’ve generated (i.e. the human genome, gene expresssion studies, etc), and using them to understand how all the different parts of the cell talk to one another.  This global approach to biology is relatively young, so understanding, visualizing, and analyzing these data is a huge, new challenge. Videos like this one, while perhaps not the most detailed representations of biology, are helpful in communicating this global view of the cell.  Plus it looks pretty cool.