Recognition and self-assembly of macromolecules. Cytoskeleton

Recognition and self-assembly of macromolecules. Cytoskeleton

How molecules find their partners through many weak bonds, how subunits build large structures by themselves, and how the cytoskeleton's three kinds of filament shape the cell and move things within it.

Contents3 sections

At a glance

  1. Macromolecules recognise their partners through many weak, noncovalent bonds that form together only where two surfaces fit, which makes binding both specific and reversible.
  2. Because the information for assembly is in the subunits, many structures build themselves: viral capsids, bacterial ribosomal subunits, lipid bilayers and the filaments of the cytoskeleton. Others need assembly factors.
  3. The cytoskeleton has three kinds of filament: actin filaments (about 7 nm across), intermediate filaments (8 to 10 nm) and microtubules (about 25 nm).
  4. Actin filaments and microtubules are polar: they grow and shrink at their ends, and motor proteins walk along them, myosins on actin, kinesins and dyneins on microtubules.
  5. Intermediate filaments are ropes with no polarity and no motors. They give cells and tissues their strength: keratins in epithelia, the lamins inside the nucleus.

Recognition: many weak bonds

Molecules in a cell find their partners by shape. Where two surfaces fit, many weak bonds can form at once: hydrogen bonds, ionic bonds, van der Waals contacts, and the hydrophobic effect, as water pushes water-avoiding patches together. Each of these bonds alone is broken easily by the thermal motion of molecules; together they hold firmly. Since they add up only where the surfaces match, the binding is specific, and since each can break on its own, it is reversible.

  • An enzyme and its substrate: the active site fits the substrate, and often closes round it as it binds (induced fit).
  • An antibody and its antigen, a hormone and its receptor.
  • A transcription factor and the bases of its DNA sequence.
  • A codon and the anticodon of a tRNA, and the two strands of DNA, matched by base pairing.

Self-assembly

Many of the cell's large structures are built from many copies of a few kinds of subunit, which bind to one another through the same kind of matching surfaces. If the information for the final structure lies in the subunits themselves, they can assemble with no template and no instructions from outside: self-assembly.

  • Tobacco mosaic virus. Its RNA and the many copies of its single coat protein, separated and then mixed in a test tube, assemble into virus particles that can infect again.
  • Ribosomal subunits. The bacterial small subunit's RNA and proteins, mixed in the right conditions, rebuild working subunits.
  • Lipid bilayers. Phospholipids in water form bilayers by themselves, their water-avoiding tails inside.
  • The cytoskeleton's filaments, each built from many copies of one subunit (actin, or the αβ-tubulin dimer) or, in intermediate filaments, of a few related proteins that pair up (keratin 5 with keratin 14, for example), and the shells (capsids) of many viruses, built from identical proteins arranged symmetrically.

Building from small identical subunits has advantages: a short gene can encode a huge structure, a faulty subunit can be left out, and the structure can be taken apart and rebuilt when the cell needs. Not everything assembles unaided, though. Some structures need assembly factors, proteins that guide the process and are not part of the finished structure: a eukaryotic ribosome needs many, and some virus heads are built on a protein scaffold that is removed afterwards. Some subunits are activated by cutting: collagen molecules form fibrils only once the ends of procollagen have been cut off outside the cell.

The cytoskeleton

The cytoskeleton is a network of protein filaments running through the cytoplasm of eukaryotic cells. It gives the cell its shape, holds organelles in place, carries cargo, separates the chromosomes in mitosis and moves the cell.

Actin filamentsMicrotubulesIntermediate filaments
Widthabout 7 nmabout 25 nm8 to 10 nm
Subunitactin, which binds ATPαβ-tubulin dimers, which bind GTPfibrous proteins, different in each tissue
Shapetwo strands wound into a helixa hollow tube of 13 protofilamentsa rope of twisted strands
Polarityyes: a fast-growing plus end, a minus endyes: a plus end, a minus end in the centrosomenone
Motor proteinsmyosinskinesins and dyneinsnone
Main jobsthe cell cortex, microvilli, crawling, the contractile ring that divides the cell, muscle contractiontracks for transport, the mitotic spindle, cilia and flagellastrength against stretching, the nuclear lamina
The cytoskeleton
The cytoskeleton drawn in four steps, every protein a shade of green. First, its three filaments one above the other at one scale: a microtubule 25 nm across, a hollow tube seen a little from its open minus end, its wall of 13 protofilaments, each a row of light α-tubulin and darker β-tubulin subunits; an intermediate filament 10 nm across, a rope of twisted strands; and an actin filament about 7 nm across, two strands of round subunits winding round each other. A plus sign and a minus sign mark the ends of the microtubule and of the actin filament; the intermediate filament has none. Next, two microtubules: one growing, the subunits at its plus end each holding a GTP, drawn as a small orange bead, with free tubulin dimers beside it; the other shrinking, its protofilaments peeling out in curls at its end and dimers falling away. Then three motors, each carrying a vesicle, a ring of membrane: kinesin, two small heads on a long stalk, and dynein, two large heads, on a microtubule, and myosin, two heads on long lever arms, on an actin filament below. Last, the core of a cilium cut across: nine doublets of microtubules in a ring round two single ones, each doublet with two dynein arms reaching toward the next, a nexin link to it and a radial spoke in toward the central pair. Step 1 of 4: Three filaments. Drawn at one scale: a microtubule 25 nm across, an intermediate filament 10 nm and an actin filament about 7 nm. Each is built from many copies of a small subunit. Microtubules and actin filaments have a plus end (+) and a minus end (−); intermediate filaments have none.−+−+

Step 1 of 4Three filaments. Drawn at one scale: a microtubule 25 nm across, an intermediate filament 10 nm and an actin filament about 7 nm. Each is built from many copies of a small subunit. Microtubules and actin filaments have a plus end (+) and a minus end (−); intermediate filaments have none.

Point at a name or a part to light it.

Three kinds of filament, each built from many copies of a small subunit. Two of them grow and shrink at their ends, and motors walk along them.

Simplified: the first two steps to scale, the motors drawn to read, the axoneme at a smaller scale; the microtubule's subunits drawn in rings, not in their slight helical stagger; the intermediate filament drawn as three strands, not its 32 to 40 chains; only β-tubulin's GTP drawn, in the cap and on free dimers; GDP not drawn; the GTP cap drawn a few rows long, where in cells it is tens of rows; the growing end drawn blunt, though its protofilaments flare a little too; each motor's chains drawn as heads and stalks; dynein's partners, such as dynactin, left out; B tubules drawn with 10 subunits; the central pair's sheath and the membrane round the axoneme left out.

13 sources
  1. Cooper GM. The Cell: A Molecular Approach, 2nd edition. Sinauer Associates, 2000. Structure and Organization of Actin Filaments.
  2. Cooper GM. The Cell: A Molecular Approach, 2nd edition. Sinauer Associates, 2000. Microtubules.
  3. Cooper GM. The Cell: A Molecular Approach, 2nd edition. Sinauer Associates, 2000. Intermediate Filaments.
  4. Cooper GM. The Cell: A Molecular Approach, 2nd edition. Sinauer Associates, 2000. Microtubule Motors and Movements.
  5. Cooper GM. The Cell: A Molecular Approach, 2nd edition. Sinauer Associates, 2000. Actin, Myosin, and Cell Movement.
  6. Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell, 4th edition. Garland Science, 2002. The Self-Assembly and Dynamic Structure of Cytoskeletal Filaments.
  7. Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell, 4th edition. Garland Science, 2002. Molecular Motors.
  8. Mitchison TJ. Localization of an exchangeable GTP binding site at the plus end of microtubules. Science. 1993;261(5124):1044–1047.
  9. Malik F, Brillinger D, Vale RD. High-resolution tracking of microtubule motility driven by a single kinesin motor. Proc Natl Acad Sci USA. 1994;91(10):4584–4588.
  10. Narita A, Usukura E, Yagi A, et al. Direct observation of the actin filament by tip-scan atomic force microscopy. Microscopy (Oxf). 2016;65(4):370–377.
  11. McIntosh JR, O’Toole E, Morgan G, et al. Microtubules grow by the addition of bent guanosine triphosphate tubulin to the tips of curved protofilaments. J Cell Biol. 2018;217(8):2691–2708.
  12. Seetapun D, Castle BT, McIntyre AJ, Tran PT, Odde DJ. Estimating the microtubule GTP cap size in vivo. Curr Biol. 2012;22(18):1681–1687.
  13. Eibauer M, Weber MS, Kronenberg-Tenga R, et al. Vimentin filaments integrate low-complexity domains in a complex helical structure. Nat Struct Mol Biol. 2024;31(6):939–949.

Actin filaments

Actin is a globular protein that binds ATP. Its subunits join head to tail into a filament of two strands wound round each other, about 7 nm across, which grows faster at its plus end. Starting a new filament is the slow step, so cells use proteins that start them where they are needed: the Arp2/3 complex branches a new filament off an old one, and formins grow long, unbranched ones. After a subunit joins, its ATP is split to ADP, which makes the older parts of the filament easier to take apart. Beneath the plasma membrane a mesh of actin filaments forms the cell cortex, which sets the cell's shape. Bundles of them hold up microvilli and the thin spikes (filopodia) of a crawling cell, a branched mesh of them pushes out its front edge, and with myosin II they form the contractile ring that pinches a dividing cell in two. In muscle, actin filaments slide past filaments of myosin II, and the muscle contracts.

Microtubules

A microtubule is a hollow tube about 25 nm across, whose wall is 13 rows (protofilaments) of α- and β-tubulin dimers. In animal cells most microtubules grow out from the centrosome, beside the nucleus, where rings of γ-tubulin anchor their minus ends, and their plus ends reach towards the cell's edge. The centrosome holds a pair of centrioles, each made of nine triplets of microtubules.

Microtubules switch between growing and rapid shrinking, which is called dynamic instability. Tubulin's GTP is split to GDP soon after it joins, so only a growing end keeps a cap of tubulin still holding GTP. GDP-tubulin is held straight only by its neighbours: if the end loses its cap, the protofilaments bend outwards, the end peels apart and the microtubule shrinks. Proteins that bind microtubules, such as tau in axons, steady them. This lets the cell rebuild its microtubules quickly: at mitosis they are pulled down and remade as the spindle, which separates the chromosomes.

  1. 1

    Kinesins carry outwards

    Most kinesins walk towards the plus end, carrying vesicles and organelles from the cell's centre towards its edge, and down an axon from the nerve cell body to its terminals.
  2. 2

    Dyneins carry inwards

    Cytoplasmic dynein walks towards the minus end, bringing cargo back to the centre and up the axon to the cell body.
  3. 3

    Myosins on actin

    Myosins walk along actin filaments, mostly towards the plus end. Myosin II makes muscle contract; others carry cargo over short distances in the cortex.

Each motor splits ATP for every step it takes. Most hold their cargo by the tail; the tails of myosin II instead pack together into the thick filaments of muscle.

Cilia and flagella are built round microtubules and bent by dynein. Their core, the axoneme, is a ring of nine pairs of microtubules round two single ones in the centre, the 9 + 2 pattern. Arms of axonemal dynein on each pair pull on the neighbouring pair; linked to one another by nexin and fixed at the base, the pairs can slide only a little past each other, so the sliding bends the axoneme. Each cilium grows from a basal body, built like a centriole. Many cells also have a single primary cilium, which has no central pair, does not beat and senses signals. The cilia of the embryo's node are the exception: they also lack the central pair, but have dynein arms and spin, which sets the left and right sides of the body.

Intermediate filaments

Intermediate filaments, found in animal cells only, 8 to 10 nm across, are built from long fibrous proteins wound into a rope. Two chains coil round each other, and two of these pairs lie side by side pointing in opposite directions, which is why the finished filament has no polarity. They bind no nucleotide and carry no motors. Their job is strength: they spread the pull on a tissue across its cells, anchored at desmosomes between cells and at hemidesmosomes to the basement membrane. Each tissue has its own kinds.

Intermediate filamentWhere
keratinsepithelial cells; hair and nails
vimentinfibroblasts, endothelial cells, white blood cells
desminmuscle
neurofilamentsnerve cells
glial fibrillary acidic proteinastrocytes
laminsthe nuclear lamina, under the inner nuclear membrane, in every nucleated cell

Because tumours usually keep their tissue's intermediate filament, pathologists stain for them to help tell where a tumour came from, keratins pointing to a carcinoma, for example.

Check yourselfAnswer, then say how sure you were: a lucky guess still counts as a weak point.

1How can an antibody bind its antigen tightly yet let go of it again?

2The RNA and coat protein of tobacco mosaic virus, separated and then mixed in a test tube, rebuild infectious virus particles. What does this show?

3Which filament is a hollow tube of α- and β-tubulin that grows out from the centrosome?

4Paclitaxel and vincristine both stop cancer cells in mitosis. How do they differ?

5A man has had sinusitis and a wet cough since childhood, is infertile, and his heart is on the right. Which protein is most likely faulty?