Protein Dressing Room Has Electronic Walls
Properly folded proteins are essential to all of life. When a polypeptide, or chain of amino acids, emerges from the ribosome translation factory on its way to becoming a protein, it looks like a useless, shapeless piece of string. It cannot perform its function till folded into a precise, compact shape particular for its job. Some short polypeptides will spontaneously fold into their “native” state, ready for work, but many of the bigger ones need help. Fortunately, the cell provides a private dressing room called the GroEL-GroES chaperonin that not only gives them privacy, away from the bustle of colliding molecules in the cytoplasm, but actually helps them get dressed (see also 05/05/2003 entry). This chaperone or “helper” machine thus not only gets the actor ready for the stage faster, but prevents misfolding that could clutter the cell with useless or harmful aggregates of protein.
A team from the Max Planck Institute, writing in Cell,1 investigated how the internal structure of this barrel-shaped molecular machine overcomes energy barriers to proper folding and speeds up the process ten-fold. They found that the inside walls of the GroEL barrel and the inside walls of the GroES lid contain protrusions that generate electrostatic and hydrophobic forces on the interior space. When the unfolded protein enters, therefore, it is subjected to gentle pressures that coax it to fold. These forces are nonspecific enough to work on hundreds of different substrates that use this general-purpose machine.
Furthermore, they found that the forces change during the entry of the nascent protein. The interior is not barrel shaped when the actor approaches the door; the GroES lid, with the help of the energy molecule ATP, guides the protein in, and then the barrel pops into its shape, providing a safe haven for folding. Moreover, the electronic walls turn on to provide that gentle nudge to get the polypeptide over its energy barriers and into the right folding pathway. When the protein has properly completed its folding after about 10 seconds in the dressing room, the door opens and the protein pops out, ready for action.
How finely tuned is this machine? The authors did some experiments on mutating the chaperone to make the barrel looser and tighter. They found that volume changes as small as 2-5% slowed down the folding considerably. The barrel volume needs to be within certain narrow limits, yet general enough to handle a variety of small, medium and large proteins.
The GroEL/GroES nano-cage allows a single protein molecule to fold in isolation. This reaction has been compared to spontaneous folding at infinite dilution. However, recent experimental and theoretical studies indicated that the physical environment of the chaperonin cage can alter the folding energy landscape, resulting in accelerated folding for some proteins. By performing an extensive mutational analysis of GroEL, we have identified three structural features of the chaperonin cage as major contributors to this capacity: (1) geometric confinement exerted on the folding protein inside the limited volume of the cage; (2) a mildly hydrophobic, interactive surface at the bottom of the cage; and (3) clusters of negatively charged amino acid residues exposed on the cavity wall. We suggest that these features in combination provide a physical environment that has been optimized in evolution [sic] to catalyze the structural annealing of proteins with kinetically complex folding pathways. Thus, the chaperonin system and its mutant versions may prove as useful tools in understanding how proteins navigate their energy landscape of folding.
1Tang et al., “Structural Features of the GroEL-GroES Nano-Cage Required for Rapid Folding of Encapsulated Protein,” Cell
We didn’t need that little senseless phrase “optimized in evolution” now, did we? The authors talked nothing else about evolution, or how natural selection could produce three independent structural features of this one machine that assists proteins in vital ways. This machine has irreducible complexity written all over it. As usual, references to evolution provide nothing but a narrative gloss on the actual facts of the story. The science involved continuing revelations inside the black box, where we see precision, efficiency, control – and design.
In the film Unlocking the Mystery of Life with its forgivably simplified animations, a nascent protein is shown floating into a smooth, barrel-shaped chamber with a lid, where it folds on itself from one end to another. This is helpful to show the general idea, but the actual process is much more complicated and interesting. For one thing, this all happens much quicker than shown, in a very crowded environment. For another, protein folding is a complex affair, wherein several domains of the polypeptide fold sequentially or simultaneously following an energy landscape (like a pinball negotiating obstacles) that leads to the completed protein. Some domains fold into a helix or sheet, or several, which then combine into larger structures. Even then, after the protein exits the chaperone, there can be subsequent modifications: multiple proteins, for instance, might be joined into complexes, with metal ions inserted (as in hemoglobin or chlorophyll), and these proteins usually become part of networks. Add to that now the exciting discovery that the walls of the chaperone barrel are interactive, coaxing the proteins to fold properly. At every stage there is coordinated, synchronized, elegant design.
Think about how these molecules operate in the blind. They do not have eyes and brains telling them where to go – yet they succeed. There is no analog in human technology; the closest, perhaps, is computer programming, but in life, at scales smaller than most of us can imagine, nano-factories operate with physical entities moving through space and time. How fortunate we are to see these marvels unfold. Our ancestors might have wondered at the mysteries of biological life, but could they in their wildest dreams have imagined the city-like organization at work at the molecular level?