Proteins Fold Who Knows How

One of the biggest mysteries remaining in cell biology is how proteins fold.  Proteins start out as chains of amino acids (polypeptides) as they exit the ribosome.  Most of them spontaneously fold into their “native” three-dimensional structures, where they will go to work as enzymes, structural materials or other key players in cell life.  About 10% of them are so complex, they need a little help.  The GroEL+GroES enzymes act like a barrel-shaped dressing room to help these proteins escape the bustle of the cytoplasm so that they can fold in private.  New work published in Cell shows that this “chaperone” device speeds up the proper folding of the polypeptide when it otherwise might get stuck on a “kinetic trap.”¹  A German team likened the assistance to narrowing the entropic funnel.  “The capacity to rescue proteins from such folding traps may explain the uniquely essential role of chaperonin cages within the cellular chaperone network,” they said.  GroEL+GroES therefore “rescues” protein that otherwise might misfold and cause damage to the cell.
    The GroEL barrel and its GroES cap spend 7 ATP energy molecules opening and closing.  The process can work in reverse, taking a misfolded protein and unfolding it as well.  It might take several rounds for a complex protein to reach its native fold.  These chaperonins operate in bacteria as well as higher organisms – and they are not the only chaperones.  “Bacterial cells generally contain multiple, partly redundant chaperone systems that function in preventing the aggregation of newly synthesized and stress-denatured proteins,” the authors said.  “In contrast to all other components of this chaperone network, the chaperonin, GroEL, and its cofactor, GroES, are uniquely essential, forming a specialized nano-compartment for single protein molecules to fold in isolation.”  This fact has been known since the 1990s.  Chakraborty et al focused on the ability of GroEL+GroES to rescue proteins from kinetic traps.  Like a stack of six-sided rings, GroEL forms a barrel-shaped container.  “Each subunit of GroEL is composed of an equatorial ATPase domain, an apical domain, and an intermediate hinge domain,” they explained.  “The apical domains form the flexible ring opening and expose hydrophobic amino acid residues toward the central cavity for the binding of non-native substrate proteins.”  GroES forms a cap or lid over this barrel, allowing the polypeptide inside to fold in isolation.  The dressing room is large enough to fold proteins 60,000 atomic mass units in size.
    What is becoming clear is that the barrel is not just a passive container.  It actually accelerates folding: “an active mechanism in promoting folding appears to operate in addition, based on the demonstration that GroEL/ES can substantially enhance the rate of folding for proteins,” increasing the folding rate by as much as 10-fold.  Whether iterative cycles of folding and unfolding in the barrel cause the acceleration, or the isolation alone prevents kinetic traps, was not known.  The team concluded that “protein confinement in the chaperonin cage has the capacity to reduce entropic folding barriers, thereby promoting the formation of native contacts.”  If so, the entropic funnel picture is apt; a narrowing funnel prevents the protein from misfolding and guides it along the way to its correct shape.
    The team also helped confirm that a net negative charge on the interior of the barrel contributes to the accelerated folding.  “These findings are consistent with recent theoretical considerations that the charged surface may induce ordered water structure, with the resulting increase in the density of water facilitating folding by enhancing the hydrophobic effect and thus promoting global protein compaction,” they said.  This interior charge contribution only works when the protein is inside the barrel.  Outside the barrel, they found that artificially induced disulfide bridges could coax their test polypeptide into the native fold.  “In view of the fact that cells contain multiple, partially redundant chaperone systems for aggregation prevention, the ability to actively promote the folding of such intermediates would explain the uniquely essential role of the chaperonin cages,” they said in conclusion.  On the other hand, the conspicuous absence of chaperonins from oxidizing cellular compartments correlates with the role of disulfide bond formation in providing an alternative mechanism to lower entropic folding barriers.”  See also the 12/28/2007 entry, last two paragraphs.     Meanwhile, scientists at Rice University have been trying to model protein folding on computers.  PhysOrg quoted them saying that “Protein folding is regarded as one of the biggest unsolved problems in biophysics.”  How proteins find their native fold through a maze of wrong folds is still not understood.  “Like a river finding the shortest route to the sea, proteins always find their way to their native states in an instant,” the article said.  “How that happens is one of life’s great mysteries.”  Somehow they do it – and quickly.  Many proteins spontaneously collapse into their proper shape in milliseconds or microseconds.  “Though the proteins assemble themselves in nature almost instantly, the Rice team’s algorithm took weeks to run the simulation.” the article said.  “Still, that was far faster than others have achieved.”  Using another analogy to show what the protein (and simulators) are up against, one researcher said that “A polypeptide chain en route to its native state encounters many energy barriers, much like when one navigates through a rugged mountain landscape.”  If you have supercomputers handy and weeks of free time, you might be able to run the Rice team’s new and improved simulation.  The spontaneous folding of proteins vastly exceeds the complexity of human attempts at spontaneous origami (see New Scientist for primitive example).
    Once folded, proteins are workhorses in the cell, performing all kinds of intricate tasks.  A recent article on PhysOrg, for instance, reported that scientists at the University of Dundee discovered an enzyme that acts like a “molecular scissors,” cutting off parts of DNA during damage repair operations.  Some proteins incorporate metals into their structure.  This adds to the difficulty of getting them into their native conformation, because they have to delicately position these highly reactive metal ions at precisely the right locations inside the fold.  An article on PhysOrg did not address the folding problem per se, but marveled at these “hives of industry” in the cell, stating that “Nearly half of all enzymes require metals to function in catalysing biological reactions” such as photosynthesis, metabolism, and respiration.  Kylie Vincent, of Oxford University’s Department of Chemistry, continued: “Both the metal and the surrounding protein are crucial in tuning the reactivity of metal catalytic centres in enzymes.”  Oxford is keen on watching how metallic enzymes work in order to imitate them.  “There is much that we can learn,” Kylie said, “from the way that micro-organisms use readily available metals to carry out these reactions while chemists often require rare and expensive metals for the same chemistry.”  Clean, green fuel cells and other inventions may come from a better understanding of these amazing strings of amino acids that fold ever-so-precisely into the most efficient molecular machines ever witnessed.

1.  Chakraborty et al, “Chaperonin-Catalyzed Rescue of Kinetically Trapped States in Protein Folding,” Cell Volume 142, Issue 1, 112-122, 9 July 2010, DOI: 10.1016/j.cell.2010.05.027.

None of these articles said anything about evolution.  Why would natural selection produce a multi-part precision folding machine like GroEL+GroES, able to fold multiple different polypeptides, when other chaperone mechanisms exist? (cf. 12/30/2002).  This is not clumsy tinkering; it is elegant extravagance showing the power of goal-directed design, utilizing an irreducibly complex machine (see 11/30/2006, bullet 7).  One can envision Charlie worrying about this and spontaneously folding into a fetal position in his isolation chamber (tomb), never to come out again.
    It’s overkill by this point, but to rub it in, you might read Robert Deyes’ review Uncommon Descent of Doug Axe’s new paper, “The Case Against A Darwinian Origin Of Protein Folds,” available for open access in the new journal, Bio-complexity.  Deyes titled his review, “Proteins Fold as Darwin Crumbles.”