Playing video games isn’t precisely rocket science but, due to Foldit, it may be molecular biology. Sort of. Solo and in groups, these amateur analysts vie to crack the most perplexing puzzles vexing molecular biologists at this time: how particular person proteins and their component amino acids fold. It’s no wonder such a buzz ensued when a 2011 publication in the journal Nature Structural & Molecular Biology reported that Foldit gamers had unraveled a key protein in Mason-Pfizer monkey virus (MPMV), the simian version of HIV, that had stymied researchers for more than a decade. Like John Henry versus the steam hammer or Garry Kasparov versus Deep Blue, Foldit players showed that humans nonetheless have a factor or two to teach machines; not like Henry, who died, or Kasparov, who lost in a rematch, the protein-folding avid gamers still have an edge over the brute-power number crunching of supercomputers. To grasp the scope of this achievement and what it might mean for the future of HIV, let us take a look at why understanding how a protein folds is so vital.


Each protein’s peculiar origami determines both its position and its potential to hook up with different molecules. It’s as if a protein had been a sequence made up of a thousand locks, all bunched in a ball: Should you needed to design a drug to have an effect on it, you’ll have to know which locks have been turned outward, and in what pattern, so that you would reduce a set of keys to suit them. Particular proteins play pivotal elements in key chains of occasions. Researchers prize these proteins because they signify a vulnerability that they will exploit to sluggish or cease a illness, together with retroviruses like HIV and MPMV. A retrovirus is a virus that carries its genetic data as ribonucleic acid (RNA) instead of DNA. These viruses transcribe their RNA into DNA, as a substitute of vice versa, completely enmeshing their genetic code into the infected cell’s genome and remodeling it into a manufacturing facility for making extra retrovirus.

Inhibiting that protein throws a monkey wrench into a retrovirus’ equipment of destruction. Unfortunately, teasing out the structure of such proteins is one of the most troublesome puzzles we know of. Imagine filling a large field with tangled Christmas tree lights, disused Slinky toys, barbed wire, duct tape and electromagnets, then shaking it and flipping it round, and at last making an attempt to guess what form you’d made. You’ve solely begun to scratch the floor of the complexity of this activity. Such complexity is more than even a supercomputer can typically handle, particularly as a result of computer systems will not be especially good at working with three-dimensional shapes. So, scientists started in search of a faster and more effective means to crack protein buildings. Their answer? Use the innate spatial evaluation abilities of the human mind. Foldit was born. Almost instantly, it began paying dividends. On this next part, we’ll take a closer look at how Foldit works, what avid gamers have completed with it and whether or not or not they cured HIV.

In Foldit, players use a easy field of tools to manipulate the form of a protein. The thought is to bend, twist, transfer and shake the protein’s facet chains and amino acid backbones such that the whole construction is packed into its optimum shape. Players know their solution works when they get rid of collisions between facet chains of atoms, cover the hydrophobic chains contained in the protein, face the hydrophilic chains outward and take away giant empty areas that threaten the stability of the protein — all of which is reflected in their rating. Thermodynamics tells us that natural methods have a tendency toward states of decrease vitality. Other physical legal guidelines, such as the mutual attraction of opposite costs, repulsion of like fees and limitations concerning how atomic bonds may be organized and rotated, are additionally inbuilt. The Foldit program abstracts the details right into a form that the attention can understand and the brain can grasp.