Techniques from computer science may help explain the tendency in biology for structures to repeat themselves.
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It is now relatively trivial to determine the order of amino acids in a protein. Figuring out how that order translates to a complicated three-dimensional structure that performs a specific function, however, is extremely challenging. But after decades of slow progress, Google’s DeepMind AI group announced that it has made tremendous strides toward solving the problem. In July, the system, called AlphaFold, was made open source. At the same time, a group of academic researchers released its own protein-folding software, called RoseTTAFold, built in part using ideas derived from DeepMind’s work.
How effective are these tools? Even if they aren’t as good as some of the statistics suggested, it’s clear they’re far better than anything we’ve ever had. So how will scientists use them?
This week, a large research collaboration set the software loose on a related problem: how these individual three-dimensional structures come together to form the large, multi-protein complexes that perform some of the most important functions in biology.
The central dogma of molecular biology holds that DNA gets transcribed into RNA, which then gets translated into proteins. Of course, there are exceptions—some viruses, like coronaviruses, forego DNA altogether and encode their genetic information in RNA genomes. Other viruses, like HIV, have RNA genomes that must be copied into DNA and then transcribed back into RNA before being made into proteins. But as a general rule, “DNA to RNA to protein” describes how information moves within cells.
A unique property of biological molecules is that they have handedness. Naturally occurring molecules occur in roughly equal mixtures of left- and right-handed varieties. This means that molecules can have identical atoms and shapes but cannot be superimposed one upon the other. Instead, they are mirror images of each other, like our right and left hands.
(This can be difficult to envision, which is why pre-meds taking organic chemistry in college spend so much time playing with those ball-and-stick molecular models.)
A spider weaving its intricate web is a bit like a person composing a song, at least in the eyes of MIT materials engineer Markus Buehler, whose research involves translating web structure into musical melodies. Together with his collaborators, he has devised a way for humans to “enter” a 3D spider web and explore its structure both visually and aurally via a virtual reality setup. Buehler described the ongoing project during a talk at the (virtual) meeting of the American Chemical Society (ACS) this week.
The work may one day lead to a means of rudimentary communication with spiders in their own “language” of web vibrations, such as when they stretch a strand of silk while building a web or when the strands vibrate in response to a gust of wind or to the presence of trapped prey. “The spider lives in an environment of vibrating strings,” Buehler said during an online press conference. “They don’t see very well, so they sense their world through vibrations, which have different frequencies.”
As we’ve reported previously, several years ago, Buehler led a team of MIT scientists that mapped the molecular structure of proteins in spider silk threads onto musical theory to produce the “sound” of silk in hopes of establishing a radical new way to create designer proteins. The hierarchical elements of music composition (pitch, range, dynamics, tempo) are analogous to the hierarchical elements of a protein structure. Much like how music has a limited number of notes and chords and uses different combinations to compose music, proteins have a limited number of building blocks (20 amino acids) that can combine in any number of ways to create novel protein structures with unique properties.
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Researchers at DeepMind say they have solved “the protein folding problem,” a task that has bedeviled scientists for more than 50 years.
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You’ve had six-minute eggs, maybe slow-cooked eggs. Now try an egg cooked forever.
Our “hidden enemy,” in plain sight.
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