Techniques from computer science may help explain the tendency in biology for structures to repeat themselves.
Tag Archives: Proteins
How the Coronavirus Steals the Sense of Smell
The virus does not infect nerve cells that detect odors, researchers have found. Instead, it attacks nearby supporting cells.
Covid-19 At-Home Testing and PCR, Rapid Testing Questions: What to Know
Facing long lines and shortages of home test kits during the latest surge, people are searching for answers about Covid tests.
Can an Athlete’s Blood Enhance Brainpower?
Scientists who injected idle mice with blood from athletic mice found improvements in learning and memory. The findings could have implications for Alzheimer’s research and beyond.
Open-sourcing of protein-structure software is already paying off
Enlarge (credit: Humphreys et. al.)
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.
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Holding a mirror to life’s key molecules
Enlarge / The left- and right-handed forms of an amino acid. Every living thing uses the left-handed form exclusively. (credit: Wikimedia Commons)
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.)
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MIT scientists study spider web structure by translating it into music
Now you can walk through a virtual spider web, using VR headset and controllers to interact with a web sonification model.
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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Getting One Vaccine Is Good. How About Mix-and-Match?
Researchers are exploring the possible benefits of pairing doses from two different Covid-19 vaccines.
Cold Tooth Pain’s Mysterious Molecular Culprit
Researchers figured out how a jolt of discomfort gets from the damaged outside of your tooth to the nerves inside it.
His Sister Died 12 Days After Suffering Mysterious Spells. Now He Had Them.
The clock was ticking. An M.R.I., a spinal tap and blood tests weren’t revealing the culprit. Could it be psychological?
Beef Is Past Its Prime
The burger and I have a juicy past. But do we have a future?
If You Squeeze the Coronavirus, Does It Shatter?
Scientists are exploring the physics of viruses, to understand how these pathogens assemble themselves — and might be rent apart.
London A.I. Lab Claims Breakthrough That Could Accelerate Drug Discovery
Researchers at DeepMind say they have solved “the protein folding problem,” a task that has bedeviled scientists for more than 50 years.
Antibodies Good. Machine-Made Molecules Better?
With help from computer algorithms, researchers designed proteins from scratch that can trounce the coronavirus in lab animals.
Nasal Spray Prevents Covid Infection in Ferrets, Study Finds
Scientists at Columbia University have developed a treatment that blocks the virus in the nose and lungs, is inexpensive and needs no refrigeration.
Spider Silk Is Stronger Than Steel. It Also Assembles Itself.
Scientists are figuring out the chemical triggers that turn the liquid stored in silk glands into a solid that’s tougher than Kevlar.
Why Does the Coronavirus Hit Men Harder? A New Clue
Women produce a more powerful immune response than do men, a new study finds.
What if the First Coronavirus Vaccines Aren’t the Best?
Dozens of research groups around the world are playing the long game, convinced that their experimental vaccines will be cheaper and more powerful than the ones leading the race today.
Your Coronavirus Antibodies Are Disappearing. Should You Care?
Declining antibody levels do not mean less immunity, experts say. Besides, two widely used tests may detect the wrong antibodies.
Mutation Allows Coronavirus to Infect More Cells, Study Finds. Scientists Urge Caution.
Geneticists said more evidence is needed to determine if a common genetic variation of the virus spreads more easily between people.
Can You Boil an Egg Too Long?
You’ve had six-minute eggs, maybe slow-cooked eggs. Now try an egg cooked forever.
Monster or Machine? A Profile of the Coronavirus at 6 Months
Our “hidden enemy,” in plain sight.
Lift Weights, Eat More Protein, Especially if You’re Over 40
Eating more protein can significantly augment the effects of lifting weights, a review of research found.
Can You Get Too Much Protein?
While some nutritionists have encouraged the protein craze, a number of experts are urging caution.