Wednesday, February 3, 2021

Take a Sequence of Amino Acids and Accurately Predict Their 3D Shape

Environmental & Science Education, STEM, Nature of Science

Ed Hessler

Did you think it would ever be possible to determine a protein's 3D shape from its amino acid sequence? The problem seemed intractable and when it could be solved involved painstaking laboratory experiments until...

The story of its solution is found in a recent science briefing in the journal Nature

As the article notes "Proteins are the building blocks of life, responsible for most of what happens inside cells. How a protein works and what it does is determined by its 3D shape — ‘structure is function’ is an axiom of molecular biology. Proteins tend to adopt their shape without help, guided only by the laws of physics."

Ewen Galloway, the writer of the essay on this 7-league step, opens this remarkable achievement with these words. "An artificial intelligence (AI) network developed by Google AI offshoot DeepMind has made a gargantuan leap in solving one of biology’s grandest challenges — determining a protein’s 3D shape from its amino-acid sequence.

"DeepMind’s program, called AlphaFold, outperformed around 100 other teams in a biennial protein-structure prediction challenge called CASP, short for Critical Assessment of Structure Prediction. The results were announced on 30 November, at the start of the conference — held virtually this year — that takes stock of the exercise."

The report describes the problem, the laboratory research and then how this "contest" was conducted--the exercise takes place each year over several months. And it is blind, i.e., the assessors don't know the names of the individuals or their affiliations." They are referred to as groups and assigned a number. The entry that satisfied the judges and met the criteria was from "Group 427). 

The significance of this solution is noted by Mohammed AlQuraishi, a computational biologist at Columbia University. “'I think it’s fair to say this will be very disruptive to the protein-structure-prediction field. I suspect many will leave the field as the core problem has arguably been solved. It’s a breakthrough of the first order, certainly one of the most significant scientific results of my lifetime.'”

Structure-function is one of the important ideas in current standards for science, K-12.. Here is a short explanation from the Next Generation Science Standards (NGSS) of why it is important, what should be learned and progression of this cross-cutting concept by grades.

There is information about the company and "the real world impact," e.g., drug discovery, protein design, and making "sense disease causing gene variations that differ between people."

Expect scientific criticism, skepticism and intense arguments on whether the problem has been solved. It is the nature of science. American astronomer Carl Sagan once wrote "Extraordinary claims require extraordinary evidence."

This video (7m 54s) from DeepMind shows and explains the making of this breakthrough.


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