Comprehensive model is first to map protein folding at atomic level

Nov 06, 2006

Scientists at Harvard University have developed a computer model that, for the first time, can fully map and predict how small proteins fold into three-dimensional, biologically active shapes. The work could help researchers better understand the abnormal protein aggregation underlying some devastating diseases, as well as how natural proteins evolved and how proteins recognize correct biochemical partners within living cells.

The technique, which can track protein folding for some 10 microseconds -- about as long as some proteins take to assume their biologically stable configuration, and at least a thousand times longer than previous methods -- is described this week in the Proceedings of the National Academy of Sciences.

"For years, a sizable army of scientists has been working toward better understanding how proteins fold," says co-author Eugene I. Shakhnovich, professor of chemistry and chemical biology in Harvard's Faculty of Arts and Sciences. "One of the great problems in science has been deciphering how amino acid sequence -- a protein's primary structure -- also determines its three-dimensional structure, and through that its biological function. Our paper provides a first solution to the folding problem, for small proteins, at an atomic level of detail."

Fiendishly intricate, protein folding is crucial to the chemistry of life. Each of the body's 20 amino acids, the building blocks of proteins, is attracted or repulsed by water; it's largely these affinities that drive the contorting of proteins into distinctive three-dimensional shapes within the watery confines of a cell. The split-second folding of gangly protein chains into tight three-dimensional shapes has broad implications for the growing number of disorders believed to result from misfolded proteins or parts of proteins, most notably neurodegenerative disorders such as Alzheimer's and Parkinson's diseases.

The model developed by Shakhnovich and colleagues faithfully describes and catalogs countless interactions between the individual atoms that comprise proteins. In so doing, it essentially predicts, given a string of amino acids, how the resulting protein will fold -- the first computer model to fully replicate folding of a protein as happens in nature. In more than 4,000 simulations conducted by the researchers, the computer model consistently predicted folded structures nearly identical to those that have been observed experimentally.

"This work should open new vistas in protein engineering, allowing rational control of not only protein folding, but also the design of pathways that lead to these folds," says Shakhnovich, who has studied protein folding for nearly two decades. "We are also using these techniques to better understand two fundamental biological questions: How have natural proteins evolved, and how do proteins interact in living cells to recognize correct partners versus promiscuous ones?"

Source: Harvard University

Explore further: The seashell-inspired material inspiring a new wave of safety gear in sport

Related Stories

Molecular chaperones help with folding

May 12, 2015

Chaperones are molecular helpers that assist other proteins with folding. One such chaperone is the so-called heat shock protein 60 (Hsp60). This protein forms structures in mitochondria that resemble barrels ...

A tale of two roads into protein unfolding

May 11, 2015

You are taking a class on origami and Mr. Otaki asks you to fold that little red piece of paper into a very elaborate design. You have to do it in a very short time. You try your best but you fail. Your origami ...

Chromosome-folding theory shows promise

Apr 28, 2015

Human chromosomes are much bigger and more complex than proteins, but like proteins, they appear to fold and unfold in an orderly process as they carry out their functions in cells.

Building scaffolds in the cell's power stations

May 06, 2015

A group of scientists led by Assistant Professor Dr. Martin van der Laan has decoded the molecular basis for the characteristic structures inside of mitochondria. Mitochondria are the powerhouses of cells ...

Recommended for you

User comments : 0

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.