Proteome

From Catherine Offord at the at The Scientist: In one recent project, for example, Schroeter and her advisor Mary Schweitzer extracted and analyzed collagen peptides from just 200 mg of an 80-million-year-old fossil of a Cretaceous-era herbivore, Brachylophosaurus canadensis, excavated in Montana. The amino acid sequences of those peptides, published last year, placed the dinosaur on a branch of the phylogenetic tree between crocodiles and basal birds such as ostriches.1 What’s more, the team’s collection of analyzable peptides from the ancient specimen suggests that there might be other fossils out there with similar molecular information hidden in them. Although the findings were controversial—some researchers still doubt that proteins can resist degradation for tens of millions of years—Schroeter is one of a Read More ›

Can protein folding complexity be formed by stochastic processes? With 14 intermediate steps?
JILA Team Discovers Many New Twists in Protein Folding

Biophysicists at JILA have measured protein folding in more detail than ever before, revealing behavior that is surprisingly more complex than previously known. . . .
They fold into three-dimensional shapes that determine their function through a series of intermediate states, like origami. Accurately describing the folding process requires identifying all of the intermediate states.
The JILA research revealed many previously unknown states by unfolding an individual protein. For example, the JILA team identified 14 intermediate states—seven times as many as previously observed—in just one part of bacteriorhodopsin, a protein in microbes that converts light to chemical energy and is widely studied in research.
“The increased complexity was stunning,” said project leader Tom Perkins, a National Institute of Standards and Technology (NIST) biophysicist working at JILA, a partnership of NIST and the University of Colorado Boulder. “Better instruments revealed all sorts of hidden dynamics that were obscured over the last 17 years when using conventional technology.”
“If you miss most of the intermediate states, then you don’t really understand the system,” he said.
Knowledge of protein folding is important because proteins must assume the correct 3-D structure to function properly. Misfolding may inactivate a protein or make it toxic. Several neurodegenerative and other diseases are attributed to incorrect folding of certain proteins.

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A frequently made claim in the scientific literature is that protein domains can be readily recombined to form novel folds. In Darwin’s Doubt, Stephen Meyer addresses this subject in detail (see Chapter 11). Over the course of this article, I want to briefly expand on what was said there. Defining Our Terms Before going on, it may be useful for me to define certain key terms and concepts. I will be referring frequently to “exons” and “introns.” Exons are sections of genes that code for proteins; whereas introns are sections of genes that don’t code for proteins. Proteins have multiple structural levels. Primary structure refers to the linear sequence of amino acids comprising the protein chain. When segments within this chain Read More ›