Junk DNA: goodbye!: ENCODE now hedging on 80% (Introduction)

by David Turell , Monday, May 11, 2020, 16:03 (1658 days ago) @ Balance_Maintained

" A spatial understanding of how DNA is packaged into a cell, and of the 3D folding that positions genes in close contact with their regulatory elements(emphasis mine), will be key to predicting an element's target genes. The NIH Common Fund has begun the '4D Nucleome' project, for instance, which aims to predict the target genes for every regulatory element. That knowledge will help to fill in the picture of how a given regulatory element influences health and disease."

Tony: I know this is an old post, but a particular line caught my eye. What regulates the protein folding spatially? What puts the protein in close proximity to the right regulatory section? How is the information of that spatial awareness stored?

Try this previous entry: Thursday, April 30, 2020, 21:28

https://phys.org/news/2020-04-hidden-symmetry-chemical-kinetic-equations.html

"In each case, the researchers demonstrated that a simple mathematical ratio shows that the likelihood of errors is controlled by kinetics rather than thermodynamics.

"'It could be a protein folding into the correct versus the incorrect conformation, an enzyme incorporating the right versus the wrong amino acid into the polypeptide chain, or a motor protein mistakenly stepping backward instead of going forward," said Igoshin, a CTBP investigator and professor of bioengineering at Rice. "All of those properties can be expressed as a ratio of two steady-state fluxes, and we found that biological properties expressed in these terms are under kinetic control."

***

"Before it folds, a protein has energy, like a ball sitting atop a hill. Folding is the downhill run from this high-energy starting point to the place where the ball stops rolling. Chemists often use a visual aid called a "free-energy landscape" to chart energy levels in chemical reactions. The landscape looks like a mountain range with peaks and valleys, and the downhill run from a protein's unfolded starting point to its fully folded finishing point can look like a mountain road that winds through a series of valleys. Even if one town along the road is lower in elevation, a traveler might have to climb hills to get from one valley to the next on the way downhill.

"'We've shown it's the barriers, the high points between valleys, that determine these ratios," Igoshin said. "The depths of the valleys don't matter.