Corporate Banner
Satellite Banner
RNAi
Scientific Community
 
Become a Member | Sign in
Home>News>This Article
  News
Return

Scientists Devise Innovative Method to Profile and Predict the Behavior of Proteins

Published: Friday, August 09, 2013
Last Updated: Friday, August 09, 2013
Bookmark and Share
A class of proteins that are made up of multiple, interlocking molecular components, enzymes perform a variety of tasks inside each cell.

However, precisely how these components work together to complete these tasks has long eluded scientists.

But now, a team of researchers has found a way to map an enzyme’s underlying molecular machinery, revealing patterns that could allow them to predict how an enzyme behaves – and what happens when this process disrupted.

In the latest issue of the journal Cell, a team of scientists led by Gladstone Institutes and UC San Francisco investigator Nevan Krogan, PhD, Texas A&M University’s Craig Kaplan, PhD, and UCSF professor Christine Guthrie, PhD, describe a new technique – called the point mutant E-MAP (pE-MAP) approach—that gives researchers the ability to pinpoint and map thousands of interactions between each of an enzyme’s many moving parts.

The researchers focused on a well-known enzyme – called RNA polymerase II (RNAPII) – and used the single-cellular yeast species S. cerevisiae as a model. Researchers had previously mapped the physical structure of RNAPII, but not how various parts of the enzyme work with other proteins within the cell to perform vital functions.

“Scientists know RNAPII’s physical structure, but this large enzyme has many distinct regions that each perform distinct functions,” said Kaplan, who is also a scientist at Texas A&M AgriLife. “We wanted to connect the dots between these regions and their function.”

In laboratory experiments, the team took a genetic approach – generating 53 variations of RNAPII, so-called RNAPII “mutants,” that each changed a specific part of RNAPII. They wanted to test each mutant against a particular function. In this way, they could link a specific region in the enzyme to a specific function.

But to do so, they had to compare each of the mutants against thousands of functions that RNAPII might be involved in within the cell – an immense task that couldn’t be accomplished by traditional methods. So the team developed the pE-MAP approach.

“Instead of crossing a single point mutant with one or two different mutants, pE-MAP lets us cross each one with more than 1,000,” said Krogan, who also directs the California Institute for Quantitative Biosciences, or QB3, at UCSF. “This gives us 1,000 data points for each mutant, which we then use to build our high-resolution profiles.”

“Until now, the only way to get similar information was to deactivate, or “knock out” specific genes within an enzyme and observe the impact,” explained Hannes Braberg, a graduate student in Krogan’s lab and the paper’s lead author. “But RNAPII is so critical that deactivating even one gene often kills the cell. So instead of knocking out the genes, we mutated them.”

The team then correlated the newly generated profiles to how well each variation of RNAPII could transcribe DNA into RNA – the enzyme’s most important function. The research team found that some of the RNAPII mutants transcribed more slowly than the others, while others were much faster. Further analysis revealed that the slow transcribers showed key similarities with each other, as did the fast transcribers. A pattern began to emerge that allowed them to predict the transcription speed – fast or slow – for each mutant.

And then the team discovered yet another phenomena related to transcription, involving a process called splicing, whereby specific stretches of non-coding RNA are cut out, and what remains is stitched back together. Previously, scientists had hypothesized that the transcription speed was related to splicing – in that fast transcribers would be less accurate splicers, and vice versa. But no one had been able to see it in action. So Guthrie, whose lab researches splicing, used the profiles generated from the pE-MAP approach to observe in real time how different transcription speeds affected splicing precision.

“When you slow down transcription, splicing gets more efficient,” said Guthrie. “We saw the opposite effect in our fast transcribers—which had long been predicted but had never before been observed. This was another testament to the power of the pE-MAP approach.”

The approach used here could be applied to studies of other enzymes, explained the authors. And what the researchers learn could then be used to develop an understanding of how mutations in enzymes like RNAPII lead to specific disease states – and may ultimately inform our ability to correct them.

This research received support from QB3, the National Institutes of Health, the National Science Foundation, the Searles Scholars Program and the W.M. Keck Foundation.


Further Information

Join For Free

Access to this exclusive content is for Technology Networks Premium members only.

Join Technology Networks Premium for free access to:

  • Exclusive articles
  • Presentations from international conferences
  • Over 2,900+ scientific posters on ePosters
  • More than 4,200+ scientific videos on LabTube
  • 35 community eNewsletters


Sign In



Forgotten your details? Click Here
If you are not a member you can join here

*Please note: By logging into TechnologyNetworks.com you agree to accept the use of cookies. To find out more about the cookies we use and how to delete them, see our privacy policy.

Related Content

Science Magazine Names CRISPR ‘Breakthrough of the Year’
In its year-end issue, the journal Science chose the CRISPR genome-editing technology invented at UC Berkeley 2015’s Breakthrough of the Year.
Monday, December 21, 2015
New Method for Screening Cancer Cells
Parallel microfiltration could lead to better treatments for a number of diseases, UCLA-led study says.
Thursday, December 03, 2015
RNA-Based Drugs Give More Control Over Gene Editing
CRISPR/Cas9 gene editing technique can be transiently activated and inactivated using RNA-based drugs, giving researchers more precise control in correcting and inactivating genes.
Monday, November 23, 2015
Double Enzyme Hit May Explain Common Cancer Drug Side Effect
Mouse study suggests genomic screening before treatment may help prevent anemia.
Wednesday, October 14, 2015
Opening the Door to Safer, More Precise Cancer Therapies
New method regulates when, and how strongly, cancer-killing therapeutic T cells are activated.
Tuesday, September 29, 2015
Scientists Create CRISPR/Cas9 Knock-In Mutations in Human T Cells
In a project spearheaded by investigators at UC San Francisco, scientists have devised a new strategy to precisely modify human T cells using the genome-editing system known as CRISPR/Cas9.
Tuesday, July 28, 2015
Delivering Drugs to the Right Place
Thomas Weimbs has developed a targeted drug delivery method that could potentially slow the progression of polycystic kidney disease.
Monday, June 29, 2015
Designing New Pain Relief Drugs
Researchers have identified the molecular interactions that allow capsaicin to activate the body’s primary receptor for sensing heat and pain, paving the way for the design of more selective and effective drugs to relieve pain.
Thursday, June 11, 2015
Genetic Markers for Detecting and Treating Ovarian Cancer
Custom bioinformatics algorithm identifies human mRNAs that distinguish ovarian cancer cells from normal cells and provide new therapeutic targets
Wednesday, May 27, 2015
Using microRNA Fit to a T (Cell)
Researchers show B cells can deliver potentially therapeutic bits of modified RNA.
Friday, November 29, 2013
Digging Deeper Into Cancer
What a pathologist looks for in a Pap test sample, but hopes not to find, are oddly shaped cells with abnormally large nuclei. The same is true for prostate and lung cancer biopsies.
Tuesday, November 19, 2013
Nanotech Method Show Promise Against Pancreatic Cancer
Researchers at UCLA's Jonsson Comprehensive Cancer Center have developed a new technique for fighting deadly and hard-to-treat pancreatic cancer.
Monday, November 18, 2013
Researchers Un-Junking Junk DNA
A study shines a new light on molecular tools our cells use to govern regulated gene expression.
Wednesday, November 13, 2013
Powerful Anti-Cancer Compound Safely Delivered
Researchers have discovered a way to effectively deliver staurosporine (STS).
Tuesday, October 22, 2013
Pan-Cancer Studies Find Common Patterns Shared by Different Tumor Types
Findings may open up new treatment options by extending therapies effective in one cancer type to others with a similar genomic profile.
Wednesday, October 02, 2013
Scientific News
Cancer Cells Kill Off Healthy Neighbours
Cancer cells create space to grow by killing off surrounding healthy cells, according to UK researchers working with fruit flies.
Cancer Drug Target Visualized at Atomic Resolution
New study using cryo-electron microscopy shows how potential drugs could inhibit cancer.
Genetic Mechanism Behind Cancer-Causing Mutations
Researchers at Indiana University has identified a genetic mechanism that is likely to drive mutations that can lead to cancer.
Future of Medicine Could be Found in a Tiny Crystal Ball
A Drexel University materials scientist has discovered a way to grow a crystal ball in a lab. Not the kind that soothsayers use to predict the future, but a microscopic version that could be used to encapsulate medication in a way that would allow it to deliver its curative payload more effectively inside the body.
"Gene Fusion" Drives Childhood Brain Cancers
Study co-led by Penn scientists highlights potential targets for future cancer therapies.
Enzyme Links Age-Related Inflammation, Cancer
Researchers have shown that an enzyme key to regulating gene expression -- and also an oncogene when mutated -- is critical for the expression of numerous inflammatory compounds that have been implicated in age-related increases in cancer and tissue degeneration.
Viral Gene Editing System Corrects Genetic Liver Disease
Penn study has implications for developing safe therapies for an array of rare diseases via new gene cut-and-paste methods.
Improving Delivery of Poorly Soluble Drugs Using Nanoparticles
A technology that could forever change the delivery of drugs is undergoing evaluation by the Technology Evaluation Consortium™ (TEC). Developed by researchers at Northeastern University, the technology is capable of creating nanoparticle structures that could deliver drugs into the bloodstream orally – despite the fact that they are normally poorly soluble.
Curing Disease by Repairing Faulty Genes
New delivery method boosts efficiency of CRISPR genome-editing system.
'Junk' DNA Plays Role in Preventing Breast Cancer
Supposed "junk" DNA, found in between genes, plays a role in suppressing cancer, according to new research by Universities of Bath and Cambridge.
SELECTBIO

Skyscraper Banner
Go to LabTube
Go to eposters
 
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
2,900+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
4,200+ scientific videos
Close
Premium CrownJOIN TECHNOLOGY NETWORKS PREMIUM FOR FREE!