Old methods prove true for studying proteins

October 17, 2020

A fresh new look at an old technique in protein biochemistry has shown that it should be reintroduced to the spectroscopy toolkit.

For decades, scientists have used nuclear magnetic resonance (NMR) spectroscopy to probe the molecular motions of proteins on various timescales. This technique has revealed aspects of enzyme reactions, protein folding and other biological processes, all on an atomic scale.

Typically, spectroscopists will gauge the rotation of NMR-active atoms in the protein backbone with and without proton irradiation to calculate a ratio known as a steady-state nuclear Overhauser effect (NOE); however, it was not always done this way.

Before steady-state NOE experiments became the norm in biological investigations, scientists would often take a greater number of measurements over the course of an irradiation experiment. This method, termed "dynamic" NOE, might seem more complicated, but according to Ph.D. student Vladlena Kharchenko, it is no more time consuming than steady-state NOE, while dynamic NOE provides additional information about protein flexibility and is far more accurate to minute biological motions in proteins.

"It works for proteins and makes studying their dynamics even more accurate," says Kharchenko, a member of ?ukasz Jaremko's lab at KAUST. "Our message to biological NMR spectroscopists is simple: 'Don't be afraid of dynamic NOE.'"

To prove the technique's worth, Kharchenko, Jaremko and their team performed a series of NMR experiments on ubiquitin, a globular protein that regulates a range of processes inside the cell. Working with Mariusz Jaremko, also from KAUST, and collaborators in Poland, the researchers collected both steady-state and dynamic NOE measurements and demonstrated that the dynamic approach is always preferable--except under a few specific conditions, such as when instrument access is limited or when proteins degrade very rapidly.

Notably, the steady-state approach proved especially prone to errors in regions of the ubiquitin protein that were flexible and disposed to moving around. The dynamic technique, in comparison, offered no such misleading results.

In light of their findings, the KAUST team hopes that other scientists with an interest in atomic-level protein mechanics will now begin to adopt, or at least reconsider, dynamic NMR methods. Kharchenko says that sometimes, "it's worth dusting off forgotten methods and checking if they fit to new emerging questions and systems of research interest."

King Abdullah University of Science & Technology (KAUST)

Related Proteins Articles from Brightsurf:

New understanding of how proteins operate
A ground-breaking discovery by Centenary Institute scientists has provided new understanding as to the nature of proteins and how they exist and operate in the human body.

Finding a handle to bag the right proteins
A method that lights up tags attached to selected proteins can help to purify the proteins from a mixed protein pool.

Designing vaccines from artificial proteins
EPFL scientists have developed a new computational approach to create artificial proteins, which showed promising results in vivo as functional vaccines.

New method to monitor Alzheimer's proteins
IBS-CINAP research team has reported a new method to identify the aggregation state of amyloid beta (Aβ) proteins in solution.

Composing new proteins with artificial intelligence
Scientists have long studied how to improve proteins or design new ones.

Hero proteins are here to save other proteins
Researchers at the University of Tokyo have discovered a new group of proteins, remarkable for their unusual shape and abilities to protect against protein clumps associated with neurodegenerative diseases in lab experiments.

Designer proteins
David Baker, Professor of Biochemistry at the University of Washington to speak at the AAAS 2020 session, 'Synthetic Biology: Digital Design of Living Systems.' Prof.

Gone fishin' -- for proteins
Casting lines into human cells to snag proteins, a team of Montreal researchers has solved a 20-year-old mystery of cell biology.

Coupled proteins
Researchers from Heidelberg University and Sendai University in Japan used new biotechnological methods to study how human cells react to and further process external signals.

Understanding the power of honey through its proteins
Honey is a culinary staple that can be found in kitchens around the world.

Read More: Proteins News and Proteins Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.