Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

For Determining Protein Structures, A New Method Boosts Precision and Speed in High-Dimensional NMR

10.01.2003


A University at Buffalo chemist has developed a new, high-throughput method for obtaining nuclear magnetic resonance (NMR) data that not only has the distinction of potentially performing orders of magnitude faster than conventional methods, but does so more cheaply and with greater precision.



The new method, described in the current online issue of the Journal of the American Chemical Society, has the potential to increase greatly the use of high-throughput NMR to determine protein structures with the ultimate goal of developing new medicines and treatments.

A patent has been filed on the method and UB is exploring licensing opportunities.


"Our method allows researchers to get the information from their NMR experiments faster, while at the same time increasing accuracy," explained Thomas Szyperski, Ph.D., UB associate professor of chemistry and biochemistry and principal author.

"It’s an important contribution to increasing the competitiveness of NMR relative to X-ray diffraction in structural biology," he said.

It also has the potential to allow scientists to take full advantage of the new, highest-field NMR machines and cryogenic probes, which reduce NMR measurement times by an order of magnitude (factor of 10).

"With this new method, we’ve increased data collection speed by orders of magnitude," said Szyperski. "For example, for the experiment published in JACS, the gain was a factor of 250, while we increased the precision of the frequency measurements three- to four-fold.

"That’s an incredible blend, which will allow us to bring the horsepower of our new ’NMR-Ferraris’ equipped with cryogenic probes on the road."

Szyperski developed the method with Seho Kim, Ph.D., formerly a postdoctoral fellow in Szyperski’s lab, as a member of the Northeast Structural Genomics Consortium, (NESGC) one of nine National Institutes of Health-funded efforts to capitalize on discoveries generated by the human genome project.

UB’s NESGC researchers are affiliated with the Strategically Targeted Academic Research (STAR) Center in Disease Modeling and Therapy Discovery at UB, sponsored by the New York State Office of Science, Technology and Academic Research.

NMR machines use very powerful magnetic fields to determine macromolecular structures. NMR experiments provide "nuclear Overhauser enhancements," or NOE’s, molecular "rulers" that allow researchers to measure distances between protons and use that information to calculate the molecular structure.

To obtain NOEs, scientists first must measure the chemical shifts, or resonance frequencies, of the atomic nuclei, which relate to the environment of each atom’s nucleus. To do so, they perform several NMR spectra experiments with multiple frequency dimensions, in which resonance frequencies are measured and correlated.

According to Szyperski, when using such multidimensional NMR, the approach scientists use for determining protein structures, it is necessary to run many such experiments with higher dimensions (higher than 2D) to measure and correlate frequencies.

"Ultimately, you want a resonance assignment for each nucleus in each atom," explained Szyperski. "So for every protein, you need to have and correlate thousands of resonance frequencies.

"The drawback is that for each additional dimension you do, the data collection takes about one or two orders of magnitude longer," he said.

For example, he explained, if two-dimensional experiments take at least several minutes, then three-dimensional experiments take several hours, four-dimensional experiments take several days and five- or six-dimensional experiments would take months or years.

"The minimum measurement times explode when the dimensions are increased," said Szyperski. "That is why five- or higher-dimensional NMR experiments never have been recorded."

At the same time, he noted, the accuracy of the measurement of the resonance frequencies obtained by these long measurement times still is not very high.

Szyperski’s method, called GFT NMR, for G-matrix Fourier Transform NMR, beats both drawbacks of multidimensional NMR: the long intrinsic measurement times and the low accuracy of the frequency measurements.

GFT NMR uses a G-matrix, which represents a system of linear equations, in conjunction with Fourier Transform, the mathematical operation used to process multidimensional NMR spectra.

"We record larger numbers of low-dimensional NMR spectra and using the G-matrix we can linearly combine them to retain the information of the high-dimensional experiment," said Szyperski. "This way, we can sample spectra much more rapidly and get not the resonance frequencies themselves, but multiple sums and differences of them, which gives us higher precision.

"With GFT NMR, you can record a five- or six-dimensional experiment in about an hour or even less -- all because your measurement times increase linearly, not exponentially -- with the number of dimensions you are involving," said Szyperski.

Used for proteins since the mid-1980s, NMR has been responsible for determining about 20 percent of the structures in the Protein Data Bank, the international repository of solved protein structures, whereas the other technique, X-ray diffraction, in use since 1962 for proteins, has determined 80 percent.

"In terms of maturity, you could say we’re about 22 years behind X-ray diffraction when it comes to solving protein structures," Szyperski admitted.

However, he added, the combination of much more powerful 900 megahertz magnets now coming online, such as the new one at the New York Structural Biology Center, to which UB researchers will have access, and new techniques, such as his, is ushering in a new era for NMR determination of proteins.

"Our approach will allow scientists to take full advantage of the highest-field NMR machines, without having to sample many high-dimensional spectra," said Szyperski.

New cryogenic probes, such as the one that UB will be receiving in the spring, supported by both the NIH grant to the NESGC and UB funds, will provide additional speed for NMR experiments.

In collaboration with Gaetano T. Montelione, Ph.D., of Rutgers University, and principal investigator on the NESGC, Szyperski is planning to develop a software package that will expedite the calculations required when using GFT NMR experiments to produce protein structures.

Ellen Goldbaum | EurekAlert!
Further information:
http://www.buffalo.edu/news/fast-execute.cgi/article-page.html?article=60200009

More articles from Life Sciences:

nachricht Scientists uncover the role of a protein in production & survival of myelin-forming cells
19.07.2018 | Advanced Science Research Center, GC/CUNY

nachricht NYSCF researchers develop novel bioengineering technique for personalized bone grafts
18.07.2018 | New York Stem Cell Foundation

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Future electronic components to be printed like newspapers

A new manufacturing technique uses a process similar to newspaper printing to form smoother and more flexible metals for making ultrafast electronic devices.

The low-cost process, developed by Purdue University researchers, combines tools already used in industry for manufacturing metals on a large scale, but uses...

Im Focus: First evidence on the source of extragalactic particles

For the first time ever, scientists have determined the cosmic origin of highest-energy neutrinos. A research group led by IceCube scientist Elisa Resconi, spokesperson of the Collaborative Research Center SFB1258 at the Technical University of Munich (TUM), provides an important piece of evidence that the particles detected by the IceCube neutrino telescope at the South Pole originate from a galaxy four billion light-years away from Earth.

To rule out other origins with certainty, the team led by neutrino physicist Elisa Resconi from the Technical University of Munich and multi-wavelength...

Im Focus: Magnetic vortices: Two independent magnetic skyrmion phases discovered in a single material

For the first time a team of researchers have discovered two different phases of magnetic skyrmions in a single material. Physicists of the Technical Universities of Munich and Dresden and the University of Cologne can now better study and understand the properties of these magnetic structures, which are important for both basic research and applications.

Whirlpools are an everyday experience in a bath tub: When the water is drained a circular vortex is formed. Typically, such whirls are rather stable. Similar...

Im Focus: Breaking the bond: To take part or not?

Physicists working with Roland Wester at the University of Innsbruck have investigated if and how chemical reactions can be influenced by targeted vibrational excitation of the reactants. They were able to demonstrate that excitation with a laser beam does not affect the efficiency of a chemical exchange reaction and that the excited molecular group acts only as a spectator in the reaction.

A frequently used reaction in organic chemistry is nucleophilic substitution. It plays, for example, an important role in in the synthesis of new chemical...

Im Focus: New 2D Spectroscopy Methods

Optical spectroscopy allows investigating the energy structure and dynamic properties of complex quantum systems. Researchers from the University of Würzburg present two new approaches of coherent two-dimensional spectroscopy.

"Put an excitation into the system and observe how it evolves." According to physicist Professor Tobias Brixner, this is the credo of optical spectroscopy....

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

Leading experts in Diabetes, Metabolism and Biomedical Engineering discuss Precision Medicine

13.07.2018 | Event News

Conference on Laser Polishing – LaP: Fine Tuning for Surfaces

12.07.2018 | Event News

11th European Wood-based Panel Symposium 2018: Meeting point for the wood-based materials industry

03.07.2018 | Event News

 
Latest News

A smart safe rechargeable zinc ion battery based on sol-gel transition electrolytes

20.07.2018 | Power and Electrical Engineering

Reversing cause and effect is no trouble for quantum computers

20.07.2018 | Information Technology

Princeton-UPenn research team finds physics treasure hidden in a wallpaper pattern

20.07.2018 | Materials Sciences

VideoLinks
Science & Research
Overview of more VideoLinks >>>