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 Decoding the genome's cryptic language
27.02.2017 | University of California - San Diego

nachricht New risk factors for anxiety disorders
24.02.2017 | Julius-Maximilians-Universität Würzburg

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Safe glide at total engine failure with ELA-inside

On January 15, 2009, Chesley B. Sullenberger was celebrated world-wide: after the two engines had failed due to bird strike, he and his flight crew succeeded after a glide flight with an Airbus A320 in ditching on the Hudson River. All 155 people on board were saved.

On January 15, 2009, Chesley B. Sullenberger was celebrated world-wide: after the two engines had failed due to bird strike, he and his flight crew succeeded...

Im Focus: Breakthrough with a chain of gold atoms

In the field of nanoscience, an international team of physicists with participants from Konstanz has achieved a breakthrough in understanding heat transport

In the field of nanoscience, an international team of physicists with participants from Konstanz has achieved a breakthrough in understanding heat transport

Im Focus: DNA repair: a new letter in the cell alphabet

Results reveal how discoveries may be hidden in scientific “blind spots”

Cells need to repair damaged DNA in our genes to prevent the development of cancer and other diseases. Our cells therefore activate and send “repair-proteins”...

Im Focus: Dresdner scientists print tomorrow’s world

The Fraunhofer IWS Dresden and Technische Universität Dresden inaugurated their jointly operated Center for Additive Manufacturing Dresden (AMCD) with a festive ceremony on February 7, 2017. Scientists from various disciplines perform research on materials, additive manufacturing processes and innovative technologies, which build up components in a layer by layer process. This technology opens up new horizons for component design and combinations of functions. For example during fabrication, electrical conductors and sensors are already able to be additively manufactured into components. They provide information about stress conditions of a product during operation.

The 3D-printing technology, or additive manufacturing as it is often called, has long made the step out of scientific research laboratories into industrial...

Im Focus: Mimicking nature's cellular architectures via 3-D printing

Research offers new level of control over the structure of 3-D printed materials

Nature does amazing things with limited design materials. Grass, for example, can support its own weight, resist strong wind loads, and recover after being...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Booth and panel discussion – The Lindau Nobel Laureate Meetings at the AAAS 2017 Annual Meeting

13.02.2017 | Event News

Complex Loading versus Hidden Reserves

10.02.2017 | Event News

International Conference on Crystal Growth in Freiburg

09.02.2017 | Event News

 
Latest News

New pop-up strategy inspired by cuts, not folds

27.02.2017 | Materials Sciences

Sandia uses confined nanoparticles to improve hydrogen storage materials performance

27.02.2017 | Interdisciplinary Research

Decoding the genome's cryptic language

27.02.2017 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>