Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Computational Biochemist Uncovers a Molecular Clue to Evolution

11.09.2008
A Florida State University researcher who uses high-powered computers to map the workings of proteins has uncovered a mechanism that gives scientists a better understanding of how evolution occurs at the molecular level.

Such an understanding eventually could lead to the development of new and more effective antiparasitic drugs.

Wei Yang is an assistant professor in FSU’s Department of Chemistry and Biochemistry and a faculty member in the university’s Institute of molecular biophysics. Working with colleagues from FSU, Duke University and Brandeis University, he recently produced remarkable computer models of an enzyme that carries the unwieldy name of inosine monophosphate dehrydrogenase, or IMPDH for short. IMPDH is responsible for initiating certain metabolic processes in DNA and RNA, enabling the biological system to reproduce quickly.

“In creating these simulations of IMPDH, we observed something that hadn’t been seen before,” Yang said. “Previously, enzymes were believed to have a single ‘pathway’ through which they deliver catalytic agents to biological cells in order to bring about metabolic changes. But with IMPDH, we determined that there was a second pathway that also was used to cause these chemical transformations. The second pathway didn’t operate as efficiently as the first one, but it was active nevertheless.”

... more about:
»Evolution »Molecular »Yang »enzyme

Why would an enzyme have two pathways dedicated to the same task? Yang and his colleagues believe that the slower pathway is an evolutionary vestige left over from an ancient enzyme that evolved over eons into modern-day IMPDH.

The finding is significant for several reasons, Yang said.

“First of all, this offers a rare glimpse of evolutionary processes at work on the molecular level,” Yang said. “Typically when we talk about evolution, we’re referring to a process of adaptation that occurs in a population of organisms over an extended period of time. Our research examines such adaptations at the most basic level, which helps scientists to develop a fuller picture of how evolution actually occurs.

“This also represents a big step forward in our efforts to create computational simulations of biological processes,” Yang said. “In this case, we first made a prediction of the enzyme structure via computer and later verified it through direct observation in a laboratory, rather than the other way around. This is a most unusual accomplishment, and one that indicates we are becoming more advanced in our ability to answer questions relating to biological functions at the molecular level.”

“Because of the key role that IMPDH plays, scientists have focused on developing new antiparasitic drugs that target it,” Yang said. “Our research will certainly contribute to this process.”

Joseph Schlenoff, the chairman of FSU’s Department of Chemistry and Biochemistry, praised Yang’s computational methods as “extremely powerful because they are rigorous, make few assumptions and approximate the complexity of the real world. The accurate predictions that result represent success that has been promised to us for so long by scientists using computers.”

Collaborating with Yang on the project were Gavin J.P. Naylor, an associate professor in FSU’s Department of Scientific Computing; Donghong Min, a postdoctoral associate in the Institute of Molecular Physics; Hongzhi Li, a former postdoc in the Institute of Molecular Physics; Clemens Lakner, a graduate assistant in the Department of Biological Science; David Swofford, a research scientist at Duke University and former FSU faculty member; Lizbeth Hedstrom, a professor of biochemistry at Brandeis University; and postdocs Helen R. Josephine and Iaian S. MacPherson, both of Brandeis.

Together the researchers wrote about their findings in a paper, “An Enzymatic Atavist Revealed in Dual Pathways for Water Activation,” that was published this summer in PLoS Biology, a peer-reviewed, open-access journal published by the Public Library of Science. Visit http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0060206 to read the paper.

Dan Herschlag, a professor of biochemistry at Stanford University, edited the paper for PLoS Biology. He praised it for its innovative approach.

“This work reveals basic aspects of how enzymes work and how they have evolved,” Herschlag said. “The study melds experiment and computation in a powerful fashion and represents a model for how to use interdisciplinary research to answer important questions.”

Wei Yang | Newswise Science News
Further information:
http://ww.fsu.edu

Further reports about: Evolution Molecular Yang enzyme

More articles from Life Sciences:

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

nachricht Pollen taxi for bacteria
18.07.2018 | Technische Universität München

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

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....

Im Focus: Chemical reactions in the light of ultrashort X-ray pulses from free-electron lasers

Ultra-short, high-intensity X-ray flashes open the door to the foundations of chemical reactions. Free-electron lasers generate these kinds of pulses, but there is a catch: the pulses vary in duration and energy. An international research team has now presented a solution: Using a ring of 16 detectors and a circularly polarized laser beam, they can determine both factors with attosecond accuracy.

Free-electron lasers (FELs) generate extremely short and intense X-ray flashes. Researchers can use these flashes to resolve structures with diameters on the...

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

NYSCF researchers develop novel bioengineering technique for personalized bone grafts

18.07.2018 | Life Sciences

Machine-learning predicted a superhard and high-energy-density tungsten nitride

18.07.2018 | Materials Sciences

Why might reading make myopic?

18.07.2018 | Health and Medicine

VideoLinks
Science & Research
Overview of more VideoLinks >>>