Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Techniques used to infer pathways of protein evolution found unreliable

11.10.2012
Experimental studies of ancestral visual pigments and their mutational variants cast doubt on simplifying assumptions widely used in evolutionary studies of proteins
A key assumption that biologists have relied on widely over the past quarter-century in studying the evolution of protein molecules is "highly questionable," according to an article published in the November issue of BioScience.

The article, by Shozo Yokoyama, a vision researcher at Emory University, summarizes experimental work that involved creating and measuring the properties of dozens of reconstructed ancestral versions of visual pigments found in the eyes of vertebrates, including humans, as well as deliberately altered variants. Yokoyama concludes that the studies he assessed "cast serious doubt" on the "fundamental principle of molecular adaptation," the bedrock of thousands of published papers based on reconstructions of evolutionary changes in a wide range of proteins. The statistical tools used by such studies are "not reliable," he writes.

In attempting to understand how proteins and their properties might have changed over time, biologists have typically made simplifying assumptions. One is that a known change at a particular spot in a protein would affect the properties of ancestral and modern forms of proteins in similar ways. That simplification makes it relatively easy for computers to infer the likely evolutionary paths that led to the forms of the proteins found in modern organisms—for example, the visual pigments found in deep-sea fishes (which live with no ultraviolet light) and the different pigments found in shallow-water fishes.

Yokoyama tested the assumptions by making the hypothesized ancestral pigments and variants of them that might have been produced by mutation, then accurately measuring their properties. The results were disturbing: the properties of related versions of proteins would often change in very different ways when the same mutation was introduced into each. Consequently, standard computational and statistical methods would rarely have identified the experimentally supported evolutionary pathway. Yokoyama expresses the hope that other researchers will start to make and test the properties of reconstructed ancestral proteins to evaluate hypotheses about their evolution, rather than relying on computational approaches.

BioScience, published monthly, is the journal of the American Institute of Biological Sciences (AIBS; www.aibs.org). BioScience is a forum for integrating the life sciences that publishes commentary and peer-reviewed articles. The journal has been published since 1964. AIBS is a meta-level organization for professional scientific societies and organizations that are involved with biology. It represents nearly 160 member societies and organizations. The article by Yokoyama can be accessed ahead of print at www.aibs.org/bioscience-press-releases/ until early November.

The complete list of peer-reviewed articles in the November, 2012 issue of BioScience is as follows. These are published online ahead of print from 11 October.

Synthesis of Experimental Molecular Biology and Evolutionary Biology: An Example from the World of Vision.

Shozo Yokoyama

Sentinels of Ecological Processes: The Case of the Northern Flying Squirrel.
Winston P. Smith
What Is Conservation Science?
Peter Kareiva and Michelle Marvier
A State-Based National Network for Effective Wildlife Conservation.
Vicky J. Meretsky, Lynn A. Maguire, Frank W. Davis, David M. Stoms, J. Michael Scott, Dennis Figg, Dale D. Goble, Brad Griffith, Scott E. Henke, Jacqueline Vaughn, and Steven L. Yaffee
A Global System for Monitoring Ecosystem Service Change.
Heather Tallis, Hal Mooney, Sandy Andelman, Patricia Balvanera, Wolfgang Cramer, Danny Karp, Stephen Polasky, Belinda Reyers, Taylor Ricketts, Steve Running, Kirsten Thonicke, Britta Tietjen, and Ariane Walz

Tim Beardsley | EurekAlert!
Further information:
http://www.aibs.org

More articles from Life Sciences:

nachricht Cryo-electron microscopy achieves unprecedented resolution using new computational methods
24.03.2017 | DOE/Lawrence Berkeley National Laboratory

nachricht How cheetahs stay fit and healthy
24.03.2017 | Forschungsverbund Berlin e.V.

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Giant Magnetic Fields in the Universe

Astronomers from Bonn and Tautenburg in Thuringia (Germany) used the 100-m radio telescope at Effelsberg to observe several galaxy clusters. At the edges of these large accumulations of dark matter, stellar systems (galaxies), hot gas, and charged particles, they found magnetic fields that are exceptionally ordered over distances of many million light years. This makes them the most extended magnetic fields in the universe known so far.

The results will be published on March 22 in the journal „Astronomy & Astrophysics“.

Galaxy clusters are the largest gravitationally bound structures in the universe. With a typical extent of about 10 million light years, i.e. 100 times the...

Im Focus: Tracing down linear ubiquitination

Researchers at the Goethe University Frankfurt, together with partners from the University of Tübingen in Germany and Queen Mary University as well as Francis Crick Institute from London (UK) have developed a novel technology to decipher the secret ubiquitin code.

Ubiquitin is a small protein that can be linked to other cellular proteins, thereby controlling and modulating their functions. The attachment occurs in many...

Im Focus: Perovskite edges can be tuned for optoelectronic performance

Layered 2D material improves efficiency for solar cells and LEDs

In the eternal search for next generation high-efficiency solar cells and LEDs, scientists at Los Alamos National Laboratory and their partners are creating...

Im Focus: Polymer-coated silicon nanosheets as alternative to graphene: A perfect team for nanoelectronics

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are less stable. Now researchers at the Technical University of Munich (TUM) have, for the first time ever, produced a composite material combining silicon nanosheets and a polymer that is both UV-resistant and easy to process. This brings the scientists a significant step closer to industrial applications like flexible displays and photosensors.

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are...

Im Focus: Researchers Imitate Molecular Crowding in Cells

Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to simulate these confined natural conditions in artificial vesicles for the first time. As reported in the academic journal Small, the results are offering better insight into the development of nanoreactors and artificial organelles.

Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

International Land Use Symposium ILUS 2017: Call for Abstracts and Registration open

20.03.2017 | Event News

CONNECT 2017: International congress on connective tissue

14.03.2017 | Event News

ICTM Conference: Turbine Construction between Big Data and Additive Manufacturing

07.03.2017 | Event News

 
Latest News

Argon is not the 'dope' for metallic hydrogen

24.03.2017 | Materials Sciences

Astronomers find unexpected, dust-obscured star formation in distant galaxy

24.03.2017 | Physics and Astronomy

Gravitational wave kicks monster black hole out of galactic core

24.03.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>