Statistics are insufficient for study of proteins' signal system

Mar 26, 2008

Ten years ago great attention was attracted by the discovery that it was possible to demonstrate signal transfer in proteins using statistical methods. In an article in the journal Proceedings of the National Academy of Science Uppsala researchers are now presenting results of experiments that contradict the theory.

Proteins govern nearly all chemical processes in the body's cells. A fundamental property of proteins is their ability to transfer signals – both within and between proteins. It is known, for example, that such signal transfer is vital to haemoglobin, which transports oxygen in the body. In that instance the mechanism has largely been clarified.

"But in other instances very little is known about the mechanisms or whether such signal transfer even occurs," says Per Jemth, who together with his research group at Uppsala University is studying whether signal transfer also occurs in small proteins.

Nearly ten years ago great attention was attracted by an article published in Science that described a method of demonstrating signal transfer in proteins by comparing their amino acid sequence. The authors recorded a statistical method of showing how certain parts of proteins change together through evolution, i.e. if a change had taken place in one part a change simultaneously took place in another part of the protein. One thus found a network of parts that seemed to belong together, and within this network signal transfer was deemed to take place.

But the Uppsala researchers saw several things that were not right about the results in the much discussed article, and by means of experiments they can now show that no more signals occur in this network than with other parts of the protein. They instead found, completely logically, that nearby parts of the protein interact more with each other than parts that are a long way apart.

"Our results thus question whether statistical methods can demonstrate signal transfer within proteins, and emphasise the importance of precise experiments to substantiate computer-based methods in protein chemistry," says Per Jemth.

The ability to predict proteins' function down to the smallest detail on the basis of their amino acid sequence is a goal that has preoccupied many researchers ever since human DNA became known. This study emphasises that experiments are needed to improve and refine the computerised methods currently in use.

"When theory, computer simulation and experiments provide the same answers the long-term goal has been attained, but there's still a long way to go."

Source: Uppsala University

Explore further: Researchers develop models to study polyelectrolytes, including DNA and RNA

add to favorites email to friend print save as pdf

Related Stories

New tool identifies therapeutic proteins in a 'snap'

4 hours ago

( —In human and bacterial cells, glycosylation – the chemical process of attaching complex sugar molecules to proteins – is as fundamental as it gets, affecting every biological mechanism from cell signaling ...

Smart gating nanochannels for confined water developed

Jun 25, 2014

Confined water exists widely and plays important roles in natural environments, particularly inside biological nanochannels. Professor Lei Jiang and his group from State Key Laboratory of Organic Solids, ...

Recommended for you

The fluorescent fingerprint of plastics

4 hours ago

LMU researchers have developed a new process which will greatly simplify the process of sorting plastics in recycling plants. The method enables automated identification of polymers, facilitating rapid separation ...

Water and sunlight the formula for sustainable fuel

9 hours ago

An Australian National University (ANU) team has successfully replicated one of the crucial steps in photosynthesis, opening the way for biological systems powered by sunlight which could manufacture hydrogen ...

Rice chemist wins 'Nobel Prize of Cyprus'

9 hours ago

Rice University organic chemist K.C. Nicolaou has earned three prestigious international honors, including the Nemitsas Prize, the highest honor a Cypriot scientist can receive and one of the most prestigious ...

Researchers create engineered energy absorbing material

10 hours ago

( —Materials like solid gels and porous foams are used for padding and cushioning, but each has its own advantages and limitations. Gels are effective as padding but are relatively heavy; gel performance ...

Solar fuels as generated by nature

10 hours ago

( —Society's energy supply problems could be solved in the future using a model adopted from nature. During photosynthesis, plants, algae and some species of bacteria produce sugars and other energy-rich ...

User comments : 0