Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Scripps Research team uncovers chemical basis for extra 'quality control' in protein production

11.12.2009
Nature's solution to age-old chemical paradox provides clues to health and disease

Even small errors made by cells during protein production can have profound disease effects, and nature has developed ways to uncover these mistakes and correct them. Though in the case of one essential protein building block—the amino acid alanine—nature has been extra careful, developing not one, but two checkpoints in her effort to make sure that this component is used correctly.

Now, scientists at The Scripps Research Institute have discovered the chemical basis for why these extraordinary efforts are necessary. The work was published in the December 10, 2009 issue of the prestigious journal Nature.

"What is shown here with the 'serine paradox' is just the tip of the iceberg," said senior author Paul Schimmel, who is the Ernest and Jean Hahn Professor and Chair of Molecular Biology and Chemistry and a member of The Skaggs Institute for Chemical Biology at Scripps Research. "In the coming years, there will be an increasing awareness of the role of mistranslation in human diseases and of how nature has struggled to find solutions to attenuate mistranslation and its consequences."

Spelling with Amino Acids and Proofreading for Errors

As letters of the alphabet spell out words, when amino acids are linked to one another in a particular order they "spell out" proteins. When amino acids are put in the wrong order, "spelling errors" (mistranslations) occur, often with devastating consequences for the health of the organism.

Normally, small RNA molecules, called transfer RNAs (tRNAs), transport specific amino acids to the ribosomes, the protein factories of cells, so that amino acids can be added to their correct place in a growing chain. At the beginning of this process, 20 tRNA enzymes, one for each of the 20 common amino acids, select the proper amino acid to be transported by a tRNA and join them together.

However, as Senior Research Associate Min Guo of the Schimmel-Yang lab, who is first author of the new paper, noted, "Sometimes there are mistakes. Where there is supposed to be alanine, there is a serine or glycine instead."

In 2006, the Schimmel-Yang lab contributed to research led by the Ackerman group at Jackson Laboratories that showed the consequences of this particular mistake in protein building for a strain of mutant mice. When the enzyme that adds the amino acid alanine to tRNAs—called alanyl-tRNA synthetase (AlaRS)—mischarges its tRNA (tRNA Ala), the error leads to the accumulation of misfolded proteins and the mice display severe neurological and other defects. Another study by the Schimmel-Yang lab showed that E. coli bacteria with a similar mutation become very sensitive to serine and glycine, dying when these amino acids (but not others) are added to the culture.

Clearly, nature has a vested interest in avoiding such costly errors.

In fact, the Schimmel-Yang group showed in a Nature and a Science paper published in January 2008 and August 2009, respectively, that nature plays it extra safe with the quality control of alanine in protein production. Alanine's tRNA synthetase, AlaRS, not only loads the tRNA with an amino acid, but also checks to make sure it attached the right one. In addition, many organisms, from bacteria to humans, have an extra freestanding "spellchecker" molecule—in the form of a protein called AlaXp—to ensure that alanine is not confused with other amino acids.

"The editing function is redundant," said Guo. "This leads to several questions: Why are the cells so sensitive to alanine mistakes in particular? Why did AlaXps evolve so early? And why are redundant proteins still present that you supposedly don't need?"

A Case of Mistaken Identity

In the new Nature paper, the scientists used a variety of techniques, including x-ray cryatallography and kinetic and mutational analysis, to answer these questions.

The results showed that one reason for the difficulty AlaRS has in distinguishing alanine from serine and glycine is that the active site on the AlaRS molecule is a large, flexible pocket. Instead of acting as a rigid lock for a single key, the cavity flexes to hold not only its target alanine, but also similar-size molecules serine and glycine.

But serine and glycine are not exactly the same size as alanine. That's where the "serine paradox" comes in. Glycine is smaller and serine is larger than alanine. Current theory would not predict that molecules that are both larger and smaller than alanine would be a problem for AlaRS.

"The reason we call it a paradox is because none of the other tRNA synthesases have a problem mis-activating both a smaller and a bigger amino acid," said Guo. "Theoretically, the tRNA synthesases should have the most problem recognizing a smaller amino acid, because a smaller one can also go into the binding pocket. The smaller one is easy to understand. Now we explain the bigger one."

Unexpectedly, the new study's results also revealed that within AlaRS's binding pocket the acidic group of Asp235 creates an extra hydrogen bond with the larger serine molecule. This additional bond turns out to be the major force that helps to secure the misplaced serine in the pocket, despite its larger size. However, x-ray analysis showed that Asp235 is also critical for holding the amino group of alanine. Attempts by the Schimmel-Yang lab (and also most likely by eons of evolution) to replace Asp235 with another residue failed. In fact, the scientists found that to make a change that would eliminate the interaction with serine would also impact negatively on the interaction with the correct amino acid, alanine. So, nature developed another solution by creating AlaXp, which is specifically designed to provide a second check and eliminate any serine that is attached to tRNA (Ala).

Together, AlaRS's large, flexible pocket and the additional hydrogen bond with serine explain the chemical basis for frequent confusion of glycine and serine for alanine and the need for additional checks to make sure that alanine, not one of its look-alikes, is incorporated into a protein when called for.

"Now we can understand why nature takes so much effort to invent two editing checkpoints," said Guo. "That's what is necessary to have the correct sequence of amino acids in a protein. To me, it's amazing that a single chemical feature can determine the fate of almost every organism on earth. Organisms from bacteria to humans share the same biological solution that nature found to this critical chemical problem."

In addition to Schimmel and Guo, authors of the paper are Yeeting E. Chong, Ryan Shapiro, Kirk Beebe, and Xiang-Lei Yang, all of Scripps Research.

This work was supported by a grant from the National Institutes of Health and by a fellowship from the National Foundation for Cancer Research.

About The Scripps Research Institute

The Scripps Research Institute is one of the world's largest independent, non-profit biomedical research organizations, at the forefront of basic biomedical science that seeks to comprehend the most fundamental processes of life. Scripps Research is internationally recognized for its discoveries in immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune, cardiovascular, and infectious diseases, and synthetic vaccine development. Established in its current configuration in 1961, it employs approximately 3,000 scientists, postdoctoral fellows, scientific and other technicians, doctoral degree graduate students, and administrative and technical support personnel. Scripps Research is headquartered in La Jolla, California. It also includes Scripps Florida, whose researchers focus on basic biomedical science, drug discovery, and technology development.

Keith McKeown | EurekAlert!
Further information:
http://www.scripps.edu

Further reports about: AlaXp Asp235 Nature Immunology RNA amino acid amino acid alanine synthetic biology

More articles from Life Sciences:

nachricht A Map of the Cell’s Power Station
18.08.2017 | Albert-Ludwigs-Universität Freiburg im Breisgau

nachricht On the way to developing a new active ingredient against chronic infections
18.08.2017 | Deutsches Zentrum für Infektionsforschung

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Fizzy soda water could be key to clean manufacture of flat wonder material: Graphene

Whether you call it effervescent, fizzy, or sparkling, carbonated water is making a comeback as a beverage. Aside from quenching thirst, researchers at the University of Illinois at Urbana-Champaign have discovered a new use for these "bubbly" concoctions that will have major impact on the manufacturer of the world's thinnest, flattest, and one most useful materials -- graphene.

As graphene's popularity grows as an advanced "wonder" material, the speed and quality at which it can be manufactured will be paramount. With that in mind,...

Im Focus: Exotic quantum states made from light: Physicists create optical “wells” for a super-photon

Physicists at the University of Bonn have managed to create optical hollows and more complex patterns into which the light of a Bose-Einstein condensate flows. The creation of such highly low-loss structures for light is a prerequisite for complex light circuits, such as for quantum information processing for a new generation of computers. The researchers are now presenting their results in the journal Nature Photonics.

Light particles (photons) occur as tiny, indivisible portions. Many thousands of these light portions can be merged to form a single super-photon if they are...

Im Focus: Circular RNA linked to brain function

For the first time, scientists have shown that circular RNA is linked to brain function. When a RNA molecule called Cdr1as was deleted from the genome of mice, the animals had problems filtering out unnecessary information – like patients suffering from neuropsychiatric disorders.

While hundreds of circular RNAs (circRNAs) are abundant in mammalian brains, one big question has remained unanswered: What are they actually good for? In the...

Im Focus: RAVAN CubeSat measures Earth's outgoing energy

An experimental small satellite has successfully collected and delivered data on a key measurement for predicting changes in Earth's climate.

The Radiometer Assessment using Vertically Aligned Nanotubes (RAVAN) CubeSat was launched into low-Earth orbit on Nov. 11, 2016, in order to test new...

Im Focus: Scientists shine new light on the “other high temperature superconductor”

A study led by scientists of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) at the Center for Free-Electron Laser Science in Hamburg presents evidence of the coexistence of superconductivity and “charge-density-waves” in compounds of the poorly-studied family of bismuthates. This observation opens up new perspectives for a deeper understanding of the phenomenon of high-temperature superconductivity, a topic which is at the core of condensed matter research since more than 30 years. The paper by Nicoletti et al has been published in the PNAS.

Since the beginning of the 20th century, superconductivity had been observed in some metals at temperatures only a few degrees above the absolute zero (minus...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Call for Papers – ICNFT 2018, 5th International Conference on New Forming Technology

16.08.2017 | Event News

Sustainability is the business model of tomorrow

04.08.2017 | Event News

Clash of Realities 2017: Registration now open. International Conference at TH Köln

26.07.2017 | Event News

 
Latest News

A Map of the Cell’s Power Station

18.08.2017 | Life Sciences

Engineering team images tiny quasicrystals as they form

18.08.2017 | Physics and Astronomy

Researchers printed graphene-like materials with inkjet

18.08.2017 | Materials Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>