PRESS-NEWS.org - Press Release Distribution
PRESS RELEASES DISTRIBUTION

Structural genomics accelerates protein structure determination

New strategy sheds light on membrane protein structure

2010-10-28
(Press-News.org) Proteins are molecular machines that transport substances, catalyze chemical reactions, pump ions, and identify signaling substances. They are chains of amino acids and the individual amino acid sequence is known for many of them. However, the functions a protein can carry out inside the cell are determined by the three-dimensional spatial structure of the protein. Establishing this so-called tertiary structure presents a great challenge to scientists. There is, thus, a lot of catching up to be done in structure analysis. To push progress, the National Institute of General Medical Sciences (NIGMS) of the USA National Institutes of Health (NIH) has invested over 500 million dollars in this field over the last ten years as part of the Protein Structure Initiative with the hope of making significant progress in medicine and biological research.

Informatics professor Burkhard Rost and Marco Punta, Carl von Linde Junior Fellow at the Institute for Advanced Study (IAS) of the TU München, are involved in this large-scale project. They are affiliated with the New York Consortium on Membrane Protein Structure (NYCOMPS), which is among nine funded membrane research centers. The NYCOMPS scientists put a special emphasis on membrane proteins. That is because they play a key role in pharmacological research. When a pharmaceutical agent enters the cell, it normally interacts first with membrane proteins. Knowing the protein structure is essential to understanding this interaction at the molecular level.

However, in the case of these very important membrane proteins, experimentally deciphering the tertiary structure is particularly difficult. For example the recombinant production of many membrane proteins is a major challenge and purification and crystallization are also difficult steps. The result: although around 25 percent of all proteins are membrane proteins, they account for less than one percent of the total number of proteins with known structures. Membrane protein structures are thus underrepresented 25-fold. Given their medical relevance, they should be much better known.

Since the experimental analysis of a membrane protein can take up to several years, the NYCOMPS scientists applied a bioinformatics strategy, the so-called homology modeling. The basic assumption of this strategy is that proteins with common evolutionary predecessors resemble each other in their amino acid sequences, as well as in their three-dimensional structure. If the structure of one of the related proteins can be determined experimentally, the remaining ones can be predicted.

In the case of the bacterial membrane protein TehA they could bring all pieces of the puzzle together. "In a screening procedure we searched for TeHA-related membrane proteins by comparing tens of thousands of amino acid sequences. Using a multistage selection process we chose 43 proteins from 38 different organisms," says TUM computational biologist Marco Punta.

Scientists at Columbia University now succeeded in experimentally determining the tertiary structure of the membrane protein TehA of the bacterium Haemophilus influenzae using X-ray crystallography. With a resolution of 0.12 nanometers (1.2 Ångstrøm), this structure is among the best crystal structures ever obtained for a membrane protein. Furthermore, the experiment harbored a surprise: The TehA membrane protein has a hitherto entirely unknown fold.

After getting to know the "TehA family," the scientists at Columbia University succeeded in deriving the structures of the individual proteins. In particular, they modeled the structure of the plant membrane protein SLAC1. Comparing this to the protein structure of TehA derived experimentally, they could build a structural model for SLAC1 – entirely without experimentation, using nothing but bioinformatics methods.

"Using this procedure we aim to have a high structure determination throughput rate. determining more protein structures in a shorter time – that was our goal, in particular for the membrane proteins. The results at hand show that this strategy can work for membrane proteins, too," says Burkhard Rost.

Ultimately, the three-dimensional structures are determined to identify the function of the proteins using mutagenesis tests. Although the membrane proteins TehA and SLAC1 are only distantly related – the overlap of the amino acid sequence is only 19 percent – the predicted tertiary structure of SLAC1 was so good that a new hypothesis on the function of the SLAC1 membrane protein could be put forward.

SLAC1 is found in the stomata of the plant Arabidopsis thaliana. Stomata control the exchange of water vapor and carbon dioxide between the plant and its environment. This is very important in photosynthesis. The membrane protein SLAC1 plays a role in this process, as well, as part of the anion channel: It influences the turgor pressure – the pressure of cell fluid on the cell wall – and thus the gas exchange of the plant cell as a reaction to environmental influences such as aridity and high carbon dioxide concentration.

SLAC1 anion channels are entirely novel in structure and, apparently, in the mechanism for ion conductance. The SLAC1 pore has a relatively uniform diameter, but in the middle a Phenylalanine-group blocks the way. The results suggest that this amino acid is turned away when the ion channel is activated through binding of a triggering protein.

INFORMATION:

END



ELSE PRESS RELEASES FROM THIS DATE:

NOAA: Tagged narwhals track warming near Greenland

2010-10-28
In a research paper published online Saturday in the Journal of Geophysical Research Oceans, a publication of the American Geological Union (AGU), scientists reported the southern Baffin Bay off West Greenland has continued warming since wintertime ocean temperatures were last effectively measured there in the early 2000s. Temperatures in the study were collected by narwhals, medium-sized toothed Arctic whales, during NOAA-sponsored missions in 2006 and 2007. The animals were tagged with sensors that recorded ocean depths and temperatures during feeding dives from the ...

Researchers find a 'liberal gene'

2010-10-28
Liberals may owe their political outlook partly to their genetic make-up, according to new research from the University of California, San Diego, and Harvard University. Ideology is affected not just by social factors, but also by a dopamine receptor gene called DRD4. The study's authors say this is the first research to identify a specific gene that predisposes people to certain political views. Appearing in the latest edition of The Journal of Politics published by Cambridge University Press, the research focused on 2,000 subjects from The National Longitudinal Study ...

Deadly monkeypox virus might cause disease by breaking down lung tissue

Deadly monkeypox virus might cause disease by breaking down lung tissue
2010-10-28
RICHLAND, Wash. -- A new study of an exotic, infectious virus that has caused three recent outbreaks in the United States reveals clues to how the virus might damage lungs during infection. The findings also suggest possible new ways to treat lung diseases in humans. Not only does the infection from monkeypox virus increase production of proteins involved in inflammation, but it decreases production of proteins that keep lung tissue intact and lubricated. The findings appear in an upcoming issue of Molecular & Cellular Proteomics. "Going into this study, we thought ...

Exposure to BPA associated with reduced semen quality

2010-10-28
Oakland, Calif.(October 28, 2010) — Increasing urine BPA (Bisphenol-A) level was significantly associated with decreased sperm concentration, decreased total sperm count, decreased sperm vitality and decreased sperm motility, according to a Kaiser Permanente study appearing in the journal of Fertility and Sterility. The five-year study recruited 514 workers in factories in China and compared workers who had high urine BPA levels with those with low urine BPA. Men with higher urine BPA levels had 2-4 times the risk of having poor semen quality, including low sperm concentration, ...

New study suggests most preschool-age children exceed daily screen time recommendations

2010-10-28
Cincinnati, OH, October 28, 2010 -- The American Academy of Pediatrics (AAP) recommends that parents limit combined screen time from television, DVDs, computers, and video games to 2 hours per day for preschool-age children. In a study soon to be published in The Journal of Pediatrics, researchers found that many children are exposed to screen time both at home and while at child care, with 66% exceeding the recommended daily amount. According to Dr. Pooja Tandon, "A majority of children under the age of 5 years in the United States spend almost 40 hours a week with ...

Many male cancer patients are missing out on sperm banking

2010-10-28
Many men – whose fertility may be at risk from cancer treatment – are not being offered the chance to store their sperm according to new research published today in the Annals of Oncology (Thursday). Guidelines from the National Institute for Health and Clinical Excellence (NICE) state that any men or adolescent boys who are receiving treatment that may leave them infertile should be offered the opportunity to store their sperm. But in a study funded by Cancer Research UK, researchers at the University of Warwick and University Hospitals Coventry and Warwickshire NHS ...

iViZ, leading on-demand security testing company, partners with Imaginet International Inc. in the Philippines

2010-10-28
iViZ Security, pioneers in on-demand penetrating testing solution in the world, announced their entry into the Phillippines market with its strategic partnership with Imaginet International Inc., a leading IT Systems Integrator and managed service provider. This partnership will also cater to companies and clients all over the Asia Pacific region. Today, companies find it increasingly challenging to manage information security to protect themselves from hackers. This is made severe by the alarmingly large number of new vulnerabilities discovered every year. In 2008 alone, ...

Kitchen Incubator Launches the First Center for Culinary Entrepreneurship in Texas

2010-10-28
Kitchen Incubator, A Center for Culinary Entrepreneurship, opened its doors on October 16 as part of downtown's "A Night in Market Square." The first of it's kind in Texas, Kitchen Incubator ("Kitchen Inc") combines commercial kitchens for rent with a unique multi-chef cafe, cooking school and culinary event venue. An extravagant grand opening, Kitchen Inc celebrated with a full day of chef demonstrations and tastings, an edible artisan market and culinary crafts. Over 1,000 guests were estimated to have attended the event throughout the evening. Prior to settling in ...

No Slippy Hair Clippy Launches Affiliate Program

2010-10-28
No Slippy Hair Clippy, creator of the world's first and finest no-slip clip for girls of all ages, is launching its Affiliate Program on October 28, 2010. The No Slippy Hair Clippy Affiliate Program offers website owners, bloggers and online entrepreneurs a quick and easy way to earn extra income, while helping to make the world prettier one girl at a time. No Slippy Hair Clippy Affiliates will earn 15% commission on all online sales made through affiliate links they place on their sites. They also get to enjoy exclusive privileges such as a 90-day return cookie, cutting-edge ...

Update on Venezuela Gold Mining: Eldora Gold Resources Canada News

2010-10-28
Update on Venezuela Gold Mining: Eldora Gold Resources Canada News - Uncertainty grips expectant gold-mining communities in Venezuela. Continuing a report on the situation of gold-mining in Bolivar State and in particular on the Las Cristinas mine in Sifontes municipality, Correo del Caroni reporter, Natalie Garcia maintains that the end of the Crystallex concession has reopened the debate on the Venezuelan State's gold-mining policies, which could be said to have failed, given current labor instability and cordons of misery south of Bolivar State. Update on Venezuela ...

LAST 30 PRESS RELEASES:

Mysterious ‘Dark Dwarfs’ may be hiding at the heart of the Milky Way

Real-world data shows teclistamab can benefit many multiple myeloma patients who would have been ineligible for pivotal trial

Scientists reveal how a key inflammatory molecule triggers esophageal muscle contraction

Duration of heat waves accelerating faster than global warming

New mathematical insights into Lagrangian turbulence

Clinical trials reveal promising alternatives to high-toxicity tuberculosis drug

Artificial solar eclipses in space could shed light on Sun

Probing the cosmic Dark Ages from the far side of the Moon

UK hopes to bolster space weather forecasts with Europe's first solar storm monitor

Can one video change a teen's mindset? New study says yes - but there’s a catch

How lakes connect to groundwater critical for resilience to climate change, research finds

Youngest basaltic lunar meteorite fills nearly one billion-year gap in Moon’s volcanic history

Cal Poly Chemistry professor among three U.S. faculty to be honored for contributions to chemistry instruction

Stoichiometric crystal shows promise in quantum memory

Study sheds light on why some prostate tumors are resistant to treatment

Tree pollen reveals 150,000 years of monsoon history—and a warning for Australia’s northern rainfall

Best skin care ingredients revealed in thorough, national review

MicroRNA is awarded an Impact Factor Ranking for 2024

From COVID to cancer, new at-home test spots disease with startling accuracy

Now accepting submissions: Special Collection on Cognitive Aging

Young adult literature is not as young as it used to be

Can ChatGPT actually “see” red? New results of Google-funded study are nuanced

Turning quantum bottlenecks into breakthroughs

Cancer-fighting herpes virus shown to be an effective treatment for some advanced melanoma

Eliminating invasive rats may restore the flow of nutrients across food chain networks in Seychelles

World’s first: Lithuanian scientists’ discovery may transform OLED technology and explosives detection

Rice researchers develop superstrong, eco-friendly materials from bacteria

Itani studying translation potential of secure & efficient software updates in industrial internet of things architectures

Elucidating the source process of the 2021 south sandwich islands tsunami earthquake

Zhu studying use of big data in verification of route choice models

[Press-News.org] Structural genomics accelerates protein structure determination
New strategy sheds light on membrane protein structure