Rules devised for building ideal protein molecules from scratch

ScienceDaily (Nov. 28, 2012) ? By following certain rules, scientists can prepare architectural plans for building ideal protein molecules not found in the real world. Based on these computer renditions, previously non-existent proteins can be produced from scratch in the lab. The principles to make this happen appear this month in Nature magazine.

The lead authors are Dr. Nobuyasu Koga and Dr. Rie Tatsumi-Koga, a husband-and-wife scientific team in Dr. David Baker's lab at the University of Washington Protein Design Institute.

The project benefited from hundreds of thousands of computer enthusiasts around the world who adopted Rosetta@home for simulating designed proteins.

Protein molecules start as an unstable, high energy chain of amino acids. This chain then begins folding into various shapes to try to achieve a stable, low energy state. The end result is its distinctive molecular structure. Rosetta@home volunteers helped the project team to plot this energy landscape from protein structure predictions.

"The structural options become fewer as the interactions that stabilize the protein selectively favor one folding pattern over others," explained Koga.

"This decline in conformation options to eventually achieve a unique, ordered structure is called a funnel-shaped energy landscape," he said, drawing a tornado-like figure on a whiteboard. The researchers came up with guidelines for robustly generating this type of energy landscape.

According to Tatsumi-Koga, these rules require the interactions among the residues in the protein's amino acid chain to consistently favor the same folded conformation in forming its molecular shape. This is made possible, for example, by defining whether a specific unit will form a "right-handed" orientation or its mirror image, and disfavor others.

The researchers, she said, synthesized the proteins they had originally designed and tested "in silico" (on the computer) and physically characterized them through "in vitro" (laboratory test tube) experiments.

They also compared the molecular structures of the computer models with these laboratory-derived proteins to see how well they matched.

Koga stressed that the project looked strictly at protein structure. He smiled as he said his group was striving toward a "platonic ideal," a reference to Plato's theory of perfect forms.

In our imperfect material world, proteins are not always optimized for their stability, but can be beset by bulges, kinks, strains, and improperly buried parts. Many diseases arise from protein malformations.

During this project, the researchers achieved a library of five ideal structures, but since filing their report have added several more.

To make them accessible to other scientists, the designs have been deposited in the Research Collaboratory for Structural Bioinformatics and the lab analysis of their chemical structure was put in the Biological Magnetic Resonance Database.

The team was not attempting to create specific new proteins that could carry out particular activities.

However, their design principles and methods, according to their report, should allow the ready creation of a wide range of robust, stable, building blocks for the next generation of engineered functional proteins.

Such proteins would be custom-made for the task, instead of repurposed from proteins with unrelated functions. The hope is that engineered proteins will be useful for drug and vaccine development, especially for formidable viruses like HIV or rapidly changing ones, like the flu.

Proteins designed to exact specifications might also prove therapeutically useful in cleaving mutated genes, and for speeding up chemical reactions important in industry and environmental reclamation.

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Story Source:

The above story is reprinted from materials provided by University of Washington. The original article was written by Leila Gray.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

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Journal Reference:

1. Nobuyasu Koga, Rie Tatsumi-Koga, Gaohua Liu, Rong Xiao, Thomas B. Acton, Gaetano T. Montelione, David Baker. Principles for designing ideal protein structures. Nature, 2012; 491 (7423): 222 DOI: 10.1038/nature11600

Note: If no author is given, the source is cited instead.

Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of ScienceDaily or its staff.

Source: http://feeds.sciencedaily.com/~r/sciencedaily/matter_energy/biochemistry/~3/Q1RqmNvqLVg/121129093949.htm

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PFT: Problem with NFL's year-round Adderall ban

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With 176 games completed, the gap has been cut from seven to two.

After a four-game sweep of our disagreements in Week 11, MDS posted another 3-1 mark in Week 12, making it very interesting over the final five weeks.

This week, we have only one disagreement.? So it?ll be down to one or back to three by Monday.? (I are good at the math.)

Of course, that doesn?t mean we?ll be right on the picks on which we agree.? But we?re doing OK.? MDS was 11-5 for Week 12, and I was 9-7.? For the season, I?m at 112-63-1, a 63.6 percent accuracy rate.? MDS is 110-65-1, which equates to 62.5 percent.

Saints at Falcons

MDS?s take: It sounds crazy to say this about a 5-6 team facing a 10-1 team, but right now the Saints are playing better football than the Falcons. Having said that, I have a hunch the Falcons will turn in their best effort of the season at home against the team that gave them their only loss.

MDS?s pick: Falcons 28, Saints 21.

Florio?s take:? An already contentious rivalry will become even more contentious now that eggs have flown into the Saints bus and former Falcons linebacker Curtis Lofton has declared that his new team, the Saints, don?t regard the rivalry as a rivalry, given that the Saints have won 11 of 13.? With the Falcons closing in on a playoff berth and sensitive about the perception that they can?t win big games at home, it?s time to drop the Saints? mark against the Falcons to 11 of 14.

Florio?s pick:? Falcons 27, Saints 24.

Jaguars at Bills

MDS?s take: Jaguars quarterback Chad Henne has been impressive enough since replacing Blaine Gabbert that I?m tempted to pick the Jags to pull off a home upset. But these are still the Jaguars, and even if Henne has improved the offense, they still have a terrible defense, plus the Bills have a big special teams edge.

MDS?s pick: Bills 27, Jaguars 23.

Florio?s take:? The Jags are riding a rare one-game winning streak.? The Bill are trying to break a not-so-rare one-game losing streak.? Home team gets the advantage, even though the Jaguars are better with Chad Henne at quarterback.

Florio?s pick:? Bills 24, Jaguars 17.

Seahawks at Bears

MDS?s take: This might be the day?s most interesting game, especially if you enjoy watching teams that play tough, physical defense. I think Seattle?s defensive front has the potential to make life a nightmare for Jay Cutler playing behind the Bears? woeful offensive line, and yet the Seahawks have struggled so much away from home that I?m taking the Bears in a close one.

MDS?s pick: Bears 14, Seahawks 13.

Florio?s take:? It?s chicken salad time for the Chicago offensive line, with failed first-round tackle Gabe Carimi being pressed into service at guard.? But Jay Cutler knows how to avoid the pressure and deliver the ball, and the Seahawks still haven?t learned how to win on the road.

Florio?s pick:? Bears 23, Seahawks 13.

Colts at Lions

MDS?s take: The Lions are playing better football than their record suggests, while the Colts are playing worse football than their record suggests. I still think Indianapolis will be a wild card team, but in this game Calvin Johnson will have a huge day against a weak secondary.

MDS?s pick: Lions 31, Colts 20.

Florio?s take:? Assuming that the Lions haven?t folded the tents after a season-crushing Thanksgiving loss, they?ve got the horses to hold off a Colts team that has yet to learn how to win away from Indy consistently.

Florio?s pick:? Lions 27, Colts 20.

Vikings at Packers

MDS?s take: Green Bay had a letdown against the Giants last week, but that won?t happen again. This is the game when the Packers pull ahead of the pack in the NFC wild card race, as well as staying within striking distance of the Bears in the NFC North.

MDS?s pick: Packers 34, Vikings 13.

Florio?s take:? Minnesota has embarked on its long-expected late-season collapse, and the Packers will be extra salty after getting peppered by the Giants.? This one could get ugly.

Florio?s pick:? Packers 34, Vikings 13.

Panthers at Chiefs

MDS?s take: It?s too late for the Panthers to get back in the playoff race, but I do see them going on a little bit of a late-season run. With Cam Newton playing well, they?ll easily win in Kansas City.

MDS?s pick: Panthers 27, Chiefs 9.

Florio?s take:? The Chiefs can?t lose every game the rest of the season, can they?? Carolina is on the road after a Monday night on the road, cramming two rounds of travel into a short week after a game in which they are feeling better about themselves than they should.? The Chiefs, if they don?t win this one, may not win another.? Ever.

Florio?s pick:? Chiefs 20, Panthers 16.

Patriots at Dolphins

MDS?s take: I like a lot about the way the Dolphins are playing, especially defensively. And the Patriots? secondary has a bad tendency to leave receivers wide open, so Ryan Tannehill may have a decent statistical game. But New England?s offense is such a well-oiled machine that I like the Patriots to get into the end zone five or six times.

MDS?s pick: Patriots 38, Dolphins 28.

Florio?s take:? The Dolphins will win if the sprinklers come on again.? And if the are loaded with hydrochloric acid and aimed at the eyes of Tom Brady and Bill Belichick.? Otherwise, advantage Pats.

Florio?s pick:? Patriots 35, Dolphins 24.

Cardinals at Jets

MDS?s take: This is a stinker of a game between two teams with all kinds of problems at the quarterback position, but it says something about how far the Cardinals have sunk that Mark Sanchez is easily the top quarterback in this game.

MDS?s pick: Jets 20, Cardinals 10.

Florio?s take:? It?s easy to assume the Jets will continue their implosion.? The schedule suggests they could win five in a row.? They may not get to 9-7, but 5-7 is looking pretty promising.

Florio?s pick:? Jets 30, Cardinals 17.

49ers at Rams

MDS?s take: I don?t think this game is going to be easy for the 49ers because St. Louis isn?t an easy place to play anymore, but in the end San Francisco just has too much power on both sides of the ball for the Rams to have much of a chance.

MDS?s pick: 49ers 24, Rams 13.

Florio?s take:? They pick up where they left off after five quarters that ended in a tie.? The Rams try to extend their 3-0-1 record in the NFC West.? The Niners are simply a better team with Colin Kaepernick at quarterback.

Florio?s pick:? 49ers 31, Rams 23.

Texans at Titans

MDS?s take: The Titans fired offensive coordinator Chris Palmer this week, as if that will fix anything. The Titans? problems go much deeper than the offensive playcalling, and the Texans ? getting a well deserved three extra days of rest following their back-to-back overtime games the last two weeks ? will look fresh and win this one handily.

MDS?s pick: Texans 41, Titans 20.

Florio?s take:? Yes, before the season I thought the the Titans, who were unexpectedly 9-7 in 2011, were poised to topple the Texans.? It hasn?t happened.? And it won?t happen for the Titans on Sunday, not with the Texans closing in on their second straight playoff berth.

Florio?s pick:? Texans 27, Titans 14.

Buccaneers at Broncos

MDS?s take: The Bucs are thin in the secondary after trading away Aqib Talib and losing Eric Wright to a suspension, and Peyton Manning is the last quarterback you want to face when you?re thin in the secondary. Manning will pick the Bucs? defense apart. The best chance the Bucs have of keeping this game close is to control the ball by running Doug Martin, but in the end Manning will just have too much for Tampa Bay.

MDS?s pick: Broncos 35, Buccaneers 24.

Florio?s take:? With Eric Wright suspended and Aqib Talib long gone, it?ll be a long day for the Bucs? porous pass defense.

Florio?s pick:? Broncos 31, Buccaneers 21.

Steelers at Ravens

MDS?s take: The Steelers need this one, but they?re not going to get it. Without Ben Roethlisberger the Steelers just aren?t a very good team, and I expect the Ravens to earn a big win that helps them pull away in the AFC North.

MDS?s pick: Ravens 23, Steelers 7.

Florio?s take:? With or without Ben Roethlisberger, the Ravens are tough to beat at home.? And even though it would be fitting for the Steelers to win in Baltimore after the Ravens won in Pittsburgh, the Ravens are the better team ? and the Steelers are on the verge of a late-season implosion.? All that?s left is for coach Mike Tomlin to vow to ?unleash hell.?

Florio?s pick:? Ravens 19, Steelers 13.

Browns at Raiders

MDS?s take: Both teams are 3-8, but they?re a different 3-8. The Browns are a 3-8 team that is playing competitive football and has a lot of young guys who look hungry. The Raiders are a 3-8 team that just wrapped up an 0-4 November in which their four losses came by a total of 90 points. The Browns will go into the Black Hole and come out with their first road win of the season.

MDS?s pick: Browns 21, Raiders 17.

Florio?s take:? The Browns are better than their record suggests.? The Raiders are worse.? With Browns players trying to save the job of their head coach (and in turn their own jobs), Cleveland has more incentive to try to emerge with a win.

Florio?s pick:? Browns 17, Raiders 13.

Bengals at Chargers

MDS?s take: The Bengals are rolling and the Chargers are reeling. Marvin Lewis will take another step toward the playoffs while Norv Turner takes another step toward the unemployment line.

MDS?s pick: Bengals 24, Chargers 14.

Florio?s take:? San Diego?s AFC North tour continues, and they wish it wouldn?t.? After losing to the Browns and to the Ravens, a surging Cincinnati team is ready to keep pushing toward their first consecutive playoff appearances in non-strike years.

Florio?s pick:? Bengals 27, Chargers 17.

Eagles at Cowboys

MDS?s take: The Eagles have given up on the season. At this point I don?t think I?d pick them to beat anyone, and I certainly won?t pick them to win on the road against a Cowboys team that still has slim playoff hopes.

MDS?s pick: Cowboys 28, Eagles 20.

Florio?s take:? Philly is in a full-blown free fall.? After seeing them lose to the lowly Panthers, I?m done picking them until next September at the earliest.? The Cowboys aren?t much better, but they?re good enough (and sufficiently healthier) to get it done.

Florio?s pick:? Cowboys 34, Eagles 20.

Giants at Redskins

MDS?s take: The Redskins have done a great job of pulling themselves back into NFC East contention, and if you want to see an interesting playoff race in December you should be rooting for the Redskins to beat the Giants on Monday night. But Robert Griffin III playing so well as a rookie has masked the fact that the Redskins have big problems on both sides of the ball. The Giants will be too much for them.

MDS?s pick: Giants 34, Redskins 17.

Florio?s take:? The Giants have awoken from their slumber.? That may not be enough to contain a streaking RG3 in his Monday night debut.? Forced to make a choice, however, let?s stick with the team that has shown that it still has the ability to periodically play up to its potential.? Especially when it has to.

Florio?s pick:? Giants 31, Redskins 27.

Source: http://profootballtalk.nbcsports.com/2012/11/28/tyler-sashs-adderall-case-highlights-the-problem-with-a-year-round-ban/related/

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Every single Apple ad now unofficially available in an iTunes playlist

Apple has always produced amazing adverts that are often as cool as its products. Thankfully one loyal Apple follower has taken the time to create a YouTube playlist that he claims includes every single television ad that Apple has created. Apple has created a lot of great ads for its products, the playlist contains a massive 485 videos.

YES, EVERY APPLE TV ADS EVER BROADCASTED! There's a lot to discover in the Playlists - Go watch! Ads missing? Let me know.

Who could forget the classic iPod ads featuring dancing silhouettes and rhythmic music, the multitude of ads based on the Mac versus PC war. More recently Apple has focused on features like the iPhone?s ability to take panoramic photographs and of course the ability to access all corners of the screen on the iPhone 5?s larger screen with one hand. Of course not all of them have been great, the recent Genius ads were a bit of a fail but there are certainly many more great ads than bad.

You can see them all over at YouTube although we don?t know how long they will last as it is not an official Apple source. If you have some time to kill and love all things Apple, you can do a lot worse than sit back and enjoy some or all of these ads. If you watch any, make sure to let us know which ones you liked best.

Source: YouTube via TNW

Source: http://feedproxy.google.com/~r/TheIphoneBlog/~3/GVpemGMUd2g/story01.htm

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Britain in free-press bullshit extravaganza

Paul Dacre is just trying to stop you from being killed

In the traditional eve-of-major-report shouting ritual, professional and amateur opinion-havers made one last bid to silence their opponents? views on free speech.

The media bullshit, led by News International, the Daily Telegraph and the Daily Mail, is focused firmly on the phrases ?300 years?, ?state-control? and ?worse than the French?.

But this has also been combined with a thinly-veiled threat to MPs tempted to vote for new regulation that they will have their fucking lives turned upside down.

The pro-regulation bullshit is a diverse collective of fancy writers, self-loathing Guardian readers and the adulterous croquet-player John Prescott.

They have rallied round the phrases ?Murdoch?, ?Murdoch? and ?Thatcher?.

Meanwhile, some of Britain?s most trusted and intelligent actors have called for tough regulations, a state-of-the-art trailer and ?2m to play themselves in the Sam Mendes adaptation of day 14 of the Leveson hearings.

Media analyst Julian Cook said: ?Like all proper British debates about important things, press freedom must be decided on the basis of vested interests, ulterior motives and dimwitted tribal nonsense.

?Otherwise how on earth would we get it completely wrong??

?

Source: http://www.thedailymash.co.uk/news/society/britain-in-free-press-bullshit-extravaganza-2012112850980

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Consumer confidence hits 4-year high

19 hrs.

Reuters

Consumer confidence rose to a four-and-a-half-year high in November as consumers became more optimistic about the outlook for the economy, according to a private sector report released on Tuesday.

The Conference Board, an industry group, said its index of consumer attitudes rose to 73.7 up from an upwardly revised 73.1 the month before, its highest since February 2008. Economists had expected a reading of 73.0, according to a Reuters poll.

October was originally reported as 72.2.

"Over the past few months, consumers have grown increasingly more upbeat about the current and expected state of the job market, and this turnaround in sentiment is helping to boost confidence," Lynn Franco, director of The Conference Board Consumer Research Center, said in a statement.

The expectations index rose to 85.1 from 84.0, while the present situation index edged slightly lower to 56.6 from 56.7.

Consumers' labor market assessment was little changed in November. The "jobs hard to get" index was flat at 38.8 percent, while the "jobs plentiful" rose to 11.2 percent from 10.4 percent.?

Analysts said the latest figures should bode well for the holiday shopping season.

"Despite the 'fiscal cliff,' Hurricane Sandy and a weaker stock market in November, households seem to be upbeat," said Ray Stone, economist and managing director for Stone & McCarthy Research Associates.?"That means they should be willing to spend money on Christmas. Shoppers won't be busting down doors, but sales should be pretty upbeat."?

Source: http://www.nbcnews.com/business/economywatch/consumer-confidence-hits-more-4-year-high-1C7277986

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Protestors In Egypt Denounce President's 'Power Grab'

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Source: http://feedproxy.google.com/~r/NewsXS_Middle_East/~3/tzOroJ8MxS8/

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jaimes Site - What do You Imply by Internet Hosting - Saunders ...

Sorry, Readability was unable to parse this page for content.

Source: http://kolmiwaklam.blogspot.com/2012/11/jaimes-site-what-do-you-imply-by.html

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How Long Will Your Discs & Drives Last?

LIFESPAN 2 to 5 years

MAX CAPACITY 650 MB

PROS Portable, cheap, and can be read by almost any modern computer. Those with gold or silver undersides last longest.

CONS Fragile, degrades easily in extreme temperatures, can even be ruined just by markers (it's best to write on the clear center ring).

Source: http://www.popularmechanics.com/technology/how-to/gadgets/how-long-will-your-discs-and-drives-last?src=rss

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Will the fiscal cliff break Grover Norquist?s hold on Republicans? (Washington Post)

Share With Friends: | | Politics - Top Stories Stories, RSS and RSS Feed via Feedzilla.

Source: http://news.feedzilla.com/en_us/stories/politics/top-stories/266532453?client_source=feed&format=rss

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10 Things to Know for Wednesday

Your daily look at late-breaking news, upcoming events and stories that will be talked about Wednesday:

1. WHY THE WHITE HOUSE IS STICKING WITH MORSI

The Egyptian leader ? despite questions about his commitment to democracy ? remains a key American partner in brokering peace between Israel and its neighbors.

2. DEMOCRATS' LATEST STANCE: NO CUTS TO SOCIAL SECURITY OR MEDICARE

As the clock ticks on the "fiscal cliff," many in the party ? emboldened by the election ? no longer want to consider cuts that once were on the bargaining table.

3. WHERE WEDNESDAY'S POWERBALL JACKPOT RANKS

The $500 million pot is the second-highest in lottery history, behind only the $656 million Mega Millions prize in March.

4. SUSAN RICE'S PROSPECTS GROW CLOUDY

The would-be secretary of state will meet with two more GOP senators Wednesday amid fresh concern about comments she made after the Benghazi attack.

5. YEARNING TO SERVE ON THE FRONT LINES

Four women sue to overturn a Pentagon rule barring females from being assigned to ground combat units.

6. HOW DROUGHT AND RISING TEMPERATURES ARE AFFECTING THE GREAT LAKES

Water levels have fallen to near-record lows on Lakes Michigan and Huron.

7. U.N. ON VERGE OF RECOGNIZING PALESTINIAN STATEHOOD

The U.S. and Israel strongly oppose the resolution, which would add weight to Palestinian claims for a state in the West Bank, Gaza Strip and east Jerusalem.

8. AMERICANS UPBEAT DESPITE LOOMING BUDGET MELTDOWN

Consumer confidence rose in November as home values increased and gas prices fell.

9. A NEW TECHNOLOGY TO TRACK STUDENTS' WHEREABOUTS

Microchips embedded in ID cards ? a purported safety measure ? will be "the next wave" in schools, one expert says.

10. SIN CITY'S LATEST ATTRACTION

Las Vegas is building a zip line that will spit tourists out of an 11-story slot machine and send them hurtling five blocks.

Source: http://news.yahoo.com/10-things-know-wednesday-103500895.html

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