Free Newsletters - Space News - Defense Alert - Environment Report - Energy Monitor
. 24/7 Space News .




EARLY EARTH
Untangling life's origins
by Staff Writers
Urbana IL (SPX) Mar 13, 2013


File image.

Researchers in the Evolutionary Bioinformatics Laboratory at the University of Illinois in collaboration with German scientists have been using bioinformatics techniques to probe the world of proteins for answers to questions about the origins of life.

Proteins are formed from chains of amino acids and fold into three-dimensional structures that determine their function. According to crop sciences professor Gustavo Caetano-Anolles, very little is known about the evolutionary drivers for this folding.

In collaboration with scientists at the Heidelberg Institute for Theoretical Studies, he has been working at the interface of molecular evolution and molecular dynamics, looking back to when proteins first appeared approximately 3.8 billion years ago to determine changes in folding speed over time.

To do this, they looked at all known protein structures as defined in the Structural Classification of Proteins (SCOP) database and mined their presence in 989 fully sequenced genomes. In a previous study, researchers in Caetano-Anolles's group used SCOP and genomic information to reconstruct phylogenomic trees that describe the history of the protein world. The current research is based on these types of trees.

"They are not the standard trees that people see in phylogenetic analysis," he said. "In phylogenetic analysis, usually the tips of the trees, the leaves, are organisms or microbes. In these, they are entire biological systems."

In contrast, the leaves of these new trees are protein domains, which are compact evolutionary units of structure and function. Proteins are usually complex combinations of several domains.

"We have a world of about 90,000 of these structures, but they seem to be always producing the same designs," he said. Over the last 10 years, he has been part of the effort to map these designs, or folds, because they are determined by the way the protein chains fold on themselves. To date, approximately 1,300 folds have been characterized.

For the current study, the researchers identified protein sequences in the genomes that had the same folding structure as known proteins. They then used bioinformatics techniques to compare them to each other on a time scale to determine when proteins became part of a particular organism. This allowed them to map protein structures and organisms onto a timeline.

Directly calculating the folding speed for all of these proteins would be impossible with today's technology, so the researchers took advantage of the fact that a protein always folds at the same points and used a measure called Size Modified Contact Order (SMCO).

Contact order is the ability of a protein to establish links between segments of the polypeptide chain. When points that are close together on the chain come together, they generally form helical structures; when distant points come together, they form beta strands that interact with each other and form sheets. Contact order measures how many of the connections are local and how many are distant. Experimental studies have shown that it is correlated with folding speed. The measure is normalized (size modified) to take protein length, which affects folding speed, into account.

They saw a peculiar pattern in the results.
"What we see is an hourglass," said Caetano-Anolles. "At the beginning, proteins seem not to be folding so fast. And then, as time progresses, there's a tendency to fold faster and faster. And then it reaches a critical point, and at this point we have a tendency that reverses, that seems to go back again to slow folding." However, the tendency toward higher speed dominates.

This point coincides with what he calls the "Big Bang" in protein evolution. Approximately 1.5 billion years ago, more complex domain structures and multi-domain proteins emerged with the appearance of multicellular organisms. Amino acid chains, which make up proteins, also became shorter at this point in time.

Why does folding speed matter?
"If the protein does not fold, in the vast majority of cases it will not have a function. So folding implies functionality. And speed of folding implies speed of achieving that functionality," he explained. "For a cell, that's very important, because if proteins are very slow folders, there is a time lag to when that function will be accessible to the cell."

Fast folders are also less susceptible to aggregation, or clumping together, so they work faster. Moreover, proteins that fold rapidly are more likely to fold correctly. Protein misfolding has been linked with diseases such as Alzheimer's.

Caetano-Anolles said, however, that this research makes an important contribution to understanding how molecules work. "The complexities of the biological functions of molecules are still poorly understood," he said.

"If we mix the world of molecular dynamics with the world of molecular evolution, we can then determine what aspects of sequences are important for molecular dynamics, and therefore, we can apply them to genetic engineering, synthetic biology, and so on."

.


Related Links
University of Illinois College of Agricultural, Consumer and Environmental Sciences
Explore The Early Earth at TerraDaily.com






Comment on this article via your Facebook, Yahoo, AOL, Hotmail login.

Share this article via these popular social media networks
del.icio.usdel.icio.us DiggDigg RedditReddit GoogleGoogle




Memory Foam Mattress Review
Newsletters :: SpaceDaily :: SpaceWar :: TerraDaily :: Energy Daily
XML Feeds :: Space News :: Earth News :: War News :: Solar Energy News





EARLY EARTH
UF scientists discover new crocodilian, hippo-like species from Panama
Gainesville FL (SPX) Mar 11, 2013
University of Florida paleontologists have discovered remarkably well-preserved fossils of two crocodilians and a mammal previously unknown to science during recent Panama Canal excavations that began in 2009. The two new ancient extinct alligator-like animals and an extinct hippo-like species inhabited Central America during the Miocene about 20 million years ago. The research expands the ... read more


EARLY EARTH
Lunar Orbiter Image Recovery Project Seeks Public Support To Retrieve Apollo Era Moon Images

China sets moon mission re-entry test

Lunar impacts created seas of molten rock

China to use modified rocket for moon landing mission

EARLY EARTH
Maryland explores adaptations strategies for survival on Mars

NASA rover finds conditions once suited to life on Mars

Curiosity Rover's Recovery Moving Forward

NASA Rover Finds Conditions Once Suited for Ancient Life on Mars

EARLY EARTH
Technology to detect Alzheimer's takes SXSW prize

Basketball legend Shaq talks tech at SXSW

UK and Kazakhstan agree collaboration in space

Wyle To Provide NASA Ongoing Support For Human Space Flight

EARLY EARTH
China's fourth space launch center to be in use in two years

China to launch new manned spacecraft

Woman expected again to join next China crew roster

China's space station will be energy-efficient

EARLY EARTH
Canadian commands space station for first time

'Goody Bag' Filled With Sample Processing Supplies Arrives on Station

ESA's Columbus Biolab Facility

SpaceX set for third mission to space station

EARLY EARTH
Vega receives its upper stage as the next mission's two primary passengers land in French Guiana

Grasshopper Successfully Completes 80M Hover Slam

Musk: 'I'd like to die on Mars'

Ariane 5 vehicle for next ATV resupply mission in Kourou

EARLY EARTH
The Great Exoplanet Debate

Earth-sized planets in habitable zones are more common than previously thought

Astronomers Observe Planets Around Another Star Like Never Before

Astronomers Conduct First Remote Reconnaissance of Another Solar System

EARLY EARTH
Breaking the final barrier: room-temperature electrically powered nanolasers

New Technique Creates Stronger, Lightweight Magnesium Alloys

Novel technique for chemical identification at the nanometer scale developed

Aspirin may lower melanoma risk




The content herein, unless otherwise known to be public domain, are Copyright 1995-2014 - Space Media Network. AFP, UPI and IANS news wire stories are copyright Agence France-Presse, United Press International and Indo-Asia News Service. ESA Portal Reports are copyright European Space Agency. All NASA sourced material is public domain. Additional copyrights may apply in whole or part to other bona fide parties. Advertising does not imply endorsement,agreement or approval of any opinions, statements or information provided by Space Media Network on any Web page published or hosted by Space Media Network. Privacy Statement