The research, published today in Proceedings of the National Academy of Sciences, is a glimpse into RNA, found in all life on Earth, and could advance a variety of research areas, including the search for new antibiotics and cures for protein-related diseases.
A simulation of the GCAA tetraloop folding: The color code is red=guanine, green=cytosine, and yellow=adenine, and dotted white lines are hydrogen bonds. There is a cyan overlay in the last 5 seconds indicating the experimentally determined structure.
Existing computational models, based on DNA rather than RNA, do not achieve the atomic level accuracy of the new model, said Angel Garcia, head of the Department of Physics, Applied Physics, and Astronomy within the School of Science at Rensselaer, and senior constellation chaired professor in the Biocomputation and Bioinformatics Constellation, who co-wrote the paper with Alan Chen, a post-doctoral fellow at Rensselaer. The new model Garcia and Chen created can simulate the folding of three known versions of a tetraloop, accurate to within one ten-billionth of a meter.
RNA is involved in many biological functions, such as building proteins, coding and decoding genes, and cellular regulation. RNA molecules are composed of strings of four different “bases” —cytosine, guanine, adenine, and uracil—mounted on a sugar-phosphate backbone. Once the sequence is assembled, the individual bases interact with their neighbors, twisting and swinging on the hinged chemical bonds that connect them to the backbone. When the process is complete, the RNA has folded into its “tertiary” structure, which influences its function. Although researchers can easily alter the sequence of molecules, without accurate computer modeling there they cannot easily see the tertiary structure of their creation.
“Right now, it takes people from molecular biologists, to virologists, to cell biologists, thousands of dollars and years of study to see the structure of an RNA they have made, altered, or are studying,” said Chen. “There are a lot of researchers working on the RNA in viruses and how it attacks the cell, and, while they’re easily able to alter the sequence, they’re essentially working without ever seeing the effects of their changes in molecular detail. Because of this, there’s a lot of trial and error, and our work aimed at helping that.”
Garcia and Chen said that, unlike DNA, which typically twists two strands of bases into a classic double-helix, RNA is single-stranded and folds onto itself, forming many unusual structures. A tetraloop is a small section of single-stranded RNA that is looped into the shape of a hairpin, the curve of which is formed by four bases. Even the sequence of bases in a tetraloop is unusual, violating a standard arrangement described by groundbreaking DNA researchers James Watson and Francis Crick.
To create an effective computational model, Garcia and Chen had to match the unique “recipe” of twisting and swinging proscribed by the interactions between the bases.
“Imagine if you try to produce a recipe of Mario Batali,” said Garcia, referring to a popular chef. “I tell you it has water, salt, fish, and pasta—go produce his recipe. The problem is, you don’t know how much of each, and in what order.”
Instead of a recipe of food ingredients, Garcia and Chen created a computational recipe for the interactions of the bases in the sequence of a tetraloop.
“The problem is one of balancing different forces. It’s the actions between the bases as they stack on top of each other, the interactions of the bases with water, the rotation of the bases relative to a sugar. Those are things that change the balance,” said Garcia.
Garcia said tetraloops are an important area of study because they appear in all organisms, particularly in ribosomes, which manufacture proteins for living cells. Statistically, there could be as many as 256 possible sequences of those four bases, but only three sequences actually appear in tetraloops. Once formed, they are highly stable, outlasting other structures when subjected to the destructive force of increasing heat.
“Tetraloops are sequences which are highly conserved throughout evolution; you find them everywhere, from bacteria to humans,” said Garcia. “From one organism to another, many things can change, but when tetraloops change, they change from one sequence of four bases to one of the other three. They stack against each other and they are hyperstable. And there is a reason for them to be arranged the way they are.”
The paper, titled “High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations,” appears in the September 16 online early edition of PNAS, and will be published in the September 20 print edition.Contact: Mary L. Martialay
Mary Martialay | EurekAlert!
Computer model predicts how fracturing metallic glass releases energy at the atomic level
20.07.2018 | American Institute of Physics
What happens when we heat the atomic lattice of a magnet all of a sudden?
18.07.2018 | Forschungsverbund Berlin
A new manufacturing technique uses a process similar to newspaper printing to form smoother and more flexible metals for making ultrafast electronic devices.
The low-cost process, developed by Purdue University researchers, combines tools already used in industry for manufacturing metals on a large scale, but uses...
For the first time ever, scientists have determined the cosmic origin of highest-energy neutrinos. A research group led by IceCube scientist Elisa Resconi, spokesperson of the Collaborative Research Center SFB1258 at the Technical University of Munich (TUM), provides an important piece of evidence that the particles detected by the IceCube neutrino telescope at the South Pole originate from a galaxy four billion light-years away from Earth.
To rule out other origins with certainty, the team led by neutrino physicist Elisa Resconi from the Technical University of Munich and multi-wavelength...
For the first time a team of researchers have discovered two different phases of magnetic skyrmions in a single material. Physicists of the Technical Universities of Munich and Dresden and the University of Cologne can now better study and understand the properties of these magnetic structures, which are important for both basic research and applications.
Whirlpools are an everyday experience in a bath tub: When the water is drained a circular vortex is formed. Typically, such whirls are rather stable. Similar...
Physicists working with Roland Wester at the University of Innsbruck have investigated if and how chemical reactions can be influenced by targeted vibrational excitation of the reactants. They were able to demonstrate that excitation with a laser beam does not affect the efficiency of a chemical exchange reaction and that the excited molecular group acts only as a spectator in the reaction.
A frequently used reaction in organic chemistry is nucleophilic substitution. It plays, for example, an important role in in the synthesis of new chemical...
Optical spectroscopy allows investigating the energy structure and dynamic properties of complex quantum systems. Researchers from the University of Würzburg present two new approaches of coherent two-dimensional spectroscopy.
"Put an excitation into the system and observe how it evolves." According to physicist Professor Tobias Brixner, this is the credo of optical spectroscopy....
13.07.2018 | Event News
12.07.2018 | Event News
03.07.2018 | Event News
20.07.2018 | Power and Electrical Engineering
20.07.2018 | Information Technology
20.07.2018 | Materials Sciences