Proteins known as the building blocks of the body can self-assemble themselves probably in a jiffy. But even the most powerful computers may take days together to mimic this process with no guarantee of success. Researchers from the Rice University claim to have unveiled a computer program that can precisely simulate protein folding much faster than previously known methods.
By employing this computer program, scientists can possibly analyze various diseases caused by proteins folded incorrectly. The researchers suggested that once the complication of protein folding is ascertained, the genetic code which serves as the operating system of all living things may be understood.
Jianpeng Ma a professor in the Department of Bioengineering at Rice University and the Department of Biochemistry and Molecular Biology at Baylor College of Medicine shared, “Protein folding is regarded as one of the biggest unsolved problems in biophysics. This is a technically challenging task, and many groups around the world have been competing for years to make the process faster and more accurate.”
Once proteins are accurately folded, they act as enzymes that seem to be very crucial to metabolism. Correctly folded proteins act as structural elements in bone, muscle and cell scaffolding. They can seemingly act as mechanisms in cell signaling and immune response. In case, the protein is not folded properly, it may become an important factor in many diseases like Alzheimer’s, cystic fibrosis, emphysema and various cancers.
Ma explained, “In the process of simulation, called sampling, the computer has to search through many, many possible structures of the protein chain to find the lowest-energy solution. A polypeptide chain en route to its native state encounters many energy barriers, much like when one navigates through a rugged mountain landscape. Speeding up the process of crossing those barriers is the key to finding the true global minimum (energy state). In our simulation, temperature is a variable that goes continuously up and down. When the temperature is higher, proteins can overcome energy barriers faster. It’s equivalent to speeding up the motion of atoms.”
it has been assumed that proteins begin as amino acid molecules floating in a cell and then follow DNA blueprints. In the DNA blueprints, the molecules called as a polypeptide appear to be strung together like beads on a necklace. It has been ascertained that each polypeptide of a given sequence folds exactly the same way into the shape, called the native state that decides its function. This entire process of the protein to its native state apparently takes place in an instant. However, scientists still seem to be unable to determine how the process is completed so quickly.
Ma added, “The single-copy approach uses only one simulation, essentially, to find the native state of the protein. This is a major plus, because anyone with reasonable computing power can run this method.”
It has been revealed that Cheng Zhang and Ma were able to reach an exceptional accuracy and speed in simulating the folding of three relatively short but well-understood proteins trpzip2, trp-cage and the villin headpiece in the presence of water molecules. This way has been supposedly suggested to be the best for simulating physiological conditions.
The researchers mentioned that employing their algorithm enabled them to achieve the simulation in weeks. Yet it was possibly much faster than what others have achieved. Ma claimed that in the presence of water which is the most stringent condition, no scientists have been able to reach to this level of accuracy for trpzip and villin.
Ma affirmed, “We can’t overstate the significance of state-of-the-art computing facilities, as well as excellent service from Rice’s Research Computing Support Group. These supercomputer resources will continue to make Rice one of the leading institutions in the field of protein folding and computational biophysics.”
Previously scientists probably employed an intensive and expensive approach wherein multiple copies of a simulation are run parallel on many computers. But during the experiment, the researchers undertook two unique strategies, continuously variable temperature and single-copy simulation.
Zhang and Ma apparently discovered that the single-copy approach also takes computational muscle to simulate a biological task that the body’s cells accomplish as a matter of course. The researchers are supposedly continuing their work on Rice’s newest supercomputer cluster, BlueBioU, for longer polypeptide sequences.
The research is published in the current edition of Journal of Chemical Physics.