Study explains core packing fractions

In living organisms, each protein – a type of biological polymer with hundreds of amino acids – exit out special functions such as catalis, molecule transport, or DNA repair. To perform these tasks, they have to be converted into specific shapes. It is a complex process that is important for life, and despite the progress in the field, there are many open questions about the process.

A search Published In PRX Life This issue throws some light on the issue, and can create new ways to design proteins for drug theraputics, novel biomaterials and other applications.

Researchers led by Corey O’Harn developed computational models for all rounded proteins in the protein data bank, an online database, and measured their internal core areas to determine how they were densely packed. Each protein had a core packing fraction of 55%. Namely, 55% of space was captured by atoms. This inspired the research team for two questions.

“Why did they all have the same value? And, especially, why is the price 55%?” The professor of O’Harn, Mechanical Engineering, Material Science, Physics and Applied Physics said. “Answer: The packing fraction stops growing when the protein core jams or hardness.”

That is, individual amino acids that produce protein core cannot be compressed further when the protein is folded. The packing fraction on which the object jams together depends largely on their size. For example, circular objects jam at a packing fraction of 64%.

“But amino acids have complex shapes,” O’Harn said.

“Some of the amino acids are quite spherical, but most of them grow due to side chains, and due to some kind of bonded hydrogen atoms. Physics of soft substances tells us that long, rugged -rugged particles are not low in the form of jam packing, which are as low value packing.”

The direction of an interesting future is whether the protein core packing fraction can be dense compared to the protein found in physical conditions. For example, protein has been studied under high pressures, mimicking the pressures in the deep ocean hydrothermal vents, which are possibly associated with the original synthesis of organic molecules.

The structural characteristics of proteins at high pressures have shown that the protein core packing fraction may increase by 58–60%. Thus, this research is also related to our understanding of the origin of life.

Alex Grigas, a Ph.D. Candidates and prominent author of paper at O’Harn Lab.

“If you change the position, pressure or temperature jump of the solvent, you may be able to pack amino acids more efficiently.”

O’Harn said that currently protein design focuses on creating new sequences of amino acids for new protein structures and functions.

“Now, this task opens the possibility that even with the same amino acid sequence, you can only design new protein structures and functions by changing folding conditions.”