In a recent study published in the Proceedings of the National Academy of Sciences on the 20th, American scientists have uncovered how hydrogen bonds facilitate protein conformation in a very short time by converting data into sound. They have also revealed the process of converting amino acids into functional folded proteins, providing a unique perspective on the sequence of hydrogen bond events that occur when proteins transition from an unfolded to folded state.
To better understand how protein folding occurs, scientists must first determine how a chain of amino acids transforms into its final form in the cellular water environment. This transformation process actually happens very quickly, taking place in approximately 70 nanoseconds to 2 microseconds.
Hydrogen bonds are essentially the attractive forces that occur when a small, positively charged hydrogen atom is in close proximity. This relatively weak attraction can bring together atoms from different amino acids in a protein. Folded proteins form hydrogen bonds internally and also with surrounding water molecules. Throughout this process, the protein continuously explores different conformations, which are intermediate states in the formation of the final 3D structure. Along the way to achieving the final conformation, the protein may sometimes hit a "dead end," then backtrack until it accidentally finds another path.
To achieve this, researchers thought of sonifying the data. This method involves converting molecular data into sound, allowing them to "hear" the formation of hydrogen bonds. They developed a software program that assigns a unique tone to each hydrogen bond. If the conditions for the correct formation of a hydrogen bond are met, the software plays the corresponding tone for that process. In essence, the program sequentially tracked the formation of tens of thousands of individual hydrogen bonds.
Numerous studies suggest that the processing speed of audio in the human brain is approximately twice that of visual data. Compared to sequences represented visually, humans are better at detecting and remembering subtle differences in a series of sounds.
Researchers emphasize that including water molecules in simulations and hydrogen bond analyses is crucial to understanding this process. Through acoustic experiments, they truly grasped how water molecules enter the correct positions in proteins and how they assist in changing the protein's conformation, ultimately leading to its folding.
Chemistry professor Martin Gruebele from the University of Illinois at Urbana-Champaign and composer/software developer Carla Scaletti co-led this new research. Image source: Fred Zwicky/American Association for the Advancement of Science EurekAlert website
