A new simulation technique offers a faster way to predict how proteins change shape using only minimal experimental data. Developed by Drexel researchers, the method could accelerate studies of hard-to-visualize proteins critical to drug development.
Published in The Journal of Physical Chemistry B, the study was led by postdoctoral researcher Salsabil Abou-Hatab with Cameron Abrams, PhD, professor and head of chemical and biological engineering.
The team demonstrated their approach on T4 lysozyme, a bacterial enzyme with well-documented structural states. Using steered molecular dynamics and temperature accelerated molecular dynamics, they identified just four key measurements called collective variables that captured the enzyme’s transition between open and closed forms.
“This study shows that with the right choice of features, we can get powerful insight into how proteins move, without needing a perfect picture of the whole process,” Abou-Hatab said. The streamlined method can simulate shape changes in both directions and works even without knowing the protein’s final structure. The approach lays a foundation for studying proteins where structural data is incomplete, potentially speeding the search for a wide-range of therapies.
