Structural biology of tumor necrosis factor demonstrated for undergraduates instruction by computer simulation

This work presents a three-dimensional (3D) modeling exercise for undergraduate students in chemistry and health sciences disciplines, focusing on a protein-group linked to immune system regulation. Specifically, the exercise involves molecular modeling and structural analysis of tumor necrosis factor (TNF) proteins, both wild type and mutant. The structure of the tumor necrosis factor type 1 receptor (TNF-R1) is also briefly explored. TNF and TNF-R1 play major roles in maintaining human immune-system homeostasis. Upon binding with TNFR-1, the TNF can activate the nuclear factor kappa B (NF-κB), eventually resulting in apoptosis or cell death. These essential features of the clinically relevant TNF family is explored within the frame work of a readily adaptable tutorial. © 2015 by The International Union of Biochemistry and Molecular Biology, 44:246-255, 2016.