Computational Analysis of the Effects of the Early Effects of Disulfide Bonds Cleavage on the Structure of Human Serum Albumin

Traditional structural biology methods have employed diffractive techniques (such as x-ray diffraction and cryo-electron microscopy, cryo-EM) or nuclear magnetic resonance (NMR) to retrieve the 3-dimensional atomistic structure of biomolecules. The high resolution of these experimental techniques, bring an important set of experimental challenges including sample preparation and operating under extreme non-physiological conditions. In addition, these techniques mostly deny much of the dynamics of biomolecules which are deemed to be essential for their functions.

Challenges are particularly evident in the investigation of proteins whereby understanding atomic arrangement and the dynamic behavior is crucial to understanding their function.

Computational physics offers the possibility to reproduce the dynamic changes of the folding of proteins. Crucially, it also offers the possibility to investigate how external factors may modify their conformation and in turn predict how their functionality may be affected.

In our group, we have demonstrated that various photosensitizer (PS) prompt laser-induced protein conformational changes. Crucial details remain unknown including: 1) which photochemical and photophysical mechanisms trigger the changes (e.g., production of reactive oxygen species (ROS), photoinduced charge transfer, etc.) and 2) the details of the secondary and tertiary structural changes. In this work we did not attempt to simulate the photoinduced mechanisms but only their effects. Under the assumption that ROS are created by the laser irradiation of PS we hypothesized a series of photoinduced changes, in particular the cleavage of disulfide bonds. We tested this hypothesis in human serum albumin (HSA), which is characterized by the presence of 17 S-S bonds. We have prepared HSA using the Charmm-Gui interface and performed molecular dynamic simulations of HSA with NAMD as a function of the number and location of disulfide bonds. We report early events (1ns) observed in the simulations.