Computational Study of Disease Related Proteins Form Electrostatic Point of View

Chitra Bahadur Karki, University of Texas at El Paso

Abstract

In the last three decades, many giant DNA viruses have been discovered. The giant viruses present a unique and essential research frontier for the study of self-assembly and regulation of supramolecular assemblies. The question on how these giant DNA viruses assemble thousands of proteins so accurately to form their protein shell, the capsids, remains largely unanswered. Revealing the mechanisms of giant virus assembly will help to discover the mysteries of many self-assembly biology problems. Paramecium Bursaria Chlorella Virus 1 (PBCV-1) is one of the most intensively studied giant viruses. Based on the high-resolution structure of PBCV-1, we implemented a multi-scale approach to investigate the interactions among capsomers, which are giant virus capsid building units. An individual PBCV-1 capsomer consists of three major capsid proteins, each of which has two jelly-roll folds, giving the whole capsomer a pseudo-hexagonal shape. Electrostatic features calculated by DelPhi show that the six vertices of a single PBCV-1 capsomer are always positive while its six grooves are alternatively positive and negative. Based on the electrostatic potential analyses for capsomer-capsomer pairs around the relatively flat area at the icosahedral 2-fold axis, three binding modes with different strengths are found, two of which are attractive while the other one is repulsive. Furthermore, a capsomer structure manipulation tool package is developed to simulate the capsid assembly process and investigate the binding funnels. Results from this tool package shows that 1. long-range electrostatic forces indeed play important roles during and after the capsid assembly; 2. the binding funnels are obvious and can be quantitatively measured. In addition, the total binding free energy of each binding mode was calculated with the MM/PBSA method after molecular dynamic simulations. Interestingly, no matter if the electrostatic binding forces are attractive or repulsive, when counting the Van der Waals, non-polar solvation and other energies, the binding free energies of the three binding modes are all negative indicating the capsid structure is very stable. Among all the binding modes, the weakest binding mode is located at the boundary of trisymmetron. This explains why the seam between two neighboring trisymmetrons becomes the breaking line when a giant virus capsid dissociates. Formulas generated for the total number of each binding mode within one capsid show the mode within trisymmetron are dominating the stabilization of the capsid which is consistent to previous observation. Results and tools generated in this work shed first light on the assembly of giant virus by providing quantitative analyses. Besides the viral capsid assembly, methods developed in this study pave the way for studying more complicated assembly process for other biomolecular structures. One quarter of the world’s population are infected by Mycobacterium tuberculosis (MTB), which is a bacterial pathogen and is one of the leading causes of death in humans. Recent evidences have demonstrated that two virulence factors, ESAT-6 and CFP-10, play crucial roles in cytosolic translocation. Many efforts have been made to study the ESAT-6/CFP-10 but the mechanism of how ESAT-6 and CFP-10 contribute to MTB cytosolic translocation and virulence is poorly understood. One recent interesting finding is that at low pH, the ESAT-6 with Post Translation Modification (PTM) dissociates from CFP-10 but the non-PTM ESAT-6 doesn’t. This work focuses on the ESAT-6/CFP-10’s dissociation mechanism. We found at low pH, the ionizable residues in both ESAT-6 and CFP-10 change their charge states significantly. The net charge of the ESAT-6/CFP-10 complex changes from -10e to +1e from pH 7 to 4. Due to the dramatic charge changes, the salt bridges at the interfaces in the complex are broken or weakened significantly, which may result in the increment of the contribution of electrostatic energy to the total binding energy of complex ESAT-6/CFP-20. The binding energy calculations using the MM/PBSA approach confirm that the electrostatic binding energy does increase at pH 4. However, the Van der Waals (VDW) binding energy decreases at pH 4, which compensates the electrostatic binding energy and thus the total binding energy remains almost the same as in pH 7. Which is in good agreement with the experiments results where the binding affinity of the complex remain almost the same at both the pH conditions. Further investigation on the VDW energy shows that the N-terminal of ESAT-6 play a significant role in strengthening the VDW binding energy and stabilizing the complex structure at low pH. The structure used for this work was derived from E.coli where the PTM is absent but in experiments on native ESAT-6/CFP-10 from MTB bacteria from humans, where PTM is present, the dissociation of complex at low pH values was observed. This gives the hint that the PTM on N-terminal of ESAT-6 may play a role in the dissociation of the ESAT-6/CFP-10 complex. After the dissociation of the complex ESAT-6/CFP-10 into the constituents, the ESAT-6 undergoes oligomerization process which then rupture the membrane to form a channel for bacterial cytosolic translocation. To simulate the oligomerization, process the M-ZDOCK and SymmDock algorithms were used to predict the structures with different number of symmetries. The predictions form docking algorithms were filtered based on some experimental facts and the final structures were embedded to membrane. The MM/PBSA analysis was implemented to obtain the binding free energies of these structures. No matter which docking algorithm, the oligomer with symmetry four had the least binding free energy per ESAT-6. So, oligomer with symmetry four could be the structure for membrane interaction.

Subject Area

Biophysics|Health sciences|Virology|Microbiology|Molecular biology

Recommended Citation

Karki, Chitra Bahadur, "Computational Study of Disease Related Proteins Form Electrostatic Point of View" (2019). ETD Collection for University of Texas, El Paso. AAI22620482.
https://digitalcommons.utep.edu/dissertations/AAI22620482

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