Exercises for Chapter 7 – Characterization via Charges

Overview: The practical exercises will be performed using the software tool Atom icChargeCalculator (ACC), because it provides both charge calculation and visual ization, and is currently the only available web application for charge calculation. A usage of the ACC is shown in the solution of demo exercise 1 and also in the ACC manual. 1. Demo exercise: Detection of the first dissociating hydrogen in 3-hydroxy benzoic acid 3-hydroxybenzoic acid contains two hydrogens, which can potentially dissoci ate. The hydrogen from the COOH group and the hydrogen from the OH group. The more positively charged hydrogen will dissociate first. Calculate atomic charges for the 3-hydroxybenzoic acid using ACC (with Bult2002 mpa para meters) and detect the first dissociating hydrogen. 2. Comparison of charges in phenol molecules and detection of correlation between charges and pKa. Download from PubChem the 3D structures of the molecules mentioned in the table below. For all the molecules calculate partial atomic charges using ACC (with Bult2002 mpa parameters). Analyze, if there is any dependency between the pKa of the molecules and the atomic charges of certain atoms. Spe cifically, focus on charges on the H and O from the phenolic OH group, the C connected to the OH group and the charges on the C atoms in the phenolic ring. Molecule Pubchem ID pKa 2,4,6-trinitrophenol 6954 0.38 2,3-dinitrophenol 6191 5.96 3-hydroxybenzaldehyde 101 8.5 2,4,6-trimethylphenol 10698 10.9 3. Comparison of charge distributions in cocaine binding sites Calculate partial atomic charges for two cocaine (PDB residue ID COC) antibod ies, specifically Anti-Cocaine Antibody M82G2 (PDB ID 1q72) and Cocaine catalytic Antibody 7A1 Fab’ (PDB ID 2ajv). Afterwards, compare charge dis tribution in cocaine binding sites. Note: In both cases, delete water and cocaine molecules before starting the charge calculation. Use ACC with default settings for the calculation. Visualize the charge distribution in ACC using the Display Mode Surface and Probe Radius 1.4. 4. Comparison of a charge distribution in activated and inhibited apoptotic proteins BAX is a protein participating in regulation of apoptosis – programmed cell death. When the cell is healthy, BAX is inactive and its C domain is tightly bound to its structure (see the figure below). During apoptosis, BAX is activated (i.e., an activator is bound to the activation site), its C domain becomes free, can insert into the mitochondrial membrane and penetrate it. It was found [8] that the activation is realized via a charge transfer and that helices 1 and 5 (see Figure 7.3) play a role in this process. In this exercise, you will compare the charge distribution in active and inhibited BAX. Calculate charges in inactive BAX (PDB ID 1f16), inactive BAX in complex with its inhibitor (PDB ID 2lr1) and active BAX (PDB ID 2k7w) via ACC. Describe how the charges in helix 1, helix 5 and the C domain changed.