ChargeCalculator:Case studies

We present a few interesting examples of use cases for ACC.

Paracetamol

N-acetyl-p-aminophenol, commonly known as paracetamol, is a widely used analgesic and antipyretic. Its mechanism of action is believed to be the inhibition of the protein cyclooxygenase 2, regulating the production of pro-inflamatory compounds. In order to study the interaction of the drug with its target, it is necessary to look at the electrostatic properties of paracetamol. Further modeling studies will also require atomic charges for paracetamol as parameters of the simulation.

We have computed atomic charges in paracetamol (experimental coordinates from wwPDB CCD). Try out this particular computation setup [| here], and make sure to use the interactive giudes for additional explanations. We have used several EEM parameter sets available in literature, in order to cover a wide range of atomic charge definitions. One or more of these might prove useful in further modeling studies. If you plan to run molecular dynamics, it is good to use charges which are compatible with the particular force field you plan to use. For instance, if the force field is known to use atomic charges based on electrostatic potential mapping, pick at least one EEM parameter set developed with this charge definition.

The results of the calculation are available [| here].

The phenolic H appears to be not only the most positive H in the paracetamol molecule, but also the second most positive atom in the entire molecule (the most positive is the amide C). The H bound to the amide N is the second most positive H, and the third most positive atom in the entire molecule. Not surprisingly, these positions represent the reaction sites for all metabolic modifications of paracetamol. While paracetamol is a very small molecule with few polar sites, the same principle can be applied in reasoning out highly reactive sites in more complex molecules.

Different EEM parameter sets produce a range of absolute values for the atomic charges. For instance, the phenolic H in paracetamol may have anywhere between +0.1e and +0.34e, depending on which EEM parameter set was used. While the trends observed within each set of charges hold true, these values cannot be compared between sets, due to the inherently different nature of the charge definitions they are based on. On the other hand, these differences might allow one set of charges to sample conformations not accessible to other sets.

Apoptosis

The protein Bax is important in regulating programmed cell death (apoptosis). Upon activation, Bax oligomerizes and causes a cascade of events which eventually leads to the death of the cell. Bax activation is a transient phenomenon believed to rely on a specific network of charge transfer. The active Bax appears in complex with a charged activator peptide, causing a few conformational changes and a shift in the total charge. The distribution of charges can be studied individually, and furhter compared between the active and inactive states.

For studying Bax activation we have calculated atomic charges for the active (PDB ID 2k7w) and inactive (pdb id 1f16) forms of bax using an eem parameter set specifically developped for proteins. Try out this particular computation setup [| here], and make sure to use the interactive giudes for additional explanations. Note that the input files were in pqr format, and contained AMBER charges as given by the program pdb2pqr. These are also available for comparison in ACC.

The results of the calculation are available [| here].

EEM allows inter-residue polarization and charge transfer, and thus the total residue charges given by EEM will deviate from the formal values of +1,0 and -1, respectively. The total residue charges given by AMBER always coincide with the formal values, as they do not account for the influence of the surrounding environment. A number of residues in the inactive Bax deviate from the formal charge, suggesting electrostatically interesting sites. Most are on the surface of Bax, but some are also inside the protein (e.g., ARG 109).

Further, we can compare the total residue charges between active and inactive Bax. For instance, the residue ARG 109 has a charge of +0.07e in inactive Bax, and +0.37e in active Bax. This significant difference may be a clue that this residue is relevant during activation. Indeed, a triple mutant at positions 109-111 shows decreased biological activity.

Note again that the absolute values of the charges are not always relevant. But the trends within a certain set of charges can hold a lot of relevant information. Moreover, not all charge differences may be of interest. For instance, when comparing between the values for highly flexible parts of the protein, the noise (differences caused by entirely different conformation and hence chemical environment) can be higher than the information content. Thus, context is always important.

Proteasome

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