Adding Hydrogen Atoms to Protein

Raw PDB files can be hydrogenated by running them as MOPAC jobs, e.g. running MOPAC with the argument 1A1A.pdb. Because it does not allow any options this way of hydrogenating a protein is not normally used. A better approach is to make up a normal MOPAC data-set that refers to the PDB file, and run that. This strategy allows options that modify how the hydrogenation is done. But first, some notes on hydrogenation, to make the process easier to understand:

Initial hydrogenation

The hydrogenation method used in MOPAC has been optimized for hydrogenating protein systems. Hydrogen atoms are added by keyword ADD-H so as to neutralize all sites, so, for example, -COO would become -COOH, SO₄ would become H₂SO₄, and O would become H₂O. Only metal atoms, such as K and Ca, are ionized

Ionization and other operations

Salt bridges

Many proteins contain salt bridges. These can be added automatically by keyword SITE=(SALT) This identifies all potential salt bridges and adds and deletes hydrogen atoms, as appropriate.

Other ionized sites

In individual proteins, some sites are known to be ionized, for example the Asp residue in the protease catalytic triad. These sites can be ionized using the simple "chain-letter residue number" approach. Thus if the triad residue Asp in chymotrypsin were to be in chain "F" and have residue number 102, then that site could be ionized using SITE=(F102(-)).

Incorrect site hydrogenated

Some systems, in particular the imidazole ring in histidine, have two sites that can be hydrogenated. If the wrong site is hydrogenated, then problems can occur, for example if one nitrogen in an imidazole ring forms a hydrogen bond with a nearby residue, then hydrogenating that site might result in a steric clash. To correct this, the protonation state of each nitrogen in the imidazole would need to be changed. This requires a more specific SITE command of the type:

SITE("[HIS]222:A.ND1"(0),"[HIS]222:A.NE2"(+))

SITE("ND1 HIS A 222"(0)," NE2 HIS A 222"(+))

In this system, the original hydrogenation incorrectly put a proton on ND1 of His222 instead of on NE2. To correct this, the SITE command re-defines ND1 as being neutral and NE2 as being a cation. When the SITE command is run, it sees that ND1 is a nitrogen atom in an unsaturated ring (think pyridine) that has a hydrogen atom attached (think pyridinium). Removal of that hydrogen atom would neutralize the charge. Similarly defining NE2 as being a cation would result in a hydrogen atom being added to that atom.

These commands can be combined to form a single command that corrects all the faults in the original hydrogenation, for example:

SITE(SALT,"[HIS]222:A.ND1"(0),"[HIS]222:A.NE2"(+),F102(-))