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large proteins. In the simulations, a solvated bc 1 complex in a phospholipid
layer simulating a membrane was constructed, having a total of 206,720 atoms.
A subset of 91,061 atoms was actually included, with 45,131 moving atoms, in
an SMD simulation. First, an algorithm was assembled to compare two known
conformations of the ISP protein in relatively rigid domains. Rotations, based
on theα - carbon atoms of the ISP in its two forms (native and stigmatellin
bound), characterize the domain movements relative to each other. (See Figure
3 of reference 22.) The algorithm identifi ed a nearly rigid - body rotation of the
water - soluble portion of the ISP (amino acid residues 73 – 196 of PDB: 1BCC
and 3BCC) with respect to the ISP ’ s transmembrane helix (aa residues 1 – 67).
The reference 22 molecular dynamics simulations were performed with the
parallel molecular dynamics program NAMD^23 using the CHARMM22 force
fi eld.^24
Before the SMD simulation can be carried out, the researchers must build
a complex cytochrome bc 1 model. The next paragraphs describe this process.
First, the reference 22 authors generated charge distribution parameters for
the cytochrome bc 1 heme cofactors. They assumed that all three hemes in the
cytochrome bc 1 complex were in the oxidized state and carried the same point
charge distribution. The carboxyl chains of the hemes (see Figure 7.25 ) were
assumed to be deprotonated with a net charge of − 2, so that the oxidized state
heme carries a − 1 charge, or in the reduced (Fe(II)) state, a − 2 charge. The
distributions of point charges on the oxidized and reduced hemes were calcu-
lated using the program GAUSSIAN - 94^25 at the Hartree – Fock level with a 6 -
311G basis set. A radius of 1.22 Å was used for the Fe atom in electrostatic
potential fi tting calculations. The reference 22 authors compared resulting
charge distributions on several groups of heme atoms for deprotonated and
protonated hemes in the reduced state, and these in turn allowed them to
identify changes in charge distribution for protonation of the oxidized heme
state. Continued calculation and manipulation of heme charge distribution
resulted in calculated charges for each heme atom, collected in reference 22 ’ s
Table 1. The authors stipulate that their calculation of heme charge distribu-
tion was adequate for the SMD simulations conducted in their work, but
added that geometry optimization and more structural information (coordi-
nates of the histidine coordinating to the heme iron, for instance) should have
been included in the heme charge distribution calculation.
The next problem was parametrization of the cytochrome bc 1 [Fe 2 S 2 ] cluster.
The Rieske [Fe 2 S 2 ] cluster in the cytochrome bc 1 complex ’ s iron – sulfur protein,
ISP, is coordinated by two cysteine residues (cys139 and cys158 in PDB: 1BCC
and 3BCC) and two histidine residues (his141 and his161). In the oxidized
state, both [Fe 2 S 2 ] cluster irons are in the Fe(III) state (overall charge is 0)
while in the reduced state, one iron is in the Fe(II) state and one remains in
the Fe(III) state (overall charge − 1). The reference 22 authors calculated the
charge distribution on the [Fe 2 S 2 ] cluster and the coordinating histidine and
cysteine residues. The atomic coordinates from the 1.5 - Å resolution structure
of the water soluble portion of the ISP from bovine heart cytochrome bc 1