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. 2004 Sep;87(3):2043–2059. doi: 10.1529/biophysj.103.038497

TABLE 8.

Comparison of rates of electron transport calculated from BD simulations with experimental values

BD simulation†
Experimental*
18-Å cutoff
20-Å cutoff
Mutant 10−6 × k2† (M−1 s−1) % WT 10−6 × k2 (M−1 s−1) % WT 10−6 × k2 (M−1 s−1) % WT
PC mutants
 WT 47 100 80 100 336 100
 D45(43)A‡ 59 126 147 184 501 149
 K46(44)A 31 66 41 52 227 68
 K53(51)A 33 70 48 60 232 69
 R93(88)A 19 40 29 37 152 45
 R93(88)Q 21 45 19 24 107 32
 R93(88)E 10 21 18 22 113 33
Cyt f mutants
 WT 40 100 – – 324 100
 Q7R 29 73 – – 236 73
 Q7E 40 100 – – 372 115
 D63A 31 78 – – 248 77
 E165A 39 98 – – 217 67
 D187A 38 95 – – 215 66
 D188A 42 105 – – 207 64
 D192A 41 103 – – 223 68
*

PC results taken from Schlarb-Ridley et al. (2002); cyt f results taken from Hart et al. (2003).

†

A total of 10,000 trajectories were completed for WT and mutant PCs at 100 mM ionic strength in the absence of Zn2+. Rates of electron transfer (k2) were calculated as described in the Methods sections for reaction coordinate cutoff distances of 18 and 20 Å. Rates obtained in the absence of the electrostatic field were not subtracted from the values shown to compare with the experimental values that would include nonelectrostatic contributions.

‡

Mutants were constructed as described in the Methods section. Residue numbers are taken from the consensus sequence (Pearson, 2000) with residue numbers from the PDB file of Phormidium PC sequence in parentheses.