Biology Reference
In-Depth Information
2. Accuracy
We think that the constants and algorithms for the calculations in these pro-
grams are appropriate, but the ambiguities in available fundamental constants,
some nuances in their application and the systematic experimental errors discussed
above conspire such that solution making by recipe is imperfect. Experience and
direct [Ca
2
þ
] measurement are the best ways to limit inaccuracies in the long run.
Indeed, blind acceptance of the calculations, and a presumption that there are no
systematic errors (in either the solution making, pH, temperature, or in the
calculations) enhances the likelihood for inaccuracies.
3. Ease of Use and Adaptability
Early versions of these programs were DOS based and developed within various
labs, with user interfaces not consistent with present day expectations. Patton's
MaxChelator has attempted to maintain a user friendly interface that has evolved
during the past 15 years. One can input either desired free concentrations of Ca
2
þ
,
Mg
2
þ
, Mg-ATP to obtain the total concentrations required or vice versa, and there
are simple intuitive screens for these inputs. We are not aware of a commercial
program that does these calculations. To ensure adaptability in this future, code
should be available as open source to maximize access for future improvements
(including by others).
Both Chelator and MaxChelator allow for additional chelators and sets of
constants to be created or changed (a useful feature), but do not allow for their
inner workings or equations to be changed. If programs were open sourced then
the inner algorithms could be changed to try out di
erent ideas. Software could be
''tweaked'' and refined to hopefully overcome its limitations. Another issue for the
future is whether there will be su
V
Y
cient interest in the continual evolution of these
software suites.
4. Other Things to be Aware of When Doing This Work
In line with the aforementioned concerns,
Patton et al. (2004)
mentioned several
precautions. First, pH control is critical (within 0.01 pH unit) especially for EGTA.
Moreover, when metals bind to chelators, H
þ
is released a
V
ecting pH, and that
increases the importance of appropriate pH bu
er choice. Second, chelators
cannot reduce free metal concentration to zero. An equilibrium is set up, and
[Ca
2
þ
] and [Mg
2
þ
] (like [H
þ
]) are always finite. If proteins or other moieties in your
system have higher a
V
Y
nity for the metal than your chelator, it can complicate
ectiveness. Contamination with Ca
2
þ
is almost always present. Third,
select the right chelator for metal concentrations of interest. Just like pH bu
chelator e
V
V
ers
which work in a range of
0.5 pH units, chelators work in a range of
0.5pK
d
0.3-3K
d
). Using too high K
d
allows contaminant Ca
2
þ
to strongly influence
[Ca
2
þ
] at the low levels, while too low K
d
will result in saturation and loss of
(
