Biogeosciences
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2006
10.5194/bg-3-311-2006
http://www.biogeosciences.net/3/311/2006/
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http://www.biogeosciences.net/3/311/2006/bg-3-311-2006.pdf
311
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2006-07-21
Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins
J. M. Dick
jedick@berkeley.edu
D. E. LaRowe
H. C. Helgeson
Department of Earth and Planetary Science, University of California, Berkeley, CA 94720-4767, USA
Thermodynamic calculations can be used to quantify environmental constraints
on the speciation of proteins, such as the pH and temperature dependence
of ionization state, and the relative chemical stabilities of proteins
in different biogeochemical settings. These calculations depend in
part on values of the standard molal Gibbs energies of proteins and
their ionization reactions as a function of temperature and pressure.
Because these values are not generally available, we calculated values
of the standard molal thermodynamic properties at 25°C
and 1 bar as well as the revised Helgeson-Kirkham-Flowers equations
of state parameters of neutral and charged zwitterionic reference
model compounds including aqueous amino acids, polypeptides, and unfolded
proteins. The experimental calorimetric and volumetric data for these
species taken from the literature were combined with group additivity
algorithms to calculate the properties and parameters of neutral and
ionized sidechain and backbone groups in unfolded proteins. The resulting
set of group contributions enables the calculation of the standard
molal Gibbs energy, enthalpy, entropy, isobaric heat capacity, volume,
and isothermal compressibility of unfolded proteins in a range of
proton ionization states to temperatures and pressures exceeding
100°C and 1000 bar. This approach provides a useful frame of
reference for thermodynamic studies of protein folding and complexation
reactions. It can also be used to assign provisional values of the net
charge and Gibbs energy of ionized proteins as a function of temperature
and pH. Using these values, an Eh-pH diagram for a reaction representing
the speciation of extracellular proteins from <i>Pyrococcus furiosus</i> and
<i>Bacillus subtilis</i> was generated. The predicted predominance
limits of these proteins correspond with the different electrochemical
conditions of hydrothermal vents and soils. More comprehensive calculations
of this kind may reveal pervasive chemical potential constraints on
the interactions of microbes with their environment.
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