24
2 A New View on Mechanism of Functional Expression …
turns out that the key quantity is the hydration entropy of the protein complex as
emphasized in the first paper [44] and revisited in a recently published book [47].
Our claim is that the entropic force generated by water is a dominant physical factor,
and the geometric characteristics of F-actin are more important than the electric-field
distribution emanated from F-actin.
2.10 Problems in Prevailing View on Functional Expression
of a Molecular Motor
No one considers that a protein must perform mechanical work against the viscous
resistance force by water during the folding. Water is not the external system: The
system of interest consists of not only the protein but also water where it is immersed.
The protein folds so that the free energy of the protein-water system can be minimized.
A self-assembly process such as protein folding spontaneously occurs and no input
of energy or free energy is necessitated. Water never hinders protein folding through
the viscous resistance force: It does drive a protein to fold as argued in Sect. 2.7.
Here, we comment on the physical difference between the EV, V ex , and the partial
molar volume (PMV), V M [38]. V M of a solute is the change in system volume
upon insertion of the solute into water under the isobaric condition. V ex is determined only by the geometric characteristics of protein structure and the molecular
diameter of water, but V M is also dependent on the average number density of water
molecules near the protein surface and the water-accessible-surface area (WASA)
[38]. A higher-density layer of water molecules is formed near the protein surface.
The number density of water molecules within this layer is significantly higher than
that in bulk water. As the WASA increases, “V ex −V M ”, which is positive, becomes
larger. V ex of the folded state is much smaller than that of the unfolded state. However,
the WASA of the folded state is much smaller than that of the unfolded state. Consequently, the values of V M of the folded and unfolded states are not significantly
different (in general, V M of the folded state is slightly larger than that of the unfolded
state) [32, 33]. (A pressure-denatured state is unique in the sense that its EV is only
slightly larger than the EV of the native state while its WASA is considerably larger
than the WASA of the native state. As a result, the PMV of the pressure-denatured
state is significantly smaller than that of the native state [38].) Hence, the system
volume does not change much during the folding under the isobaric condition. Moreover, the pressure P is only 1 atm. It follows that PV ~ 0 (V is the change in
system volume and PV is the mechanical work performed by the system) and
the system performs essentially no mechanical work. This is true for any biological self-assembly process. For the binding of MDM2 and p53NTD [24], 0 < PV
<< k B T (T = 298 K). For the apoPC folding, 0 < PV << k B T is corroborated both
experimentally [33] and theoretically [32].
For actomyosin, for instance, the system of interest consists of not only myosin
and F-actin but also water in which ATP, ADP, and Pi are dissolved. Hydration of
2 A New View on Mechanism of Functional Expression …
turns out that the key quantity is the hydration entropy of the protein complex as
emphasized in the first paper [44] and revisited in a recently published book [47].
Our claim is that the entropic force generated by water is a dominant physical factor,
and the geometric characteristics of F-actin are more important than the electric-field
distribution emanated from F-actin.
2.10 Problems in Prevailing View on Functional Expression
of a Molecular Motor
No one considers that a protein must perform mechanical work against the viscous
resistance force by water during the folding. Water is not the external system: The
system of interest consists of not only the protein but also water where it is immersed.
The protein folds so that the free energy of the protein-water system can be minimized.
A self-assembly process such as protein folding spontaneously occurs and no input
of energy or free energy is necessitated. Water never hinders protein folding through
the viscous resistance force: It does drive a protein to fold as argued in Sect. 2.7.
Here, we comment on the physical difference between the EV, V ex , and the partial
molar volume (PMV), V M [38]. V M of a solute is the change in system volume
upon insertion of the solute into water under the isobaric condition. V ex is determined only by the geometric characteristics of protein structure and the molecular
diameter of water, but V M is also dependent on the average number density of water
molecules near the protein surface and the water-accessible-surface area (WASA)
[38]. A higher-density layer of water molecules is formed near the protein surface.
The number density of water molecules within this layer is significantly higher than
that in bulk water. As the WASA increases, “V ex −V M ”, which is positive, becomes
larger. V ex of the folded state is much smaller than that of the unfolded state. However,
the WASA of the folded state is much smaller than that of the unfolded state. Consequently, the values of V M of the folded and unfolded states are not significantly
different (in general, V M of the folded state is slightly larger than that of the unfolded
state) [32, 33]. (A pressure-denatured state is unique in the sense that its EV is only
slightly larger than the EV of the native state while its WASA is considerably larger
than the WASA of the native state. As a result, the PMV of the pressure-denatured
state is significantly smaller than that of the native state [38].) Hence, the system
volume does not change much during the folding under the isobaric condition. Moreover, the pressure P is only 1 atm. It follows that PV ~ 0 (V is the change in
system volume and PV is the mechanical work performed by the system) and
the system performs essentially no mechanical work. This is true for any biological self-assembly process. For the binding of MDM2 and p53NTD [24], 0 < PV
<< k B T (T = 298 K). For the apoPC folding, 0 < PV << k B T is corroborated both
experimentally [33] and theoretically [32].
For actomyosin, for instance, the system of interest consists of not only myosin
and F-actin but also water in which ATP, ADP, and Pi are dissolved. Hydration of