Urry D.W. (Ed.) What Sustains Life? : Consilient Mechanisms for Protein-Based Machines and Materials
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References
325
28.
M.F. Colombo, D.C. Rau, and V.A. Parsegian,
"Protein Solution in Allosteric Regulation: A
Water Effect on Hemoglobin." Science, 256,
655-659,1992.
29.
C. Bohr, K.A. Hasselbalch, and A. Krogh,
"Uber einem in biologischen Beziehung
wichtigen Einfluss, den die Kohlensaurespan-
nung des Blutes auf dessen Sauerstoffbinding
ubt."
Skand.
Arch. Physiol., 16, 401^12,
1904.
30.
Christian Bohr was the father of quantum
physicist Niels Bohr.
31.
J.A.V. Butler, "The Energy and Entropy of
Hydration of Organic Compounds." Trans.
Faraday Soc, 33, 229-238,1937.
32.
H.M. Berman, J. Westbrook, Z. Feng, G.
GilUland,
T.N.
Bhat, H. Weissig, I.N. Shindyalov,
and PE. Bourne, "The Protein Data Bank."
Nucleic Acids Res., 28, 235-242, 2000.
33.
E. Martz, "FrontDoor to Protein Explorer
1.982 Beta" Copyright © 2002. Website:
proteinexplorer.org.
34.
D.W. Urry and J.W Pettegrew, "Model Systems
for Interacting Heme Moieties. II. The Ferri-
heme Octapeptide of Cytochrome." /. Am.
Chem.
Soc, 89, 5276-5283,1967.
35.
J.R.H. Tame and B. Vallone, "The Structures of
Deoxy Human Haemoglobin and the Mutant
Tyra42 His at 120K." Acta Crystal. D, 56,
805-811,2000.
36.
M. Paoli, R. Liddington, J. Tame, A. Wilkinson,
and G. Dodson, "Crystal Structure of T State
Haemoglobin with Oxygen Bound at all Four
Haems." /. Mol. Biol, 256,775-792,1996.
37.
The choice of the crystal structure of Paoh
et al.,^^ with each of the heme sites occupied by
oxygen (while remaining in the T state), goes to
the primary purpose, which is to determine
the effect of binding the very polar oxygen
molecule to the heme on the hydrophobicity of
heme and to assess its influence on proximal
groups through AGap. As such, this crystal pro-
vides a challenging test of the consilient mech-
anism to see if the effects of AGap are apparent
even though changes in quaternary structure
are limited. For our purposes, the structure will
be delineated as oxyHb(T).
38.
J. Vojtechovsky, J. Berendzen, K. Chu, L.
Schlichting, and R.M. Sweet, "Implications for
the Mechanism of Ligand Discrimination and
Identification of Substrates Derived from
Crystal Structures of Myoglobin-Ligand Com-
plexes at Atomic Resolution." Protein Data
Bank, Structure Files, 1A6N and 1A6M.
39.
A. Brzowowski, Z. Derewenda, E. Dodson, G.
Dodson, M.J. Grabowowski, R. Liddington, T
Skarzynski, and D. Valley, "Bonding of Molec-
ular Oxygen to T State Human Haemoglobin."
Nature, 307, 74-76,1984.
40.
R.C. Liddington, Z. Derewenda, G. Dodson,
and D. Harris, "Structure of the Liganded T
State of Haemoglobin Identifies the Origins of
Cooperative Oxygen Binding." Nature, 331,
725-728,1988.
41.
R.C. Liddington, Z. Derewenda, E. Dodson, R.
Hubbard, and G. Dodson, "High resolution
crystal structures and comparisons of T state
deoxy and two liganded T state hemoglobins: T
(aoxy) Haemoglobin and T (met) Haemoglo-
bin." /. Mol. Biol, 228, 551-579,1992.
42.
C. Rivetti, A. MozareUi, G.L. Rossi, E.R. Henry,
and W.A. Eaton, "Oxygen Binding by Single
Crystals of Haemoglobin." Biochemistry, 32,
2888-2906,1993.
43.
D. Voet and J.G. Voet, Biochemistry, 2nd
Edition, John Wiley & Sons, New York, 1995,
p.
226.
44.
See, for example, "Sickle Cell Anemia." Ency-
clopedia Britannica, 2002.
45.
W.A. Eaton and J. Hofrichter, "Sickle Cell
Hemoglobin Polymerization," Adv. Prot.
Chem.,
40, 63-279,1990.
46.
M. Manno, A. Emanuele,
V.
Martorana, PL. San
Biagio, D. Bulone, M.B. Palma-Vitorelli, D.T
McPherson, J. Xu,T.M. Parker, and D.W. Urry,
"Interaction of Processes on Different Time
Scales in a Bioelastomer Capable of Per-
forming Energy Conversion." Biopolymers, 59,
51-64,
2001.
47.
E Sciortino, K.U. Prasad, D.W. Urry, and M.U.
Palma, "Self-assembly of Bioelastomeric
Structures From Solutions: Mean Field Critical
Behavior and Flory-Huggins Free-energy of
Interaction." Biopolymers, 33, 743-752,1993.
48.
PL. San Biagio and M.U. Palma, "Spinodal
Lines and Flory-Huggins Free-energies for
Solutions of Human Hemoglobins HbS and
HbA." Biophys. J., 60, 508-512,1991.
49.
PL. San Biagio and M.U. Palma, "Solvent-
induced Forces and Fluctuations: A Novel
Comparison of Human Hemoglobin S and A."
Comments Theor Biol, 2, 453^70,1992.
50.
D.W. Chung, IE. Harris, and E. Harris,
"Nucleotide Sequences of the Three Genes
Encoding for Human Fibrinogen." Adv. Exp.
Med. Biol, 281, 39-48,1990.
51.
Z. Yang, J.M. Kollman, L. Pandi, and R.F.
Doolittle, "Crystal Structure of Native Chicken
326
7.
Biology Thrives Near a Movable Cusp of Insolubility
Fibrinogen at 2.7 A Resolution." Biochemistry,
40,12515-12520,2001.
52.
D.W. Urry, T.L. Trapane, and K.U. Prasad,
"Phase-structure Transitions of the Elastin
Polypentapeptide-water system Within the
Framework of Composition-Temperature
Studies." Biopolymers, 24,2345-2356,1985.
53.
M.W. Mosesson, K.R. Siebenlist, and D.A. Meh,
"The Structure and Biological Features of
Fibrinogen and Fibrin." Ann. N.Y.
Acad.
Sci.,
936,11-30, 2001.
54.
G. Spraggon, S.J. Everse, and R.S. Doolittle,
"Crystal Structures of Fragment D from
Human Fibrinogen and its Crosslinked Coun-
terpart from Fibrin." Nature, 389,455-462,1997.
55.
S.J. Everse, G. Spraggon, L. Veerapandian, M.
Riley, and R.F. Doolittle, "Crystal Structure of
Fragment Double D from Human Fibrin with
Two Different Bound Ligands." Biochemistry,
37,
8637-8642,1998.
56.
L.C. Serpen, M. Sunde, and C.C.F Blake, "The
molecular basis of amyloidosis." Cell. Mol Life
Sci., 53, 871-887,1997.
57.
Amyloid deposits are fibrous protein structures
of high p-sheet content that are identified
microscopically from their staining characteris-
tics,
giving a green birefringence when stained
with the dye Congo red.
58.
R.B. Wickner, K.L. Taylor, H.K. Edskes, M.-L.
Maddelein, H. Moriyama, and B.T. Roberts,
"Prions in Saccharomyces and Podospora spp.:
Protein-based Inheritance." Microbiol. Mol.
Biol. Revs., 63, 844-861,1999.
59.
J.S. Griffiths, "Self-replication and Scrapie."
Nature, 215,1043-1044,1967.
60.
S.B. Prusiner, "Novel Proteinaceous Particles
Cause Scrapie." Science, 216,136-144,1982.
61.
S.B. Prusiner, "Scrapie Prions." Annu. Rev.
Microbiol., 43, 345-374,1989.
62.
The word scrapie evolved from the habit of
sheep with the disease to "scrape off" their
coats by rubbing against available surfaces such
as trees, apparently due to an itching symptom
characteristic of the disease.
63.
S.B. Prusiner, D.C. Gajdusek, and M.P. Alpers,
"Kuru with Incubation Periods Exceeding Two
Decades." Ann. Neurol., 12,1-9,1982.
64.
The term spongiform encephalopathy arises
from the appearance of the brain tissue
wherein the brain is riddled with lacunae or
vacuoles giving rise to a sponge-like
appearance.
65.
P Brown, PP Liberski, A.
Wolff,
and D.C.
Gaj-
dusek, "Resistance to Steam Autoclaving After
Formaldehyde Fixation and Limited Survival
After Ashing at 360 Degrees C: Practical and
Theoretical Limitations." /. Infect. Dis., 161,
467-472,1990.
66.
D.M. Taylor, H. Eraser, I. McConnell, D.A.
Brown, K.A. Lanza, and G.R. Smith, "Decont-
amination Studies with the Agents of Bovine
Spongiform Encephalopathy and Scrapie."
Arch.
Virol., 139, 313-326,1994.
67.
An advantage of using elastic protein-based
polymers as scaffoldings for soft tissue
restoration as discussed in Chapter 9 would
be to overcome the problem of infectious
prions.
68.
J. CoUinge, K.C. Sidle, J. Meads, J. Ironside, and
A.F.
Hill, "Molecular Analysis of Prion Strain
Variation and the Aetiology of 'New Variant'
CJD."
Nature, 383, 685-690,1996.
69.
Health Canada—Canada Comminicable
Disease Report, Vol. 22-17. Website:
http://www.hc-sc.gc.ca/hpb/lcdc/publicat/ccdr/
96vol22/dr2217ec.html.
70.
See the "Kimball's Biology Pages" Website:
http://users.rcn.com/jkimball.ma.ultranet/
BiologyPages/W/Welcome.html, specifically,
http://users.rcn.com/jkimball.ma.ultranet/
B iology Pages/P/Prions. html.
71.
D.W. Urry and C.-H. Luan, "Proteins: Structure,
Folding and Function." In Bioelectrochemistry:
Principles and Practice, G. Lenaz, Ed.,
Birkhauser Verlag AG, Basel, Switzerland,
1995,
pp. 105-182.
72.
When using the data for
AGHA
of Table 5.3 with
the values
AGHACGIU)
= + 0.75 kcal/mole-
pentamer and
AGHA(G1U")
= -i- 3.72kcal/mole-
pentamer, five peptide units would sum to give
the an equivalent AGgp of an ionized glutamate
residue. If a sufficient concentration of edge
chains of a p-sheet could be experimentally
prepared and examined by NMR, the lack of
adequate peptide hydrogen bonding might be
observable by distinctive chemical shifts
of the CO and NH peptide atoms of the edge
P-chain.
73.
H. Inouye, J. Bond, M.A. Baldwin, H.L. Ball,
S.B. Prusiner, and D.A. Kirschner, "Structural
Changes in a Hydrophobic Domain of the
Prion Protein Induced by Hydration and by Ala
-^ Val and Pro -^ Leu Substitutions." /. Mol.
Biol., 300,1283-1296, 2000.
74.
The designation PIOIL indicates that the
proline (Pro, P) residue 101 of the normal
sequence has mutated to give a leucine (Leu,
L) residue, and similarly the A ^ V designation
References
327
without enumeration of the residue number
means a less hydrophobic alanine (Ala, A)
residue has been mutated to a more oil-like
valine (Val, V) residue.
75.
D.D. Laws, H-M.L. Bitter, K. Liu, H.L. Ball, K.
Kaneko, H. Wille, RE. Cohen, S.B. Prusiner, A.
Pines,
and D.E. Wemmer, "Solid-state NMR
Studies of the Secondary Structure of a Mutant
Prion Protein Fragment of 55 Residues that
Induces Neurodegeneration." Proc. Natl
Acad.
ScL U.S.A., 98,11686-11690, 2001.
76.
S.B. Prusiner, "Molecular Biology of Prion
Diseases." Science, 252,1515-1522,1991.
77.
W. Swietnicki, R. Petersen, P. Gambetti, and
W.K. Surewicz, "pH Dependent StabiUty and
Conformation at the Recombinant Human
Prion Protein PrP (90-231)." /. Biol. Chem.,
272,
27517-27520,1997.
78.
S.
Hornemann and R. Glockshuber, "A Scrapie-
like Unfolding Intermediate at the Prion
Protein Domain PrP (121-231) Induced by
Acidic pH." Proc. Natl.
Acad.
Sci. U.S.A., 95,
6010-6014,1998.
79.
H. Wille, M.D. Michelitsch, V. Guenebaut, S.
Supattapone, A. Serban, EE. Cohen, D.A.
Agard, and S.B. Prusiner, "Structural Studies of
the Scrapie Prion Protein by Electron Crystal-
lography." Proc. Natl.
Acad.
Sci. U.S.A., 99,
3563-3568,2002.
80.
D.R. Booth, M. Sunde, V. Bellotti, C.V.
Robinson, W.L. Hutchinson, RE. Frazer, P.N.
Hawkins, CM. Dobson, S.E. Radford, C.C.F
Blake, and M.B. Pepys, "Instability, Unfolding
and Aggregation of Human Lysozyme Variants
Underlying Amyloid Fibrillogenesis." Nature,
385,
787-793,1997.
81.
Z. Xu and PB. Sigler, "GroEL/GroES: Struc-
ture and Function of a Two-stroke Folding
Machine." / Struct. Biol., 124,129-141,1998.
82.
Z. Xu, A.L. Horwich, and PB. Sigler,
"The Crystal Structure of Asymmetric
GroEL-GroEs-(ADP)7 chaperonin complex."
Nature, 388, 741-750,1997.
83.
C.B. Anfinsen, "Principles that Govern the
Folding of Protein Chains." Science, 181,
223-230, 1973. The Anfinsen principle is that
the sequence of a protein dictates the full three-
dimensional structure that it would form, that
is,
sequence dictates protein folding and assem-
bly. The need for molecular chaperones sug-
gests that the correctly folded protein, the
lowest energy structure, is not always the result
and that the problem arises out of improper
hydrophobic associations. Interestingly, the
need for molecular chaperones is greatest when
temperature is elevated. They were first identi-
fied as heat shock proteins, which are just the
conditions where metastable hydrophobic asso-
ciations would occur. The rise in temperature
from that of the cusp of insolubility to the insol-
uble hydrophobically associated state occurred
without opportunity for the protein to sort out
the lowest energy, hydrophobically associated
state.
Thus, biology employs a polar cage that
ensures hydrophobic dissociation and then
systematically decreases polarity of the cage by
hydrolysis of ATP with phosphate release to
allow for correct hydrophobic re-association.
84.
See references 4 and 5 of Chapter 1.
85.
J.
Wang and D.C. Boisvert, "Structural Basis for
GroEL-assisted Protein Folding from the
Crystal Structure of (GroEL-KMgATP)i4 at 2.0
A Resolution."/. Mol. Biol., 327,843-855,2003.
86.
K. Braig, Z. Otwinowski, R. Hedge, D.C.
Boisvert, A. Joachimiak, A.L. Horwich, and P.B.
Sigler, "The Crystal Structure of Bacterial
Chaperonin GroEL at 2.8 A." Nature, 371,
578-586,1994.
87.
K. Braig,
P.
Adams, and A.T Brunger, "Confor-
mational VariabiHty in the Refined Structure of
the Chaperonin GroEL at 2.8 A Resolution."
Nature Struct. Biol., 2,1083-1094,1995.
88.
Such an apolar-polar repulsion became appar-
ent on analysis of the data in Figure
5.31.
In that
case,
even though Model Protein v, (GVGVP
GVGFP GEGFF GVGVP GVGFP GFGFP)42
(GVGVP), was completely unfolded and the
carboxylates were free to reach out for water
unperturbed by the other, there still remained
a measured repulsion of 2.4kcal/mole-carboxy-
late.
The freedom of motion of the otherwise
random coil structure was constrained from a
range of conformations by the 2.4kcal/mole
repulsion between carboxylate and the more
hydrophobic phenylalanine (Phe, F) residues.
89.
Calculations of the surface
AGHA
values are
necessarily very gross until they are given per
nanometer squared and until a set of rules are
developed to take into consideration the extent
of residue exposure to the surface and espe-
cially the exposure of the charged or polar
component of the functional side chain to the
surface.
90.
R. Lovat and J.C. Preiser, "Antioxidant Therapy
in Intensive Care." Curr Opin. Crit. Care, 9,
266-270,
2003.
91.
D.W. Urry, H. Sugano, K.U. Prasad, M.M. Long,
and R.S. Bhatnagar, "Prolyl Hydroxylation of
328
7.
Biology Thrives Near a Movable Cusp of Insolubility
the Polypentapeptide Model of Elastin Impairs
Fiber Formation." Biochem. Biophys. Res.
Commun., 90,194-198,1979.
92.
R.S. Bhatnagar, R.S. Rapaka, and D.W. Urry,
"Interaction of Polypeptide Models of Elastin
with Prolyl Hydroxylase." FEBS Lett., 95,
61-64,1978.
93.
L.M. Barone, B. Faris, S.D. Chipman, P Toselli,
B.W. Oakes, and C. Franzblau, "Alteration of
the Extracellular Matrix of Smooth Muscle
Cells by Ascorbate Treatment." Biochchim.
Biophys. Acta, 840,245-254,1985.
94.
E.R. Peacock, Jr., Wound Repair, W.B.
Saunders, Philadelphia, 1984, pp.
56-101.
95.
D.W. Urry, "Entropic Elastic Processes in
Protein Mechanism. II. Simple (Passive) and
Coupled (Active) Development of Elastic
Forces."/. Protein Chem.,7,81-114,1988, espe-
cially Figure 12.
96.
D.W. Urry, R.S. Bhatnagar, H. Sugano, K.U.
Prasad, and R.S. Rapaka, "A Molecular
Basis for Defective Elastic Tissue in
Environmentally Induced Lung Disease." In
Molecular Basis of Environmental Toxicity,
R.S.
Bhatnagar, Ed., Ann Arbor Scientific
Publishers, Inc., Ann Arbor, MI, pp. 515-530,
1980.
97.
J.G. Clark, C. Kuhn, and R.P Meacham, "Lung
Connective Tissue." Int. Rev. Connect. Tissue
Res.,
10, 249-331,1983.
98.
P.J. Stone, "The Elastase-Antielastase Hypoth-
esis of the Pathogenesis of Emphysema." Clin.
Chest Med., 4,405-412,1983.
99.
G.L. Snider, "Two Decades of Research in the
Pathogenesis of Emphysema." Schweiz Med.
Wochenschr., 114, 898-906,1984.
100.
A.
Janoff,
"Elastases and Emphysema. Current
Assessment of the Protease-Antiprotease
Hypothesis." Am. Rev. Respir Dis., 132,
417^33,1985.
101.
C. Kuhn, S.-Y. Yu, M. Chraplyvy, H.E. Linder,
and R.M. Senior, "The Induction of Emphy-
sema with Elastase. II. Changes in Connective
Tissue." Lab. Invest., 34, 372-380,1976.
102.
M. Osman, S. Keller, Y. Hosannah, J.O. Cantor,
G.M. Turino, and I. Mandl, "Impairment of
Elastin Resynthesis in the Lungs of Hampsters
with Experimental Emphysema Induced by
Sequential Administration of Elastase and
Trypsin." 105, 254-258,1985.
103.
D. Voet and J.G. Voet, Biochemistry, 2nd Ed.,
John Wiley & Sons, New York, 1995.
104.
J.G. White, "Ultrastructural Features of
Erythrocyte and Hemoglobin Sickling." Arch.
Intern. Med., 133, 545-562,1974.
105.
G.W Dykes, R.H. Crepeau, and S.J. Edelstein,
"Three-dimensional Reconstruction of 14-
Filament Fibers of Hemoglobin S."/. Mol. Biol.,
130,451^72,1979
106.
ID. Harper and PT Lansbury, Jr., "Models of
Amyloid Seeding in Alzheimer's Disease and
Scrapie: Mechanistic Truths and Physiological
Consequences of the Time-dependent Solubil-
ity of Amyloid Proteins." yln«M. Rev. Biochem.,
66,
385-407,1997.
8
Consilient Mechanisms for
Protein-based Machines of Biology
8.1 Thesis
Biology thrives near a movable cusp of insolu-
bility, and the forces that, in a positively cooper-
ative manner, power the molecular machines
of biology drive spatially localized hydropho-
bic protein domains back and forth across
thermodynamically movable water-solubility-
insolubilitv divides.
8.1.1 Further Considerations of the
Volume Title
This chapter is the principal focal point for the
question asked in the title, What Sustains Life?
The obvious answer, of course, is that protein
machines access energy available in the envi-
ronment and convert it to those forms of energy
required for Life to flourish. The specific
rejoinder in the title speaks of "Consilient
Mechanisms for...." In our usage, consilient
mechanism means a particular "common
groundwork of explanation,"^ whereby protein-
based machines access the whole range of avail-
able energies and convert those energies to
the many energy forms required to build and
operate the structures that constitute the func-
tional living entity.
A more complete technical description of the
consilient mechanisms of concern to biological
energy conversion encompasses two distinct
but interlinked physical processes of hydropho-
bic association and of elastic force development.
The latter results from a generally appUcable
mechanism of entropic elastic force arising
from the damping of internal chain dynamics
on deformation of an interconnecting chain
segment that began with significant kinetic
freedom. The fundamentals of hydrophobic
association are embodied within the com-
prehensive hydrophobic effect, expressed in
terms of the Gibbs free energy of hydrophobic
association,
AGHA-
As developed in Chapter 5,
the operative component of
AGHA
is the
apolar-polar repulsive free energy of hydra-
tion, AGap. Extensive studies on systematically
varied elastic-contractile model proteins
demonstrate that AGap derives from the
competition for hydration between apolar
(hydrophobic) and polar (e.g., charged)
groups.
The rejoinder in the title continues, "Protein-
based Machines " Biology's protein-based
machines group into three functional cate-
gories: (1) those of the electron transport chain
that produce the proton concentration gradient
by pumping protons from one side to the other
of the inner mitochondrial membrane; (2) those
that synthesize adenosine triphosphate (ATP),
principally ATP synthase of the inner mito-
chondrial membrane that utilizes the proton
gradient to produce ATP; and (3) those many
ATPases that use ATP in carrying out the
essential functions of the Hving cell. Arguably,
the protein-based machine most vital to energy
conversion in living systems is ATP synthase
of the inner mitochondrial membrane. This
proton-powered rotary motor produces nearly
90%
of the ATP, the energy coin, of biology.
329
330
8. Consilient Mechanisms for Protein-based Machines of Biology
ATP and equivalent nucleotide triphosphates
(NTPs) power essentially all subsequent
protein-based machines of biology, either
directly or indirectly.
The crucial protons that fuel ATP synthase
result from the action of four complexes, four
protein-based machines, of the electron trans-
port chain within the inner mitochondrial mem-
brane. Of the four, Complex III (ubiquinone:
cytochrome c oxidoreductase^) provides a
particularly reveaUng protein-based machine,
wherein the power of AGap achieves ready
recognition in the role of proton gatekeeper
and wherein a single strand of protein chain,
stretched by hydrophobic association, provides
for the elastic force development essential for
subsequent domain movement resulting in
electron transfer. Accordingly, the hydrophobic
and elastic consiUent mechanisms, in our view
as developed in Chapter 5 and given example
below, provide salient insight into the function
of Complex III and, as we shall also see, into
the function of ATP synthase and the myosin II
motor of muscle contraction.
For the casual observer, muscle contraction
presents the most notable ATPase-based
protein machine of biology. Specifically, the
Unear myosin II motor of striated muscle most
signifies the motion of mammalian Life, as
exemplified by the discus thrower mentioned in
the introduction to Chapter 2. In particular, the
powerstroke of the myosin II motor provides
another stunning example of the hydrophobic
consiUent mechanism. In this case, binding of
the very polar ATP molecule or an equivalent
chemical analogue disrupts hydrophobic asso-
ciation that becomes re-estabHshed in the
absence of ATP, for example, in the near-rigor
state.^
The myosin II motor in part illustrates
the case of the hydrophobic consilient mecha-
nism by providing insight into the physical basis
for what Rayment and his colleagues described
as a thermodynamic instability in their insight-
ful paper, "Revised Model for the Molecular
Basis of Muscle Contraction.'"^ Therefore, a
short restatement of the physical bases for the
pervasive hydrophobic and elastic consilient
mechanisms follows, initially in a qualitative
sense and then in a more detailed sense in the
subsequent parts of section 8.1.
8.1.2 Representation of the Movable
Cusp of Insolubility
The experimental endothermic heat of the
inverse temperature transition of hydrophobic
association symbolizes the hydrophobic con-
siUent mechanism. That symbol, the sign of the
cusp of insolubihty, is recognized in Figures 1.1
and 7.1. Different nonthermal energy inputs
power biology's protein-based machines
through the inverse temperature transition
by moving the cusp of insolubility along the
temperature axis.
8.1.3 Moving the Cusp of Insolubility
The physical basis of the hydrophobic con-
silient mechanism draws from the comprehen-
sive hydrophobic effect in the form of a Gibbs
free energy of hydrophobic association, AGHA,
and the size of the cusp of insolubihty deter-
mines the magnitude of
AGHA-
Hydrophobic
hydration provides the dominant thermody-
namic contribution to
AGHA-
The foremost
functional component of
AGHA
is the change in
apolar-polar repulsive free energy of hydra-
tion, AGap, which arises from the competi-
tion for hydration between apolar (hydropho-
bic) and polar (e.g., charged) groups. AGap
dictates the interchange of structural states of
protein domains from hydrophobically associ-
ated (insoluble) to hydrophobically dissociated
(soluble). Thus, as developed in Chapter 5 with
designed elastic-contractile model proteins,
AGap is the thermodynamic quantity that moves
the cusp of insolubility; it drives spatially local-
ized hydrophobic domains of model proteins
back and forth between solubility and insolu-
bility, and, in doing so, it catalyzes the set of
energy conversions extant in biology.
8.1.4 Positive Cooperativity
The AGap-driven interconversion between
states of solubility and insolubility exhibits
positive cooperativity and as such becomes
the physical basis for the allosteric effect of
Monod.^ Thus, AGap, demonstrated with
designed model proteins, results in a positively
cooperative interchange between hydrophobic
8.1 Thesis 331
association (insolubility) and hydrophobic
dissociation (solubility) that constitutes the
movable cusp of insolubility. Therefore^ we ask,
are the Gibbs free energy of hydrophobic asso-
ciation and its operative apolar-polar repulsive
free energy of hydration relevant to the molecu-
lar machines of biology? In other words, does
Monod's "second secret of Life''^'^ reside within
the particulars ofAGap?
As shown in Chapter 5, the molecular basis
of positive cooperativity and the source ofAGap
arise from changes in the competition for
hydration that result when converting a func-
tional group from a more polar to a less polar
state and vice versa. When the polar species
becomes neutralized, for example, H^ + -COO"
-^ -COOH, or -NH3^ -> -NH2 + H% or an oxi-
dized state -> a reduced state, or MgATP"^ +
H2O -^ MgADP- + HPO4-2 + H\ the remaining
less polar (the less charged, bold-faced) product
no longer destructures as much hydrophobic
hydration. The resulting reconstitution of suffi-
cient additional hydrophobic hydration drives
hydrophobic association, because the (-TAS)
term becomes more positive and overwhelms
the inherently negative AH term. In short,
AG(solubility), which equals AH - TAS,
becomes positive and solubiUty is lost.
Limitations in the amount of polar hydration,
arising due to the competition for hydration
with hydrophobic groups, result in large shifts
in pKa values and in reduction potentials and
associated changes in positive cooperativity
(see Figure 5.20). These hydrophobic-induced
shifts in the free energy of the more polar state
of functional groups, that is, groups that can
occur in two or more states of polarity, are
central to the hydrophobic consilient mechanism
for energy conversion by controlling hydropho-
bic association/dissociation.
8.1.5 Contractility as the Coupling of
Hydrophobic Association and Elastic
Force Development
Hydrophobic association within a protein chain
constitutes an element of contraction. From our
design and study of elastic-contractile model
proteins, a contraction comprises two distinct
but interlinked physical processes. They are
hydrophobic association between domains
within the protein construct and the associated
development of an elastic force within inter-
connecting chain segments.^
The experimental condition of isometric con-
traction, the development of elastic force at
fixed extension, most clearly brings to light the
role of the elastic element of contraction. At
this stage one begins to recognize two con-
silient mechanisms—the hydrophobic con-
silient mechanism for hydrophobic association
and the elastic consilient mechanism for the
fundamental process of elastic force develop-
ment. The coupled physical processes of
hydrophobic association/dissociation and
changes in elastic force constitute key aspects
of function and efficiency of contractile
protein-based machines. Working in combina-
tion, the hydrophobic and elastic consilient
mechanisms are considered relevant to the
function of the Rieske Iron Protein movement
of Complex III and of the myosin II Hnear
motor, most notably during isometric contrac-
tions (see sections 8.3.4 and 8.5.3).
8.1.6 On the Relevance of
Hydrophobic and Elastic Consilient
Mechanisms to Biology's Protein-
based Machines
Before proceeding further with these introduc-
tory comments, the reader should be aware that
professionals in the specialized areas have
proposed mechanistic detail for a number of
biology's protein-based machines. None of
those descriptions, however, has considered
what we describe as the comprehensive
hydrophobic effect. Although an awareness of
hydrophobic effects is pervasive with a long
history going back most notably to Edsall in
1935^
and Butler in 1937,^° there remains an
absence of the concept of a competition for
hydration between apolar and polar groups for
hydration, that is, of the AGap component of the
comprehensive hydrophobic effect. Conse-
quently, there is no appreciation of the domi-
nance of AGap as a controlling element within
AGHA-
AS a result, the proposed fundamental
role of AGap within protein mechanisms has
been absent.
332
8. Consilient Mechanisms for Protein-based Machines of Biology
Similarly for the elastic consilient mecha-
nism, elastic force development can be the
result of hydrophobic association resulting in
the damping of internal chain dynamics within
interconnecting chain segments, as we believe
occurs in Complex III of the electron transport
chain and the myosin II motor. Ideal or
reversible elastic force development does not
require random chain networks and it does not
arise directly from changes in solvent entropy.
Furthermore, the apolar-polar repulsive free
energy of hydration,
AGap,
can provide a repul-
sive force that elastically constrains a protein
segment providing an elastic impulse that can
result in efficient motion, as we beUeve occurs
in ATP synthase.
Accordingly, the perspectives in Chapter 5,
developed on elastic-contractile protein-based
polymers, introduce new concepts into the func-
tional description of biology's protein-based
machines. As with the introductory comments
in Chapter 7, the footnote relevant to reactions
toward new concepts in science is repeated here
in footnote form.^^
8.1.7 Our Platform from Which
to Explore Energy Conversion
in Biology
Furthermore, to the best of our understanding,
de novo design of the family of elastic model
protein-based machines, described in Chapter
5,
and the extensive exploration of mechanism,
presented therein only in part, stand unparal-
leled in the development of an understanding
of energy conversion by protein-based ma-
terials. As such these demonstrated energy
conversions, using de novo designed molecular
machines, present a firm and warranted foun-
dation on which to explore the relevance of the
hydrophobic and elastic consilient mechanisms
to biology's protein-based machines.
This chapter discusses key protein-based
machines of biology to demonstrate the rele-
vance of the hydrophobic and elastic consilient
mechanisms. The objective in this chapter,
therefore, is to investigate selected examples of
biology's protein-based machines and to look
at the molecular level for a coherence of
phenomena with the designed elastic model
protein-based machines described in Chapter 5.
Accordingly, the following constitutes the
second of two chapters that address the third
assertion of this book, the assertion of biologi-
cal relevance, as introduced in Chapter 1. The
order in which we consider protein-based
machines of biology will follow the natural flow
of energy conversions in respiration from the
redox-driven proton pumps, to the proton-
driven rotary protein motor that produces ATP,
and to a protein motor that utilizes ATP as the
source of energy with which to drive function.
8.1.8 The Comprehensive
Hydrophobic Effect: Can This Be a
Consilient Mechanism for the Energy
Conversions of Biology?
Can the comprehensive hydrophobic effect,
developed in Chapter 5, be a consilient mecha-
nism, a "common groundwork of explanation,"^
for biology's protein-based machines? We put
forward the point of view that a "common
groundwork of explanation" does indeed
pertain to the function of the diverse protein-
based machines that sustain Life. The "common
groundwork of explanation" resides in the
thesis that introduces this chapter. Simply
restated, biology thrives by means of control-
ling the association (insolubility) and dissocia-
tion (solubiHty) of hydrophobic domains of
protein-based machines to achieve the essential
energy conversions that sustain Life. Sur-
prisingly, the extensively studied myosin II
motor of muscle contraction provides a pre-
viously unrecognized and clear demonstration
whereby addition of polar phosphate disrupts
hydrophobic association and phosphate
removal drives the hydrophobic association
that provides the powerstroke of contraction
(see section 8.5.3).
8.1.8 J Brief Considerations Relevant to
the Comprehensive Hydrophobic Effect
To date the sigmoid curve in Figure 5.10 offers
perhaps the most effective introduction to the
comprehensive hydrophobic effect. It is a plot
of the reference temperature, either Tb or Tt,^^
for the onset of the inverse temperature transi-
8.1 Thesis
333
tion
for
hydrophobic association versus AGHA,
the Gibbs free energy
of
hydrophobic associa-
tion. Calculation
of
AGHA utilizes
the
heat
of
the inverse temperature transition obtained
on
a series
of
(GVGVP)-based polymers
in
which
guest pentamers (GXGVP)
are
introduced
where
X is
each
one of the
naturally occurring
amino acid residues
as
well
as
biologically
relevant chemical modifications thereof
and
attached relevant protein prosthetic groups
(see Tables
5.2 and
5.3).
For an
inverse temper-
ature transition
for
hydrophobic association,
the heat
of the
transition
itself,
under experi-
mental conditions
in
Figures
1.1 and 7.1,
becomes
the
Gibbs free energy
for
hydropho-
bic association, which
by
Equation
5.10b is
written.
AGHA(Z)
-
AHt(ref)
-
AHt(;f).
8.1.8.1.1
The
Comprehensive Hydrophobic
Effect Resolves Three Categories
of
Amino
Acid Residues
Figure
5.10
dehneates
the
dependencies
of
AGHA
on
Tt,
or its
equivalent Tb, into slopes
of
three categories—that
of the
aliphatic hydro-
carbons, that
of
the aromatic hydrocarbons, and
that resulting from
the
interaction
of
charged
species with host hydrophobic residues.
The
slopes define
the
entropy change attending
hydrophobic association
for
each category. The
first category, defining
the
central part
of the
sigmoid, contains
the
amino acid residues that
differ only
by the
number
of
aliphatic hydro-
carbons (e.g., -CH2-,
-CH-,
-CH3), namely.
Leu, He, Val, Pro,
Ala, and
Gly. These purely
aliphatic amino acid residues define
a
linear
relationship between
AGHA
and Tt
(obtained
from temperature profiles
for
aggregation)
or
Tb (obtained from differential scanning
calorimetry data).
The
slope
for
peptides
containing only aliphatic hydrocarbons
and
peptide groups,
the
first category,
is
ASHA
= 80
cal/deg-mole(GXGVP).
The
aliphatic amino
acid residues give
a
large change in AGHA (or
in
ASHA)
for a
small change
in Tt or
Tb.
The second category, shown
at low
tempera-
ture,
involves
the
amino acid residues with aro-
matic side chains, namely,
Phe and
Trp, which
define
a
steeper dependence
of
Tt versus
AGHA-
Tyr with
its
phenolic hydrogen
is
within
the
cluster
of
aromatic residues
but is
displaced
from
the F-W
line. This
low
temperature
segment
for
aromatic residues exhibits
a
slope,
when defined
by the
data points
for F
and W,
of
ASHA
= 14cal/deg-mole(GXGVP).
The third category
in
Figure
5.10 is at
high
values
of
Tb
or Tt and is
defined
by the
charged
residues
K^ and
E~, with
a
slope
of
ASHA
= 7
cal/deg-mole(GXGVP).This slope results from
the competition
for
hydration between apolar
and charged species.
The
effectiveness
of the
formation
of
charged species
in
destructuring
hydrophobic hydration
is
most readily seen
as
large increases
in
Tt(Tb)-values that result from
charge formation.
8.1.8.1.2
Source
of the
Different Slopes
for
Aliphatic
and
Aromatic Amino Acid Residues
For
the
inverse temperature transition
of
hydrophobic association,
the
temperature
for
the onset
of the
transition,
Tt or
Tb,
is
approxi-
mately AHt/ASt, where
AHt (the net
endother-
mic heat
of
the transition)
and
ASt
(the
entropy
change
for the
transition) derive from
the
change
in
structure
and
change
in
amount
of
water attending
the
transition from hydropho-
bic hydration
to
bulk water.
The
pentagonal
dodecahedral structure
of
hydrophobic hydra-
tion surrounding
a
simple aliphatic hydrocar-
bon
gas, due to
Stackelberg
and
Miiller,^'^
appears
in the
lower part
of
Figure 2.8.
As
long
as
the
hydrophobic group
is
comprised
of
noncyclic saturated hydrocarbons,
as in the
series
of
aliphatic residues
L, I, V, P, A, and
G
of the
first category
in
Figure
5.10, the
pentagonal dodecahedral hydration structure
remains quite representative.
In
other words,
as
long
as the
series
of
amino acid residues
is
essentially described
by a
change
of a
-CH2-
or
-CH3 hydrocarbon unit,
as in the
first category,
it
is
reasonable that
a
common slope
for a Tt
versus AGHA plot would
be
experiment-
ally observed.
The
AGHA/CH2
~
-Ikcal/
deg-mole(GXGVP).
For
an
aromatic hydrocarbon,
as in the
phenyl group, -CeHs,
of
phenylalanine (Phe, F),
however, only the arrangement
of
water around
the periphery
of the
aromatic ring could begin
to approximate
a
portion
of the
pentagonal
334
8. Consilient Mechanisms
for
Protein-based Machines
of
Biology
dodecahedral arrangement.
The
water mole-
cules hydrating
the top and
bottom surfaces
of
the
planar aromatic structure would
be
expected
to
associate with different values
for
AHt
and ASt on
formation
of
hydrophobic
hydration.
Thus,
the slope
in
the Tb versus
AGHA
plot
for
aromatic, unsaturated cycHc groups
would
be
expected
to
differ from that
of
simpler aliphatic hydrocarbons.
As
shown
in
Figure
5.10, the
slope
for
aromatic groups
is
steeper than that
for
aliphatic groups.
8.1.8.1.3
Source
of the
Slopes
for
Amino
Acid Residues with Different Charged
Functional Groups
The slope defined
by the
data points
for
KVOF
and E70F, which
is due to the
charged states
of
Model Protein
x',
(GVGVP GVGVP GK^GVP
GVGVP GVGVP GVGVP)22(GVGVP),
and
Model Protein
i,
(GVGVP GVGVP GEGVP
GVGVP GVGVP GVGVP)36(GVGVP),
results from
the
hydrophobic hydration
re-
maining after formation
of the
-NHs^
and the
-COO"
states, respectively. When
the
host
polymer
is
poly (GVGVP),
the
formation
of
the charged species, -COO", destroys more
hydrophobic hydration than does
the -NHs^
charged species. Thus
the
position
of a
charged
species along this slope indicates, among other
things, the relative effectiveness
of
that charged
species
to
destructure hydrophobic hydration
in order
to
achieve
its own
hydration.
If we continue along this slope
in
Figure
5.10
to 860°C, which
is the
TfValue obtained
on extrapolation
to one
-Ser-O-POa
= per
(GVGIP)
on
phosphorylation
of the
serine
(S)
in poly[30(GVGIP),(GRGDSP)], a
AGHA
of
8kcal/mole-phosphate
is
found. Accordingly,
the phosphate group becomes recognized
as
a remarkably effective charged species
in
destructuring hydrophobic hydration.
In
fact,
phosphate
is the
most effective species that
we
have found
for
disrupting hydrophobic associ-
ation (see Table 5.2),
and its
capacity
to
change
AGHA approximates
its
free energy
of
hydroly-
sis.
In our
view, this element constitutes
the
primary process whereby
the
rotary motor,
ATP synthase,
and the
linear motor, myosin
II,
function.
8.1.8.1.4
Net
Heat Changes
for the
Inverse
Temperature Transitions
of the
Comprehensive Hydrophobic Effect
Are
Endothermic
Due to the
Conversion
of
Hydrophobic Hydration
to
Bulk Water!
Solubility
is
governed
by the
Gibbs free energy
for solubilization, AG(solubility)
= AH -
TAS.
The early work
of
Butler^^ established
the
remarkable
and
fundamental finding that for-
mation
of
water around hydrophobic groups
is
exothermic, that is,
the
formation
of
hydropho-
bic hydration constitutes
a
favorable exother-
mic reaction.
He
further demonstrated that
solubility
of
organic molecules containing
hydrophobic groups
in
water becomes lost
because
the
(-TAS) term
is
positive
for the
CH2
group
and
grows faster with each added
CH2
than
the
favorable, negative
AH
term
(see
Chapter
5,
section 5.1.3.3). During
an
inverse
temperature transition, solubility
of
hydropho-
bic groups
is
lost
on
raising
the
temperature,
that
is,
hydrophobic groups associate because
raising
the
temperature increases
the
magni-
tude
of the
positive (-TAS) term. Accordingly,
this reverse change
of
hydrophobic hydration
to bulk water,
as
occurs during
an
inverse tem-
perature transition, should
be an
endothermic
transition,
as it is.
Putting aside changes
in
hydration that
are
the fundamental defining feature
of
inverse
temperature transitions,
the
physical associa-
tion
of the
model protein molecules containing
hydrophobic groups
is
expected
to be of the
opposite sign, that
is, to be
exothermic, arising
from effects such
as van
der Waals interactions.
In preparation
of
Figure 5.10, the
net
endother-
mic AHt was used
to
calculate AGHA- The pres-
ence
of an
exothermic component resulting
from physical association
of
model protein
chains
was not
explicitly considered.
As it
should
be,
AGHA, calculated from the heat
of
the
inverse temperature transition
for
hydrophobic
association,
is the net
result
of all
changes
in
energy that attend
the
inverse temperature
transition. Nonetheless,
an
understanding
of
the
comprehensive hydrophobic effect
is
incom-
plete without some sense
of the
relative mag-
nitudes
of the
dominant endothermic
and the
smaller exothermic components.