Urry D.W. (Ed.) What Sustains Life? : Consilient Mechanisms for Protein-Based Machines and Materials

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2.4 Essential Energy Conversions That Sustain Life

Respiration

2 oxidized flavins

oxidized nicotinamides

a. glycolysis ir^ j j

transition reaction 10 redUCea

+ 24H+ + 24e-

gluCOSe

Krebs cycle

I6CO2I 4ATP

nicotinamide^

*'2

reduced flavins

FIGURE

2.11.

Simplified schematic representation of the energy conversion steps of respiration are shown.

See text for more discussion.

Electrons, obtained by oxidation of

reduced nicotinamides and flavins, flow through

the electron transport chain (a series of pro-

teins with associated groups that cyclically

become oxidized and reduced) in the inner

mitochondrial membrane ultimately to oxygen

with regeneration of water, H2O, while

pumping protons (acid) across the inner mito-

chondrial membrane into the intermembrane

space between the inner and outer mitochon-

drial membranes.

The

1,000-fold

greater concentration of

protons (acid) of the intermembrane space

return across the inner mitochondrial mem-

brane and produce chemical energy, in the

form of ATP.^^ As in photosynthesis, the ATP

results from the protein-based machine ATP

synthase.

Key intermediate energy-converting steps

common to both photosynthesis and respiration

are (1) the cyclic reduction and oxidation of

nicotinamides and flavins coupled to the

pumping of acid (protons) from one side to the

other of

membrane and (2) the return of acid

(protons) across the membrane coupled to pro-

duction of ATP.

2.4.2 Key Molecular Players Change

Charge in Both Photosynthesis

and Respiration

As seen above, the two primary molecular

players of photosynthesis and respiration are

nicotinamide and ATP. Both of these key mol-

ecules effect change in the charge of a protein

machine during its function. In particular.

oxidized nicotinamide is positively charged,

and, on reduction (on addition of negative elec-

trons),

it becomes uncharged (more oil-like,

more hydrophobic). ATP can add a negatively

charged phosphate to a protein machine to

make it less oil-like, and removal of the phos-

phate dramatically increases the oil-like char-

acter of the protein machine. The decrease of

charge in model proteins, as in going from

vinegar-Uke to more oil-Uke by means of reduc-

tion of nicotinamide or by means of dephos-

phorylation, can drive hydrophobic folding

(association of oil-like groups).^^'^^

2.4.3 Key Molecular Players Perform

Mechanical Work in Model Proteins

Reduction of oxidized nicotinamide attached to

an elastic model protein lowers the transition

temperature and drives hydrophobic folding,

that is, reduction drives contraction with the

lifting of a weight,^^ as depicted in Figures 2.6C

and 2.9 reaction

(Hi).

The process is reversible;

re-oxidation of the attached nicotinamide

returns the elastic model protein to its original

unfolded state. ATP attaches one of its three

charged phosphates to an elastic model protein

and yields ADP This phosphorylation, the addi-

tion of the super vinegar-Hke phosphate group,

causes unfolding of the hydrophobically folded

model protein.^^ Subsequent removal of the

phosphate drives hydrophobic folding, that is,

dephosphorylation can drive contraction with

the lifting of a weight. Both molecular players

of the key steps of photosynthesis and respira-

tion have been used to perform mechanical

What Sustains Life? An Overview

work with properly designed model proteins.

The cydic reduction/oxidation and the cydic

dephosphorylation/phosphorylation achieve

one contraction/relaxation cyde with the con-

sumption of two electrons and a proton and

with consumption of one phosphate of the ATP

molecule, respectively.

2.4.4 Relationship of Key Molecular

Players to Protons

Further direct analogy to the key intermediate

steps of photosynthesis and respiration com-

bines reduction of positively charged groups (to

drive hydrophobic folding) with performing

chemical work of changing the concentration of

protons, of pumping protons. It further com-

bines protonation of negatively charged groups

(to drive hydrophobic folding) with performing

the chemical work of energizing a phosphate

plus ADP to form ATP.

The justification for this view of ours is in the

demonstration that making a model protein

more oil-like can increase the affinity of car-

boxylates for protons up to a millionfold,^°

whereas an increase of only some 3,000-fold is

required to pump protons for the relevant steps

of photosynthesis and respiration.

As noted above in Figures 2.6C and 2.9

reaction (///), the reduction of a nicotinamide

attached to a model protein lowers the folding

temperature by increasing hydrophobic hydra-

tion and, therefore, drives folding at body

temperature.^^ Importantly, however, when

the model protein also contains a negatively

charged carboxylate, -COO", increasing the

hydrophobicity by reduction of the nicoti-

namide forces the functional vinegar-like, neg-

atively charged carboxylate group to become

uncharged and more oil-like by the uptake of a

positive proton, ¥t (see Figure 2.12B).^^ Also

directly, the association of proton, H^, with a

negatively charged R-group, for example,

-CH2-CH2-COO", on a model protein lowers

the folding temperature and drives hydropho-

bic folding at body temperature (See Figure

2.6B). Furthermore, protonation of a negatively

charged -COO" group increases hydrophobic-

ity and is expected, in our view, to energize an

attached phosphate. Pi, such that it would have

the capacity to phosphorylate ADP to produce

ATP (see Figure 2.12A). ATP

is,

again, the basic

source of energy that produces motion and per-

forms other biological functions. This combin-

ing of two different functional groups within

the same molecular machine becomes central

to the use of designed elastic-contractile model

proteins to provide insight into the mechanism

for fundamental processes of photosynthesis

and respiration. The point to retain is that the

studies on designed elastic-contractile model

protein demonstrate the correct energy consid-

erations to perform the indicated energy con-

versions, but different structures may be used

to harvest properly output energies other than

mechanical.

2.4.5 Immediate Energy Sources for

the Motion of Muscle Contraction

The source of energy for muscle contraction is

ATP.

During one cycle of contraction and relax-

ation, ATP is bound, spUt into the products of

ADP and Pi (or PO/"), and the products are

sequentially released.^^ The triggering mecha-

nism for contraction, however, is the release of

calcium ion (Ca^^) from nearby stores into the

muscle cell, where the calcium ions bind to car-

boxylates of the muscle proteins.

This sudden increase in Ca^^ concentration

also constitutes an energy requirement for con-

traction. In fact, calcium pumps in the cell mem-

brane use ATP to pump calcium ion out of the

cell into nearby storage compartments to be

held in readiness for release through trans-

membrane channels that are electrically trig-

gered to open by a nerve impulse. Thus, the

energy to drive contraction of the voluntary (or

striated) muscle of the discus thrower comes

directly from ATP and from an increase in

calcium ion concentration, with the latter also

being achieved through expenditure of ATP.

What can be demonstrated with model

proteins functioning as contractile molecular

machines is that two of the most effective

means of lowering the temperature of an

inverse temperature transition to drive con-

traction are positively charged calcium ions

(Ca^^) binding at paired negatively charged

carboxylates (COO~) to decrease net charge

H+

protonation

due to

concentration

of protons

ADP ATP

oil-like

hydration

energizes

phosphate

Spontaneous,

because curve b

shifts to be curve a

of Figure

2-06A

0 carboxylate (COO"-) @ protonated carboxylate (COOH) # oil-like residue

H+

because

increased

affinity

for

protons

spontaneous

because transition

temperature below body

temperature

(i.e.,

in Figure

2-06A

curve b shifts to a)

A reduced nicotinamide @ protonated carboxylate (COOH)

FIGURE

2.12. The thermodynamics of the special-

structured pentagonally arranged water molecules

around oil-like groups, as in Figure 2.8, is such that

too much leads to loss of solubility with the result of

hydrophobic association. This kind of water is indi-

cated by the halo. On the side where there is no halo,

charged groups have destructured the hydrophobic

hydration in the process of achieving their required

hydration. This is indicated by the absence of halo.

A Both carboxylates and phosphates destructure

water on one side. Protonation of the carboxyls

allows restoration of

much hydrophobic hydration

that the phosphate is at high energy due to lack of

adequate hydration, just as inadequate hydration

results in hydrophobic-induced pKa shifts that are a

measure of the increase in free energy of carboxy-

lates.

The phosphate is so energized as to be able to

add to ADP to form ATP with restoration of the

complete halo of hydrophobic hydration with the

result of insolubility and contraction. B The com-

bination of carboxylates and positively charged

oxidized nicotinamide destructure the hydrophobic

hydration, the halo, on one side of the structure.

Reduction of the nicotinamide converts a charged

group to a hydrophobic group and restores so much

hydrophobic hydration that the pKa of the carboxy-

late is higher than the pH of the solution. The car-

boxylate starved for hydration pulls a proton out of

solution; the halo is restored, and insolubility and

contraction result. This constitutes the pumping of

protons driven by reduction of the nicotinamide.

What Sustains Life? An Overview

(see Figures 5.15 and 5.27) and dephosphoryla-

tion to remove charge (see Table 5.2).TTiese are

the most immediate energy-converting events

of muscle contraction.

2.5 Synthetic Model Protein

Machines Emulate Energy

Conversions of Photosynthesis,

Respiration, and Motion

2.5.1 Model Protein Machines in the

Coupling of Functions

Seen through the looking glass of energy con-

version, a living organism constitutes the

successful integration of many proteins func-

tioning as molecular machines. By definition, a

machine converts energy from one form to

another, and an engine is the particular

machine that performs useful mechanical work,

for example, lifting a weight or throwing an

object. Overall, therefore, the discus thrower

functions as a complex molecular engine having

converted the chemical energy derived from

the intake of food into the useful mechanical

work of throwing the discus. In doing so, the

discus thrower has successfully utilized many

coordinated molecular machines, proteins, of

different energy-converting functions. In addi-

tion to the coordination of different machines,

there is also the important coupUng of functions

within a single molecular machine.

Here we describe the coupling of functions.

A function involves any chemical entity that

can exist in either of two states, and by the con-

siUent mechanism the two states differently

affect hydrophobic hydration to a significant

extent. Two functions become coupled when

the more polar state of each decreases

hydrophobic hydration while the more

hydrophobic state of each increases the poten-

tial for hydrophobic hydration. The two func-

tions can be a chemical couple such as

-C007-C00H and a redox couple such as

the interconvertible states of oxidized nicoti-

namide/reduced nicotinamide.

With both functional groups in the same

model protein in their more polar states, that is,

ionized and oxidized, an electrical or electro-

chemical energy input to produce the reduced

state of the redox couple by making the model

protein more hydrophobic brings about the

chemical energy output of the increase in affin-

ity of a carboxylate for its proton. The bases of

the coupling of functions are the insights of the

consilient mechanism arising from the coher-

ence of the simpler contractile processes of

Figure 2.6. In fact, the common form of the

graphs of Figure

2.6,

independent of the energy

source, underscores the unifying element of

controlling hydrophobic hydration as shown

in Figure 2.9. Accordingly, de novo-designed

elastic-contractile model proteins experimen-

tally demonstrate the coupling of functions.^^

The biomolecular machines of living organ-

isms convert the chemical energies of food and

molecular oxygen, O2, through many different

energy-conversion steps, to the mechanical

work of motion to maintain Life and to the

construction of the macromolecules and cel-

lular structures that form living cells. The key

steps,

however, are the coupling of oxidation

to proton release and reduction to proton uptake,

and the coupling of proton transmembrane

flow to phosphorylation of ADP to form ATP.

In the following we use the molecular struc-

ture of the elastic-contractile model protein, as

exemplified in the simplified structural repre-

sentations in Figures 2.5,2.6, and

2.9,

to demon-

strate a principle that is transferable to protein

machines of different configurations, such as

linear and rotary motors. The fundamental

principle arises out of the competition for

hydration between apolar (oil-like) and polar

(e.g., charged) groups, given the technical term

of an apolar-polar repulsive free energy of

hydration and represented as AGap.^ Chapter 5

details the experimental foundation and analy-

sis giving rise to AGap, which may also be

thought of as a water-mediated repulsion

between hydrophobic and charged species.

Chapters 7 and 8 demonstrate the relevance of

AGap to molecular machines of biology.

2.5.2 Synthetic Model Protein

Machines Pump Protons on Reduction

Oxidized nicotinamide is more vinegar-like due

to its positive charge; this is indicated in Figure

2.9 by reaction (///) and in Figure 2.12B by the

2.5 Synthetic Model Protein Machines Emulate Energy Conversions of Photosynthesis

R-group with an open circle containing a plus

also contains carboxylates indicated by an open

circle with a negative sign. Like the carboxylate

in Figure 2.9 of reaction (/), charge destructures

the pentagonally structured waters surrounding

oil-like groups. Reduction of (addition of

negative electrons to) oxidized nicotinamide

makes it more oil-like and results in a more

complete shell of hydrophobic hydration sur-

rounding the second structure of Figure 2.12B.

When oxidized nicotinamide, attached to a

model protein with an inverse temperature

transition above body temperature, is reduced,

more low entropy water forms; the inverse tem-

perature transition drops below body tempera-

ture and increases the apolar-polar repulsion

between oil-like groups and carboxylates. The

consequence is a shift in the pKa of the car-

boxylate, resulting in protonation, followed by

completion of the shell of hydrophobic hydra-

tion and hydrophobic folding and contraction

represented in Figure 2.12B^^ (see also Figure

2.9 and the graphical representations in Figure

2.6).

The result of reduction is the uptake, that

is,

the pumping, of protons. Thus, reduction

pumps protons, i.e., causes the uptake of

protons, and, ahhough the structure of the

elastic-contractile model protein is inadequate to

localize a concentration buildup of protons, the

same physical principle applies as demonstrated

with the protein-based machines of the electron

transport chain (see Figures 8.12 through 8.25

of Chapter 8 and related text).

If reduction of the oxidized nicotinamide

were to occur in an appropriately structured

and carboxylate-containing protein within a

membrane, however, the pickup of proton by

the carboxylate could occur from one side of a

membrane, thereby lowering the concentration

on that side, and on oxidation the proton

release could occur to a confined space on the

other side, thereby increasing the proton con-

centration within the confined space on the

other side. Our proposal is that the cyclic reduc-

tion and oxidation of redox couples within the

thylakoid membrane of chloroplasts and within

the inner mitochondrial membrane achieves

proton pumping by means of

AGap,

the aqueous

mediated repulsion between oil-like and

charged groups that disrupts association of oil-

like groups to open access on one side and then

the other of these membranes (again, see

Figures 8.12 to 8.25 of Chapter 8 and related

text).

The resulting proton concentration gradi-

ent, as described by Mitchell's chemiosmotic

hypothesis,^^ provides the energy for phospho-

rylation of ADP to form ATP as noted below

and discussed more extensively in the text asso-

ciated with Figures 8.26 to 8.36 of Chapter 8.

2.5.3 Synthetic Elastic-contractile

Model Protein Machines to

Energize Phosphates

Both reduction of a positively charged nico-

tinamide and the protonation of a negatively

charged carboxylate increase the oil-Hke nature

of a protein. Both remove vinegar-like charge.

Phosphate, however, is super vinegar; one phos-

phate attached to a model protein is equivalent

to three or four carboxylates in its capacity to

disrupt hydrophobic association by destructur-

ing hydrophobic hydration. When the model

protein, functioning as a biomolecular machine,

is made more vinegar-like by binding of phos-

phate, the affinity of carboxylates for protons

is less (so too is affinity of a negative for a

positive charge as in ion-pair formation). The

1,000-fold

higher concentration of proton on

one side of the membrane could, however, still

drive protonation from that side of the

membrane.

Now, making the model protein more oil-hke

by protonation of several carboxylates allows

much more pentagonally structured water to

form, as schematically depicted in the Figure

2.12A. This, in our view, energizes the highly

charged phosphate, as it competes for its own

hydration by destructuring the waters hydrat-

ing the oil-like groups in an effort to obtain

the hydration that it requires. With a properly

designed active site, the phosphate could

escape the energetically charged situation by

adding to an ADP molecule to form ATP

when faced off against a sufficiently oil-like

surface.

This scenario, however, would not provide

for the most efficient energy conversion

because the phosphate, so activated, could have

a significant probability of hydrolytic cleavage

with release of heat. Too often the result could

What Sustains Life? An Overview

be the production of thermal energy instead of

the desired chemical energy. As was noted in

Chapter 1 and as will be treated in some detail

in Chapter 8, biology has evolved a remarkably

efficient rotary motor that spatially separates

the protonation of carboxylates from the acti-

vation of phosphate. Nonetheless, from the

perspective presented in Chapter 8, the same

physical process, a counterintuitive competition

for hydration between oil-like domains and

vinegar-like species, obtains at both sites. First,

however. Chapter 5 develops an extensive

experimental and analytical basis for the water-

mediated repulsion between oil-like and

vinegar-like groups, the apolar-polar repulsive

free energy of hydration, AGap.

2.5.4 Synthetic Model Protein

Machines Pump Iron

One of the more dramatic ways to increase the

oil-like character of a model protein function-

ing as a biomolecular machine is to neutralize

the charge on a pair of carboxylates by ion

pairing to a calcium ion with its double positive

charge. Ion pairing of calcium ion with car-

boxylate ion lowers the transition from above

to below body temperature, as shown in lower-

ing the cusp of insolubility of Figure 1.1 and as

is apparent in Figure 2.6A. As in Figures 5.15

and 5.27, this allows the waters of oil-like

hydration to form with the consequence of low-

ering the transition temperature so much that

it forces hydrophobic folding and drives con-

traction. Interestingly, the trigger for muscle

contraction is calcium ion binding to a pair of

carboxylates.

The very most dramatic way to increase the

oil-like nature of a model protein is the removal

of an attached phosphate. This is demonstrated

in Figure 2.12A. Calcium ion binding to a pair

of carboxylates is second only to protonation of

a carboxylate in driving hydrophobic associa-

tion (See Figures 5.27 and 5.34). Thus, the com-

bination of calcium ion binding to a pair of

carboxylates followed by phosphate removal,

as occurs in muscle contraction, provides

perhaps the most potent means of bringing

about hydrophobic association and the associ-

ated contraction. It is our view that hydropho-

bic association caused through lowering the

cusp of insolubility, as represented in Figure 1.1,

provides the primary driving force for muscle

contraction, as will be shown in part below

in Figure 2.17 for the hydrophobic association

that occurs in the cross-bridge of the myosin II

motor in its rigor-like state and that is dissoci-

ated in the ATP bound state.

2.6 Progression to Biology's

Machines from Model

Protein Machines

2.6.1 Equivalence of Energy

Conversion to Biology's Proteins yet

Structural Limitations of Elastic-

contractile Model Proteins

Designed elastic-contractile model proteins

served to elucidate the consiUent mechanism

for energy conversion. With proper design,

they remarkably perform mechanical work

using five different energy inputs. Furthermore,

as shown by Steinberg and coworkers,^"^ there

are designs whereby a continuous band of

cross-linked elastic-contractile protein can

provide a continuous driving force for rotary

engines. The rotary engine contains two sepa-

rated baths, one that drives contraction and the

second that effects relaxation. In all, elastic-

contractile model proteins functioning by the

consilient mechanism are capable of demon-

strating more than 15 classes of pairwise energy

conversions.

It is important to realize that the principles

so derived are independent of a specific mole-

cular structure. The requirements of the mole-

cular constructs are that they can exist in water,

exhibit adequate elasticity or flexibility, and

contain oil-like groups in variable spatial rela-

tionship to vinegar-like groups with the latter

being capable of occurring in states of different

degrees of vinegar-like character.

Much fundamental science came from the

study of elastic-contractile model proteins. The

elastic-contractile model proteins provided

the molecular system for realizing the correct

description of elasticity.^ Furthermore, compe-

tition for hydration between oil-like and polar.

2.6 Progression to Biology's Machines from Model Protein Machines

for example, charged, groups came conclusively

from numerous designed elastic-contractile

model proteins and their characterization us-

ing a number of different physical methods.

Chapter 5 presents this in some detail.

Despite these extraordinary virtues, elastic-

contractile model proteins are structurally

limited and thereby are themselves unable to

take full advantage of the principles to which

they gave rise. Biological protein-based

machines, however, provide the fertile ground

of examples wherein the consilient mechanism

can be given generality. A progression of

gedanken images from the elastic-contractile

model proteins, based on a pentameric repeat

with translational symmetry, demonstrate

approaches to the very diverse structures of

biology's protein-based machines. The remain-

der of this section begins a succession of steps,

and Chapters 7 and 8 carry the argument

directly to a number of the protein machines of

biology.

2.6.2 ATP Synthase Common to Most

Living Systems

As impUed by Figure 2.10, which shows details

of photosynthesis, ATP synthase plays the

central role for the production of ATP in pho-

tosynthetic plants, which ATP is used in the syn-

thesis of carbohydrate and all other organic

molecules of plants and as the energy source to

power the protein-based machines of plants. As

similarly indicated in Figure 2.11 for details of

respiration, the same ATP synthase provides

nearly 90% of the ATP produced in the oxida-

tion of glucose to carbon dioxide and water.

Because of the central role of ATP in the syn-

thesis of biomolecules and in powering

biology's machines, it is not unreasonable to

consider ATP synthase to be the most impor-

tant protein-based machine of biology.

As introduced in Chapter

ATP synthase is

in reality a pair of mechanically coupled rotary

motors; the Fo-motor driven by the proton

gradient provides the mechanical output of a

rotating shaft, and the Fi-motor driven by the

rotating shaft produces ATP from ADP and Pi

(inorganic phosphate, P04~^).

2.6.2.1 The Fo-motor of ATP Synthase

The Fo-motor presents a simplistic utilization

of the consiUent mechanism. The repulsion,

between a vinegar-like carboxylate of a cleat of

a wheel and the sea of oil of a cell membrane,

becomes an attraction on protonation,^^ and

the wheel rotates one cleat into the oily

membrane as a second cleat rotates into a

suf-

ficiently polar/aqueous position for a carboxyl

to release its proton to the other side of

the membrane. The direction of rotation of

the wheel and importantly of the axle (the

y-rotor) that extends from the wheel depends

on the frequency with which protons enter

and leave from each side of the membrane.

This straightforward demonstration of the

consilient mechanism will be considered in

more detail in relation to Figures 8.26 through

8.30.

2.6.2.2 The Fj-motor: ATP Synthesis

by Changing Repulsion Between the

Oil-like Surface of the Rotor and the

Charged Nucleotides at the Origin of

Water-filled Clefts

The same repulsive interaction, AGap, between

an oil-like surface and charges associated with

the nucleotides occurs in the synthesis of ATP

from ADP and Pi by the Fi-motor—the second,

the extramembrane, component of ATP syn-

thase. As noted above, the intramembrane

component functions to rotate an axle-like

projection, called the y-rotor, from the center

of an intramembrane rotary motor driven by

protons.

In the extramembrane component the y-

rotor forms the stem and core of an orange-

shaped structure comprised of six sections,

three a-subunits and three p-subunits, arranged

as threefold symmetrical (aP) pairs, designated

(ap)3.

The key element of the consilient

mechanism appUed to ATP synthase is that the

y-rotor exhibits three faces of very different

hydrophobicity. In our view, rotation of the

y-rotor by the Fo-motor causes the very

hydrophobic side of the rotor to be spatially

opposed, through a water-filled cleft, to the cat-

alytic site containing the most charged state.

What Sustains Life? An Overview

FIGURE

2.13.

Shown is one complete cycle of the Fi-

motor of ATP synthase on filling all catalytic sites

with nucleotide and with a y-rotor that has three

faces of very different hydrophobicities, that is, of

very different oil-like character. As discussed in

Chapter 8, the relative oil-like character of the three

faces compare as -20kcal/mol-face for the most oil-

like,

+Okcal/mol-face for an essentially neutral face,

and +9 kcal/mol-face for the least oil-like face. The

least oil-like face would allow ADP and Pi to enter

the catalytic site. As the Fo-motor rotates the dark-

ened, oil-like face of the rotor toward the catalytic

site containing ADP plus Pi, the repulsion between

the oil-like face and the filled site causes the ADP

plus Pi to relax the repulsion by forming ATP. As

rotation brings the oil-like face into complete oppo-

sition to the now ATP-fiUed site, the ATP molecule

is expelled from the site. As the rotor continues on

its way ADP again enters the catalytic site, followed

by Pi. In this mechanism the noncatalytic ATP-

containing site would have the function of repelling

the most oil-like side of the rotor sufficiently to

prevent hydrophobic associations that would

produce a frictional drag on the rotor and decrease

efficiency and rate of energy conversion.

ADP and

Pi.

This face-off raises the free energy

of the reactants, that

is,

increases the magnitude

of AGap, and results in formation of the less

charged ATP. Figure 2.13 shows this cyclic

process with all sites containing nucleotide and

with the three sides of the y-rotor, as described

in more detail in the figure legend. Molecular

details are discussed in the text that describes

Figures 8.31 through 8.37.

2.6.3 Filament Assembly from a

Clam-shaped Globular Protein

From the perspective of the consilient mecha-

nism, the assembly of filaments as required for

muscle contraction and the necessary move-

ment of components within the cell involves

hydrophobic association/dissociation between

composite subunits. The actin thin filament of

2.6 Progression to Biology's Machines from Model Protein Machines

muscle contraction and the microtubules of

intracellular transport present two relevant

examples. Both pose the same challenge to the

consilient mechanism. Assembly of the actin

filament requires ATP and assembly of micro-

tubules requires structurally and energetically

equivalent GTP (guanosine triphosphate).

Thus,

how could binding a triphosphate to a soluble

subunit unit bring about hydrophobic assembly,

when, by the consiUent mechanism, the tri-

phosphate should be disrupting hydrophobic

association? The issue is approached below by

considering dimerization of a hydrophobically

closed clam-shaped monomer.

2.6.3.1 Disrupting Intramolecular

Hydrophobic Association to Form

Intermolecular Hydrophobic Association

Phosphorylation initiated dimerization by

hydrophobic association is illustrated in Figure

2.14. In Figure 2.14A, a closed clam-shaped

globular protein, representing globular G-actin,

is held closed by hydrophobic association; but

phosphorylation near the mouth destroys a sig-

nificant amount of the hydrophobic hydration

and allows the clam-shaped globular protein to

open^^in analogy to the unfolding of our elastic

model protein on phosphorylation.^^ The resid-

ual hydrophobic hydration of the open state,

however, becomes the driving force for associ-

ation, that is, for the dimerization shown in

Figure 2.14B.

2.6.3.2 Treadmilling in Formation and

Maintenance of Actin and Microtubular

Tracts for Motion

Addition of a third dimension to the two-

dimensional representation in Figure 2.14B

provides an additional hydrophobic face for fil-

ament growth. Growth of the actin filament

occurs at one end by the conversion of

monomeric globular G-actin to filamentous F-

actin on ATP binding. In this case ATP binding

equates to the phosphorylation in Figure 2.14B.

Dissociation to form a G-actin occurs on

hydrolysis, giving ADP and Pi at the opposite

end of the filament. Release of

Pi,

leaving ADP

allows for recovery of the monomeric form with

ADP release.

Thus,

there is a treadmilling with

ATP-dependent growth at the positive end and

hydrolysis-dependent dissociation at the nega-

tive end.

In the case of microtubules the unit that adds

or leaves is an ap heterodimer called tubulin.

2.6.4 Deriving Contraction from a

Hydrophobically Closed Clam-shaped

Globular Protein

2.6.4.1 Adapting the Clam-shaped

Globular Protein Motif to Approach a

Sliding Filament Element of Contraction

In Figure 2.15, the clam-shaped globular

protein motif is adapted to demonstrate one

of many possible ways that the control of

hydrophobic folding could achieve motion by

means of a sliding filament/cross-bridge model

for muscle contraction. In this case the increase

in energy of the attached and energized phos-

phate allows that water become the receptor

molecule for the high-energy phosphate rather

than a molecule of ADP.

We hasten to clarify the purpose of Figure

2.15,

which is to exemplify the compliant nature

of a mechanism based on the repulsion

between oil-like and vinegar-like groups. It

shows the ease of a conceptual progression

from the more obvious phosphorylation control

of opening and closing of a clam-shaped

globular protein to a more involved swinging

cross-bridge/sliding filament process.

2.6.5 A First Step in Putting

an ATPase Motor to Work,

Controlling Association with a

Complementary Surface

The families of proteins that consume ATP

while functioning as protein-based machines

are called ATPases. Muscle contraction, just

noted

above,

a member of the family of linear

(contractile) protein motors that also includes

ATPases that walk along protein tubules and

transport elements from one part of the cell to

another. Another class of protein motors that

uses ATP rotary and nonrotary ion pumps

transports ions from one side to the other of the

What Sustains Life? An Overview

pentagonally

arranged water ^

FIGURE 2.14. A Phosphorylation Driven Unfolding.

A clam-shaped globular protein exhibits an opening

fluctuation but closes due to the formation of too

much hydrophobic hydration. Phosphorylation of

the site near the mouth of the clam-shaped globular

protein destructures so much hydrophobic hydration

in the process of achieving its own hydration that the

equilibrium is shifted to the open state. B Phospho-

rylation Driven Dimerization. On association of

complementary surfaces containing hydrophobic

hydration, an insolublilization of oil-like groups

occurs such that dimerization results.