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

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1.2 Four Principal Assertions of "What Sustains Life?"

• Herbicides, pesticides, fertilizers, and growth

factors can be released by the phase separa-

tion mechanism.

• Time, location, and amount of release can

be controlled by the phase separation

mechanism.

• Such effective and efficient use can

limit extent of harmful side effects to the

environment.

1.2.4,7

Design of Nonmedical

Applications: Biodegradable Plastics

1.2.4.7.1

Problems of Present Plastics

• Presently, plastics are made from petroleum,

an exhaustible resource.

• Preparation of petroleum-based plastics

utilizes toxic and noxious chemicals.

• Both preparation and the plastic pro-

ducts themselves pollute and deface the

environment.

• Because they are not biodegradable, plastics

disposal at sea means death to marine life.

1.2.4.7.2

Protein-based Materials Can

Be Thermoplastics

• With proper design, proteins can be plastics

and even thermoplastics.

• Protein-based plastics can be designed to

melt 100°C below their decomposition

temperatures.

• Such protein-based thermoplastics can be

processed as melts.

• Protein-based thermoplastics can be molded

as desired or extruded and pulled into fibers

(see Fig.

1.10).

1.2.4.7.3

Protein-based Plastics Can

Be Programmed for Different Rates

of Biodegradation

• Protein-based plastics can be prepared by

living cells, renewable resources, without the

usual necessity of resorting to toxic and

noxious chemicals.

• Protein-based plastics can be designed for

a given environment to biodegrade in time

periods ranging from days to decades.

FIGURE 1.10. Thermoplastics are polymers that melt

at a temperature well below thermal decomposition

such that they can be melted and formed into a

desired shape as a melt. Shown are three thermo-

plastics, two are plastics of our daily use and a third

is a designed protein-based thermoplastic that melts

at 160°C and does not decompose until the temper-

ature is raised above 250°C. The protein thermo-

plastic can be programmed to biodegrade with

half-lives ranging from days to decades when in an

aqueous environment.

• Global environmental concerns result in

ever-mounting costs for disposal of solid

waste.

• Solid waste of non-degradable petroleum-

based plastics, and the toxic and hazardous

Introduction

chemicals of their production buttress

concerns.

• The result is demand for polymers, like

protein materials, that are biodegradable, of

benign production, and from renewable

resources.

• The Martime Pollution (MARPOL) Treaty

of 1995 and the Plastic Pollution Research

and Control Act of 1987 prohibit, disposal of

plastics at sea due to damage to the marine

environment.

• Protein-based plastics can be environmen-

tally friendly and could even represent

healthful products from tobacco plants.

• Rather than death to marine life, program-

mably biodegradable plastics can mean food

for the fishes.

1.2.4.8

Design of Nanosensors: The

Ultimate in Sensors, Detection of a

Single Molecule

• Using atomic force microscopy, it is possible

to obtain the smooth force-extension profile

of a single elastic model protein chain.

• Insertion of a globular protein sensing

element within an elastic model protein

chain results in a force-extension profile that

contains the unfolding peak for the single

globular protein.

• Binding of a single molecule to a highly selec-

tive site on the globular protein component

can change the unfolding peak in the force-

extension profile.

• When the selective site binds a single mole-

cule of nerve gas or of an explosive, the

changed profile would provide the ultimate

in detection, that of detection of a single

molecule, with the renowned selectivity of

protein to limit false positives.

In summary, there is promise that one can

harness the consilient, phase separation mech-

anism in the design of materials to extend and

improve quahty of life at both individual and

societal levels.

References

E. Schrodinger, What is Life? Cambridge Uni-

versity Press, Cambridge, England. First pub-

lished in 1944, Canto edition with "Mind and

Matter" and Autobiographical Sketches, forward

by R. Penrose, 1992.

Origin of Life reference:

Eigen,

Steps towards

Life: A Perspective on Evolution. Oxford Uni-

versity Press, Oxford, England, 1992.

I. Prigogine and I. Stengers, Order Out of

Chaos:

Man's New Dialogue with Nature. Bantum

Books, New York, 1984, p. 13.

E.O. Wilson,

Consilience:

The Unity of Knowl-

edge.

Alfred E.

Knopf,

New York, 1998, p. 8.

Consilient is the adjective form of the noun

consilience.

As defined in Webster's Third New

International Dictionary, the term consilience

contains the sense that there exist pervasive, fun-

damental laws of nature underlying related dis-

ciplines that provide a common groundwork of

understanding. Here we refer to the consilient

mechanism as a water-dependent, pervasive, fun-

damental process by which the macromolecules

of living organisms function and evolve. The

term originates from William Whewell in The

Philosophy of the Inductive Sciences, London,

1840.

In Chapter 5 a second consilient mecha-

nism is introduced that relates to the mechanism

for a near ideal elasticity that is important to effi-

cient protein-based machines wherein mechani-

cal energy becomes important.

6. Webster's Third New International Dictionary,

Merriam-Webster, Inc., Springfield, MA, 1993,

557.

D.W. Urry and T.M. Parker, "Mechanics of

Elastin: Molecular Mechanism of Biological

Elasticity and its Relevance to Contraction." /.

Muscle

Res.

Cell

Motil, 23,541-557,2002. Special

Issue, Mechanics of Elastic Biomolecules. H.

Granzier, M. Kellermayer,

Linke, Editors.

8. J. Monod, "On Symmetry and Function in

Biological Systems." In Nobel Symposium 11:

Symmetry and Function of Biological Systems at

the Macromolecular Level, A. Engstrom and B.

Strandberg,

Eds.

Almqvist & Wiksell Forlag AB,

Stockholm, 1968, p. 1527. Also reprinted in

Selected Papers

in Molecular Biology by Jacques

Monod, A.

Lwoff,

and A. UUmann,

Eds.,

Acade-

mic Press, New York,

1978,

p. 708.

9. M.F. Perutz, "Mechanisms of Cooperativity and

Allosteric Regulation in Proteins." Q. Rev.

Biophys., 22, 139-236, 1989. Reprinted in book

form as referenced below (in ref. 16).

10.

These data stand as a challenge to those many

computational programs presently in use for cal-

culation of protein structure and function that

treat water as a uniform dielectric without

more specific consideration of the energetics of

References

hydration. From our studies, treatments of

detailed water structure and interactions are

required to properly describe protein structure

and function, including the competition for

hydration, which is expressible as a repulsion

between oil-like and vinegar-like (e.g., charged)

groups of protein.

11.

C.B. Bauer, H.M. Holden,

J.B.

Thoden, R. Smith,

and I. Rayment, "X-ray Structures of the Apo

and MgATP-bound States of Dictostelium dis-

coidium Myosin Motor Domain." / Biol Chem.,

275,

38494-38499, 2000.

12.

E. Martz, Front Door to Protein Explorer 1.982

org.

13.

As noted in the opening paragraph of the Pro-

logue and in the initial paragraphs of Chapter 3,

of this book, Thales of Miletus launched scien-

tific investigation in the sixth century

with the

inquiry "What is the world made of?" His simple

answer of "water" has been suggested as deriv-

ing "perhaps from seeing that the nutriment of

all things is moist and kept alive by

it... ."^^ In recognition of Thales' having initi-

ated our quest and because of the central role

that water fills in function of the protein-based

machines that sustain Life, we refer to this key

water as the "waters of Thales."

14.

D.J. Boorstin, The Seekers: The Story of Man's

Continuing Quest to Understand His

World.

Random House, New York, 1998, p. 22.

15.

A.J. Fisher, C.A. Smith, J. Thoden, R. Smith, K.

Sutoh, H.M. Rayment, and I. Rayment, "Struc-

tural Studies of Myosin: Nucleotide Complexes:

A Revised Model for the Molecular Basis of

Muscle Contraction." Biophys. /., 68, 19s-28s,

1995.

16.

M.F. Perutz, Mechanisms of Cooperativity and

Allosteric Regulation in Proteins. Cambridge

University Press, Cambridge, England, 1990,

Preface, p. x.

17.

D.W Urry,

Haynes, H. Zhang, R.D. Harris, and

K.U. Prasad, "Mechanochemical Coupling in

Synthetic Polypeptides by Modulation of an

Inverse Temperature Transition." Proc. Natl.

Acad Sci. U.S.A., 85, 3407-3411,1988.

18.

These results of 18 years ago, demonstrating the

capacity of de wovo-designed model protein-

based machines for the conversion of chemical

energy into mechanical work, remain unex-

plained by the computational methodologies

currently in use to describe the function of

protein-based machines of biology.

19.

P.D.

Boyer, "The Binding Change Mechanism for

ATP Synthase—Some Probabilities and Possi-

bilities." Biochim. Biophys. Acta, 1140, 215-250,

1993.

20.

P.D. Boyer, "Catalytic Site Occupancy During

ATP Synthase Catalysis." FEBS Lett., 512,29-32,

2002.

21.

J.P. Abrahams, A.G.W. LesHe, R. Lutter, and IE.

Walker, "Structure at

2.8

A Resolution of Fi-

ATPase from Bovine Heart Mitochondria."

Nature, 370, 621-628,1994.

22 K. Kinosita, Jr., R. Yasuda, and H. Noji, "Fi-

ATPase: A Highly Efficient Rotary ATP

Machine." In Essays in Biochemistry: Molecular

Motors, G. Banting and S.J. Higgins, Eds.,

Portland Press, London, England, 2000,

pp.

3-18.

23.

PL. Privalov, "Cold Inactivation of Enzymes."

C R. Biochem. Mol. Biol, IS, 281-305,

1990.

24.

It may be noted that present calculations of

protein structure and function neglect the pres-

ence of so much internal water. In calculations,

a quantity called the dielectric constant, required

in electrostatic calculations of the energy of

interaction between charges, is utilized. The

value of the dielectric constant of bulk water is

about 80, and commonly the assumption is made

that the value shifts at the surface of the protein

from 80 to 5 or less within the protein. The pres-

ence of the "waters of Thales" raises concern

about such assumptions. Similarly, in Chapter 5,

particularly in Figure 5.30, the experimental

values could only be approximated by electro-

static calculations when a value of 5 or less was

used, whereas direct measurement of the dielec-

tric constant for the model protein system

required that the value within the model pro-

tein motor be no less than 65. These points

provide substantial support for the consilient

mechanism.

25.

D.W. Urry, "Function of the Fi-motor (Fj-

ATPase) of ATP synthase by Apolar-polar

Repulsion through Internal Interfacial Water."

Cell Biol Int., 33(1), 44-55, 2006.

26.

E.O. Wilson, Consilience: The Unity of Knowl-

edge. Alfred E.

Knopf,

New York, 1998, p. 298.

What Sustains Life? An Overview

2.1 Introductory Comments

2.1.1 Dilemma of a Disordering

Universe Yet Life Systems of

Increasing Order

The physicist looks at the expanding universe,

disassembUng toward disorder, and views

increasing disorder as the inevitable flow in

nature. The chemist burns the oils that have

accumulated over the millennia in the earth's

crust and energizes molecules to react. On a

smaller scale, the chemist sees the march

toward disorder; the oils become dispersed and

disordered gases, and the excited new mole-

cules become dormant. Both physicists and

chemists look at living organisms—propagat-

ing, assembling, growing—and wonder, how

can living matter act in such an inverse way to

the nonliving matter of their experiences? On

the other hand, biochemists and biophysicists

look at molecular systems of a dissected

organism and successfully describe a still func-

tional component in terms of the equilibrium

laws of physics and chemistry. So, how can

living matter seem so different from nonliving

matter?

The timely access to forms of energy—light,

carbon dioxide, and water for plants and food,

oxygen, and water for animals (and plants in

the dark)—has been known for more than a

century to provide the nourishment for living

organisms. The energies accessible to the living

organism, transformed by components of the

living organism

itself,

result in the characteris-

tics that define Life—metabolism, growth,

reproduction, responsiveness, adaptability, and

motion. How can the energy sources of light

and food, along with the additional chemical

energies represented, for example, by supplies

of oxygen, carbon dioxide, and water, result in

these attributes of living organisms?

2.1.2 Familiar Energy Conversions

The sun's energy unevenly heats the surface of

the earth and evaporates water from the seas.

Solar energy drives the energy consuming

water-to-vapor phase transition and creates

moisture-laden warm air masses. Clashes

between cold and warm moist air masses cause

energy-releasing condensation of water vapor

to rain drops. Resulting winds as extreme as

hurricanes and tornadoes disfigure the earth's

surface—uproot trees, demoUsh man-made

structures, and cause waves that transform

shorelines. The rains become rivers that carve

mountain ranges into grains of sand and

remodel flood plains. These processes continue

the march toward less order.

Looking at man-made machines, ignited fuels

create heat and expanding, disordering gases

that propel rockets and jet planes and drive

pistons of the internal combustion engines of

our motor vehicles. These familiar, natural and

man-made energy conversions, which produce

motion and perform mechanical work, are all

associated with changes in temperature and

increases in disorder. The primary energy

conversions of living organisms, however.

2.1 Introductory Comments

occur spontaneously within, without significant

changes in temperature and often with a com-

ponent of increasing order.

2.1.3 The More Enigmatic Energy

Conversions of Living Organisms

The seemingly mysterious motions of Life

"come spontaneously from within, in the blink

of an eye, in the twitch of a muscle, in the

sudden kick of a runner, in the jerk and press

of a weight lifter,"^ and in the abrupt burst of

motion of the discus thrower.

The discus thrower stands motionless, discus

in hand. In response to an entirely internal

signal, he bursts into circular motion of ever

increasing rotational speed; he releases the

discus that soars along an arching trajectory

and falls to the ground. The discus thrower

again becomes motionless except for the

heaving of his chest, taking in molecular oxygen

(O2) and giving off carbon dioxide (CO2) and

water (H2O). Conversion of glycogen from

chemical energy storage depots in the muscles

to glucose and oxidation of this carbohydrate

molecule give rise to CO2 and H2O and replen-

ish ATP (adenosine triphosphate), the im-

mediate universal biological energy currency,

utilized for the muscle contractions that pro-

pelled the discus. All of this happens without a

significant change in temperature.

2.1.4 Proteins Catalyze Energy

Conversions

Proteins perform the energy conversions that

sustain Life; they consist of carbon (C), hydro-

gen (H), oxygen (O), nitrogen (N), and a more

limited number of sulfur (S) atoms. Proteins are

polymers, long-chain molecules. The individual

links of the chain are amino acids joined in

formation of the peptide bond, -CONH-.

Accordingly, this chain structure may also be

called a polypeptide. The resulting protein

polymers are sequences of 20 different

monomer units, the amino acid residues, to

form poly(-HNCHRCO-), as depicted in

Figure 2.1A.

Different side chains, designated as R-

groups, distinguish the 20 naturally occurring

amino acid residues. An R-group can be oil-

like, containing only carbon and hydrogen, for

example, -CH2CH(CH3)2; or the R-group can

be vinegar-like^ with a functional group, for

example, -CH2COOH, in which the carboxyl,

-COOH, part can dissociate to give acid, ff (a

proton with its positive charge), and the nega-

tively charged carboxylate -COO". The R-

group can even be neutral like the simple

hydrogen, -H, of glycine. (See Table 5.1 for the

molecular structures of the 20 naturally occur-

ring R-groups.)

The constrained ahgnment of oil-like and

vinegar-like groups along a protein chain, as

shown in Figure 2.1B, confounds the familiar

adage "oil and vinegar don't mix." Nonetheless,

the same forces that cause oil and vinegar to

separate affect the chain's behavior. The forces

that exist between oil-like and vinegar-like

groups distributed along the chain compel the

chain to fold in such a way as to separate oil

from vinegar. This brings oil-like side chains

together, as demonstrated in Figure 2.1C, in a

manner that separates oil-like groups from

vinegar-Uke groups. In the process this associa-

tion of oil-Uke groups shortens the chain length.

The complete separation of oil-like side chains

from water occurs by association of chains or

chain segments, as indicated in Figure 2.ID.

These structural changes are referred to as

hydrophobic (water fearing) folding (Fig. 2.1C)

and hydrophobic assembly (Fig. 2.1D). In short,

the sequence of amino acid residues controls

the way a protein folds^ and functions as the R-

groups variously attempt to segregate, as oil

from vinegar and as oil from water.

The tendency to fold and assemble hydro-

phobically in this way varies remarkably with

the presence and state (charged or uncharged)

of certain R-groups. The vinegar-Uke side

chains can transform to become more oil-like.

Changes in chemical groups of proteins, includ-

ing vinegar-like R-groups and other bound

chemical groups, control folding and assembly

through shifting the balance between being

more oil-like and being more vinegar-like. In

fact, these reversible chemical changes in

vinegar-like side chains and additional bound

chemical groups provide the means whereby

proteins catalyze energy conversions.

19 19 19 19

+H3N-C-C-N-C-C-N-C-C -N-C-C •

H .H H , H H . H H

Amino

Terminal

Residue

]

Third Amino

I Acid Residue'

What Sustains Life? An Overview

N-

' 1

Rn-

-c-

-N-

Rn-

-c-

-N-

Rn-

-c-

-N-C-Ct

H H

Carboxyl

Terminal

Residue

oil-like

O vinegar-like

showing oil-like residues on one side

and vinegar-like on the other

showing oil-like side

FIGURE

2.1.

The phase transition of oil-Uke groups

separating from water produces motion. A A protein

is described as a polypeptide chain molecule with

dif-

ferent side chains, R-groups.

The side chains delin-

eated simply as oil-like and vinegar-like (e.g.,

charged), are distributed along the chain.

The sep-

aration of oil-like groups from vinegar-like groups

and the association of oil-like groups to form oil-like

oil-like residues separated

from vinegar-like residues

and from water

domains result in folding that shortens the chain. D

The folded chains associate to complete the separa-

tion of oil-like domains from water while maintain-

ing the vinegar-like groups in water at a distance

from the oil-like domains. In reality, the steps shown

in C and D occur simultaneously and in a coopera-

tive manner.

2.1.5 Boundless Potential of

Biosynthesis to Produce Proteins of

Varied Sequence

Proteins perform the w^ork that sustains Life.

The genius of biological synthesis of proteins,

however, is that it matters relatively little how

complex the linear alignment of the available

20 R-groups, and it matters only in a limited

way how energetically unfavorable the result-

ing linear alignment, that

is,

the sequence, of R-

groups that form the protein. The information

for the protein sequence resides independently

in the nucleic acid sequence, and the energy

required to produce a nucleic acid sequence is

independent of the protein sequence it specifies

and, therefore, independent of the interaction

energies within the resulting protein sequence.

Separating the complexities and probabilities

of preparation from the complexities of perfor-

mance strikes advantage readily appreciated by

peptide chemists and thermodynamicists.

In our experience with the model proteins

of the type considered below, a wide range

of sequences can be designed, constructed, and

expressed to a useful degree in the organism

Escherichia coli, a generally symbiotic bac-

terium of our intestinal tract. Therefore, setting

aside the perennial issue of sufficient research

funds,

the design of model proteins to develop

and demonstrate concepts of energy conversion

becomes limited primarily by one's imagina-

tion. The fidelity and diversity of sequences

possible with genetic engineering is without

parallel among all known chain molecules.

Accordingly, an extraordinary potential now

2.1 Introductory Comments

exists to develop an understanding of the forces

involved in energy conversion (i.e., in protein

function). Such an understanding also has the

potential to provide advanced materials for the

future.

The example of the basic sequence from

which the designed set of diverse protein-based

machines evolved follows. By means of well-

established techniques of recombinant DNA

technology, many genes, that is, many different

DNA sequences, have been constructed for the

many designed model protein-based machines.

For example, one gene has been prepared for

the basic sequence that encodes for 251 repeats

of a five-residue sequence. It is the elastic-

contractile model protein, designated as

(glycyl-valyl-glycyl-valyl-prolyl)25i and abbrevi-

ated as (GVGVP)25i. The G stands for glycine

(Gly) with the hydrogen atom, -H, for the

R-group; the V for valine (Val) with the

-CH2(CH3)2 side chain; and the P for proline

(Pro) with the -CH2-CH2-CH2- R-group that

bridges from the attachment backbone C to the

N of the same residue, as shown in Figure 2.2.

The structure of this pentamer with a 10-atom

hydrogen bonded ring, called a p-turn, and the

single chain folding pattern for (GVGVP)25i, a

heUcal structure called a p-spiral, are given in

Figure 2.2."^

Production of (GVGVP)25i gives an example

of successful genetic engineering to produce

the designed model proteins that provide the

experimental basis for the perspectives

reported in this volume. Figure 2.3 shows an

example of the results from a single fermenta-

tion run of E. coli that has been genetically

transformed to produce (GVGVP)25i. At the

end of the fermentation period the cells are

broken (lysed), and the lysate is centrifuged

cold to remove cellular debris. At low temper-

ature the model protein is soluble, but then it

phase separates on heating to body tempera-

STEP1

STEP 2

FIGURE

2.2.

The folding pattern of the repeating five

residue sequence of elastin, which for the secondary

structural reason of the P-turn (step 1) is defined as

(Val^-Pro^-Gly^-Val'-GlyO giving poly(VPGVG).

For a large number of repeats, this should be recog-

nized as equivalent to poly(GVGVP). In step 2, the

chain of repeating pentamers folds into a helical

structure called a

^-spiral.

For the complete descrip-

tion, several P-spirals associate to form a twisted fil-

ament, a cross-section of which is shown in Figure

2.1D. (Reproduced from Urry,"^ with permission of

www.WorldandIJournal.com)

GlyS

Gly3

Pro2

VaP

What Sustains Life? An Overview

FIGURE

2.3. A Mass of the elastic-contractile model protein, (GVGVP)25i, from a single fermentation run of

E. coli. B Suitably transformed to produce the protein material.

ture.

Centrifugation of a warmed solution

results in the mass of elastic-contractile model

protein of Figure 2.3A. Under these conditions

this model protein gives the appearance of glis-

tening taffy. In a visual demonstration of the

physical properties in Figure 2.3B, pulling on

the viscoelastic model protein readily forms a

long fine strand.

2.2 Our Window on What

Sustains Life

2.2.1 Motion as an Index of Life

Albert Szent-Gyorgyi, perhaps the first person

to know the excitement of seeing the motion

of Life outside of the living organism, began a

review^ of his remarkable studies w^ith the state-

ment, "Motion has always been looked upon as

the index of life."^ Szent-Gyorgyi, while promi-

nent in the resistance in Hungary during World

War II and while in sanctuary within the

Swedish Embassy in Budapest, had removed

the contractile proteins from skeletal muscle,

fashioned them into a thick fiber, added the

necessary chemicals, and saw the fiber contract.

2.2.2 Designed Model Proteins

That Contract

By means of the design, and originally the

chemical synthesis, of model proteins, our

window on what sustains Life begins somewhat

analogously. In the midst of a less lethal con-

troversy on the nature of protein elasticity, we

designed a series of elastic-contractile model

proteins, fashioned them into fibers or bands,

and on adding the appropriate source of energy

visually observed the bands contract to produce

motion and perform the mechanical work of

lifting a weight. Not unlike the studies of Szent-

Gyorgyi, an energy source produced motion;

but, now man-made, the model proteins had

produced the motion.

In addition to changes in concentrations of

chemicals (chemical energy) to drive contrac-

tion of the Szent-Gyorgyi demonstration, we

have now seen each of the sources of thermal

energy, pressure-volume energy, chemical

energy, electrical energy (reduction and oxida-

tion),

and Ught, acting on a particular functional

R-group,

reversibly drive contraction and relax-

ation, that

is,

result in demonstration of mechan-

ical energy by a properly designed model pro-

tein. In

all,

six energies can be interconverted. In

each case of contraction at constant tempera-

ture,

the energy input alters the vinegar-like or

oil-like character of the R-groups. These ener-

gies,

the same that living organisms utilize, have

been employed in graphic, visual demonstra-

tions of pumping iron, that

is,

of the performance

of work by synthetic model proteins formed into

contracting and relaxing elastic bands that lift

and lower weights (See Figure 2.4).^'^'^

2.2 Our Window on What Sustains Life

2.2.3 Model Proteins Convert

Additional Energies That Sustain

Living Organisms

The same molecular process of the separation

of oil-like and vinegar-like groups that con-

verted the five different energies into motion

(pumping iron) can be used to convert any of

those five energies from one into the other.

Model proteins have been designed such that

electrical energy of reduction (adding elec-

trons) converts into the chemical energy of

picking up acid (pumping protons). Further-

more, evidence from studies of the model pro-

teins suggests that the chemical energy input of

a change in acid concentration can convert into

the chemical energy output of forming ATP.

These energy conversions represent funda-

mental energy transformations essential to the

existence of plants and animals. Herein begins

the foundation of a previously unrecognized

and likely dominant mechanism for protein

function.

2.2.4 De A^ovo-designed Model

Protein-based Machines

The de novo-designed elastic-contractile model

proteins—not modeled after, or copies of, con-

tractile or other generally recognized energy-

converting proteins—begin with a part of the

mammalian elastic protein. Then functional

groups, designed into the elastic model protein,

allow responses to different energy inputs and

FIGURE

2.4.

The lefthand side shows

representative

sheet of y-irradiation cross-linked elastic-contractile

model protein, designed for the conversion of an

input energy into the output of pumping iron, per-

forming mechanical work of lifting a weight. The

righthand side shows the synthetic protein machine

lifting a weight in response to an energy input,

(Reproduced from Urry.^)

What Sustains Life? An Overview

allow coupled pairs of different functional

groups to be included. In this way the energy

input, to which one functional group responds,

converts, as the output energy, into the energy

form to which the other functional group is

responsive. For example, adding negative elec-

trons to an attached positive group makes it

more oil-like and forces a negatively charged,

vinegar-like group to become more oil-like by

doing the work of picking up a proton. In this

case the electrical energy input of adding elec-

trons results in the chemical work of pumping

protons.

These experimental demonstrations of our

capacity to design model proteins that perform

key biological energy conversions constitute our

access to the question o/What Sustains Life.

2.3 Energy Sources Cause

Proteins to Fold, Assemble,

and Function

2.3.1 Certain Body Tissues and

Proteins Lift Weights on Raising

the Temperature

The underlying physical property, relevant to

the above energy conversions, was evident as

early as 1880 in a publication by Charles S.

Roy.^ Roy attached a 50-g weight to a

cm wide

strip of human aorta, heated it from the tem-

perature of a cool British laboratory to body

temperature, and observed the strip of aorta

contract and lift the weight. Repeatedly and

reversibly, heating caused contraction (shorten-

ing) and cooling caused relaxation (extension).

Roy recognized this to be an exception "to the

general rule that heat causes expansion and

cold contraction." The macromolecule in the

aortic wall responsible for this counterintuitive

property is the connective tissue protein elastin,

but also involved is the actomyosin complex of

smooth muscle that exhibits a related heat rigor

(see Chapter 7).

The aorta, the major artery leaving the heart,

experiences great demand to expand as the

blood enters it on contraction of the heart's left

ventricle. To sustain this demand, two thirds

of the total protein in the aorta, as it courses

through the chest, is elastin, the mammahan

elastic protein. Part of the energy of the con-

tracting heart is stored as mechanical energy in

the stretched aortic wall. After the aortic valve

closes to prevent flow back into the heart, this

stored energy continues to propel the blood

into distant smaller arteries just as a filled

balloon expels its contents. The relationship

between elastic storage of energy and Roy's

observed contraction driven by heating is

central to understanding both the basis of elas-

ticity and the mechanism of muscle contrac-

tion.^ This will be treated in Chapter 8.

2.3.2 Elastin is Cross-Unked and

Contains Repeating Sequences of

Amino Acid Residues

Elastin is a chain molecule comprised of a

string of nearly 800 linearly linked amino acid

residues. The long chains are cross-linked into

an extended network, which on spreading

would appear much as the wires of a chain-link

fence. Because of the cross-links, the chain

molecules do not flow irreversibly passed each

other during stretching, such that, after stretch-

ing, the elastic fibers can recoil to their original

resting state.

The most striking and the longest sequence

between cross-links of the elastin chain mole-

cule of pigs^^ and cattle^^ contains a repeating

sequence of five amino acid residues to pro-

duce a repeating pentamer, designated as

poly(GVGVP) (see Fig. 2.2 and the associated

text).

As described in relation to Figure 2.2, the

capital letter G stands for the glycine amino

acid residue, -HNCH2CO-;V stands for the oil-

like valine residue, -HNCHRCO-, with an oily

(hydrocarbon) R-group of -CH(CH3)2; and P

stands for -NCHRCO-, with R being the

hydrocarbon, -CH2CH2CH2-, bridging over

from the N to the C of the CH.

The synthetic elastic model protein, com-

prised of long chains of more than 200 repeat-

ing pentamers, constitutes the starting point for

our exploration of how biologically accessible

energy can be converted into the energy forms

that sustain Life. When fashioned into a cross-

linked fiber or sheet, as in Figure 2.4A, it

exhibits a 10-fold greater shortening on heating