Cell, Vol. 92, 291–294, February 6, 1998, Copyright ©1998 by Cell Press
The Cell as a Collection Overview
of Protein Machines: Preparing the
Next Generation of Molecular Biologists
with the macroscopic world, these protein assemblies
contain highly coordinated moving parts. Within each
protein assembly, intermolecular collisions are not only
restricted to a small set of possibilities, but reaction C
depends on reaction B, which in turn depends on reacBruce
Alberts
President, National Academy of Sciences
2101 Constitution Avenue NW
Washington, D.C. 20418
Professor, Department of Biochemistry and Biophysics
tion A—just as it would in a machine of our commonUniversity of California, San Francisco
experience (Alberts, 1984).San Francisco, California 94143
Underlying this highly organized activity are ordered
conformational changes in one or more proteins driven byIntroduction
nucleoside triphosphate hydrolysis (or by other sources
of energy, such as an ion gradient). Because the confor-We have always underestimated cells. Undoubtedly we
mational changes driven in this way dissipate free en-still do today. But at least we are no longer as naive as
ergy, they generally proceed only in one direction.we were when I was a graduate student in the 1960s.
An earlier brief review emphasized how the direction-Then, most of us viewed cells as containing a giant
ality imparted by nucleoside triphosphate hydrolysesset of second-order reactions: molecules A and B were
allows allosteric proteins to function in three differentthought to diffuse freely, randomly colliding with each
ways: as motor proteins that move in a polarized fashionother to produce molecule AB—and likewise for the
along a filament or a nucleic acid strand;as proofreadingmany other molecules that interact with each other indevices
or “clocks”that increase the fidelityof biologicalside a cell. This seemed reasonable because, as we had
reactions by screening out poorly matched partners;learned from studying physical chemistry, motions at
and as assembly factors that catalyze the formation ofthe scale of molecules are incredibly rapid. Consider an
protein complexes and are then recycled. (See figure 1enzyme, for example. If its substrate molecule is present
in Alberts and Miake-Lye, 1992.)
at a concentration of 0.5mM, which is only one substrate
Since the time of that review, the number of protein
molecule for every 105
water molecules, the enzyme’s
assemblies that are recognized to employ such devices
active site will randomly collide with about 500,000 molhas
substantially increased. In particular, the nearly ubiqecules
of substrate per second. And a typical globular
uitous use of energy-driven conformational changes
protein will be spinning to and fro, turning about various
to promote the local assembly of protein complexes,
axes at rates corresponding to a million rotations per
thereby creating a high degree of order in the cell, has
second.
become universally recognized. A simple generic diaBut,
as it turns out, we can walk and we can talk
gram of such a process is presented in Figure 1.
because the chemistry that makes life possible is much
We have also come to realize that protein assemmore
elaborate and sophisticated than anything we stublies
can be enormously complex. Consider for example
dents had ever considered. Proteins make up most of
the spliceosome. Composed of 5 small nuclear RNAs
the dry mass of a cell. But instead of a cell dominated
(snRNAs) and more than 50 proteins, this machine is
by randomly colliding individual protein molecules, we
thought to catalyze an ordered sequence of more than
now know that nearly every major process in a cell is
10 RNA rearrangements as it removes an intron from an
carried out by assemblies of 10 or more protein moleRNA
transcript. As cogently described in this issue of
cules. And, as it carries out its biological functions, each
Cell by Staley and Guthrie (1998), these steps involve
of these protein assemblies interacts with several other
at least eight RNA-dependent ATPase proteins and one
large complexes of proteins. Indeed, the entire cell can GTPase, each of which is presumed to drive an ordered
be viewed as a factory that contains an elaborate net- conformational change in the spliceosome and/or in its
work of interlocking assembly lines, each of which is bound RNA molecule. As the example of the spliceocomposed
of a set of large protein machines. some should make clear, the cartoons thus far used to
Consider, as an example, the cell cycle–dependent depict protein machines (e.g., Figure 1) vastly underestidegradation
of specific proteins that helps to drive a mate the sophistication of many of these remarkable
cell through mitosis. First a large complex of about 10 devices.
proteins, the anaphase-promoting complex (APC), se- Given the ubiquity of protein machines in biology, we
lects out a specific protein for polyubiquitination (King should be seriously attempting a comparative analysis
et al., 1996; Zachariae et al., 1996); this protein is then of all of the known machines, with the aim of classifying
targeted to the proteasome’s 19S cap complex formed them into types and deriving some general principles
from about 20 different subunits; and the cap complex for future analyses. Some of the methodologies that
then transfers the targeted protein into the barrel of the have been derived by the engineers who analyze the
large 20S proteasome itself, where it is finally converted machines of our common experience are likely to be
to small peptides (Baumeister et al., 1998 [this issue]). relevant. For example, modern machines comprised of
subsystems from different “domains” (i.e., mechanical,
Ordered Movements Drive Protein Machines electrical, fluid, thermal) are often analyzed by an enWhy
do we call thelarge protein assemblies that underlie ergy-based approach. Here a mathematical description
cell function protein machines? Precisely because, like of the machine is achieved by considering certain scalar
functions that represent the system energy (i.e., kineticthe machines invented by humans to deal efficiently
Cell
292
dissipate energy. Any particular part of a machine might
be modeled as consisting of one or more of these basic
constituent elements. It seems reasonable to expect
that different, but analogous approaches could profitably
be applied to the protein machines that underlie
the workings of all living things.
Should We Expect a Protein Machine to Be
Well Engineered?
It is not hard to see why protein machines are advantageous
to cells. A mere glance at the collection of articles
in this issue of Cell should suffice to prove the point.
Compare for example the speed and elegance of the
machine that simultaneously replicates both strands of
the DNA double helix (Baker and Bell, 1998 [this issue])
with what could be achieved if each of the individual
components (DNA polymerase, DNA helicase, DNA primase,
sliding clamp) acted instead in an uncoordinated
manner.
But the devil is in the details. What, for example, has
been the advantage to the higher eukaryotic cell of adding
additional polypeptide chains to the DNA replication
apparatus, while retaining the same basic functions as
found in the bacterium E. coli and its viruses (Stillman,
1994)? And to what extent has the design of presentday
protein machines been constrained by the long evolutionary
pathway through which the function evolved,
rather than being optimally engineered for the function
at hand?
At least for protein synthesis on the ribosome, the
evolutionary history—dating back to an “RNA world”—is
thought to have played a predominant role (Green and
Noller, 1997; Wilson and Noller, 1998 [this issue]). And
when one examines the other protein assemblies known
to operate in cells—such as the various complexes of
RNA polymerase and its sets of accessory factors that
catalyze transcription in eukaryotes—one is sometimes
reminded of the many irrational complexities of a Rube
Figure 1. How the Energy Derived from Nucleoside Triphosphate Goldberg cartoon (Tjian, 1996; Greenblatt, 1997; KadoHydrolysis
Makes Possible the Localized Assembly of Protein Comnaga,
1998 [this issue]). But perhaps this is only because
plexes
we still understand so little of what the cell needs to
In this schematic, the protein serving as a catalytic assembly factor
accomplish with each of its various protein assemblies.
either exchanges GDP for GTP, or is phosphorylated by a protein
About ten years ago, I was struck by the speed andkinase using ATP. In either case, the added phosphate (P) activates
the elegance of the protein machine that replicates DNAthis protein (green) to bind the red protein, which induces a conformational
change that causes the blue protein also to bind. As indi- (Alberts, 1987) in comparison to what I viewed then as a
cated, this generates a very tight complex, in which each of the slow and ponderous ribosome. This led to a speculation:
three proteins stabilizes the others in the complex. Loss of the those present-day reactions that evolved early in the
indicated phosphate by hydrolysis then provides the energy needed
history of life on the earth (like protein synthesis) should
to release the green protein, allowing it to be reused repeatedly as
have originated in a cell dominated by RNA catalysis;a local factor for assembling the other two proteins.
these reactions might therefore remain relatively inefficient,
due to constraints traceable to their evolutionary
history. In contrast, those present-day reactions thatand potential energy) and the work done by external
forces. The laws of nature are then enforced by applica- evolved later (like DNA replication), in a cell dominated
by protein catalysis, could beexpected to be much moretion of first principles to arrive at the so-called equations
of motion (Meirovitch, 1970; Ogata, 1992). efficient (Alberts, 1986). The complexity of the spliceosome
might support this view, if one assumes that RNAAt the heart of such methods is the simplification and
idealization of a real world machine as a composition splicing was a very early event that predated the existence
of cells rich in proteins. However, the argumentof discrete elements. Engineersrecognize certainfundamental
behaviors in nature and then create an idealized has certainly been weakened by the unexpected complexity
of DNA transcription processes in eukaryotes,element to represent each of those behaviors. Most
simply, they classify elements as those that store kinetic which I would have predicted to mimic DNA replication
in their elegance and their simplicity.energy, those that store potential energy, and those that
Overview: Protein Machines
293
Answers to puzzling questions like these will require by thermodynamic and kinetic factors, as well as an
ability to use new developments in chemistry and phys-that we acquire a muchmore complete understandingof
the manyprotein assemblies that carryout the important ics as appropriate tools, will often be vital for success.
From my point of view, the education that we arefunctions of the cell.
offering today to young biologists in our colleges and
universities isseriously in needof a major rethinking. The
How Should We Educate the Next Generation good news is that biology has become an increasingly
of Molecular Biologists? popular major for our undergraduates, and there is no
This brings me to the central point of this introduction. reason whywe cannot excite allof them about science—
A careful reading of this volume should convince every- whether budding researchers, premedical students, or
one of at least two things: first, that we have made those aiming for other professions. But the bad news
incredible progress in deciphering what we know today is that far too many of our introductory courses are
about protein assemblies; and second, that we still have tedious surveys of an entire field—as if, for example,
an enormous amount more to learn. Thus, for example, one could hope to gain any real understanding of all of
our current drawings of the structure of the nuclear pore biology in a single year. And in an era where there is a
complex seem reminiscent of the sketches of houses uniform push for exposing K-12 students to “science as
that are drawn by young children, and they probably inquiry,” as emphasized in the National Science Educabear
a similar relation to the real thing. Determining the tion Standards (National Research Council, 1996, 1997),
structure of this fascinating cellular component, approx- it remains hard to find any evidence of inquiry in most
imately 25 times larger than a ribosome (Ohno et al., of our introductory college science laboratories.
1998 [this issue]), remains a daunting challenge that will Most important for the future of our field, the departprobably
require methodologies not yet developed. And mental structures at most universities seem to have thus
what new techniques will allow us to follow the kinetics far prevented any major rethinking of what preparation
and structure of each of the intermediatesinvolved in the in mathematics, what preparation in physics, and what
many fascinating transport reactions that occur deep preparation in chemistry is most appropriate for either
within the lipid bilayer membrane? (See Matlack et al., the research biologists or the medical doctors who will
1998 [this issue]). be working 10 or 20 years from now. The result is a
Even when we know the detailed structure of a protein major mismatch between what today’s students who
assembly at an atomic level, as we do for the chaparonin are interested in biology should be learning and the
GroEL-GroES, much will remain to be studied. As the actual course offerings that are available to them. It is
article by Bukau and Horwich (1998) makes clear, any largely for this reason, I believe, that so many talented
real understanding of the function of a protein machine young biologists feel that mathematics, chemistry, and
will require not only its resting structure in atomic detail, physics are of minor importance to their careers.
but also a knowledge of the kinetics and energetics of It is my hope that some of the young scientists who
each of its reaction intermediates. New techniques will read this issue of Cell will come to the realization that
need to be developed to facilitate such research. But, much of the great future in biology lies in gaining a
as always in biology, it will be crucial to define the key detailed understanding of the inner workings of the cell’s
parameters that need to be determined, since much many marvelous protein machines. With this perspecmore
can be measured than should be measured. Out- tive, students may well be motivated to gain the backstanding
prototype investigations that are clearly ex- ground in the quantitative sciences that they will need
plained and reexplained in review articles and textbooks to explore this subject successfully. But they will need
can help both to shape this exciting new field and to the faculty in our colleges and universities to lead them.
recruit young scientists to it.
Many of my generation fear that the molecular biology Acknowledgments
revolution that we have just been through has made
I am indebted to Jonathan Alberts for his explanations of how engi-biological research look deceptively easy. Perhaps as
neers analyze machines, Mei Lie Wong for preparation of the figure,
a result, we generally find that even our most talented
and Teresa Donovan for manuscript preparation.
graduate students lack the background in the physical
sciences that they are likely to need to decipher the References
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