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Contributors to This Issue
Cele Abad-Zapatero, Abe Clearfield, Marcia Colquhoun, Philip
Fanwick, Judy Flippen-Anderson, Curtis Haltiwanger, Mary Jane
Heeg, Frank Herbstein, James Hurley, John E. Johnson, Jeanette
Krause Bauer, Russ Miller, Alex McPherson, Gary Newton, Alan
Pinkerton, Ron Stenkamp, R.M. Sweet, Tom Terwilliger, Patrick
Van Roey, Charles Weeks
Notes of a Protein Crystallographer
Genomics, Proteomics and The Secret of Life : A Faustian Dialog.
The publication of the entire genome of Mycobacterium tuberculosis
(Cole et al., 1998), the tubercle bacillus responsible for the
death of so many members of the human species, represents another
milestone in the development of what has been called experimental
genomics. In a broad sense, this term refers to the efforts to
systematically obtain the complete nucleotide sequence of the
genome of important and relevant organisms of the earth ecosystem.
The ultimate goal is to complete the entire human genome by 2005.
The related areas of functional and computational genomics will
complement and enhance the impact of the data gathering efforts.
It has been only three years since J. Craig Venter published
the random sequencing and assembly of the first complete DNA
from the free living bacterium Haemophilus influenzae
completed, by the novel "shotgun cloning" (Fleischman
et al., 1995). Since then, we have seen in rapid succession entire
genomes of several microorganisms representing important biological
classes ranging from E. coli (Blattner et al., 1997) to
B. subtilis (Kunst et al., 1997) and to S. cerevisiae
(Goffeau et al., 1997).
A glimpse at the figures that keep appearing from the complete
projects is sobering. For example, the entire genome of B.
subtilis (an important member of the class of Gram-positive
bacteria) contains 4,214,810 base pairs. They code for approximately
4,100 proteins, 42% of which have unknown functions. Among those
encoded proteins there are 18 transcription factors and 77 ATP-binding
transport proteins. Many of these new sequences represent important
biotechnology findings related to the production and transport
of antibiotics (Hoch & Losick, 1997).
The amount of information, the quantity and quality of our knowledge
of the biological systems that surround us was unimaginable only
a few years ago. The idea of obtaining the three dimensional
structure of all (or a sizable subset ) of the proteins coded
by these millions of bases could wet the appetite of the novice
crystallographers and sharpen the tools of the well-seasoned
ones (see for example Chayen & Helliwell, 1998; Pennisi,
1998). The possibility of mapping structurally the majority of
the macromolecular structures playing critical roles in the human
body appears to be within reach in the not too distant future.
Undoubtedly, the knowledge so gained will be extremely valuable
to find novel antibiotics, to understand the molecular basis
of many known and unknown diseases in animals and men, and to
design potent and efficacious drugs against them. Detailed knowledge
of the genomes of various microorganisms will pave the way to
understand rare metabolic pathways that could help in solving
environmental problems. These are just a few of the immediate
applications. One can only make conjectures as to the unexpected
findings.
All of these futuristic vistas notwithstanding, I can see myself
clad in a white robe as a young, Faustian, thirsty-for-insight,
macromolecular crystallographer in front of Mephistopheles having
the following conversation:
- I want to know the secret of life.
- I presume you mean beyond the DNA double helix and the genetic
code.
- Yes of course. Those are past history.
- What do you want to offer in return?
- I am willing to sacrifice love or happiness for the ultimate
knowledge.
- Normally those two things come together.
- Fine!. Let us not go into details. I'll put both on the scale.
- You, macromolecular crystallographers, have your own view of
what the secret of life is.
- I suppose we do. I'll be more specific. Can you put at my fingertips,
the complete three-dimensional structure of all the macromolecular
components encoded in the E. coli genome?
- Of course I can, but remember your personal love and happiness
must be on the other side of the scale. At what resolution?
-Good point. Refined at least to 1.2 Å resolution.
- I certainly can in exchange for your unhappy existence, totally
deprived of love. Are you ready? Are you sure you want to do
this?
- Why do you keep on insisting on the conditions? What do you
mean am I sure? You are supposed to entice me.
- I mean that if I were to sacrifice my love and my happiness
for the secret of life, I'd better be sure of what I really understand
by that.
Am I sure? Are we sure? Albert Szent-Györgyi (1893-1986),
the Hungarian biochemist who isolated Vitamin C from extracts
of paprika from his native land, wrote in the preface to one
of his books the following parable:
If you give a dynamo to a chemist, the first thing he will do
is to submerge it in HCl and analyze what substances are deposited
during and after the reaction, and which gases are given away.
If you give it to a molecular biologist (of his time), he will
take it apart, disassemble it, characterize each and everyone
of its parts and then he will put it back together again. Now,
he argued, if you were to point out to these scientists that
the dynamo works because of changes with time of something called
"magnetic flux", they will call you a "vitalist".
A person who needs to invoke an "Elan vital" to explain
biological phenomena. (I truly believe the book is "Introduction
to a Submolecular Biology". I apologize to the reader because
much to my disappointment, I have not been able to find the complete
quote and citation of this comparison. However, what I wrote
reflects the essence of the text as it appears in my old notes).
Any person contemplating a musician playing an instrument can
certainly relate to the following analogy. We can take a musical
instrument (i.e. an oboe) from the hands of the musician playing
it. We can disassemble it and make a detailed analysis of each
individual part; then, we can put it back together again. Our
language might betray us when we leave the instrument on the
table saying that the instrument is "lifeless" without
the musician playing it. In fact, it is not the person as a unique
demiurge that originates music. Rather, it is the flow of air
circulating within the cavities and interstices of the instrument,
as channeled and diverted by the action of its valves and keys,
that produces the sound that we call music.
Similarly, as important as the molecular components are for life,
we should not forget the interplay of flows and forces that support
it. The currents of multiple ions, protons and electrons; the
pressures created by chemical gradients; the pulses of electric
currents and polarization potentials; the molecular migrations
and myriad of feedback loops. All are critical elements of the
living cell. It is precisely the cessation of these fluxes and
rhythms that mark the absence of life. Our constitutive parts
will remain long after the termination of the ephemeral wind
of life. Our challenge is to understand how our beautiful macromolecular
structures permit, facilitate and maintain that fragile and intangible
state that we call living.
References
Fleischman, R. D. et al (1995) Science 269, 496-512.
Blattner , F. R. et al. (1997) Science 277, 1453-1462.
Chayen, N.E. & Helliwell, J. R. (1998) Physics World 11,
no. 5, 43-4.
Kunst, F. et al. (1977) Nature 390, 2249-256.
Goffeau, A. et al. (1997) Nature 387, 5-105.
Hoch, J. A. & Losick, R. (1997) Nature 390, 237-238.
Pennisi, E. (1998), Science, 279, 978-979.
Cele Abad-Zapatero
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