Pistons and Proofreading: A
review of some articles relevant to the teleological perspective.
By Mike Gene (
From Otterman et al. 1999. A Piston Model for Transmembrane
Signaling of the Aspartate Receptor. Science
285; 1751-1754.
The aspartate receptor
is a trans-membrane protein that binds aspartate through its domain on the
outside of the membrane and thus undergoes a slight conformational change so
that its domain on the cytoplasmic side of the membrane can interact with other
proteins to ultimately control the direction in which the flagellum spins.
Otterman et al. have determined the mechanism by which this trans-membrane
protein shape-shifts. The receptor exists as a dimer (two interacting
polypeptide chains). Each polypeptide chain contains two alpha-helices that
span the length of the membrane in parallel. Otterman et al. describe a
piston-like movement of this polypeptide chain, where one alpha-helix moves
against another after aspartate binding. This piston-like movement is then
thought to alter the conformation of the cytoplasmic domain into an active
state. What is most interesting is that the changes are small and subtle. They
write:
"The proposed piston
mechanism would transmit a 1 angstrom conformational change in the periplasmic
domain as a 1 angstrom change to the cytoplasmic domain. If the 1 angstrom
change in the cytoplasmic can be perceived by the downstream methylation and
phosphorylation enzymes, then amplification occurs. A small conformation change
can certainly be detected by the discriminatory power of enzymes, as
exemplified by isocitrate dehydrogenase and restriction enzyme substrate
recognition. Although it is possible that the 1 angstrom movement is
structurally amplified further within the receptor cytoplasmic domain, this
does not seem to be necessary for signal transduction." (p. 1753).
If Otterman et al. are
correct about these subtle changes behind signal transduction, this highlights
just how finely-tuned the cellular environment is. The Darwinian paradigm
almost always tacitly assumes a sloppy intracellular state. But if the bacterial flagellar
"decision" to swim or tumble rests on a 1 angstrom change in the
conformation of a piston-like protein, the degree of specificity inherent in
cells is absolutely astounding. For those with some basic biochemistry
knowledge, one angstrom is about the distance which separates the central alpha
carbon from its covalently linked nitrogen atom in an amino acid. That's a
very, very subtle shift.
From Silivan et al. 1999. Insights into Editing from an
Ile-tRNA Synthetase Structure with tRNA and Murpirocin. Science 285; 1074-1077.
Extending the theme of
specificity mentioned above, it is quite fascinating to realize that the
phenomena of proofreading is more common than once thought. Most students of
molecular biology learn that DNA replication involves proof-reading, where
misincorporated bases are removed before synthesis of the newly-forming strand
of DNA resumes. Yet proofreading also seems to be involved in the charging of
tRNAs (when the proper amino acid is attached to the proper tRNA). An extreme
example concerns the tRNAs for isoleucine, threonine, and alanine, where amino
acids must be discriminated on the basis of one methyl group. Pauling estimated
that the enzyme which attached isoleucine to its proper tRNA could only
distinguish between isoleucine and valine by a factor of 5, yet fewer than 1 in
3000 errors occurs. This has always suggested a proofreading component to
charging, whereby mismatched amino acids are removed.
Silivan et al. have used
crystal data and modeling to propose one such proofreading mechanism. It turns
out that the enzyme that attaches amino acids to their appropriate tRNAs have
two active sites, a synthetic domain and an editing domain, separated by about
34 angstroms. The basic story seems to be that the acceptor stem of the tRNA
(the region where amino acids are bound) can adopt two conformations, such that
mismatched amino acids end up in the editing domain where hydrolysis takes
place and properly matched amino acids remain in the synthetic domain. The
exact mechanism of this shifting between two domains is not currently
understood.
What is interesting
about this study is not just the proofreading that takes place, but that the
general mechanism of proofreading is analogous to that which is used by the DNA
polymerase when it synthesizes DNA. If
the Silivan model holds up, this means that the process of DNA replication and
tRNA charging employ a similar mechanism not due to common descent. Put
simply, we see an abstract engineering-like principle at work here, where the
same basic logical strategy (a dynamic competition between synthetic and
editing functions) is being employed in very different proteins carrying out
very different processes. For me, it is hard to resist the subtle implications
of design, where not only is proofreading itself an echo of design, but that
the same basic logic of a proofreading mechanism only serves to amplify this
echo. In fact, this may even be considered an example of molecular convergence.
From Yoshizawa et al. 1999. Recognition of the Codon-Anticodon
Helix by Ribosomal RNA. Science 285;
1722-1725.
Now here's a study that combines
aspects of both studies mentioned above, namely, proofreading and finely-tuned
specificity.
Proof-reading not only
occurs when DNA is replicated and when tRNA is charged with amino acids, but
also seems to be involved in the codon-anticodon interaction that takes place
between mRNA and tRNA during the process of translation (protein synthesis).
Translation takes place in the ribosome and the proofreader appears to be 16S
rRNA (a component of the ribosome). Various experiments have found that there
are two residues in 16S rRNA that are essential, such that mutations of these
residues are lethal. The residues are two adenines, at positions 1492 and 1493.
Yoshizawa use an elegant
approach to uncover the reason why these residues are so important - they
apparently form the core of the proofreading. Here's the basic story. The
adenines at positions 1492 and 1493 are positioned in the A site of the
ribosome (the region where new tRNAs shuttle in to donate their amino acids).
Charged tRNAs bind to mRNA in the A site through the interaction between the
3-bp codon of the mRNA and the 3-bp anticodon of the tRNA. If the correct tRNA
binds to the correct codon, the 2' OH groups on the mRNA can form hydrogen
bonds with the N1 component of the adenines at positions 1492 and 1493. This is
thought to stabilize the condon-anticodon interaction and thus transmit changes
to further the elongation process. On the other hand, if an improper
codon-anticodon interaction takes place, the mispairing of bases alters the conformation
of the mRNA so that it doesn't interact with the adenines on the 16S rRNA and
no stabilization occurs. This is thought to increase the dissociation rates
(and slow elongation) of the improperly-paired tRNA and codon.
In the end, when you consider these three stories, they all converge on the
theme of specificity. This is especially true of proof-reading. We find
proofreading in the replication of DNA, the charging of tRNAs, and in the
actual process of translation. Yet why proofread if specificity is not
important? That is, the very act of proofreading is prima facie evidence of
specificity. This may quite relevant to Bill Dembski's approach, as the reality
of specificity is expressed by the very process of proofreading. What's more,
the specificity implied by proofreading appears to be essential for life.
Mutations in the proofreading component of the rRNA are lethal. And aminoacyl
synthetases that charged tRNAs with a 20% error rate would also probably be
lethal (this is a good experiment for the design paradigm - remove the editing
domain on these enzymes and see if it is lethal). Furthermore, the
proof-reading ability itself is dependent on finely-tuned positioning. Like a
fractal image, specificity repeats itself on smaller and smaller levels. Are we
really looking at the products of sloppy chemistry jury-rigged by natural
selection?