ScienceWeek

SCIENCE-WEEK

A Weekly Email Digest of the News of Science

A journal devoted to the improvement of communication
between the scientific disciplines, and between scientists,
science educators, and science policy makers.

August 6, 1999 -- Vol. 3 Number 32

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Books must follow sciences, and not sciences books.
-- Francis Bacon (1561-1626)

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Contents of This Issue:

1. On Aesthetics as a Guide to Theory
2. Large-Scale Structures in the Universe
3. Protein Folding: On Oleg Ptitsyn
4. Structural Mechanisms of Endocytosis
5. Immunology: T-Cell Synapses
6. On DNA Vaccines

In Focus: On the Genetic Code vs. Human Language

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1. ON AESTHETICS AS A GUIDE TO THEORY
Every branch of science has its stories of elegant theories
immediately acclaimed by everyone and then subsequently proved to
be completely wrong. Usually, one important driving force behind
the immediate acclamation is the elegance of the theory, its
aesthetic aspects. In general, we have a tendency to look for
symmetries and other elegant relations in nature, and when we
find them we feel a certain exhilaration. But there is no a
priori reason, after all, why the laws that govern natural
processes must follow human notions of aesthetics, and indeed an
argument can be made that the search for and appeal of such
aesthetic laws may be based merely on certain properties of the
human nervous system, properties that make certain symmetries and
simplicities appealing. In many cases where an acclaimed elegant
theory turns out to be completely wrong, there is indeed a
feeling of surprise: How could this possibly be wrong? Usually,
it is a case of an apparently reasonable but false premise
forming the basis of an elegant but false theoretical
construction.
... ... In an essay on elegant scientific theories subsequently
proved to be wrong, John Maynard Smith (University of Sussex, UK)
suggests that the cleverest idea in the history of science that
turned out to be wrong was a proposition published by Francis
Crick, John Griffith, and Leslie Orgel in 1957, a proposition
often called "the comma-free code". The essentials of the story
are as follows:
     1) Upon publication of the Watson and Crick model of DNA in
1953, there was an immediate (and somewhat frenzied) interest
among biologists (and some physicists) in unraveling the
mechanics of the genetic code as apparently expressed in the
sequence of nucleotide bases that constitute DNA. An important
consideration was that whatever the code was, it made possible
the coding of the 20 different amino acids found in proteins.
Since 4 nucleotide bases were involved, it was apparent that the
basis of the code could not be nucleotide doublets, since a
doublet basis would yield 4^(2) or only 16 possible amino acids.
It was thus assumed that the code involved a nucleotide triplet
basis, which would yield 4^(3) or 64 possible coded amino acid
entities. But given a discrete triplet basis for the code, how
does the cell know which triplets to read, since there are no
markers in DNA to separate the triplets? Also, why are there only
20 amino acid possibilities? In their 1957 paper, Crick et al
suggested that it is implausible to suppose that translation of
the code starts at the beginning of a gene and "counts off in
threes". Instead, Crick et al suggested that only some of the
triplets are meaningful, in the sense of specifying an amino
acid, that no matter in what order these meaningful triplets are
arranged, none of the "out-of-frame" triplets must be meaningful,
and that a message can be read in only one way. Assuming this is
the basis for the code, the largest number of meaningful triplets
was shown to be precisely 20. With caution, Crick et al
concluded: "We present the solution here because it gives the
'magic number' 20, so that our answer may perhaps be of
biological significance."
     2) But despite the caution of Crick et al, in 1957 and for
several following years, nearly the entire scientific community
acclaimed the proposal as one of extreme elegance and
significance. No matter the elegance, the idea had to be
completely abandoned in the face of subsequent evidence. We now
know that of the 64 possible triplets, 61 triplets do specify an
amino acid with enough redundancies so that only 20 amino acids
are actually entrained. We also know that the reading of the
coded nucleotide sequence does indeed start at the beginning of a
gene and effectively "count off in threes". Ironically, the
evidence against the 1957 Crick et al proposal was provided
shortly afterward in 1961 by Crick himself and another group of
co-authors, who postulated:
... ... a) A group of 3 bases codes one amino acid.
... ... b) The code is not of the overlapping type.
... ... c) The sequence of the bases is read from a fixed
starting point.
... ... d) One particular amino acid can be coded by one of
several triplets of bases.
The 1957 proposal of Crick et al involved assumptions and
arguments contrary to items (c) and (d) above, assumptions and
arguments that produced an elegant theory predicting the coding
of precisely 20 amino acids, but a theory which turned out to be
completely wrong.
     3) John Maynard Smith is not the first to focus on the idea
of the Crick et al 1957 proposal as an example of elegance
leading theory astray. As Smith notes, Horace Freeland Judson, in
his classic history of molecular biology, _The Eighth Day of
Creation_, writes of the comma-free code: "An idea of Crick's
that was the most elegant biological theory ever to be proposed
and proved wrong." [Judson, p.315].
-----------
John Maynard Smith: Too good to be true.
(Nature 15 Jul 99 400:223)
QY: John Maynard Smith, School of Biological Sciences, University
of Sussex, Falmer, Brighton BN1 9QG UK
-------------------
Summary by SCIENCE-WEEK [http://scienceweek.com] 6Aug99
-------------------
Related Background:
ON BEAUTY AND TRUTH IN SCIENTIFIC THEORIES
There is an old adage, particularly in the physical sciences,
that of two theories arising from the same set of facts, one
theory beautiful and the other theory ugly, the beautiful theory
is more likely to be correct. There are indeed theories that are
difficult or impossible to test that have extensive and expansive
lives because of their aesthetic appeal, and that are discarded
with great reluctance when testing of the theory does eventually
become possible. ... ... J. McAllister (University of Leiden,
NL), in a review of the relation between the aesthetic properties
of scientific theories and their acceptance by the scientific
community, notes that many scientists claim to be able to tell by
means of aesthetic judgment how close a theory is to the truth,
but that in fact it often happens that a theory that is aesthet-
ically innovative strikes most scientists as ugly when it is
first put forward. For example, Kepler's theory of planetary
motions was initially considered ugly because it involved
ellipses rather than circles; Newton's theory of gravitation was
considered ugly because it postulated action at a distance;
quantum electrodynamics was first considered ugly for relying on
nonstandard mathematical operations for renormalization; and,
indeed, there is the famous rejection of quantum theory by
Einstein because he felt it lacked aesthetic appeal. Noting that
what is called beautiful changes as society and science change,
McAllister concludes the evidence that any aesthetic property of
theories is a sign of truth is at present scarce.
QY: James W. McAllister [mcallister@rullet.leidenuniv.nl]
(American Scientist Mar/Apr 1998)


2. LARGE-SCALE STRUCTURES IN THE UNIVERSE
As currently defined, the field of "cosmology" is the study of
the entire observable Universe treated as a single entity. Three
recognized central questions in this field are a) What did the
Universe look like at the dawn of time? b) How did it grow and
develop into what we live in today? c) What forms of matter, both
ordinary and exotic, does the Universe contain? Related to all
three of these questions are relatively recent observations
concerning the large-scale structure of the Universe,
particularly the structure of the distribution of the galaxies.
Each galaxy consists of a relatively local assemblage of hundreds
of millions or billions of stars, with enormous distances between
the galaxies. A cube set down at random in the Universe would
need to have sides 10 million light years long to contain, on
average, one galaxy. Apparently, however, the galaxies are not
distributed randomly in space: most are in groups or clusters,
pulled together by gravity. Some clusters contain many hundreds
of galaxies, and the clusters and groups are themselves arranged
in still larger filamentary or sheetlike structures. The
existence of such large-scale structures is a serious constraint
on cosmological models, and difficult to reconcile with the
"Cosmological Principle", which is the idea that the Universe
overall is homogeneous and isotropic.
... ... Stephen D. Landy (College of William and Mary, US)
reviews current work in the mapping of large-scale structure in
the Universe, the author making the following points:
     1) On all scales observed thus far by astronomers, galaxies
appear to cluster and form intricate structures -- presumably
through physical processes that were dominant during the early
expansion of the Universe and later through gravitational
interactions.
     2) Over the past several years, technological advances have
enabled astronomers and cosmologists to probe the arrangement of
galaxies at great distances, and the naive notion that at some
scale the Cosmos becomes uniform has been replaced by an
appreciation that the large-scale structure of the Universe must
be understood in terms of random processes: the homogeneity and
isotropicity of the Universe is true only in a subtle statistical
sense.
     3) As one moves from our own Galaxy to the entire observable
Universe, clumpiness finally gives way to smoothness. A galaxy is
a lump of stars, gas, dust, and unclassified "*dark matter". It
agglomerates with other galaxies to form galaxy clusters, the
largest bodies in the Universe held together by gravity. The
clusters, in turn, are clumped together into superclusters and
*walls, separated by voids of nearly empty intergalactic space.
Up to some scale, thought to be approximately 100 million light-
years, these progressively larger structures form a *fractal
pattern, i.e., they are equivalently clumpy on every scale. But
between this scale and the size of the observable Universe, the
clumpiness gives way to near uniformity.
     4) So-called "cold dark matter models" are now the most
popular explanation for the growth of structure in the
distribution of galaxies. The premise of these models is that
most of the mass in the Universe resides in some unseen ("dark")
and relatively massive type of particle. The particle is "cold"
because it is massive and travels slowly. The particle interacts
with ordinary matter only via the force of gravity, and could
also account for the apparent *missing mass in galaxies and
galaxy clusters. The observed "*power spectrum" of the
distribution of galaxies in the Cosmos generally follows the
predictions of the cold dark matter models. But the power
increases dramatically on scales of 600 million to 900 million
light years, and this discrepancy indicates that the Universe is
much clumpier on those scales than current theories can explain.
-----------
Stephen D. Landy: Mapping the Universe.
(Scientific American June 1999)
QY: Stephen D. Landy, College of William and Mary 757-221-4223
-----------
Text Notes:
... ... *dark matter: In general, in this context, the term "dark
matter" refers to material whose presence can be inferred from
its effects on the motions of stars and galaxies, but which
cannot be seen directly because it emits little or no radiation.
It is believed that at least 90 percent of the mass in the
Universe exists as some form or dark matter.
... ... *walls: In this context, the term "walls" refers to
structured distributions of galaxies, e.g., a clustering 750
million light-years long, 250 million light-years wide, and 20
million light-years thick.
... ... *fractal pattern: A fractal is a geometrical shape whose
structure is such that magnification by a given factor reproduces
the original object. During the past several decades, the idea
that fractal geometry is an appropriate geometry to describe
nature has been proposed by many researchers. The mathematical
constructs involved are appealing because of their symmetries,
and as in the development of many appealing ideas, the use of the
term "fractal" has increased to the point where experimental
observations in all the sciences are being analyzed and
interpreted as examples of systems with apparently fractal
properties. To the mathematician, however, the definition of the
property of "fractality" involves a quantitative requirement of
infinitely many orders of magnitude of power-law scaling of the
parameters of the system -- certainly at least a spanning of many
orders of magnitude.
... ... *missing mass in galaxies and galaxy clusters: In
galaxies, particularly in spiral galaxies, the "missing mass
problem" concerns our inability to account for the motions of
stars at the edges of the galaxy using estimates of galactic mass
based on luminosities of the galaxy members. At the level of
clusters of galaxies, the missing mass problem is more a question
of assumptions concerning the physical basis of nonuniform
distributions of galaxies. In both cases, it is a matter of
asking what one would need to postulate in order to explain
observational data.
... ... *power spectrum: In this context, the term "power
spectrum" is synonymous with frequency spectrum, but the term
"frequency" refers not to a distribution of events in time, but
rather to a distribution of points (galaxies) in space.
Essentially, the same mathematics used to analyze event
frequencies can be used to analyze distribution frequencies. The
power spectrum considered here is a Fourier transform of the
autocorrelation function familiar in event frequency analysis
(e.g., analysis of neuron outputs), but in this case applied to
spatial distribution frequencies. The essential idea is that
given a distribution of a large number of points in space, one
can apply well-known analytic techniques to determine the degrees
of local and global randomness of the distribution. Thus, in this
context, galaxies are treated as points. One of the graphics in
the Landy paper is a map of the distribution of 3 million
galaxies, each galaxy a point which contains billions of stars.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 6Aug99
-------------------
Related Background:
ON THE NATURE OF DARK MATTER
Joel R. Primack (University of California Santa Cruz, US)
presents a commentary on a paper by E. Gawiser and J. Silk
(University of California Berkeley, US) ((Science 29 May 98
280:1405), Primack making the following points: 1) One of the
fundamental issues facing cosmologists concerns the evidence that
observable matter in the universe makes up only a fraction of
what is needed to explain the properties of the universe. A large
portion of matter in the universe must therefore be unobserved,
or "dark matter". 2) In current cosmology, "hot" dark matter is
defined as particles that were still moving at nearly the speed
of light at about a year after the big bang. "Cold" dark matter
is defined as particles that were moving sluggishly at that time.
Neutrinos are the standard example of hot dark matter, although
other more exotic possibilities have been discussed. 3) Gawiser
and Silk (ref. cited above) conclude that of all the currently
popular cosmological models, the only one whose predictions agree
with the data on the cosmic microwave background anisotropies and
the large-scale distribution of galaxies is the cold + hot dark
matter model, with 70% of the matter cold dark, 20% hot dark, and
10% ordinary matter (baryonic). 3) There are 3 species of
neutrinos, and there are mounting astrophysical and laboratory
data suggesting that neutrinos oscillate from one species to
another, which can only happen if they have nonzero mass. As
dark-matter candidates, neutrinos are entities with masses that
may be 10^(-5) of the mass of the electron, but with an expected
density more than 8 orders of magnitude greater than the density
of electrons and protons in the universe. Neutrinos, therefore,
can provide a substantial fraction of dark matter. 4) The success
of the cold + hot dark matter model in fitting the cosmic
microwave background and galaxy distribution data indicates that
this type of model should be investigated in more detail.
QY: Joel R. Primack (joel@physics.ucsc.edu)
(Science 29 May 98 280:1398) (Science-Week 19 Jun 98)
-------------------
Related Background:
A GRAVITATIONAL DIFFUSION MODEL WITHOUT DARK MATTER
R.J. Britten (California Institute of Technology, US) presents a
model that without dark matter quantitatively describes the flat
rotation curves of galaxies and the mass-to-light ratios of
clusters of galaxies. The hypothesis is that the agent of
gravitational force is propagated as if it were scattered with a
mean free path of about 5 kiloparsecs. As a result, the force
between moderately distant masses separated by more than the mean
free path diminishes as the inverse first power of the distance,
following diffusion equations, and describes the flat rotation
curves of galaxies. The force between masses separated by less
than 1 kiloparsec diminishes as the inverse square of the
distance. The excess gravitational force (ratio of 1/r:1/r^2)
increases with the scale of structures from galaxies to clusters
of galaxies, but there is reduced force at great distances
because of the approximately 12 billion years available for
diffusion to occur. This model with a mean free path of about 5
kiloparsecs predicts a maximum excess force of a few hundredfold
for galactic clusters with dimensions of a few megaparsecs. With
only a single free parameter, the predicted curve for excess
gravitational force vs. size of structures fits reasonable well
with observations from those of dwarf galaxies through galactic
clusters. Under this diffusion model, no matter is proposed in
addition to the observed baryons plus radiation, and thus the
proposed density of the universe is only a few percent of that
required for closure. The author suggests that although the model
does not follow from present calculations based on the general
theory of relativity, it is not necessarily inconsistent with the
general theory because the diffusing gravitational elements might
be interpreted as spatial curvatures (e.g., distortions of the
metric inducing distortions in adjacent regions). The author
further suggests there is much at stake because of the scale of
the intellectual investment and the subtle arguments in cosmology
that make use of the general theory of relativity, and that the
challenge of a theory of intrinsic "beauty" may not be met at
this time because "beauty" is a subtle concept.
QY: Roy J. Britten (rbritten@etna.bio.uci.edu)
(Proc. Natl. Acad. Sci. US 31 Mar 98 95:3351)
(Science-Week 1 May 98)
-------------------
Related Background:
ON THE AGGREGATION OF YOUNG GALAXIES IN A DARK-MATTER UNIVERSE
The term "semi-analytic modeling" refers to a quantitative
modeling procedure in which empirical data are used in places to
fix the values of parameters or functions, rather than deriving
these from theoretical principles. N-body simulations, which
usually require extraordinary computational resources, are
simulations involving calculations of interactions of a large
population of entities. "Dark matter", which is thought to
comprise as much as 90% or more of the mass of the universe, is
undetectable except by gravitational effects, and "cold dark
matter" refers to dark matter particles created with low velocity
dispersions in the early universe. At the present time, computer
simulations and empirical observations of galaxy clustering favor
the idea that most dark matter in the universe is cold dark
matter. ... ... Governato et al (7 authors at 3 installations, UK
DK US) report the use of a combination of theoretical techniques
(semianalytic modeling and n-body simulations) to show that large
concentrations of young galaxies (i.e., galaxies in existence
when the universe was one-tenth of its current age) should be
quite common in a universe dominated by cold dark matter, and
that such galaxy concentrations are the progenitors of the rich
galaxy clusters seen today. The authors suggest these clustering
properties of primeval galaxies will be compared with data
collected in the near future, and that the comparison will be a
test of our current understanding of galaxy formation within the
framework of a universe dominated by cold dark matter.
QY: C.S. Frenk (c.s.frenk@durham.ac.uk)
(Nature 26 Mar 98) (Science-Week 10 Apr 98)
-------------------
Related Background:
NO EVIDENCE OF NEARBY GALACTIC OR INTERGALACTIC HYDROGEN RESERVES
Neutral hydrogen gas is the material from which galaxies and
stars are made, and its distribution is therefore of interest.
Also, neutral hydrogen may contribute to the so-called inter-
stellar "dark matter", the existence or non-existence of which
remains one of the fundamental unresolved problems of modern
astronomy, since dark matter has been proposed as the explan-
ation, among other things, for the calculated masses of galaxies
from gravitation theory being 10 to 100 times the masses apparent
from their luminosities. Since it has been suggested by a number
of astronomers that large reservoirs of neutral hydrogen are
hidden in dark intergalactic clouds or in dim galaxies, surveys
of interstellar neutral hydrogen are of some importance in this
context. Now Martin Zwaan and Ertu Sorar (University of
Groningen, NL; University of Pittsburgh, US) report that an
analysis of data from the 300-meter Arecibo radio telescope in
Puerto Rico, which can detect neutral hydrogen out to 200 million
light years, indicates there is no significant neutral hydrogen
beyond that already known to be associated with known sources --
no significant neutral hydrogen in dark clouds and none in so-
called "low-surface-brightness" or dim galaxies. Assuming the
local universe is not atypical, it will now be difficult to
propose neutral hydrogen as a candidate for a significant
contribution to dark matter, or to propose that protogalactic
"mists" still exist in our vicinity.
QY: E. Sorar, Univ. Pittsburgh (412) 624-7488
(Science 29 August 1997) (Science-Week 12 Sep 97)


3. PROTEIN FOLDING: ON OLEG PTITSYN (1929-1999)
Proteins are polymers consisting of long chains of amino acid
residues, but that is only the beginning of their functional
chemistry. In biological systems, proteins assume various complex
high-order configurations ("folding"), and it is these
configurations that usually determine the roles of proteins as
biochemical entities in the biological system. An important goal
of molecular biology is to understand the structural and
functional features of proteins, in particular the mechanisms
responsible for specific protein folding. In recent decades, one
of the leading personalities in the field of protein folding was
Oleg Ptitsyn (1929-1999). For nearly 30 years, Ptitsyn advocated
the concept of the "molten globule" as a key intermediate in
protein folding. Ptitsyn's fundamental idea that proteins can
adopt compact structures without the close-packed side-chain
interactions characteristic of *native proteins is now implicit
in virtually every discussion of the subject.
... ... C.M. Dobson and R.J. Ellis (2 installations, UK) present
a biographical essay on Oleg Ptitsyn, the authors making the
following points:
     1) Ptitsyn was born in Leningrad in 1929, and he received a
doctorate in physics from the University of Leningrad at the age
of 25. His early work was on the physics of polymers at the
Institute of High Molecular Weight Compounds in Leningrad, but he
soon became interested in proteins and began work on protein
folding. With others, Ptitsyn founded the Institute of Protein
Research in Pushchino, a town approximately 70 miles from Moscow.
     2) In the early 1970s, Ptitsyn speculated that the protein-
folding problem might be made much simpler if a polypeptide chain
folds first into a flexible state with the usual positioning of
*helices and sheets, but without the intricate and detailed
packing of the various side chains found in a fully native
protein. There was no experimental evidence for this proposal at
that time, but soon such evidence began to emerge from studies of
*protein denaturation in various laboratories.
     3) Ptitsyn introduced the strategy of a combination of
physical methods to search for this new state of proteins. The
name "molten globule" was first used by Akiyoshi Wada in Japan.
The Ptitsyn laboratory subsequently made the major advance of
identifying species in kinetic experiments that fitted Ptitsyn's
definition of a molten globule, and then relating this state to
the mechanism of the folding process itself.
     4) Concerning Ptitsyn the person, the authors write: "Oleg
Ptitsyn was a gentle, kindly person, whose diminutive and
bustling figure was familiar around the conference and lecture
halls of the world... He died on 22 March, just before he was due
to give a lecture at the University of Warwick, during one of his
frequent trips to Britain. It was as he would have wished. He
died, as he had lived, earnestly engaged in the practice of
science, and looking forward to intense discussions about his
latest ideas."
-----------
C.M. Dobson and R.J. Ellis: Oleg Ptitsyn (1929-1999).
(Nature 8 Jul 99 400:122)
QY: Christopher M. Dobson [chris.dobson@chem.ox.ac.uk]
-----------
Text Notes:
... ... *native proteins: The "native" state or configuration of
a biological macromolecule is the functional state or
configuration ordinarily assumed by the molecule in the
biological system in which the molecule occurs.
... ... *helices and sheets: The "primary structure" of a
polypeptide chain is the actual sequence of amino acid residues;
the "secondary structure" is a low-order folding of the chain;
the "tertiary structure" is a high-order folding of the molecule.
Concerning the secondary structure, there are two main types: the
alpha configuration is a spiral configuration in which successive
turns of the helix are held together by hydrogen bonds; the beta
configuration is a configuration in which the chain is almost
fully extended and hydrogen bonded to an adjacent polypeptide
chain, with successive chains often involved to form "sheets".
... ... *protein denaturation: Usually irreversible complete
protein unfolding (without rupture of peptide bonds) and loss of
catalytic activity if the protein is an enzyme.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 6Aug99
-------------------
Related Background:
ON THE CHEMICAL PHYSICS OF PROTEIN FOLDING
... ... C.L. Brooks et al present a short review of protein
folding from the perspective of chemical physics, and with a
focus on the work of their own group, the authors make the
following points: 1) The question of the mechanism of protein
folding was once thought to be entirely analogous to the question
of mechanism in intermediary metabolism or classical organic
chemistry: the essential classical idea was that a protein
folding pathway involves a series of discrete intermediates. Such
discrete intermediates do occur in the late stages of protein
folding, but to answer the practical questions of structure
prediction and design, a new viewpoint on folding is required. 2)
The authors suggest this new viewpoint is that of chemical
physics rather than that of classical chemistry, and that the
chemical physics view requires a new set of theoretical ideas,
computational techniques, and major advances in experimental
methodology. 3) The authors suggest the theoretical framework for
the new chemical physics approach to protein folding should be
that of "*energy landscape theory", which asserts that "a full
understanding of the folding process requires a global overview
of the energy landscape." 4) The authors propose that the protein
folding energy landscape resembles a partially rough funnel
riddled with energy traps where the protein can transiently
reside. There is no unique pathway but a multiplicity of
convergent folding routes toward the native state... The authors
state that the essence of the funnel energy landscape idea is
competition between the tendency toward the folded state and
trapping because of "ruggedness" of the funnel. 5) Concerning
theoretical modeling, the authors point out that simulations with
detailed atomic models are extremely intensive numerically, so
that the number and size of systems that can be studied is
limited. Simulation models of intermediate complexity have
therefore been used. 6) Concerning experimental approaches to
exploring the energy landscape of protein folding, there are
various new methods involving the physical monitoring of folding
from an unfolded state, for example, monitoring in the
microsecond range following initiation of folding by a
nanosecond-scale step-change in ambient temperature. The authors
conclude: "Experiments are beginning to build up a *phase diagram
of folding kinetics that can be used to test and refine
theoretical models."
-----------
C.L. Brooks et al (4 authors at 3 installations, US)
Chemical physics of protein folding.
(Proc. Natl. Acad. Sci. US 15 Sep 98 95:11037)
QY: Charles L. Brooks, Scripps Research Institute 619-784-1000.
-----------
Text Notes:
... ... *energy landscape: The "energy landscape" here refers to
the contours of what is essentially a classical energy/entropy
diagram, with the native configuration state positioned at the
bottom of a deep potential well, in this case a funnel with sides
containing miniature energy wells or "traps".
... ... *phase diagram: A classical graphical representation of
the equilibrium relationships between phases of a chemical
system.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 23Oct98
-------------------
Related Background:
ON THE THERMODYNAMIC HYPOTHESIS OF PROTEIN FOLDING
Proteins are macromolecules that assume specific high-order
configurations, with each type of protein molecule folding into
the specific configuration necessary for its function. There are
two central aspects of this folding: it occurs extremely rapidly,
on the order of milliseconds to minutes after first synthesis of
the polymer, and the final configuration achieved is always
identical for each type of protein. Thus, protein A rapidly folds
into the protein A-conformation, and protein B rapidly folds into
the protein B-conformation. The question is how does this happen?
What are the variables that control these events? Experimental
techniques in the study of protein folding often involve
"denaturation" and "renaturation" of proteins in vitro.
Denaturation is the elimination of the folding of a protein by
changing ambient conditions such as temperature and pH, and
renaturation is the refolding of the protein molecule into the
native state following restoration of the original ambient
conditions. ... ... Govindarajan and Goldstein (University of
Michigan, US) present a theoretical analysis of current ideas
concerning protein folding. In 1969, C. Levinthal pointed out
that it is impossible for an unfolded protein to find the native
state (its final configuration) by randomly searching through the
entire space of possible conformations. This led Levinthal to
postulate that a protein must follow a specific path to the final
configuration, and therefore folding must be under kinetic
control (i.e., under the control of a specific sequence of
reactions). According to Levinthal, if the final folded state
turned out to be one of lowest configurational energy, it would
be a consequence of the biological evolution of specific chemical
reaction sequences ("kinetic control"), and not of physical
chemistry and the laws of thermodynamics ("thermodynamic
control"). In contrast to this idea of Levinthal, C. Anfinsen in
1973 concluded from the results of his numerous denaturation-
renaturation experiments that the native state of the protein is
indeed the global minimum of free energy, a conjecture that he
called the "thermodynamic hypothesis" of protein folding. The
debate between these two viewpoints of kinetic control and
thermodynamic control has continued for more than two decades,
with numerous experimentalists and theoreticians investigating
whether proteins reach their global free energy minimum in a
pathway-independent manner under thermodynamic control, or
whether the protein molecule follows a specific pathway to a
possibly local free energy minimum under kinetic control.
Govindarajan and Goldstein now report an exploration of the
validity of the thermodynamic hypothesis of protein folding by
simulation of the evolution of protein sequences, investigating
whether what is proposed by the thermodynamic hypothesis could
result through the process of protein evolution, the approach
involving certain assumptions concerning the effects of random
mutations on protein evolution. The authors report that their
results suggest that even if protein folding is under kinetic
control, a specific kinetic sequence will evolve so that the
native state of the protein molecule is most often the state of
minimum free energy. They point out that one consequence of this
is that theoretical methods that predict protein structure by
means of algorithms and search strategies not apparently
available to the protein itself may still be relevant as long as
the model produces an eventual state of minimum free energy.
QY: Richard A. Goldstein (richardg@umich.edu)
(Proc. Natl. Acad. Sci. US 12 May 98 95:5545)
(Science-Week 26 Jun 98)
-------------------
Related Background:
ON SIMULATED EVOLUTION AND PROTEIN FOLDING
... The "bioinformatics" approach is based on the idea of
recognition and identification in a protein of a new sequence of
amino acids similar or identical to other sequences in other
proteins for which structure and function are known. But this
approach encounters difficulties because of a lack of
understanding of what features of sequences have evolved to
encode stability and fast folding in proteins, and a lack of
understanding of which features are functional and which features
are adventitious. Better understanding of general principles that
govern kinetics and thermodynamics of protein folding can help to
reveal the signatures of protein sequences that are related to
folding. ... ... Mirny et al (3 authors at Harvard University,
US) report a study of sequences of fast-folding model proteins 48
residues long, the sequences generated by an "evolution-like
selection" toward fast folding. They report that such fast
folding model proteins exhibit a specific folding mechanism in
which all transition state conformations share a smaller subset
of common contacts (folding nucleus). The authors suggest their
results and analysis imply that for each protein structure there
is a small number of positions that are most crucial for fast
folding into that structure. Protein sequences that fold fast
into that structure may have evolved by placing into those
strategic folding-nucleus positions amino acids that provide
stabilization of the folding-nucleus.
QY: Eugene I. Shakhnovich (shakhnov@chemistry.harvard.edu)
(Proc. Natl. Acad. Sci. US 28 Apr 98 95:4976)
(Science-Week 12 Jun 98)
-------------------
Related Background:
BROWNIAN DYNAMICS SIMULATIONS OF PROTEIN FOLDING
Protein folding occurs on a time scale ranging from milliseconds
to minutes for a majority of proteins. Computer simulation of
protein folding, from a random configuration to the native
structure, is nontrivial due to the large disparity between the
simulation and folding time scales. In order to overcome this
limitation, simple models with idealized protein subdomains,
e.g., the diffusion-collision model, have gained some popularity.
The diffusion-collision protein-folding mechanism postulates the
early-stage formation of fluctuating quasiparticles (micro-
domains), which may be incipient secondary structures (alpha-
helices and beta-sheets) or hydrophobic clusters. These micro-
domains move via diffusion, and their coalescence leads to the
formation of folded proteins. Thus, the diffusion-collision model
reduces the complexity of the folding process from a consider-
ation of individual amino acids to that of the properties of a
few microdomains and their interactions. ... ... Rojnuckarin et
al (3 authors at 2 installations, US) present an analysis of the
folding of a 4-helix protein bundle within the framework of a
diffusion-collision model. Even with the simplifying assumptions
of a diffusion-collision model, a direct application of standard
Brownian dynamics methods would consume 10,000 processor-years on
current supercomputers. The authors circumvented this difficulty
by invoking a special Brownian dynamics simulation. They report
that a coarse-grained (i.e., crude) model of the 4-helix bundle
can be simulated in several days on current supercomputers, and
that such simulations yield folding times that are in the range
of time scales observed in experiments.
QY: Sangtae Kim (kim01@aa.WL.com)
(Proc. Natl. Acad. Sci. US 14 Apr 98 95:4288)
(Science-Week 15 May 98)
-------------------
Related Background:
A MODEL FOR BETA-HAIRPIN FOLDING IN PROTEINS
To be biologically active, proteins must adopt specific tertiary
configurations, a specific "folding". Although many natural
proteins spontaneously refold once they have been forced to
unfold, synthetic proteins are often produced in an insoluble
unfolded state and are thus inactive and useless until correctly
folded. One important aspect of protein folding is the kinetic
process, the rate at which folding occurs. Were a single
conformation to be found by random searching of all the possible
conformations, the number of years required would range from
10^(7) to 10^(66). In actuality, protein folding occurs on the
scale of microseconds, so there is clearly much yet to be learned
about these macromolecules. Probabilistic analysis of the
kinetics and energetics of a system of entities can be made
within the framework of the theory of statistical mechanics, and
the application of this theory is an important part of current
research into protein folding. In general, protein chains fold
into alpha-helices or beta-sheet structures, and the minimal
beta-structural element is the "beta-hairpin", a turning of the
polypeptide chain that has the shape of a hairpin. As far as
experimental methods are concerned, analysis of folding kinetics
in response to temperature variation is one of the key experi-
mental procedures, and there are now sophisticated methods for
temperature control provided by the coupling of computers and
laser physics. One such method is laser "temperature jump"
spectroscopy, which involves jump-heating (jump-discontinuity
heating) of a small volume of aqueous solution in a short time
domain coupled with spectroscopy in some part of the electro-
magnetic spectrum. Munoz et al (4 authors: National Institutes of
Health, US) used a nanosecond laser temperature jump apparatus
coupled with laser fluorescence excitation to study the kinetics
of folding of a protein beta-hairpin consisting of 16 amino acid
residues, and they report that folding of the beta-hairpin occurs
at 6 microseconds at room temperature, which is 30 times slower
than alpha-helix formation. The authors offer a statistical
mechanical model that provides a structural explanation for their
observations.
QY: Victor Munoz [vmunoz@helix.nih.gov]
(Nature 13 Nov 97) (Science-Week 5 Dec 97)
-------------------
Related Background:
A SYNTHETIC OLIGOMER THAT MIMICS PROTEIN FOLDING
The existence of helical folding in polymers such as proteins and
nucleic acids is of extreme importance in biological systems, but
biological polymers are not the only polymers to assume such
special folding arrangements. Beta-peptides, for example, non-
biological polymers synthesized from beta amino acids, form
helices stabilized by hydrogen bonds. Now Jeffrey S. Moore et al
(University of Illinois Urbana-Champaign, US) report that syn-
thetic oligomers with an all-carbon backbone, linear phenyl-
acetylenes with ester-substituted benzene rings linked to one
another by acetylene groups, spontaneously fold into a stable
helical configuration in acetonitrile, and that this apparently
involves a "solvophobic" mechanism similar to the hydrophobic
collapse model of protein folding in water. In both systems, the
phenylacetylene oligomers and biological proteins, hydrophobic
groups associate to form a compact structure that excludes the
solvent. The phenylacetylene oligomers have longitudinal cavities
that might be used for binding metals and other reactive species.
The authors also suggest such systems could be used in the design
and construction of synthetic enzymes.
QY: J. S. Moore, Univ. Illinois Urbana-Champaign, Chemistry (217)
333-0722 (Science 19 Sep 97) (Science-Week 3 Oct 97)
-------------------
Related Background:
PROTEIN-FOLDING MECHANISMS IN PROKARYOTES VS. EUKARYOTES
In biological systems, proteins are the molecules that do most of
the biological work, and the various proteins are the ultimate
expression of the genome of any organism. As polymers, proteins
are similar to the polymers known to polymer chemists, but the
chemical activities of proteins (and their biological functions)
depend mostly on higher-order folding into specific configur-
ations rather than on quasi-crystalline backbone arrays, as is
often the case in non-biological polymer chemistry. It is these
specific configurations that are responsible for the important
specificity and high catalytic power of the proteins that are
enzymes. The configurations, in turn, are an ultimate result of
amino acid sequences which form the backbone of proteins,
sequences which are not simple, as are the backbone sequences of
most non-biological polymers, but are specific, cryptic (coded),
and heterogenous. It is now recognized that complex proteins
usually have more than one folding domain, each involving a
sequence of 100 to 300 amino acids. The entire folding
architecture of a complex protein must be precisely constructed
in order for protein functionality to exist. Which provokes the
question of how the specific folding of particular proteins is
ensured by the biological system. The answer is evident for
simple proteins in vitro: the final configuration is
predetermined by the amino acid sequence, there being a single
energetically favored configuration that will always be attained
at equilibrium. This is Anfinsen's Rule, first proposed by the
protein biochemist C. B. Anfinsen more than 30 years ago. In
vivo, however, and particularly for complicated proteins, the
situation is more involved. This week W. J. Netzer and F. U.
Hartl (Sloan Kettering Cancer Center, NY US; Max Planck Inst.
Biochemistry, Martinsried DE) report an analysis of the
differences between protein folding in prokaryotes (organisms,
such as bacteria, without membrane-bound organelles such as the
nucleus) and eukaryotes (organisms with membrane-bound
organelles). Perhaps the most interesting difference is that in
prokaryotes protein folding is delayed until translation (final
synthesis by the ribosome) is completed (post-translational
folding), while in eukaryotes folding of each protein domain
occurs as each domain is translated (co-translational folding).
One result is that new prokaryote proteins can often be
misfolded. There are helper proteins at work in both prokaryotes
and eukaryotes to chaperon the proteins to their final
configurations, but there is still more possibility for errors in
the prokaryotes. One important consequence of this analysis is
that when bacteria are genetically engineered to synthesize human
protein for clinical use, the susceptibility of prokaryote
protein synthesis to folding errors must be considered.
(Nature 24 Jul 97) (Science-Week 8 Aug 97)


4. STRUCTURAL MECHANISMS OF ENDOCYTOSIS
The term "endocytosis" refers in general to any process in which
materials are taken into a biological cell by membrane-bound
vesicles that pinch off from the plasma membrane. When the
material taken up consists of large fragments or whole organisms,
the process is called "phagocytosis". "Receptor-mediated
endocytosis" is a specialized type of endocytosis that brings
specific macromolecules into the cell. Many hormones, *growth
factors, *lymphokines, and nutrients, enter the cell in this
manner. During receptor-mediated endocytosis, the external ligand
first binds to its corresponding plasma membrane receptor; the
receptor-ligand complex then becomes concentrated in specific
regions of the plasma membrane, regions called "coated pits".
Each coated pit is an infolding of the plasma membrane whose
cytoplasmic surface is coated with a polyhedral lattice
constructed from the protein clathrin. The clathrin molecule
consists of 3 large polypeptide chains and 3 small polypeptide
chains organized into a 3-pronged structure, a "triskeleton", and
clathrin triskeletons polymerize with one another to form the
polyhedral lattice. After ligand-receptor complexes have become
clustered within a coated pit, the invaginated membrane pinches
off and becomes internalized as a coated vesicle. This coated
vesicle is initially surrounded by a cage of clathrin molecules,
but this clathrin coat is quickly shed, and vesicles soon
accumulate in what is known as the "endosome compartment" of the
cell. Nearly all the details of the above brief description of
receptor-mediated endocytosis were completely unknown several
decades ago; our current picture is a result of intensive
research in many laboratories, research combining electron
microscopy, biochemistry, and molecular biology.
... ... M. Marsh and H.T. McMahon (2 installations, UK) present a
review of recent research on endocytosis, with a focus on
developments in the clathrin-mediated endocytic pathway. The
authors make the following points:
     1) The uptake, or endocytosis, of extracellular material
into cells in membrane-bound vesicles has been of great interest
to cell biologists for most of this century. The many functions
in which endocytosis plays a role include *antigen presentation,
nutrient acquisition, *clearance of apoptotic cells, pathogen
entry, receptor regulation, and *synaptic transmission.
     2) Concerning clathrin-mediated endocytosis, a high-
resolution 3-dimensional view of the clathrin coat is beginning
to emerge. Clathrin-coated vesicle formation is a complex process
dependent on, and regulated by, the activities of a set of
intracellular proteins that are recruited through various
protein-protein and protein-lipid interactions. *Phosphorylation
and dephosphorylation are apparently key regulators of these
interactions and of the activities of the involved proteins, but
the precise order in which the different components act at each
step of the process remains to be solved.
     3) Of all the coat-mediated transport events characterized
so far in cell biology, endocytic clathrin-coated vesicles are
unique in their degree of complexity. This may reflect a need for
a higher order of control to coordinate clathrin-mediated
endocytosis in various important processes: e.g., the rapid
recovery of synaptic vesicles membranes, or cellular responses to
environmental stimuli.
     4) The authors conclude: "The developments seen over the
past couple of years will continue; new insights and structures
will be published soon. The challenge for the new century will be
to understand how these structures interact to drive endocytosis.
-----------
M. Marsh and H.T. McMahon: The structural era of endocytosis.
(Science 9 Jul 99 285:215)
QY: M. Marsh [m.marsh@ucl.ac.uk]
-----------
Text Notes:
... ... *growth factors: Growth factors are peptide hormones that
regulate the growth of cells and tissues.
... ... *lymphokines: (interleukins) Hormones secreted by certain
antigen-processing cells of the immune system, the hormones
causing immune cells specific for the antigen to proliferate.
... ... *antigen presentation: In general, "antigen presentation"
refers to the presentation of antigens on the surfaces of
antigen-presenting cells of the immune system. In order for an
antigen to be presented on the surface of such a cell, the
antigen must first by taken up by the cell via endocytosis. [See
report #5, this issue of SW.]
... ... *synaptic transmission: This is a general term referring
to the events mediating the membrane-to-membrane interaction
between a neuron and another neuron, or a neuron and a muscle or
gland cell, or a neuron and a sensory receptor cell. The junction
is called a "synapse", and in many cases junction transmission
involves release and uptake of "transmitter" substances.
... ... *Phosphorylation: In general, the process of introducing
a phosphoric acid group into a molecule. Biochemical
phosphorylation reactions are of importance in the trapping of
energy, in the formation of biosynthetic intermediates during
metabolic processes, and in the control of the activity of many
enzymes and other proteins.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 6Aug99
-------------------
Related Background:
EVIDENCE FOR INTACT SYNAPTIC VESICLES IN ENDOCYTOTIC CYCLE
Neurotransmitters are chemical substances released at the
terminals of nerve axons in response to the propagation of an
impulse to the end of that axon. The neurotransmitter substance
diffuses into the synapse, the junction between the presynaptic
nerve ending and the postsynaptic neuron, and at the membrane of
the postsynaptic neuron the transmitter substance interacts with
a receptor. Depending on the type of receptor, the result may be
an excitatory or an inhibitory effect on the postsynaptic nerve
cell. Synaptic vesicles are the packets of neurotransmitter
substance formed in the presynaptic axon terminals, and when
transmitter substances are released, they are released as
packets, the vesicle membrane apparently fusing with the
presynaptic membrane to release the transmitter molecules. After
fusion of synaptic vesicles with the presynaptic membrane and
secretion of the contents of the vesicles into the synaptic cleft
("exocytosis"), the vesicular membrane is retrieved by
endocytosis (internalization) for re-use. ... ... Murthy and
Stevens (Salk Institute, US) used a fluorescent membrane dye with
quantitative fluorescence microscopy to test the classical model
of synaptic vesicle recycling, and they report that the amount of
dye per vesicle taken up by endocytosis equals the amount of dye
a vesicle releases on exocytosis. The authors therefore conclude
that the internalized vesicles do not, as the classical view
proposes, communicate with intermediate endosome-like intra-
cellular compartments during the recycling process. They suggest
their results are compatible with a model of vesicle recycling in
which endocytosis occurs mainly through internalization of
vesicle-size membrane patches that are exposed to the extra-
cellular space and which then remain intact throughout the
vesicle recycling pathway.
QY: Charles F. Stevens [cfs@salk.edu]
(Nature 2 Apr 98) (Science-Week 24 Apr 98)


5. IMMUNOLOGY: T-CELL SYNAPSES
     The so-called "adaptive immune system" of vertebrates, the
system that responds in an adaptive manner to specific pathogen-
derived or non-pathogenic foreign chemical entities, provides a
protective system that distinguishes foreign proteins from the
proteins of the organism itself. The foreign material (or part of
the foreign material) that is recognized as such by the immune
system is denoted by the term "antigen". Usually the antigen is a
protein or protein-attached moiety (hapten) that has entered the
bloodstream of the animal, e.g., the coat protein of an infecting
virus, or the cell-surface protein of a malignant cell. Exposure
to an antigen initiates an immune response that specifically
recognizes the antigen and destroys it.
     Adaptive immune responses are in general the responsibility
of white blood cells (leukocytes), particularly the so-called B-
and T-lymphocytes (B-cells and T-cells), and in addition large
amoeba-like cells called "macrophages". The lymphocytes are named
after the tissue that produces them: in mammals, B-cells mature
in bone marrow, while T-cells mature in the thymus gland. There
are an estimated 10^(12) immune system cells in the human body,
enough to constitute a large organ if they were all assembled
together. In general, the term "lymphocyte" refers to any cell
that circulates in the "lymph", a blood-plasma-like fluid
circulating separately but connected to the blood system.
     The adaptive immune system has many mechanisms to destroy an
antigen invader, with the responses generally categorized into
two types, the "humoral response" and the "cell-mediated
response".
     The humoral response depends primarily on B-cells, aided by
certain "helper T-cells" which provoke proliferation of B-cells,
and involves the secretion of specific antibodies by B-cells, the
antibodies consisting of proteins of the immunoglobulin class
that bind to specific antigens.
     The cell-mediated immune response is executed by both helper
T-cells and a class of T-lymphocytes called cytotoxic T-cells
("killer T-cells"), which attack host cells that have been
infected by a pathogen. In the cell-mediated immune response,
T-cells may also begin a T-cell proliferation process as a result
of contact with an "antigen-presenting cell" (see below), the
proliferation involving cellular specialization (differentiation)
and the production of a large number of specific-antigen-
activated T-cells from a single progenitor cell (clonal
expansion).
     The basic function of the T-cell in recognizing a target
antigen involves the use of T-cell surface receptors to recognize
an antigen when it is presented on the surface of another cell,
either an infected target cell or an immune system antigen-
presenting cell. In the former case, various antigen fragments of
the infecting intracellular pathogen are transported to the host-
cell surface; in the latter case, immune system cells specialized
to present antigens on their surfaces are involved, the antigens
derived from engulfment (phagocytosis) and fragmentation of the
pathogen. In both cases, the antigen is presented on the cell
surface by a special protein called "major histocompatibility
complex" (MHC), and in order for the antigen to be recognized by
the T-cell, the antigen must be presented by one of the MHC group
of proteins. It is apparently the combination of the antigen
peptide fragment and MHC protein which is recognized by the T-
cell receptor.
     In general, then, T-cells have various roles in immune
responses: there are types of T-cells involved in the humoral
immune response and types of T-cells involved in the cell-
mediated immune response. But in both cases, T-cell receptors
interact with antigen-MHC complexes presented by an "antigen-
presenting cell": in the case of the humoral immune response, the
antigen-presenting cell is a host immune system cell which
presents to the T-cells an antigen-MHC entity derived from the
pathogen, and the T-cells (in this case, helper T-cells) are then
involved in antibody production by B-cells; in the case of the
cell-mediated immune response, the antigen-MHC-presenting cell is
an infected host cell, the responding T-cells are helper T-cells
and cytotoxic T-cells, with both helper T-cells and cytotoxic T-
cells indirectly and directly involved, respectively, in the
destruction of the infected host cell. Another generalization is
that the humoral immune response is primarily directed against
extracellular pathogens or pathogen derivatives, while the cell-
mediated immune response is primarily directed against
intracellular pathogens (or, in special cases, malignant host or
foreign tissue cells).
     There is some evidence that when T-cell proliferation
occurs, a sustained engagement of T-cell receptors with antigen-
presenting host-cell surface complexes is necessary, with the
recognition by the T-cell of an antigen-MHC entity then involving
an actual long-term (e.g., minutes or hours) juxtaposition of the
T-cell and antigen-presenting cell. This juxtaposition, the
details of which are not yet clearly understood, is called the
"immunological synapse". The physical juxtaposition of the cells,
an actual binding of their two surfaces at one or more points, is
apparently mediated by so-called "adhesion molecules", which are
active not only in relation to immunological synapses, but also
in relation to other processes involving both intercellular
adhesion and adhesion of cells to the extracellular
macromolecular matrix. Recent evidence indicates the
immunological synapse consists of a central cluster of T-cell
receptors surrounded by a ring of adhesion molecules.
... ... A. Grakoui et al (7 authors at 2 installations, US), in
an experimental study of immunological synapses, the study
including real-time imaging and quantitative analysis of a model
system consisting of planar lipid bilayers on glass supports
mimicking the plasma membranes of antigen-presenting cells. The
authors incorporated fluorescent-labelled MHC peptides and
relevant adhesion molecules into the bilayers, and then added
living T-cells to the system, the T-cells forming points of
contact with ligands in the bilayer. The authors report their
results indicate that immunological synapse formation involves an
active and dynamic mechanism that allows T-cells to distinguish
potential antigenic ligands. Initially, T-cell receptor ligands
are engaged in an outermost ring of the nascent synapse.
Transport of these complexes into the central cluster is
dependent on T-cell receptor-ligand interaction kinetics.
Finally, formation of a stable central cluster at the heart of
the synapse is apparently a determinative event for T-cell
proliferation.
-----------
A. Grakoui et al: The immunological synapse: A molecular machine
controlling T cell activation.
(Science 9 Jul 99 285:221)
QY: Michael L. Dustin [dustin@immunology.wustl.edu]
-------------------
Summary by SCIENCE-WEEK [http://scienceweek.com] 6Aug99
-------------------
Related Background:
AN X-RAY CRYSTALLOGRAPHY STUDY OF T-CELL ANTIGEN RECEPTORS
An antibody is a protein molecule produced by the immune system
of vertebrate organisms, the molecule designed to specifically
interact with a particular invading foreign chemical entity
called "an antigen". Antibodies are produced and released by so-
called "B-cells" of the immune system, and antibody production is
part of the response of the immune system response to invasion by
foreign biological material. Another part of the immune system
response is the activation of various types of T-cells, whose
genomes are modified by interaction with foreign entities so that
T-cells can produce receptors that will then specifically recogn-
ize these entities. In general, the interaction of specific
antigens with specific cell receptors is the basis for the oper-
ation of the immune system, and there is much research effort
concerned with unraveling the details of the molecular inter-
actions. The T-cell receptors are apparently cell surface
glycoproteins involving 4 types of polypeptide chains: alpha,
beta, gamma, and delta, with variable (V) or constant (C) reg-
ions, and the T-cells receptors are either the alpha-beta variety
or the gamma-delta variety, with associated differences in
antigen recognition mechanisms. ... ... Li et al (6 authors at 3
installations, US AU) report the crystal structure of the
V(variable)-delta domain of a human gamma-delta T-cell antigen
receptor at 1.9 angstroms resolution. The authors suggest their
results provide the first direct evidence that gamma-delta T-cell
antigen receptors are structurally distinct from alpha-beta
T-cell antigen receptors, and that recognition of certain
antigens by gamma-delta T-cell antigen receptors may resemble
antigen recognition by antibodies.
QY: Roy A. Mariuzza [mariuzza@indigo2.carb.nist.gov]
(Nature 29 Jan 98) (Science-Week 13 Feb 98)
-------------------
Related Background:
MECHANISMS FOR IMMUNE SYSTEM T-CELL MIGRATIONS
Hyaluronate, the salt of hyaluronic acid, is a viscous substance
found in extracellular matrices, especially in connective tissue.
It essentially acts as an intercellular cement. Leukocytes are
white blood cells, and lymphocytes are a type of leukocyte
responsible for the immune response. There are two classes of
lymphocytes: 1) the B-cells, when presented with a foreign
chemical entity (antigen), change into antibody producing plasma
cells; and, 2) the T-cells interact directly with foreign
invaders such as bacteria and viruses. Extravasation is simply
the movement of lymphocytes, particularly the T-cells, from blood
capillaries, through the capillary walls, and into the
extracellular spaces in a tissue. CD44 is a protein, a lymphocyte
cell surface marker that appears to be important for lymphocyte
extravasation at inflammatory sites. Heather C. DeGrendele et al
(3 authors at University of Texas Southwestern Medical Center,
US) report that interactions between CD44 and hyaluronate are
involved in the targeting of lymphocytes to specific
extralymphoid effector sites, and that CD44 is therefore part of
the repertoire of adhesion receptors that can be used by
leukocytes during extravasation.
QY: Pila Estess [estess.pila@pathology.swmed.edu]
(Science 24 Oct 97) (Science-Week 14 Nov 97)


6. ON DNA VACCINES
     In the previous report in this issue (SW 6 Aug 99 #5), some
of the details concerning the adaptive immune response were
outlined. Once B-cells have been stimulated to proliferate by
helper T-cells, most of the proliferating B-cells increase in
size and begin secreting large amounts of antibody specific for
the antigen that provoked T-cell activation. But antibody-
secreting B-cells (called "plasma cells") are not the only cell
type produced by B-cell proliferation. A small fraction of the
proliferating B-cell population is set aside as a reserve
population of cells directed specifically against the stimulating
antigen. Such cells, called "memory B-cells", are
indistinguishable in appearance from unstimulated lymphocytes and
do not secrete antibody. But if the organism is exposed to the
same antigen a second time, the reserve population of antigen-
specific memory cells rapidly proliferates and differentiates
into antibody-secreting plasma cells, thereby allowing the
"secondary immune response" to a given antigen, an immune
response that occurs more rapidly and produces more antibody than
the initial or "primary immune response". The effectiveness of
the secondary response is the basis for the rarity of diseases
such as chicken pox or mumps occurring more than once in a given
individual, and it is an effective secondary immune response
which is the objective of administration of a vaccine.
     Standard vaccines are of two general types, those based on
killed pathogens or on antigens isolated from pathogens, and
those based on "attenuated" live pathogens whose replication and
viability is limited. The disadvantage of the former type of
vaccine is that killed pathogens or antigenic fragments do not
enter host cells, and thus provoke only the humoral immune
response, which is often not sufficient immunity. With the second
type of vaccine, the attenuated live pathogen (usually a virus)
does enter host cells, but there is always some danger that a
full-blown disease will be caused in individuals whose immune
system is compromised, for example, in cancer patients undergoing
chemotherapy, AIDS patients, and the elderly. Such individuals
may also contract disease from people who have been recently
inoculated with attenuated live virus. Another problem with live-
virus vaccines is that certain viruses easily mutate to entities
with restored virulence.
     A solution to the vaccine problem would be to find a method
that results in the production of a small amount of specific
pathogen-related antigen by normal host cells, this production
activating, without disease, a primary immune response that
includes the cell-mediated response, and this in turn resulting
in a sufficient secondary immune response when the actual live
pathogen is subsequently encountered. The use of so-called 
"genetic vaccines" ("DNA vaccines") is an effort in this
direction, an effort of considerable current interest.
Essentially, the idea is to transfer via genetic engineering only
part of the genetic machinery of the pathogen to host cells, the
part that codes for pathogen-specific antigen, with the
translocated genetic machinery fragment unable by itself to cause
disease, but yet still able to express the antigenic protein and
thus activate the cell-mediated immune response.
... ... D.B. Weiner and R.C. Kennedy (2 installations, US)
present a review of developments in the use of genetic vaccines,
the authors making the following points:
     1) In the 1950s and 1960s, experiments unrelated to vaccine
development indicated that delivery of genetic material into the
cells of an animal could trigger some synthesis of the encoded
proteins as well as trigger the production of antibodies targeted
against those proteins. Antibody production, in fact, became one
method of demonstrating that a given gene was indeed generating
its protein.
     2) In the 1970s and early 1980s, the ability of foreign
genes taken up and inserted in the host genome to prompt an
immune response gained attention, this time in connection with a
disappointment: Researchers attempting to develop gene therapy
(the delivery of genes to correct inherited and other genetic
defect disorders) found that proteins made from therapeutic genes
were occasionally destroyed in animals receiving the genes, the
cause of the destruction an immune reaction to unfamiliar
proteins.
     3) In the early 1990s, a small number of laboratories began
exploring whether the unwanted immune responses to the protein
products of foreign genes might be useful for vaccination. There
was considerable skepticism at first, but soon independent groups
demonstrated that the concept was sound. Studies during the mid-
1990s revealed that DNA vaccines delivered into cells could
stimulate the immune system of rodents and primates to generate
B-cell, cytotoxic T-cell, and helper T-cell responses against
many different pathogens and even against certain cancers.
     4) Since the mid-1990s, many more researchers have turned
their attention to DNA vaccines, and the technology has advanced
to the initiation of human trials focused on safety. The earliest
trial began in 1995, when *plasmids containing HIV genes were
delivered to patients already infected by that virus. In 1996,
for the first time, new genes coding for HIV or influenza virus
proteins were injected as vaccines into healthy individuals.
     5) Thus far, studies have not identified any serious side
effects of DNA vaccines. The authors suggest, however, that as
with traditional vaccines, there will probably be a need to
combine DNA vaccines with generalized immune system stimulators
("adjuvants") in order to elicit the strong immune responses
required to shield recipients from future infections.
-----------
D.R. Weiner and R.C. Kennedy: Genetic vaccines.
(Scientific American July 1999)
QY: David B. Weiner, University of Pennsylvania 215-898-5000.
-----------
Text Notes:
... ... *plasmids: A plasmid is an extra-chromosomal piece of
DNA, often circular, mostly in bacteria but also in yeast,
capable of independent replication and also capable of
translocation to other organisms of the same or other species. 
By means of genetic engineering, it is possible to insert foreign
DNA fragments into plasmids, and then use the plasmids as
vehicles to translocate the DNA fragments into the genetic
machinery of animal cells.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 6Aug99
-------------------
Related Background:
PROSPECTS FOR USE OF DNA VACCINES IN PUBLIC HEALTH
There is apparently a growing interest among medical researchers
in the potential for the use of DNA vaccines in public health. In
a DNA vaccine, the gene for the antigen of interest is cloned
into a bacterial plasmid that is genetically engineered to
augment the expression of the inserted gene in mammalian cells.
After injection into an animal, the plasmid enters a host cell,
where it remains in the nucleus as an episome without being
integrated into the DNA of the cell. Subsequently, using the
metabolic machinery of the host cell, the plasmid DNA in the
episome directs the synthesis of the antigen it encodes. In a
commentary on DNA vaccines, R.A. Seder and S. Gurunathan
(National Institute of Allergy and Infectious Diseases, US)
state: "DNA vaccines have the potential to induce potent and
perhaps long-term cellular immunity. A theoretical limitation of
the method is that the cytotoxic T cells evoked by the vaccine
may kill the very cells that produce the immunizing antigen. And
as might be expected at this stage of development, there is
concern regarding the safety of DNA vaccines in humans. There is,
however, little evidence to suggest that the DNA in these vectors
integrates into the host genome, induces tumors, or generates
pathogenic antibodies against DNA."
(New England J. Med. 22 Jul 99) (SW Bulletin 23 Jul 99)


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IN FOCUS: ON THE GENETIC CODE VS. HUMAN LANGUAGE
"The analogy between the genetic code and human language is
remarkable. Spoken utterances are composed of a sequence of a
rather small number of unit sounds, or phonemes (represented, at
least roughly, by the letters of the alphabet). The sequence of
these phonemes first specifies different words, and then, through
syntax, the meanings of sentences. By this system, the sequence
of a small number of kinds of unit can convey an indefinitely
large number of meanings. The genetic message is composed of a
linear sequence of only four kinds of unit. This sequence is
first translated, via the code, into a sequence of 20 kinds of
amino acid. These strings of amino acids fold to form three-
dimensional functional proteins. Through gene regulation, the
right proteins are made at the right times and places, and an
indefinite number of morphologies can be specified. Thus in both
systems a linear sequence of a small number of kinds of unit can
specify an indefinitely large number of outcomes. But there is
one respect in which the two systems cannot usefully be compared.
In language, the meanings of sentences depend on the rules of
syntax. These rules are formal and logical. In contrast, the
'meaning' of the genetic message cannot be derived by logical
reasoning. Thus, although the amino acid sequence of the proteins
can be simply derived from the genetic message, the way they fold
up to form three-dimensional structures, and the chemical
reactions they catalyze, depend on complex dynamic processes
determined by the laws of physics and chemistry. It does not seem
possible to draw a useful comparison between the way in which
meaning emerges from syntax, and that in which chemical
properties emerge from the genetic code."

-- John Maynard Smith and Eors Szathmary: _The Origins of Life_
   (Oxford University Press, Oxford 1999, p.169)
[J.M. Smith is at the University of Sussex, UK; E. Szathmary is
at the Institute for Advanced Study Budapest, HU]


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