biopolymers conquering the giants
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Biopolymers Conquering the giants Editorial overview Anne Dell*, Barbara imperialit and Larry McLaughlinz
Addresses
*Imperial College of Science, Technology and Medicine,
Wolfson Laboratories, Exhibition Road, London, SW7 2AY, UK;
e-mail:[email protected]
tDivision of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, CA 91 125, USA; e-mail:
*Department of Chemistry, Boston College, 140 Commonwealth
Avenue, Boston, MA 02167, USA; e-mail:[email protected]
Current Opinion in Chemical Biology 1997, 1: 523-525
http://biomednet.com/elecref/1367593100100523
0 Current Biology Ltd ISSN 1367-5931
In this issue of Current Opinion in Chemical Biofogy, we
have used a broad definition of biopolymers that goes beyond the traditional view of ‘biopolymers’ as simply proteins, oligonucleotides or polysaccharides. The reviews in this issue include the study of systems which, at the molecular level, are united by the common theme that they are assemblies of simple building blocks. The subject areas have been chosen to include highly complex assemblies, chimerical structures involving more than a single biopolymer class, synthetic systems, and molecules that are biosynthesized using nonstandard machineries. It is evident from this perspective that the traditional view of biopolymers has not been eclectic enough for the tastes of many chemists; there is clearly the desire to take on and conquer increasingly larger systems and yet understand them with the same kind of precision that has been demanded for significantly simpler molecules. This research is driven by the increasing willingness of chemists and biologists to adopt a fearless attitude towards the inclusion of new approaches and techniques-each article in this issue is characterized by a blend of organic synthesis, spectroscopic studies, and state-of-the-art molecular biology and biochemical approaches.
DNA repair is critically important to the health and long-term function of most complex organisms, but the study of such processes is hampered by two characteristics. The various repair enzymes are typically present only in very small quantities, and the enzyme targets, DNA lesions, occur as infrequent but finite events. The manner in which such enzymes recognize and repair specific lesions which occur infrequently against a background of essentially normal DNA sequence/structure is a salient example of macromolecular recognition. In order to better understand both the recognition processes and the subse- quent catalytic events which characterize these enzymes,
Schlrer, Deng and Verdine (pp 526-531) describe the use of rationally designed noncleavable substrate analogues that can be used to ‘trap’ various repair enzymes. The use of transition state mimicry appears to have been the most successful approach in these studies. Their review describes the elegant use of nucleoside and DNA chemistry to generate biopolymer analogues that contain single sites capable of attracting and then trapping various DNA repair enzymes.
Catalytic RNA continues to attract the interest of a number of scientists, not only because it appears to contradict the central dogma of biochemistry- that RNA has a role in information transfer and biological struc- ture, but it is proteins that bear the responsibilty for biological catalysis- but also because of its potential to provide insights into new and unique biochemical catalysis. The review by Verma, Vaish and Eckstein (pp 532-536) describes the state of understanding for one of the smallest naturally occurring catalytic RNAs, the hammerhead ribozyme. In spite of the structural data available for this catalyst -including crystallographically derived structures that describe primarily the ground state structure-the catalytic mechanism has remained elusive. It is clear that the role of the requisite metal cofactor(s) is intimately linked to catalysis in this complex. Many of the studies described by Verma et al: involve chemical synthesis of functionally altered RNA catalysts with a view towards locating critical interactions, or metal binding sites and then monitoring how the RNA catalyst responds when these interactions are perturbed. These chemical approaches have been very effective in elucidating some aspects of this ribozyme’s catalytic mechanism.
The review by Gibney, Rabanal and Dutton (pp 537-542) highlights recent progress on rational de novo design and synthesis of proteins with desired functions. This field is of tremendous importance since the ability to design novel proteins with a predetermined function has obvious implications for developing new molecules such as pharmaceutical agents and catalysts. It is a challenging area because the rules governing the folding of a polypeptide into a functional three-dimensional structure are not fully understood, and even if a thermodynamically stable tertiary structure is achieved, the dynamics of the folded state are not always optimized for function. Progress in overcoming these problems and the importance of designing a well defined hydrophobic protein core are described in this review. Of note here are two examples which show that, by altering less than half of the total amino acids of a protein, a predominantly P-sheet protein
524 Biopolymers
can be converted into an a-helical construct. The design
of active sites is also discussed, concentrating on the idea
of engineering a protein scaffold to which, for example, a
range of cofactor binding sites can be introduced with ease.
Several groups have been successful in designing such
proteins and it appears that design of novel, functional
proteins is an achievable goal that is closer than we think.
Post-translational protein modification has long been
considered a complicated process, with a scarcity of
definitive rules concerning the specificity and precise
structural and functional roles of each distinct modifi-
cation. Research in many cases has been hampered by
a dearth of methods for preparing discretely modified
peptides and proteins for rigorous studies. This situation
is particularly serious in the field of enzyme catalyzed
protein glycosylation. The review by Meldal and St Hilaire
(pp 552-563) shows that tremendous progress is being
made in the synthesis of defined glycopeptide conjugates.
Both synthetic and chemoenzymatic methods may now be
used for preparative scale production of single glycoforms
for studies on the roles of glycopeptides in areas such as
cell adhesion and immunology. In addition, these synthetic
methodologies have recently enabled the combinatorial
production of glycopeptide libraries.
Mootz and Marahiel’s article (pp 543-551) on the non-
ribosomal assembly of peptide antibiotics emphasizes
that nature often finds different ways to accomplish
similar tasks. Although ribosomal polypeptide synthesis
is often considered the ‘rule’ for the biosynthesis of
amino acid-based polyamides, the assembly of many
peptidyl antibiotics and siderophores is carried out using
an alternate ATP-driven process. This biosynthetic route
allows the inclusion of nonproteinogenic amino acids
and modifications including racemization, N-methylation,
and cyclization to afford conformationally rigid natural
products with important biological functions. The biosyn-
thesis of the cyclic peptide antibiotics is template-driven,
however, in contrast to ribosomal peptide synthesis, where
the product ternplating is provided at the protein level.
The article highlights how far the field has developed
since its original formulation by Fritz Lipmann in the
late 1960’s [l]. A structural understanding of these
modular peptide synthetases is now allowing researchers to
generate novel complexes composed of different domains
from different pathways, enabling the production of new
products, therefore engineering an even greater diversity
in biosynthesis of cyclic polyamide natural products.
Although the architecture of lipid bilayers as the funda-
mental building blocks of biomembranes is well under-
stood, the fact that all membranes contain lipids which can
aggregate to form nonbilayer structures remains an enigma.
De Kruijff (pp 564-569) presents an overview of this
polymorphic behavior of lipids with particular reference
to their involvement in membrane structural organization
and membrane protein function. The review examines
the paradoxical existence of nonbilayer membrane lipids
bearing in mind that membranes are actually con-
structed as bilayers, and relates the intrinsic properties of
nonbilayer-forming lipids to the biophysical requirements
for the maintenance of a functional membrane system.
Reference is made to membrane protein-lipid interactions
and optimal packing within the membrane. Emphasis is
placed on recent observations that directly link inverted
cubic lipid phases (see Figure lc, page 565) with protein
function and a variety of biological processes. These
latter processes range from mechanisms of fusion, the
action of anaesthetics, membrane protein transport and
protein insertion. Finally, the exciting observation that
nonbilayer lipids can be instrumental in facilitating the
crystallization of membrane proteins suitable for high
resolution structural analysis is presented.
The chemical diversity of isoprenoid compounds leads
into an interesting new frontier in biopolymer studies.
The review by Kellogg and Poulter (pp 570-578) defines
the current understanding of polyisoprene biosynthesis.
The stepwise assembly of two simple five carbon building
blocks (isopentenyl diphosphate, IPP, and dimethallyl
diphosphate, DMAPP) affords polyisoprenes of impor-
tance in a broad variety of cellular processes including
signal transduction and redox control. This review il-
lustrates the application of a powerful combination of
complementary X-ray crystallographic and site-directed
mutagenesis studies to the study of farnesyl diphosphate
synthase. Together, these efforts have led to a deeper
understanding of the mechanism of action of the isoprene
chain assembly enzymes and the source of chain length
control which ultimately dictates the biological function of
the released isoprenoid products.
The review by Chatterjee (pp 579-588) discusses the
structure and biosynthesis of the cell wall of Mycobacterium
tuberculosis, which is the focus of much innovative research
addressing the mechanism of action of several old drugs
and seeking targets for new drugs to treat tuberculosis.
The mycobacterial cell wall is a unique structure among
bacteria, consisting of complex polysaccharides coated
with a highly impermeable lipid barrier comprised of my-
colic acids. The mycolic acids are attached to the periphery
of giant arabinogalactans which, in turn, are joined to the
peptidoglycan layer of the wall via a phosphodiester-linked
disaccharide. This disaccharide, one residue of which is
rhamnose (a sugar not found in humans), might prove to
be the Achilles heel of mycobacteria, since its targeted
deletion should deprive the organism of its protective coat.
Embedded in the arabinogalactan framework are other
important glycopolymers such as the lipoarabinomannans.
Several decades of heroic structural work, in which the
cell wall architecture has been probed in finer and finer
detail has delineated the covalent structures of all the
major cell wall constituents. This structural work has
provided essential underpinning for investigating cell
wall biosynthetic pathways, both at the biochemical and
Editorial overview Dell, Imperiali and McLaughlin 525
genetic levels, which are being vigorously explored at the
present time. Whether or not it will be possible to explain
mycobacterial disease pathology in terms of the known
components of the bacterial envelope as they exist in
the intact mycobacterium remains to be seen. hlutants
unable to elaborate defined cell envelope constituents are
badly needed to allow scientists to address the role of
each component in the survival and/or pathogenicity of
the organism. Fortunately, as documented in this review,
our understanding of the mycobacterial cell is now so well
advanced that progress in deciphering the functions of cell
wall constituents and using the consequent knowledge to
design new drugs for combating tuberculosis is likely to
be rapid, thus the new few years promise to be an exciting
time in this area.
Choosing topics for the Biopolymer section of Currerrt
Opinion in Chemical Biology was not an easy task for the
editorial team. On the one hand there were almost too
many choices-after all, the majority of the biochemical
literature focuses on some aspects of biopolymer chem-
istry-on the other hand we were competing for the
hottest subject areas with other equally eager review
journals. We hope that the articles we have selected
convey the excitement that abounds at the interface
of chemistry and biology as researchers grapple with
the challenges posed by macromolecular systems. In
these articles it is evident that the scientific approaches,
developed in specialized fields of chemistry, for the study
of transformations of relatively low molecular weight
molecules are now being applied to far more complex
systems. With atomic detail, researchers are able to
assess the subtle responses by analog biopolymers in
biological systems, thereby allowing them to make more
detailed interpretations of the interactions and reactions
that take place at the macromolecular level in ways not
previously thought possible. Recent developments suggest
that specific, macromolecular information can be gleaned
in ever more complex systems.
These articles exemplify the amazing progress that is
being made to unravel complex molecular architecture, to
define biosynthetic pathways, to target these pathways in
the development of new drugs and to improve on nature
by de NOVO synthesis.
Reference 1. Lipmann F: Nonribosomal peptide synthesis on polyenzyme
templates. Accounts Chem Res 1973, 6:361-367.