523

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:adell@ic.ac.uk

tDivision of Chemistry and Chemical Engineering, California

Institute of Technology, Pasadena, CA 91 125, USA; e-mail:

imper@imppig.caltech.edu

*Department of Chemistry, Boston College, 140 Commonwealth

Avenue, Boston, MA 02167, USA; e-mail:Larry.McLaughlin@bc.edu

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.