SCIENCE/TECHNOLOGY
Pasteur's Legacy To Modern Science Celebrated At Symposium In His Honor • Chemists and biologists share insights on the roles of stereospecificity and molecular recognition in biological systems Ron Dagani, C&EN Washington ouis Pasteur made a name for himself in both chemistry and biology. He was one of those rare scientists who was conversant in two distinct disciplines. Today, 100 years after his death, most chemists and biologists still work in separate labs and attend separate meetings. So it was fitting that last month in New York City the spirit of Pasteur brought chemists and biologists together to communicate with each other and celebrate research advances in their fields. The symposium, "Stereospecificity and Molecular Recognition," was held on the Manhattan campus of Rockefeller University. The United Nations Educational, Scientific & Cultural Organization and the Pasteur Institute in Paris organized a series of six international symposia this year—'The Year of Louis Pasteur"—to commemorate the French scientist's monumental achievements. The Rockefeller symposium was the fifth in that series and the only one to take place in North America. In his keynote address opening the three-day conference and in additional writings, Arthur Kornberg, professor emeritus in the department of biochemistry at Stanford University School of Medicine, spoke eloquently about the "century-old rift that has separated the cultures of chemistry and biology." The division, he suggests, may be driven by basic differences in the emotional and cultural patterns of chemists and biologists. Chemists, Kornberg said, focus on molecules. "They seek the challenge of
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a molecule with many chiral centers at the very limit of synthetic difficulty and vie to obtain it in the fewest steps with the best yield. They obtain precise data with relatively few and elegant techniques. To them, the chemical monotony of proteins and nucleic acids overrides their biological importance." Biologists, on the other hand, "focus on complex phenomena in cells and organisms, using a wider range of techniques with less precision. They welcome mysteries and complexities, and some are disappointed when the veil over a phenomenon lifts to expose molecular details. "In essence, for the chemist, the chemistry of biologic systems is either too mundane or too complex. For the biologist, the intricacies of organic synthesis and the mathematical rigor of physical chemistry are beyond reach and irrelevant." Pasteur, however, was remarkable in
being able to bridge both cultures. Born in 1822, he started out as a chemist, albeit with only an "average" scholastic record. At the age of 26, while working as a lab assistant in chemistry, Pasteur discovered that tartaric acid exists as two stereoisomeric forms. This became "a major foundation of chemistry that has also had profound ramifications in biology," Kornberg pointed out. After this promising start, Pasteur "turned completely to fundamental biologic questions, such as the seeming spontaneous generation of microbes and the mysterious fermentation of the sugar in grapes to alcohol," Kornberg noted. The French researcher also "felt driven to attack pressing social problems," such as diseases of wine and diseases of people. "In his brilliant solutions to these questions, he also founded the disciplines of microbiology and immunology. Yet, in his preoccupation with biologic and clinical is-
Symposia recognize Pasteur's contributions to science This year, scientists throughout the world are observing the 100th anniversary of Louis Pasteur's death. Among the commemorations were six international symposia organized jointly by the United Nations Educational, Scientific & Cultural Organization and the Pasteur Institute in Paris. The symposia highlighted "current progress in the fields of Pasteur's major discoveries, and illustrate[d] their universal impact on biological sciences, and their applications to health, agriculture, industry, and the environment," according to Maxime Schwartz, director general of the Pasteur Institute. The symposia were held around the world, in recognition of Pasteur's role as a missionary for science." The symposia were as follows: • "From Spontaneous Generation to Molecular Evolution," in Rio de Janeiro, in February. • "Epidemiology and Public Health,"
in Hanoi, Vietnam, in March. • "Etiology and Pathogenesis of Infectious Diseases," in Dakar, Senegal, in April. • "Microbes, Environment, and Biotechnologies," in Papeete, Tahiti (French Polynesia), in May. • "Stereospecificity and Molecular Recognition," in New York City, in September. • "Vaccines, One Hundred Years After Louis Pasteur," in Paris, also in September. Each symposium was held at a site that has some connection to Pasteur. For example, the New York City meeting was held at Rockefeller University. The university was founded in 1901 as the Rockefeller Institute for Medical Research, which was modeled after the Pasteur Institute, founded by Pasteur himself in 1887. The two institutions have often collaborated on research.
OCTOBER 9,1995 C&EN
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SCIENCE/TECHNOLOGY sues, he strayed from his chemical heritage and neglected the chemical basis of the phenomena he had done so much to clarify/7 Now, a century later, Kornberg said, scientists are poised "to complete the cycle from chemistry to biology started by Pasteur, by reducing discoveries in biology back to their chemical roots." Most of the talks given in the symposium were, in fact, selected to illustrate how biological problems are reduced to a set of chemical questions," said John Kuriyan, a structural biologist who was trained as a chemist. Kuriyan and Stephen K. Burley, both professors at Rockefeller University and investigators at Howard Hughes Medical Institute (HHMI), were the two members of the five-person organizing committee who did most of the legwork for the symposium. Of course, the chemical questions revolved around the key molecules of life—DNA, RNA, and proteins—and interactions between such biomolecules. For example, Stephen C. Harrison, a professor of biochemistry and molecular biology at Harvard University and an HHMI investigator, opened the technical part of the meeting by reviewing what is known about the architecture of protein-DNA complexes involved in the regulation of transcription. This talk, as Kuriyan commented to C&EN later, began by considering "a very complicated phenomenon in biology, [such as] how a cell responds to its environment by altering the production of proteins or altering its read-
out of the genetic library." In the end, Kuriyan said, Harrison was able to reduce the phenomenon "to physical chemical interactions occurring directly between organic groups on the protein and groups on the DNA" and mediated by interactions such as hydrogen bonding. The expanse of chemical and biological knowledge on view at the symposium obviously went far beyond the scientific understanding of Pasteur's day. But it was all closely related to Pasteur's original discovery of molecular chirality. The idea that molecules have distinct shapes and that a living cell will respond to one molecular shape and not another was the conceptual underpinning of the meeting, Kuriyan pointed out. Or, in his own words: "The shapes of molecules are the driving elements of life." Sometimes, though, nature uses chiral building blocks to make structures that don't distinguish between right- and left-handed molecules. A case in point is a family of enzymes called racemases, which have a remarkable property: Although they are chiral like all other proteins, they don't care about the chirality of the substrates they act upon, according to Gregory A. Petsko, a professor of biochemistry and chemistry at Brandeis University in Waltham, Mass. In fact, their biological function is to convert one enantiomer into another. Petsko and his coworkers have studied the 3-D structures of two members of this family and have found that they both use the same strategy to "ignore" chirality. The racemases have a "functionally symmetric" reactive site that contains two basic amino acid residues oriented in such a way that they can abstract a proton from a chiral center of the substrate, whether the center has an R or S configuration. Studying exactly how the enzymes do this "has told us a great deal about how chiral [molecules] can be dealt with in chemistry and biotechnology," Petsko said. The chiral theme also is central to the work of chemistry professor Jacqueline K. Barton of California Institute of Technology. Her research has focused on designing chiral transition-metal complexes that target and probe specific sites along DNA and RNA. In collaboration with chemistry professor Nicholas J. Turro of Columbia University, Kornberg: Pasteur had brilliant solutions Barton has used luminescent metal
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OCTOBER 9,1995 C&EN
Barton: chiral transition-metal complexes probes to explore how the DNA double helix could function as a molecular wire. These experiments involve measuring electron transfer between a donor complex and an acceptor complex that are intercalated at different sites along a DNA double helix. Barton and coworkers have shown that the double helix is efficient at mediating electron transfer over very long distances (41 A). But for facile electron transfer to occur, they found, the metal complexes must be intercalated into the helix, rather than being attached to it in some other way. The reason for this is that intercalation is a Ti-stacking interaction and it allows the complexes to couple to the array of stacked aromatic heterocycles that forms DNA's stairway—the "ft-way" along which the electrons travel. The chirality of the metal complex influences the rate and efficiency of electron transfer, Barton noted. That's because the right-handed isomer stacks more effectively into the DNA double helix, thereby affording better coupling and more efficient electron transfer. Does nature take advantage of DNA's ability to act as a wire? That question can't be answered yet. But this ability may be something "that nature has to worry about," Barton said. As revealed in her talk, Barton and coworkers have found evidence that long-range electron-transfer reactions can play a role in mechanisms for DNA damage. The results are intriguing because scientists have speculated for a long time that electrons moving through a DNA helix
could be involved in the development of cancer. As was amply evidenced at the symposium, researchers are making headway in understanding the principles behind nature's design of nucleic acids and proteins. But the true test of whether one understands a design principle is to use it to construct a structure that hasn't been seen before, said Peter S. Kim, a biology professor at Massachusetts Institute of Technology and an HHMI researcher. Kim and his coworkers in recent years have been investigating protein structures known as coiled coils—two or more helices corkscrewed around each other. This is a common biological motif that shows up in structural proteins such as those found in muscle, skin, and hair, in regulatory proteins such as the 'leucine zipper," and on the surfaces of certain viruses, such as influenza virus. All of the known coiled coils, though, have a left-handed superhelical twist. Pehr B. Harbury, who worked in Kim's lab as a graduate student and is now a postdoctoral research associate at the University of California, Berkeley, set his sights on designing and making a right-handed coiled coil. Harbury had already written a computer program that correctly and efficiently predicts amino acid sequences that will fold themselves into a lefthanded coiled coil. To give the program its most rigorous test yet, he adapted it to predict a sequence that would form a right-handed coiled coil. Then he synthesized the sequence and confirmed that it does indeed form the expected structure in solution. The next step, Kim said, is to make the design method more general than just for coiled coils, "which are a very simple type of protein structure." As procedures of greater generality and sophistication become available, scientists expect to use them to probe more complicated protein-protein or proteindrug interactions. Just as studying artificial proteins is leading to important insights into nature's design strategy, so is the study of artificial nucleic acids. In an effort to understand how life evolved based on RNA and DNA, Albert Eschenmoser, professor emeritus of organic chemistry at the Swiss Federal Institute of Technology in Zurich, and his coworkers have synthesized several different
types of "potential nucleic acid alternatives" and compared their functional properties, such as base pairing, to those of natural nucleic acids. In this way, they hope to identify nucleic acid analogs that could have played a role in the evolution of life and understand the reason these analogs are not the biomolecules that nature relies on today. In his Pasteur symposium lecture, Eschenmoser focused on pyranosylRNA (p-RNA), a synthetic isomer of RNA in which the familiar ribofuran-
ose sugar (a five-membered ring) has been replaced by a ribopyranose sugar (a six-membered ring). This pyranosyl isomer, Eschenmoser reported, has "exceptional" properties. For example, it is "not only the strongest, but also the most selective oligonucleotide pairing system known so far." It is selective in the sense that its base pairing is restricted to the WatsonCrick type, with no involvement from the other base-pairing schemes that are biologically important. This pairing se-
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Pyranosyl-RNA is an isomer of RNA
lectivity arises from structural characteristics of the p-RNA backbone, such as its lower flexibility compared to the RNA or DNA backbone. Nevertheless, Eschenmoser pointed out, p-RNA actually forms more stable double-stranded pairing complexes than does RNA or DNA. p-RNA also is better able to resist hydrolysis than RNA. The work has led Eschenmoser to ask, "Can p-RNA self-replicate?,/ Recent experiments in his lab indicate that p-RNA is able to replicate in the absence of enzymes under "potentially natural conditions," in contrast, so far as is known, to RNA. And that brings up another question—one that can't be answered yet: Could p-RNA have been a forerunner of RNA? A different type of artificial system, under investigation at Scripps Research Institute in La Jolla, Calif., has led to the creation of another chemical species that has not been found in nature—a DNA enzyme. Gerald F. Joyce, an associate professor of chemistry and molecular biology at Scripps, produced cata-
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investigations may have implications for how life evolved on Earth, other organic chemists are building artificial chemical worlds that have much less resemblance to the biomolecular realm. Two chemistry professors who typify this approach and who discussed their work at the symposium are Jean-Marie Lehn of Louis Pasteur University in Strasbourg, France, and Julius Rebek Jr. of MIT. The chemical worlds of Lehn and Rebek are based on molecular recognition and self-assembly. Lehn has learned how to use these principles to build up different types of supramolecular assemblies by using metal ions as the "glue." For example, by placing in solution suitable metal ions and oligobipyridine strands, he can orchestrate the spontaneous formation of "helicates"—complexes in which two or three organic strands are helically wrapped around a string of three or more metal ions. The metal ions control the conformation of the organic components, and metal-nitrogen interactions hold the complexes together. The latest twist on this theme, Lehn revealed at the symposium, is the selfassembly of double-helical complexes that are circular, rather than linear. These circular helicates contain a central chloride ion that is very strongly bound and might be serving as the template for their formation, Lehn noted. Rebek's supramolecular complexes, by contrast, are held together by hydrogen bonds acting between self-complementary parts of identical molecules. For example, Rebek and coworkers designed an organic molecule that has selfcomplementary edges and just the right amount of built-in curvature so that two such molecules will dimerize to form a spherical complex. This complex, whose design was inspired by the architecture of a tennis ball, also can serve to encapsulate an atom or small molecule, such as methane. Lately, Rebek told his listeners, his group has designed and built monomers that self-assemble into more complex shapes that can trap larger molecules, such as benzene. Lehn's and Rebek's talks were included in the symposium's program primarily as "expositions of chemistry," Rockefeller's Kuriyan told C&EN. "They were not aimed at explaining or utilizing some biological principle, but they were very interesting [because they gave us] a flavor for the kinds
of molecules organic chemists [can California, Berkeley, and HHMI, is one of those organic chemists who has had make]." Synthetic organic chemistry tradition- a marked impact on biology. His studally has been a very "self-contained" ies have focused on the mechanisms of field, with its own language and its own molecular recognition and catalysis in concepts, Kuriyan noted. Now, as this biological systems and on designing field "moves into the mainstream of bi- molecules with novel biological funcology, it is having a tremendous im- tion. Schultz began his talk firmly in pact—precisely because organic chem- biological territory, with a discussion of ists can make compounds that can inter- catalytic antibodies. But as the lecture fere with biology, thereby teaching us progressed, it became clear that he has much more on his mind these days. how [a biological system] works." Schultz and his coworkers have been Peter G. Schultz of the University of
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working to extend the range of combi natorial chemistry, in which large col lections, or libraries, of distinct molecu lar entities are synthesized in parallel and then screened for potentially use ful properties. His lab and others' labs have been involved in screening librar ies consisting not only of antibodies and other biomolecules, but also poly mers and small organic molecules. Schultz's goal, though, is to extend the combinatorial approach to the entire periodic table. This has led him and his coworkers to prepare and screen librar ies of solid-state materials, such as high-temperature superconductors (C&EN, June 26, page 7). In his lecture, a whirlwind survey of research from his lab, Schultz noted that high-temperature superconductors tend to have complex compositions and structures, and have been discov ered largely by trial and error. The combinatorial approach is one way to carry out that discovery process more systematically and efficiently, he be lieves. And to be sure, a "huge amount of chemistry" is waiting to be discov ered in unexplored regions of the solidstate realm, he said. Schultz ended up taking his mostly biologically minded listeners down (what was for them) a surprising and unfamiliar avenue. But his take-home message fit in beautifully with the "two cultures" theme of the sympo sium: namely, that chemistry has a lot to learn from biology, and biology has a lot to learn from chemistry. •
New techniques enhance structure-activity work A group of industrial chemists and several academic collaborators are fo menting revolution in the normally se date field of quantitative structureactivity relationships (QSAR). They are developing a series of QSAR tech niques they hope will replace some tra ditional QSAR concepts that they be lieve are over the hill. In QSAR, mathematical "descriptors" of molecular structure are used as a ba sis for predicting chemical and physical properties or biological activity. QSAR is widely used for drug discovery, among other applications. For example, it can be employed to predict partition coeffi cients, lipophilicities, or relative reactivi-
