Division Awards for 2010

Founders Travel Awards

Dr. Jeremiah Hanes, Tadhg Begley Research Group, Cornell University.

To support the participation of students and/or post-docs at the Winter Enzyme Mechanisms Conference.

Tom Bruice, Bill Jencks, and Myron Bender, as a mechanism to foster collegial interactions within the community of chemists and biochemists interested in understanding the chemical basis for enzymatic catalysis and the regulation of enzyme action, founded the Winter Enzyme Mechanisms Conference in 1969. The passing of William P. Jencks on January 5 of 2007 coincided with the 20th meeting of the Winter Enzyme Mechanisms Conference in St. Petersburg, Florida, and this loss was felt keenly by many senior participants at that conference. The interest in recognizing Bill’s many contributions to mechanistic enzymology, in a manner that would help to ensure the vibrancy of the community that he helped to create, resulted in the creation of the “Founders Travel Award”, which will support the participation of students and/or post-docs at the Winter Enzyme Mechanisms Conference. The ACS Biological Chemistry Division will manage the investment of funds contributed for this award and has established the process for the competitive selection of the awardees.

Dr. Jeremiah Hanes was selected as the recipient of the first Founders Travel Award. This award was presented to Dr. Hanes on January 4, 2009 at the 21st meeting of the Winter Enzyme Mechanisms Conference in Tucson, Arizona. Dr. Hanes completed his Ph.D. with Ken Johnson at the University of Texas, and then moved to become a postdoctoral fellow with Tadhg Begley at Cornell University. The audience at this conference paid close attention to Jeremiah’s stimulating talk on the “Characterization of a New Vitamin B6 Biosynthetic Pathway”.

The ACS Chemical Biology Lectureship

Professor Alanna Schepartz, Department of Chemistry, Yale University.

For contributions that have had a major impact on scientific research in the area of Chemical Biology.

This award recognizes the work of Professor Alanna Schepartz on the application of chemical principles to understand and control biological recognition and function. Jointly sponsored by ACS Chemical Biology and the ACS Division of Biological Chemistry, the lectureship is cooperatively administered by Editor-in-Chief Laura L. Kiessling and the Division. The lectureship, awarded annually at the Spring ACS National Meeting, is a testament to the strong relationship between the journal and the division.

Professor Schepartz has made major contributions in three different areas of chemical biology: protein-DNA recognition and transcriptional activation; the development of miniature proteins that bind specifically and with high affinity to protein and DNA ligands; and the development of ?-peptides as protein ligands and as building blocks of protein-like structures.

Professor Schepartz’s contributions in the area of transcriptional activation focused largely on basic region-leucine zipper (bZip) proteins. She and her co-workers used a combination of chemical and biophysical techniques to probe the importance of basic region orientation and DNA bending for specificity. Their elegant demonstration that these proteins bind to DNA as monomers before dimerizing on the DNA surface provided insight into the means by which many classes of transcription factors achieve a high degree of spebut cificity without falling into kinetic traps. Finally, the Schepartz group also revealed the mechanisms of action behind the viral proteins Tax and pX, which exert their effects through bZip transcription factors.

This work led to an interest in designing stabilized ?-helices that could be used for both protein and nucleic acid recognition. Professor Schepartz’s approach was to incorporate recognition elements a small, stable domain from the avian pancreatic polypeptide, which is formed from an ?-helix packed against a polyproline helix. The stability and binding affinity of these miniature proteins was optimized using directed evolution to provide highly specific recognition modules. Using the ?-helical surface, Schepartz and her coworkers have developed miniature proteins that target bZip recognition sites, the anti-apoptotic protein Bcl-XL, and the oncogene hDM2. They have also used the polyproline helix to target EVH1 domains from cytoskeletal regulatory proteins and SH3 domains of Src-family kinases.

The third area in which Professor Schepartz and her colleagues have made major contributions is that of ?-peptide foldamers. They developed a strategy for stabilizing 14-helical structures in water, leading to the first ?-peptide inhibitor of a protein-protein interaction. They used this structure to design a ?-peptide combinatorial library, which allowed for the selection of more potent inhibitors. Most surprisingly, Schepartz and co-workers have discovered a ?-peptide that assembles into a defined quaternary structure. This discovery provided the first demonstration that synthetic polymers other than natural biopolymers can assemble into protein-like structures, in spite of the fact that many believed that ?-amino acid polymers represented privileged structures.

Finally, in addition to her scholarly work, Professor Schepartz has also made important contributions to the community through her service on the BNP Study Section and as an associate editor for the Journal of the American Chemical Society. She has also been a dedicated teacher, as evidence by her mentorship of over sixty graduate students and postdoctoral associates and her engaging teaching of introductory organic chemistry to undergraduates.

Eli Lilly Award in Biological Chemistry

Professor Alice Y. Ting, Department of Chemistry, Massachusetts Institute of Technology.

For outstanding research in biological chemistry of unusual merit and independence of thought and originality.

This award recognizes Professor Ting’s groundbreaking contributions in the development of new fluorescent probes and reporters for imaging protein interactions and activities in cells. Her innovative work is a remarkable demonstration of the critical role of chemistry in our efforts to understand the biological world.

The importance of genetically encoded fluorescent proteins for the study of biological molecules, pathways, and events in living cells is well documented. Indeed, the discovery and development of fluorescent proteins for use in modern cell biology was recognized with the Nobel Prize in Chemistry in 2008. In spite of the importance of these molecules, fluorescent proteins are both bulkier and dimmer than fluorescent organic dyes, limiting their sensitivity and versatility. Professor Ting’s goal has been to develop techniques that combine the genetic encodability of fluorescent proteins with the advantages of small molecule probes. The versatility of her methods allows the attachment not only of fluorescent dyes but also photoaffinity labels and crosslinkers.

Professor Ting’s approach has been to engineer several ligases to accept substrates appended with a small molecule probe with the desired function. These ligases also recognize peptide substrates as small as 13 amino acid residues. These peptide tags can be genetically appended to the protein of interest, allowing any protein to be modified by the ligase-substrate pairs. Professor Ting and her group directed their early efforts at modifying proteins on the cell surface, attaching both small molecules and quantum dots to the extracellular domains of a variety of different proteins. More recently, they have turned their attention to labeling intracellular proteins in living cells with promising results. Finally, Ting has developed a clever approach to study protein-protein interactions on the surface of living cells, using biotin attachment by proximity to detect proteins that have formed a complex in vivo.

Professor Ting and her co-workers have also applied their methods for the study of interesting biological problems, including receptor-mediated uptake of the low-density lipoprotein particle. More recently, they have discovered truly interesting interaction dynamics between proteins at neuronal synapses. With the continued development of these technologies, and with the selection of these exciting biological systems, Professor Ting is poised not only to answer important questions of her own but to have a major impact on the way that cell biology is done by others.

Pfizer Award in Enzyme Chemistry

Professor Vahe Bandarian, Department of Chemistry & Biochemistry, University of Arizona.

For outstanding work in enzyme chemistry where the presence of enzyme action is unequivocally demonstrated.

This award recognizes Professor Bandarian’s work on various aspects of the biosynthetic pathways for bacterial secondary metabolites. He and his colleagues have undertaken these studies with an eye toward understanding the pathways and chemical transformations that underlie the biosynthesis of these natural products, the mechanisms for the evolution of catalysts in these pathways, and the broader issues involving evolution of secondary metabolic pathways in bacteria.

Professor Bandarian is especially noted for the identification and characterization of the gene cluster responsible for the production of the deazapurine natural products toyocamycin and sanguvamycin in Streptomyces rimosus. Although this class of compounds was discovered more than four decades ago, the biosynthetic pathways that produced them had remained elusive. Professor Bandarian applied contemporary technology and careful molecular logic to clone the genes for the production of 7-deaza-7-cyanoguanine (preQ0), the modified base in these antibiotics. Importantly, this modified base is also a key intermediate in the conversion of GTP to the hypermodified base queuosine, which is found at the wobble base position of tRNAs in a wide variety of organisms. The activities of three of the four enzymes involved in this pathway were previously unknown; all three mediate novel catalytic transformations.

In addition to identifying the enzymes responsible for the production of preQ0, Dr. Bandarian and his colleagues have explored a range of problems in deazapurine production, including its relationship to the folate biosynthesis pathway. They have identified a new nitrile hydatase, ToyJKL, which is responsible for converting toyocamycin into sanguvamycin. They have also explored the relationship among various classes of GTP cyclohyrolases, showing that a single mutation in a class II hydrolase is sufficient to alter the reaction course.

Professor Bandarian’s work is a tour de force at the cutting edge of microbial bioinformatics, natural product biosynthesis, metabolomics, and the de-oprhaning of open reading frames of unknown function. The set of publications describing the reconstitution of the synthesis of preQo in vitro is transformative in that it opens this field of biosynthesis and sets the stage for detailed studies of these enzymes and the reactions they catalyze. In addition, the broader evolutionary questions that Dr. Bandarian poses will no doubt provide new surprises with equally rich biochemistry to be explored.

Repligen Award in Chemistry of Biological Processes

Professor Ronald T. Raines, Department of Biochemistry, University of Wisconsin, Madison.

For outstanding contributions to the understanding of the chemistry of biological processes with particular emphasis on structure, function and mechanism.

This award recognizes Professor Ronald Raines’s contributions to and wide-ranging impact on science at the interface of chemistry and biology. Dr. Raines is an outstanding scholar and unusually deep thinker who has applied his talents to a broad array of problems. He is perhaps best known for his work in two major areas of biological chemistry: unleashing the therapeutic potential of ribonucleases; and understanding the chemical basis for the unusual stability of collagen. To these problems and others, he has brought a clear understanding of both chemical principles and biology, leading his science toward real world applications from new materials to anticancer agents.

Professor Raines and his group began their work on RNase A in the early 1990s, exploring biochemical questions about its catalytic mechanism. At the time, few could have predicted that this venerable model system, arguably the most thoroughly studied of all enzymes, was to lead to a powerful new anti-cancer agent. Prof. Raines carried out state-of-the-art studies that led to important insights into the energetics of catalysis. Turning his attention to the biological role of this enzyme, he reasoned that ribonucleases could be made toxic if they escaped binding by the endogenous ribonuclease inhibitor that protects cellular RNAs from invading ribonucleases. Using careful structure-function studies, he and his co-workers engineered catalytically functional RNase A analogues that evaded the inhibitor. These ribonucleases were indeed toxic to cells, with a marked preference for killing cells of a cancerous origin. Raines extended this work to RNase 1, the human analogue of RNase A, designing an inhibitor-evasive analogue that is now in human clinical trials as a cancer therapeutic. More recently, he and his colleagues have extended the realm of cytotoxic ribonucleases to diseases other than cancer. They have cleverly used circular permutants of ribonuclease to create artificial zymogens that can be activated by any designated protease. To date, he and his group have applied this approach to engineer ribonuclease analogues that are activated by the proteases associated with the human pathogens that cause malaria, hepatitis C, HIV-AIDS

Professor Raines’s second area of focus is collagen, the most abundant protein in animal cells. Post-translational modification of collagen by the enzyme prolyl-4-hydroxylase markedly increases the conformational stability of the collagen triple helix. For 25 years, the prevailing paradigm had been that this enhanced stability arises from water-mediated hydrogen bonding between the hydroxyl group of 4-(R)-hydroxyproline (Hyp) residues and a main-chain oxygen. Recognizing that the hydroxyl group could also have stereoelectronic consequences that stabilize the desired conformation, Raines and his co-workers cleverly demonstrated that collagen triple helices in which the Hyp residues are replaced by 4-(R)-fluoroproline are extraordinarily stable. As fluorine is unable to form strong hydrogen bonds, this work and subsequent structural studies provided strong support for the importance of n ? ?* interactions between adjacent peptide bonds for stabilizing the conformation of the polyproline type-II helices found in collagen. Prof. Raines and his co-workers have exploited these findings to design self assembling, stable synthetic collagen triple helices with native-like lengths that are leading to new strategies for healing wounds.

In addition, Professor Raines’s versatility has led to important contributions in several other areas. He is internationally recognized for his development of new technologies to ligate polypeptides in a traceless fashion. He has also provided important insights regarding the roles of redox buffers in cellular homeostasis. More recently, he has turned his attention to the generation of biofuels, developing a one-step process to convert lignocellulosic biomass into highly promising fuel precursors.

Finally, Professor Raines also brings his intellectual rigor and enthusiasm for science to his service and teaching activities. He was the Chair of the NIH Study Section for Synthetic and Biological Chemistry (B), where he was an important advocate for the support of young investigators. As a research mentor, he has trained over 50 graduate students and postdoctoral scholars, 19 of whom hold tenured or tenure-track positions at academic institutions. His laboratory has also been extremely hospitable to undergraduate students; indeed, Raines has published 29 peer-reviewed journal articles with Wisconsin undergraduates as co-authors. These accomplishments highlight the commitment and energy Professor Raines directs not only his own vigorous research program, but also to the future of biological chemistry.

The Gordon Hammes ACS Biochemistry Lectureship

Professor Perry Frey, University of Wisconsin-Madison, Institute for Enzyme Research.

Professor Perry Frey, whose penetrating analyses of enzyme mechanisms have captivated the scientific community for more than 45 years, has been selected to present the second Gordon Hammes ACS Biochemistry Lecture at the 2010 ACS National meeting. The choice of Professor Frey recognizes his work on many problems, which has expanded the frontiers of the field of enzyme mechanisms.
Frey began his independent career by establishing the chemical mechanisms for the reactions catalyzed by uridine diphosphate galactose 4 epimerase (UDP-Gal epimerase) and galactose 1 phosphate uridylyltransferase. His work with the sugar epimerase provides an instructive example of the use of the substrate uridylyl group to anchor the reacting sugar at an enzyme active site where there are almost no specific sugar-protein interactions. This allows for oxidation of the sugar C-4 hydroxyl by a tightly bound NAD cofactor, rapid rotation of the 4-keto-sugar intermediate, and reduction of this intermediate to form epimerized product. Frey recognized early on that site-directed mutagenesis would revolutionize the study of enzyme mechanisms, and he used this as a tool in studies on both UDP-Gal epimerase and galactose 1-phosphate uridylyltransferase. He obtained X-ray crystal structures of wildtype and mutant enzymes in collaboration with Hazel Holden. This provided the structural information needed to draw mechanistic pictures for these two enzymatic reactions orders of magnitude more detailed than anything previously obtained from classical kinetic and structure-reactivity studies.
Frey was one of the leaders in the development of methods for the synthesis of nucleoside pyrophosphorothioates with chiral [18O]-labeled phosphorothioate groups, and in the use of these chiral compounds to determine the stereochemical course of enzyme-catalyzed thiophosphoryl transfers. Studies by Frey and several others were so successful that essentially all of the important mechanistic stereochemical problems relating to enzyme-catalyzed nucleophilic substitution reactions at tetravalent phosphorus were solved in less than fifteen years. During this time he also carried out important studies on the bond-order and charge delocalization at phosphorothioates.

Frey noted around 1994 an observation from 1972 by Robillard and Schulman that the proton bridging the ? nitrogen of His57 and the carboxyl group of Asp102 in the active site triad of chymotrypsin has an unusual downfield 1H-NMR resonance of 18 ppm. This anomalous chemical shift shows that the magnetic environment of the hydrogen-bonded active site triad proton is very different from that for hydrogen bonded protons in water, and is consistent with a much greater stability for this hydrogen bond compared to hydrogen bonds in aqueous solution. Frey followed his reevaluation of literature data with experimental work of his own design, that helped delineate the differences in the structure and stability of hydrogen bonds in water compared with hydrogen bonds in the highly organized and less polar environment of enzyme active sites. These thorough experiments and carefully argued conclusions have helped to draw the scientific community towards a consensus opinion about the contribution of hydrogen bonds to the rate acceleration for enzymatic reactions.

Frey’s studies on the bacterial enzyme lysine 2,3-aminomutase have provided critical insight into the mechanism of action of this member of the large radical SAM superfamily of enzymes. Lysine 2,3-aminomutase catalyzes the interchange of hydrogen and an amino group between adjacent carbon atoms, which is characteristic of adenosylcobalamin-dependent reactions. However, the protein catalyst does not contain or require this coenzyme and proceeded by a completely mysterious reaction mechanism. Frey has shown that the enzyme uses both S adenosyl methionine (SAM) and pyridoxal phosphate (PLP) as cofactors. The adenosyl group of SAM plays same mechanistic role as the B12-adenosyl group in the transport of hydrogen between substrate carbons. The ?-pyridyl carbon of PLP was shown to play a role similar to that of the cobalamine cobalt in mediating the skeletal rearrangement of substrate. Several hypothetical mechanisms for the generation of radicals by the reaction of SAM with the protein iron-sulfur center were considered, and strong evidence obtained to support a mechanism in which formation of a complex between the sulfonium sulfur of SAM and the iron-sulfur center is accompanied by an inner sphere electron transfer that occurs in concert with homolytic cleavage of the C-S bond in SAM.

Perry Frey has contributed heavily to the intellectual fabric of the community in which he has been a leader. His recently published book, Enzymatic Reaction Mechanisms, will be the definitive text on this subject for the next twenty years, or longer. He has served as associate editor of the Journal Biochemistry since 1992, as co-chair GRC on Enzymes, Coenzymes and Metabolic Pathways and, as Chair of the organizing committee of the Winter Enzyme Mechanisms Conference. Professor Frey’s lecture at the 240th ACS National meeting in Boston (August, 2010) will be an important event in the history of Biochemistry and the Division of Biological Chemistry, who are joint sponsors of this lectureship.

Division Awards for 2009

Eli Lilly Award in Biological Chemistry

Scott K. Silverman, Department of Chemistry, University of Illinois.

For outstanding research in biological chemistry of unusual merit and independence of thought and originality.

This award recognizes Professor Silverman’s pioneering studies of deoxyribonucleic acids as functional molecules, which is focused on developing unusual and important chemical applications for DNA beyond the storage of genetic information.

Natural ribozymes were discovered in 1982 and the first artificial deoxyribozyme was reported in 1994. Professor Silverman has developed a creative and highly productive research program to develop new DNA catalysts and original applications for these catalysts. This work has made the scientific community aware of the tremendous potential of catalytic DNA.

A long-standing challenge has been the synthesis of large RNAs with nonlinear branched or lariat topologies, which form as intermediates of RNA splicing reactions. Silverman has identified a host of deoxyribozymes that efficiently ligate RNA substrates of the appropriate physiological size, and which are suitable for the preparation of RNAs with nonlinear branched or lariat topologies. These relatively low molecular weight deoxyribozymes have been prepared by commercial suppliers of oligonucleotides, and are broadly available for use by members of the nucleic acid community.

The development of new deoxyribozymes that have direct applications towards the solution of problems in biological chemistry is a hallmark of Silverman’s work. These deoxyribozymes make use of readily available nucleoside triphosphates or 2’-3’ nucleoside cyclic phosphates as nucleotidylyl donors for the synthesis of RNA. Silverman then proceeded to use these new deoxyribozymes in creative investigations of the mechanism for proof reading for natural RNA splicing, and he has carried out experiments to test the hypothesis that branched RNAs form as intermediate of retrotransposition.

In recent years Silverman has expanded his repertoire of deoxyribozymes beyond those, which use RNA as substrates. He has identified deoxyribozymes that catalyze the classic Diels-Alder reaction with the same efficiency as ribozymes. He has expanded DNA catalysis to the realm of peptide synthesis, by selecting deoxyribozymes that catalyzes the nucleophilic attack of a phenol side chain of tyrosine at a 5’-triphosphate RNA to form a Tyr-RNA nucleopeptide linkage. These experiments are laying the groundwork for the use of deoxyribozymes in the synthesis of large molecular weight protein conjugates, such as glycoproteins.

In summary, Silverman’s accomplishments have fully demonstrated the potential of deoxyribozymes to produce new enabling technologies of profound importance. His future work will serve as the training ground for our next generation of scholars.

Pfizer Award in Enzyme Chemistry

Professor Virginia W. Cornish, Department of Chemistry, Columbia University.

For outstanding work in enzyme chemistry where the presence of enzyme action is unequivocally demonstrated.

This award recognizes Professor Cornish’s work, which combines modern techniques in synthetic organic chemistry and molecular biology, to manipulate nature’s machinery in order to carry out new chemistry. This research spans many areas in Chemical Biology, from site specific incorporation of amino acid analogs into proteins, to selective labeling of proteins in living cells, to the directed evolution of enzymes with novel activities, which is the primary work honored by the Pfizer award in enzyme chemistry.

Most methods developed to select for cells that have evolved novel enzymatic activities are limited to a narrow and specific set of reactions that can be used to either complement a growth deficiency or to reverse cell death. Professor Cornish has developed a “chemical complementation” system for the directed evolution of enzymes with new properties. This work builds on traditional complementation assays that are specific for a handful of enzyme-catalyzed reactions. The more general method that she has developed links enzyme catalysis to cell survival, and is based upon the covalent coupling of two tethered small molecule ligands that result in the triggering of a transcriptional activator, and hence, reporter gene transcription.

Professor Cornish first supervised the design of a small molecule three-hybrid system based on a dexamethasone-methoxtrexate heterodimer. This small molecule system is now being applied successfully by the biotechnology industry for the identification of drug targets. She next showed, using ?-lactamase as a model enzyme, that the small molecule three-hybrid system could be used to link enzyme catalysis to the transcription of reporter genes in yeast. This work set the stage for the directed evolution of an enzyme, with enhanced catalytic activity, which catalyzes the synthesis of carbohydrates from ?-fluoro glycosyl donors. Professor Cornish has shown that this glycosynthase activity may be detected as covalent coupling of tethered sugar acceptor and ?-fluoro sugar donor substrates. The chemical combination of these tethered substrates then leads to the transcription of a reporter gene in vivo.

Professor Cornish is a noted teacher and mentor. Her first Ph.D. student, Dr. Hening Lin, is now an assistant professor in the Department of Chemistry and Chemical Biology at Cornell University. Dr. Larry Miller, a postdoctoral fellow in her laboratory, is now assistant professor of Chemistry at the University of Illinois at Chicago Circle.

Repligen Award in Chemistry of Biological Processes

Frank M. Raushel, Department of Chemistry, Texas A&M University.

For outstanding contributions to the understanding of the chemistry of biological processes with particular emphasis on structure, function and mechanism.

This award recognizes Professor Raushel’s sophisticated kinetic and structural studies on enzymes, which have provided an in depth understanding of how substrates are bound, intermediates are
shuttled, and transition state are stabilized in the catalysis of multistep enzymatic reactions.

Professor Raushel’s work is notable for the diversity of enzymatic reactions studied, and the depth of these investigations. His work has provided fundamental insight into the mechanism of action of a variety of enzymatic reactions, including arginosuccinate lyase, arginosuccinate synthase, dihydroorotase, glycogen synthase, luciferase and selenophosphate synthase. This work has consistently extended the boundaries of research on the mechanism of enzyme action.

Raushel’s signal contribution over the past twenty years is the elucidation of the mechanism by which carbamoyl phosphate synthetase (CPS) coordinates the function of three widely separated active sites to catalyze the four distinct chemical reactions required to produce carbamoyl phosphate from bicarbonate, glutamine and ATP. He first showed by purely biochemical experiments that the separate steps of the overall enzymatic reaction take place at distinct domains of the protein. He then established a collaboration with Hazel Holden and Ivan Rayment at the University of Wisconsin to solve the crystal structure for CPS. This structure confirmed all of his earlier conclusions about the domain structures for this enzyme and led to the identification of three active sites. These structures define the mechanism by which ATP hydrolysis is coupled to chemical bond formation, and for protection of the high-energy reaction intermediates from reaction with solvent. The three active sites at CPS are widely separated, but the highly unstable reaction intermediates are never released to solvent, passing instead from one site to another through two tunnels, one of which is nearly 100 Å in length. In subsequent work, Raushel and coworkers have characterized the single-molecule transport of these intermediates through the protein milieu.

Raushel is also interested in the phosphotriesterase responsible for the bioremediation of organophosphate pesticides and has conducted a series of penetrating studies to establish the mechanism of action of this enzyme. Structural studies, in collaboration with Holden, revealed that the active site holds a binuclear metal center, which is used to stabilize a nucleophilic hydroxide. An additional unusual feature of the phosphotriesterase is the posttranslational carboxylation of an amino side-chain of an active site lysine to generate a bridging carbamate ligand in the metal cluster.

In summary, Frank Raushel is the complete package: an insightful and highly prolific researcher who is a noted pioneer in a well-developed area of biological chemistry, a conscientious mentor to students,
and a selfless contributor to the national, and international biochemistry communities.