Major research collaborations Joining Center of Excellence in Genomic Sciences molecular science, Massachusetts General Hospital natural history, and The Scripps Research Institute University of Texas medicine University of Washington NSF Chemical Bonding Center NASA Astrobiology Institute The Templeton Foundation synthetic biology systems biology planetary biology Contact information Web: www.ffame.org H N CH N C N R Donor H C C email: [email protected] O: Acceptor N N Donor R C H C Acceptor C N: Acceptor Tel: 352 271 7005 :O HC C H puDDA Fax: 352 271 7076 Donor N N pyAAD R H HC CH N :O N R Acceptor Street Address: H H C C Donor N N N Donor C H C The Westheimer Institute Acceptor N N: :O Acceptor HC C H puADA 1115 NW 4th Street, Gainesville FL 32601 Donor C N pyDAD R H

Post Address: H HC CH N N N R Donor The Westheimer Institute H C C Acceptor O: :N N Acceptor Donor R C H P.O. Box 13174, Gainesville FL 32604-1174 C N genomic biology paleobiology :O puDAA Acceptor Donor HC C H C N pyADD R H HC CH :O N N R H H C C Acceptor Donor N :N N Acceptor Donor R C H C C N puAAD chemical genetics geobiology N Donor Acceptor HC C H H C O: pyDDA R

astrobiology

O human biology C H H O O H H HO C C H

H C N O H H C H NH2

12 About Frank H. Westheimer Education for the 21st Century scientist

Frank Westheimer moved easily between Themes in 21st Century science chemistry, biology and computation long The Institute faculty offer tutorials on topics that are not often found before it was fashionable. By doing so, he showed how polydisciplinarity generates dis- in formal graduate programs in the sciences, but which are critical covery. Frank provides the inspiration for the for professional performance in science in the 21st century. polydisciplinary work done at the Institute. Trained at Dartmouth, Harvard, and Fund raising: Funding is the key to successful science. Institute Columbia, Frank worked at the University of trainees have their skills in this area developed in both formal and Chicago and Harvard. In his career, he devel- informal settings. oped three paradigms that today unify Intellectual property and technology transfer: In the future, chemistry and biology. pioneering scientific research will need to rely less on peer review First, Frank was an early practitioner of physical organic chemistry, which studies how chemical reactions occur. The reactions that he studied include those where mechanisms, and more on return from technology that it generates. molecules are oxidized or reduced, gain or lose phosphate, or release carbon dioxide. Institute trainees each submit a patent application which they Frank then turned to study the analogous reactions in biology. He began by prosecute pro se,to learn how this process works. seeking catalysis in amino acids, then metal ions, and then in enzymes themselves. Verbal presentation: The key to successful scientists is the ability to His work encouraged the study of enzyme mechanism, which today is key to the development of pharmaceuticals and diagnostic tools. convey scientific ideas verbally, to students, peers, and the public. Frank also introduced computation to molecular science. He founded molecular Every lecture at the Institute is recorded, so that trainees can review mechanics, and did the first computational studies of organic acids and bases. their performance with the aid of coaches. Today, molecular mechanics is key to all biological computation. Outreach: A key to successful science is contact to the public. As with those of other generalists of the last century, Frank’s contributions are so fundamental that it is difficult to believe that they were resisted when they were Institute trainees are involved in ongoing outreach activities ranging introduced. "Tierchemie ist Schmierchemie" (biochemistry is messy chemistry) was from elementary schools to the adult population, and also in activities the view of German chemists who surveyed the mixing of biology with chemistry. that measure the success of outreach using quantitative metrics. Modern society has benefited from science that is done without such blinders. Creative thinking: Much of modern training in science avoids issues Frank in 2003 asked where “our blind spots are now?” The Institute works to identify and remove these. We hope to have the same impact in the next century as basic as logic and creativity. Institute trainees are involved in both as Frank had in the last. formal and informal programs to enhance skills in both areas. Westheimer, F. H. (2003) Reflections. J. Biol. Chem. 278, 11729 Technology transfer

A new organization for basic and applied research Technology developed by Institute scientists supports commercial products in many industries. The modern university as we know it may not be the most important developer of Bayer Diagnostics research and technology in the coming millennium. Its collegiate and departmental EraGen Biosciences divisions are well recognized barriers to innovation and multidisciplinarity. Its Bristol-Myers Squibb governance hinders technology transfer. The Westheimer Institute has constructed an bioMerieux innovative organizational structure to match its innovative science, and to meet the Firebird Biomolecular needs of research in science and technology in the new millennium. Alantos Gilead The Westheimer Institute is a part of the Foundation for Applied Molecular Evolution Eurogentec Glen Research Firebird Biomoleclar Sciences 2 11 Graduate studies at the Westheimer Institute Pioneering science Outstanding professional competence. Graduate students receiving Synthetic biology. If you understand life, you should be able to re- their Ph.D. at the Institute select a specific craft in which to build an create it. Institute scientists founded synthetic biology, which recreates outstanding professional competence. This places them in the top 10% emergent properties of living systems by constructing artificial systems. of individuals at the same professional level in this craft. Depending on Together with Harvard and Scripps, the Institute hosts one of four their choice, the student is apprenticed to the appropriate member of the Chemical Bonding Centers funded by the National Science Foundation, Institute faculty: committed to developing this new field. Area Faculty Systems biology. Genetics always acts within a complex biological Software engineering Dr. Chamberlin setting.. Institute scientists work as part of a Center of Excellence in Synthetic organic chemistry Dr. Hutter Genomic Sciences funded by the National Institutes of Health. The Enzymology and protein chemistry Dr. Benner Institute develops tools to enable systems biology, quantitatively analy- Molecular biology Dr. Carrigan zing the biomolecules from biology. These tools today help improve the Genetics and molecular evolution Dr. Gaucher care of some 400,000 patients annually living with infectious diseases. Polydisciplinarity. Graduate students receiving their Ph.D. at the Genomics. With funding from the National Institutes of Health, the Institute are also expected to have outstanding undergraduate Institute works to improve genome sequencing and re-sequencing tools, competence in each of the following areas. offering the potential of personalized medicine based on genetic analysis., Area Faculty and ways to understand the human genome sequence. Philosophy of science Dr. Carrigan Structure theory in molecular science Dr. Hutter Paleogenetics. Any system, natural or synthetic, is better understood if Geology and paleontology Dr. Benner one understands both its structure and its history. Institute scientists Mathematical analysis in science Dr. Chamberlin invented the field of paleogenetics, which resurrects ancestral genes from Cellular and organismic biology Dr. Gaucher ancient organisms for laboratory study. This adds experimental Course work substance to historical narratives that join chemistry with biology. The Institute faculty offer tutorials for credit for enrolled graduates, Planetary biology. Life on Earth has evolved together with the planet students, postdoctoral fellows, and visiting scientists. and the cosmos; each cannot be understood without understanding the others. Institute scientists work with scientists at University of Courses Washington as part of the NASA Astrobiology Institute to understand Mathematical logic, modeling and analysis life from the molecule to the cosmos. Organic reaction mechanisms Enzymatic reaction mechanism Chemical genetics. One goal of chemical genetics is to manipulate The history of the cosmos, the Earth and its biosphere biological systems using small molecules. Institute scientists invented Metabolic pathways and their regulation dynamic combinatorial chemistry, which allows a type of natural selec- Eukaryotic genetics and cell biology tion to be used to create biologically active small molecules. This tool is Organization of biological systems used today in pharmaceutical companies to generate new therapies. Evolutionary biology and molecular evolution The origin of life and extraterrestrias. One longstanding problem in Medical genetics biology asks how life began. With support from the NASA Exobiology Modern problems in human disease, diagnostics, and therapeutics program and the Templeton Foundation, Institute scientists use their understanding of chemical reactivity, natural history, and planetary science to build models for how the first genetic systems took hold on Earth, how genetic systems might appear in alien life living on other planets, and what features of the life we know are universal.

10 3 Synthetic genetics and synthetic biology The RNA world first?

The ability to synthesize is a test of understanding rooted deeply In 1962, Alex Rich suggested that life began with catalytic RNA. A in molecular science. Nearly 20 years ago, Institute scientists began decade ago, Institute scientists combined chemistry and genomics to a program to understand molecules central to genetics by produce a model for the RNA world. synthesizing new backbones and nucleobases for DNA and RNA. Benner, S. A., Ellington, A. D., Tauer, A. (1989) Modern metabolism as a palimpsest of the RNA world. Proc. Nat. Acad. Sci. 86, 7054-7058 This led to the first artificial H N CH N C N R Donor genetic system , having 12 ge- H C C Origin of life O: netic letters instead of the 4 in Acceptor N N Donor R C H C Acceptor C N: Acceptor Did RNA support the first life on Earth? natural DNA. Institute scient- :O HC C H puDDA Institute scientists have joined the geology of ists have now combined organ- Donor N N pyAAD borate minerals with mechanistic organic ic synthesis, enzymology, and R H HC CH chemistry to suggest “yes”. N molecular biology to generate :O N R Acceptor H H C C Ricardo, A., Carrigan, M.A., Olcott, A.N., Benner, S.A. Donor N Colemanite, a borate mineral a molecular biology to support N N Donor (2004) Borate minerals stabilize ribose. Science 303, 196 C H C this artificial genetic system., Acceptor N N: that stabilizes ribose :O Acceptor HC C H puADA showing that is can support Donor C N pyDAD Darwinian evolution. R H Physical organic chemistry and the origin of genetics Piccirilli, J. A., Krauch, T., Moroney, S. E., Benner, S. A. (1990) Extending H HC CH The Institute laboratories use mechanistic chemistry to understand how N the genetic alphabet. Enzymatic N N R Donor H C C life might have originated on Earth, with a model that has the incorporation of a new base pair into Acceptor O: :N N Acceptor DNA and RNA. Nature 343, 33-37 Donor R C H appropriate complexity (shown below). C N :O puDAA Acceptor Donor C HC H O H OH OH C N O OH HCHO, A new field: Synthetic biology enolization pyADD primary C HO O HO OH HO OH R H OH OH nucleophile HC CH C2,3 H H aldol at primary center H H HCHO, primary H H H H H H H H H H Institute scientists are credited N H C nucleophile aldol at secondary center :O N R Acceptor H H OH H H O H H OH H H C C retroaldol OH OH OH as founders of synthetic Donor N C4 HO HO crowded bond :N N Acceptor HO biology as a field . This field re- Donor R C H C HO H H HO H H H OH H H C N puAAD HCHO, primary C nucleophile HCHO, secondary C nucleophile HCHO, secondary N Donor C nucleophile creates the emergent properties Acceptor HC C H H OH C O: H H OH H H H H O H H H H HO CH2 H H O H H OH pyDDA of living systems using arti- O not observed, OH OH R C5 HO OH HO OH HO Shigemasa et HO HO al. 1994] ficial molecular architectures. HO H OH HO H H OH HO H H [4, 18% HO CH H H HO CH H 2 2 Shigemasa [3, 46% Shigemasa et al. 1994] no enolization; et al. 1994] OH OH HCHO, secondary C no elimination, Institute scientists have joined A synthetic DNA with 12 genetic letters nucleophile HCHO, secondary retroaldol gives C2 C nucleophile + C3 HCHO, primary C nucleophile OH HCHO, secondary OH scientists from Harvard and C6 C nucleophile H H O H H OH H H HO CH Synthetic biology in the clinic H H H2C OH H H H H OH H H 2 Scripps in a Chemical Bonding H H H2C OH H HO OH O only one enol HO OH HO OH 3 + 3 HO [5, 13% HO CH2 H OH no enolization; HO OH Shigemasa et Alternative genetic systems sup- HO H O HO CH retroaldol gives HO CH2 H Center funded by the National no interesting retroaldol 2 OH al. 1994] OH 2 x C3 2 + 4 HO H OH only one enol OH OH Science Foundation. This team port diagnostics tools that improve HCHO, secondary C nucleophile HCHO, secondary HCHO, secondary C nucleophile HCHO, primary C nucleophile is committed to developing arti- the health of 400,000 patients each C nucleophile OH OH OH OH OH C7 H H HO CH2 H ficial genetic systems capable year worldwide, helping physi- H H O H H H H H C OH H H H HO CH2 H H 2 H H H2C OH H OH H H H2C OH OH HO OH OH OH HO OH of Darwinian evolution. cians provide personalized care to HO O HO HO OH HO HO CH2 OH HO CH HO CH HO H HO CH 2 2 HO CH2 O Benner, S. A., Sismour, A. M. (2005) manage infections by the HIV and 2 HO H O H H HO H OH H H OH OH OH OH HCHO, secondary OH HCHO, secondary HCHO, C nucleophile Synthetic biology. Nature Rev. Genetics retroaldol to C2 + C5 C nucleophile HCHO, secondary retroaldol to C3 + C4 primary C no enolization; C nucleophile no enolization nucleophile hepatitis B and C viruses. retroaldol to C3 + C4 no retroaldol OH 6, 533-543 OH OH OH isolated OH H H HO CH2 H H H H2C OH O H H HO CH H OH C8 H H H2C OH HO CH2 2 OH OH OH HO O Bain, J. D., Chamberlin, A. R., Switzer, C. Y., Benner, S. A. (1992) Ribosome incorpor- HO HO HO HO CH2 HO CH2 HO H O H H HO H HO CH2 H H HO CH2 O H H OH OH ation of non-standard amino acids into a peptide through expansion of the genetic code. FormosePathway05_05_23.cdx OH OH no enolization; continued chain growth and no enolization; continued chain growth and Nature 356, 537-39 retroaldol -> C2 + bC6 termination; retroaldol -> 2 x C4 retroaldol -> C3 + bC5 termination; retroaldol -> 3 + C5 Benner, S.A. (2004) Understanding nucleic acids with synthetic chemistry. Acc. Chem. Res. 37, 784-797 As simple as possible, but not simpler. A scheme showing possible paths for the formation of carbohydrate on early Earth. 4 9 Exobiology and alien genetics Bioinformatics and computational biology Institute scientists were the first to do an exhaustive matching of a modern How might alien genetics be recognized? protein sequence database, and constructed one of the first bioinformatics NASA missions to Mars, Titan, and elsewhere workbenches. They were also the first to generate a naturally organized make this no longer an academic question. genome sequence database. Dr. Stephen Chamberlin, now at the Institute, led Institute scientists do Earth-based research to the software engineering team that converted this to a commercial product inform NASA in its search for life in the galaxy. Many forms of alien life have that was placed in the pharmaceutical industry. been conceived by science fiction Gonnet, G. H., Cohen, M. A., Benner, S. A (1992). Exhaustive matching of the entire writers. Which are reasonable? protein sequence database. Science 256, 1443-1445

Second generation models for DNA O O Evolution holds the key to protein folding … O O - P N NH S N NH The repeating charge in the O O The toughest problem in protein science O N N NH2 N N NH2 backbone of DNA and RNA has O O been regarded as an inconveni- was recast when Institute scientists showed NH NH O 2 O 2 ence. Synthetic biology at the that it was possible to predict the folded - P O N N S N N O O structure of a protein by analyzing its O N N H N N H Institute has shown that this O O feature is a key to molecular divergent evolution. In a feat called ”a major breakthrough”, the fold of protein kinase, NH2 NH2 recognition in DNA, and may be a O O O - P N S N was successfully predicted de novo in 1990; O O universal for life in the cosmos. O N O N O many successful predictions have followed. O strand-strand O Benner, S.A., Hutter, D. (2002) Phosphates, interactions can DNA, and the search for nonterrean life: A O 286 be anywhere second generation model for genetic 313 274 301 molecules. Bioorg. Chem. 30, 62-80 307 7 active site Evolutionary bioinformatics 262 12 helps understand the adaptation of Organic compounds on Mars 152 Peptide the obesity protein leptin (2003) 153 131 Binding Site 22 The 1976 Viking mission reported 241 42 156 186 201 124 no organic molecules on Mars. general base 237 … and biomolecular function g-phosphate ATP Institute scientists applied organic Binding 46 182 Site reactivity and planetary science to When set in the context of na- 115 48 predict structures for Martian 61 161 67 tural history, protein sequence Peptide organic molecules. These may 74 Binding 163 evolution also informs about Site support human habitation on Mars. 177 ++ protein function. Led by Eric 84 Mg 212 111 166 Gaucher, Institute scientists

Weird life 226 develop new tools to detect

beta strand with when the function of a protein While most focus on water as a solvent for life, water is one of the bend indicated changes during evolution, and scarcer fluids in the solar system. More abundant is supercritical alpha helix 103 93 genetic changes that cause dihydrogen-helium mixtures (gas giant planets), liquid dinitrogen coil, loop, or turn disease. (Triton), and ammonia-water eutectics (Titan). Institute scientists The predicted structure of protein kinase (1990) serve on a panel of the National Academy of Sciences to define the Benner, S.A., Cannarozzi, G., Chelvanayagam, G., Turcotte, M. (1997) Bona fide predictions of limits of organic life in the cosmos. protein secondary structure using multiple sequence alignments. Chem. Rev. 97, 2725-2843 Benner, S. A., Ricardo, A., Carrigan, M. A. (2004) Is there a common chemical model Benner, S. A., Chamberlin, S. G., Liberles, D. A., Govindarajan, S., Knecht, L. (2000) Functional for life in the universe? Curr. Opinion Chem. Biol. 8, 672-689 inferences from reconstructed evolutionary biology involving rectified databases. An evolutionary approach to functional genomics. Research Microbiol. 151, 97-106

8 5 Joining chemistry with natural history Natural history and human disease Any system,, natural or man-made, can be better understood if one A problem in modern genomics is that there is understands both its structure and its history. Yet molecular science has too much of it. Institute scientists encountered been largely separated from natural history in the modern academy. One mission of the Institute is to fuse the physical sciences with natural this when they were approached by resear- chers in pig reproductive biology. Pigs have history, making it largely unique in academic research institutions. three genes to convert testosterone to estrogen; one would seem to be enough. Combining com- A new field: putation, geology, paleontology, physiology, An Old World pig shortly and genetics, Institute scientists built a hypo- Experimental paleogenetics after large litters emerged thesis that these helped pigs have large litters.

Institute scientists were the first to Gaucher, E.A., Graddy, L.G., Simmen, R.C.M., Simmen, F. A., Kowalski, A.A., Schreiber, D.R., Liberles, D.A., Janis, C.M., Chamberlin, S.G., Benner, S.A. (2004) Planetary biology of resurrect ancestral genes from an- cytochrome P450 aromatase from swine. BMC Biology. 2, 19 cient organisms for study in the labora- tory. Paleogenetics puts experimental A digestive enzyme of Diacodexis, data be-hind historical narratives that which lived 40 million years ago, was The new field of planetary biology resurrected to understand the connec- provide a heuristic understanding of tion between biomolecular physiology Human biology is also shaped by “function” in biological systems. For and a changing environment. changing environment in a changing example, resurrected proteins from Jermann, T.M., Opitz, J.G., Stackhouse, J., Benner, S.A. (1995) Reconstructing planet. 60 million years ago, the an- ancient ruminant digestive tracts the evolutionary history of the artioda- cestors to modern humans lost the showed the evolution of ruminants ctyl r ibonuclease superfamily. Nature gene to make vitamin C, presumably adapting to global climate change. 374, 57-59 because they inhabited a fruity rain forest rich in the vitamin. But then, At what temperature did bacteria live 3 billion years ago? geological events led to the cooling and drying of the planet, and the loss of much of the rain forest. Humans Astrobiology asks about our left the vitamin C-rich forest, acquir- most distant ancestors, including ed the disease scurvy, and then lost Human disease is dominated by incom- bacteria that lived three billion another gene, allowing urate to accu- plete adaptation of human ancestors to a change in their environment, diet, and years ago. Institute scientists resur- mulate. Urate replaces the anti- lifestyle. rected proteins from bacteria of oxidant vitamin C, but causes gout. that antiquity, and showed that Further misadaptation is involved in these were optimally active at 65 obesity, diabetes, and hypertension. °C. This suggests that bacteria near the root of the eubacterial tree Planetary biology and cancers were thermophiles. The prostate emerged in the lineage leading to modern humans about Gaucher, E. A., Thomson, J. M., Burgan, 150 million years ago. With it came a disease cluster associated with M. F., Benner, S. A. (2003) Inferring the an incompletely adapted tissue, including prostate hyperplasy and Structure of a bacterial elongation paleoenvironment during the origins of factor; one over 3 billion years old bacteria based on resurrected ancestral prostate cancer. Retracing the natural history of prostate helps us was resurrected for study in the lab. proteins. Nature 425, 285-288 understand the diseases of the tissue.

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