Fritz Lipmann Research Articles

The Power of Phosphate

This paper concerns the development of a central tenet of modern biochemistry: that cellular metabolism coordinates biological energy supply through the cyclical making and breaking of “energy-rich” phosphate bonds. This interpretation of intermediary metabolism was comprehensively set forth in two review articles published nearly simultaneously (though independently) in early 1941 by German biochemist Fritz Lipmann and Danish biochemist Herman Kalckar. Lipmann and Kalckar first met in the early 1930s in Copenhagen, where they were in frequent contact until 1939, when both left Denmark. Despite the similar claims advanced in Lipmann’s and Kalckar’s reviews, the two men’s presentations differed substantially with respect to their descriptions of “energy-rich” phosphate bonds and their target audiences. In order to explore the circumstances behind these divergences, this paper utilizes a “parallel lives” approach. By analyzing Lipmann’s and Kalckar’s lives in parallel, particular institutional contexts emerge as having been especially significant in shaping their differing interpretations of the power of phosphate bonds. The period that Lipmann spent in muscle researcher Otto Meyerhof’s laboratory (1927–30) conditioned his physiological interpretation of the role of phosphate bonds in cellular energy metabolism. Kalckar’s time at California Institute of Technology (1939–40)—where he was in regular communication with chemists such as Linus Pauling—played the most significant role in his decision to present the power of phosphate bonds from a chemical perspective. Ultimately, an examination of the life stories behind Lipmann’s and Kalckar’s 1941 reviews illuminates how older physiological perspectives were combined with recent advances in theoretical chemistry to explain how energy flows through living organisms.

On the trail of steroid aromatase: The work of Kenneth J. Ryan

On the trail of steroid aromatase: The work of Kenneth J. Ryan

Protein kinases in tune.

This issue of IUBMB Life, suggested by kinase aficionado Michael P. Walsh, plays homage to one of the largest gene families in humans, the protein kinases. The >500 members in this family are the instruments nature uses to relay information throughout the cell and, with the discovery of secreted kinases, outside the cell. Every instrument not only has a precise and finely controlled role in the symphony that controls cell function, but is itself finely tuned for perfect pitch. When these instruments are not in tune, the ensuing cacophony is causal in disease. We begin this issue with a review by Taylor and colleagues who cover the history of protein kinases, from their discovery to the elucidation of the first structure of a kinase, that of protein kinase A (PKA); this remains the gold standard to which all other kinases are compared and has provided enormous insight into how these enzymes work. Ahuja and colleagues then take the theme of PKA to discuss how it is tuned like a violin (see also cover showing violin notes for Mozart's Symphony number 40). Kikkawa then describes the history and rationale leading to the discovery of protein kinase C, a biochemical tour de force in which he participated as a graduate student with Yasutomi Nishizuka at Kobe University, Japan in the 1970s. The issue then moves to receptor tyrosine kinases, with a review by Jura and colleagues on their structures and how these inform on their mechanism of action. Shah and Kim then provide a review on using chemical biology to identify the substrates of kinases. This is followed by a review by An and Brognard on an emerging function of kinases as tumor suppressors. Last, Taggliabracci and colleagues describe the newly discovered class of mammalian secreted protein kinases and puts them in context of secreted kinases in bacteria and parasites. In addition to highlighting the protein kinase family tree, this issue also illustrates the chemistry branch of the remarkable family tree that has given rise to the current generation of scientists working on protein kinases (Fig. 1); the physiology branch which led to the discovery of protein kinases is described in the opening review by Taylor and colleagues and in that of Kikkawa (who links also to Tony Hunter, who discovered phospho-tyrosine 1). All of our authors are in some way related to Phoebus Aaron Theodore Levene who, with his student Fritz Lipmann, identified phosphoserine in the egg white protein vitullin, thus discovering protein phosphorylation 2. Five of our corresponding authors are direct descendants of Lipmann, who is their academic great or great great grandfather, and two of our authors are second cousins by relation of their mentors having trained descendants of Levene. But this family tree goes back to August Kekulé, whose vision of a snake biting its tail as he dozed by the fire led him to realize the heterocyclic structure of benzene, a conceptual break-through that allowed the subsequent determination of complex heterocyclic structures such as those found in ATP. He, in turn, trained Adolf von Baeyer, who developed a method for numbering such heterocyclic compounds, who in turn trained Emil Fischer. In addition to Fischer projections for 3D representation of chiral molecules and his work on purines and sugars, he also opened the field of protein chemistry by discovering several amino acids, showing that the amino acid constituents of proteins are joined by peptide bonds, and synthesizing oligopeptides 3. It is the unique properties of these amino acids that tune kinase function to their perfect pitch. And as if this is not enough kinase-related chemistry in the family tree, the discovery of ATP was made by a trainee of Levene, the German chemist Karl Lohman 4, 5. Thus, this is not only a story of kinases, but a story of mentorship. We hope that this issue inspires the next generation of kinase researchers.

At the Intersection of Chemistry, Biology, and Medicine

After an undergraduate degree in biology at Harvard, I started graduate school at The Rockefeller Institute for Medical Research in New York City in July 1965. I was attracted to the chemical side of biochemistry and joined Fritz Lipmann's large, hierarchical laboratory to study enzyme mechanisms. That work led to postdoctoral research with Robert Abeles at Brandeis, then a center of what, 30 years later, would be called chemical biology. I spent 15 years on the Massachusetts Institute of Technology faculty, in both the Chemistry and Biology Departments, and then 26 years on the Harvard Medical School Faculty. My research interests have been at the intersection of chemistry, biology, and medicine. One unanticipated major focus has been investigating the chemical logic and enzymatic machinery of natural product biosynthesis, including antibiotics and antitumor agents. In this postgenomic era it is now recognized that there may be from 105 to 106 biosynthetic gene clusters as yet uncharacterized for potential new therapeutic agents.

In memoriam: S. Harvey Mudd.

S. Harvey Mudd died January 21, 2014, succumbing to pneumonia after heart surgery. On hearing of his death a colleague noted “We have lost a generation of Biochemistry in a single man”. Harvey was the acknowledged international authority on diseases of methionine metabolism. He wrote the chapters on methionine and sulfur metabolism in the last four editions of “Metabolic Basis of Inherited Disease”, a source of information used world-wide. Physicians all over the world suspecting a metabolic defect involving methionine in a patient would routinely consult him and send samples for analysis. His devotion to discovering the underlying reasons for the patient’s complications was legendary. Dr. Mudd was born in 1927 in Bryn Mawr, Pennsylvania. He grew up in an academic family and signed his papers S. Harvey Mudd in order to distinguish himself from his father, Stuart Mudd, also a well-known scientist who served as Chairman of the Department of Microbiology at the University of Pennsylvania. His mother, Dr. Emily B. H. Mudd, founded the Marriage Council of Philadelphia and was a Professor in the Department of Psychiatry, also at the University of Pennsylvania. After high school Harvey enlisted in the Navy in 1945. Soon after the Second World War ended he was discharged, having served less than a year. He attended Harvard University and graduated cum laude with an AB degree in 1949. A formative influence on his lifelong commitment to science was the following summer he spent as a student in the laboratory of Dr. George Wald. Wald was a spellbinding speaker and inspirational teacher who subsequently received the Nobel Prize in 1967 for his work on the pigments of the eye and the role of vitamin A in vision. Following this, Harvey entered Harvard Medical School and managed to spend the summer of 1950 in the laboratory of another Nobel laureate, Fritz Lipmann. Lipmann was a brilliant and innovative thinker who conceived the concept of high-energy bonds in biochemistry and also discovered Coenzyme A. In 1953 Harvey received an M.D. degree from Harvard and then completed his internship at Massachusetts General Hospital. He then returned to Lipmann’s laboratory as a Research Fellow for two years where he studied the uncoupling of oxidative phosphorylation. It was during this time he met and married Marion Heinrich in 1955. Because Harvey’s initial period in the Navy was less than one year, he was subject to the draft of M.D.s that was in place during the Korean War. At that time a limited number of newly graduated M.D.s were selected to serve in the Public Health Service at the National Institutes of Health, a much sought after position. Harvey was selected to work in the laboratory of Dr. Giulio Cantoni in 1956 and remained at NIH for his entire career. Dr. Cantoni was the discoverer of S-adenosylmethionine (AdoMet), the principal doHow to Cite this Article: Blom HJ,Stabler S, Wagner C. 2015. In Memoriam: S. Harvey Mudd.

Falk Herbert Weih (1959-2014).

Image credit: Published with permission from the FLI © 2013 Sven Döring/Agentur Focus We announce with deep sorrow the passing of our friend and colleague Prof. Dr. Falk Weih, who lost his two-year battle with colon cancer at the age of 54 on 28 October 2014. Falk was known to many investigators in the fields of immunology, signal transduction and gene expression as a dedicated researcher in pursuit of understanding the role of RelB, a member of the nuclear factor-κB (NF-κB) family of transcription factors, and associated biological pathways. In the late 80s, Falk started his career in the laboratory of Prof. Günther Schütz at the German Cancer Research Center (DKFZ, Heidelberg), where he studied the interaction of methylated DNA and transcription factors at the tyrosine aminotransferase promoter 1. He published several papers in high impact journals during this period, already giving an indication of his highly focused and inquisitive mind 2-4. After completing his Ph.D., Falk joined the laboratory of Dr. Rodrigo Bravo at the Bristol-Myers Squibb Pharmaceutical Research Institute in Princeton, USA, as a postdoc. Drawn to the various aspects of NF-κB pathways, he generated several mouse models to understand the function of these proteins. During this phase, guided by the analysis of the RelB knockout mouse, Falk also developed his interest in inflammation 5-7. He also met his wife, Debbie, during this time and together they continued this line of research. Falk and Debbie returned to Germany in 1997, where Falk continued studies on the in vivo function of RelB at the Institute of Toxicology and Genetics in Karlsruhe. In 2004 he was appointed Professor of Immunology at the Friedrich Schiller University, Jena, and set up his laboratory at the Leibniz Institute for Age Research (Fritz Lipmann Institute) in Jena. Among Falk's 70 publications, significant contributions to the understanding of the non-canonical NF-κB pathway and various aspects of RelB function can be counted. These include roles in lymphoid organ development, and the transcriptional regulation of chemokines and cell adhesion molecules involved in secondary lymphoid tissue organization and function 8, 9. Moreover, his group demonstrated the specific roles of both RelA and RelB in the differentiation of natural killer T and IL-17+ γδ T cells 10-12, as well as a role for non-canonical NF-κB signaling in B-cell development and function 13, 14. Falk's research interests also extended beyond the immune system, as shown by his recent publication on the function of different NF-κB proteins during neuronal regeneration and adipocyte differentiation and function 15. In spite of Falk's struggle with cancer during the last year of his life, he continued to have meetings with students, postdocs and collaborators. He was also a critical reviewer, sensitive mentor and friend, open to many long and fruitful discussions. Falk enjoyed sharing social activities, motor cycling, horseback riding, photography and music, all of which helped maintain a balance between work and private life. Falk leaves a rich scientific heritage and many of his students and colleagues will follow on in his research path and benefit from his teachings and methodologies. We will miss him and keep him in our memories. Falk is survived by Debbie, his wife, who shared his passion for biological research and life. We would like to thank Debbie, Ronny Haenold, Marc Riemann and Buket Yilmaz for comments and the Fritz Lipmann Institute (FLI) for the photograph (commissioned by the FLI © 2013 Sven Döring/Agentur Focus).

Coenzyme A and its derivatives: renaissance of a textbook classic.

In 1945, Fritz Lipmann discovered a heat-stable cofactor required for many enzyme-catalysed acetylation reactions. He later determined the structure for this acetylation coenzyme, or coenzyme A (CoA), an achievement for which he was awarded the Nobel Prize in 1953. CoA is now firmly embedded in the literature, and in students' minds, as an acyl carrier in metabolic reactions. However, recent research has revealed diverse and important roles for CoA above and beyond intermediary metabolism. As well as participating in direct post-translational regulation of metabolic pathways by protein acetylation, CoA modulates the epigenome via acetylation of histones. The organization of CoA biosynthetic enzymes into multiprotein complexes with different partners also points to close linkages between the CoA pool and multiple signalling pathways. Dysregulation of CoA biosynthesis or CoA thioester homoeostasis is associated with various human pathologies and, although the biochemistry of CoA biosynthesis is highly conserved, there are significant sequence and structural differences between microbial and human biosynthetic enzymes. Therefore the CoA biosynthetic pathway is an attractive target for drug discovery. The purpose of the Coenzyme A and Its Derivatives in Cellular Metabolism and Disease Biochemical Society Focused Meeting was to bring together researchers from around the world to discuss the most recent advances on the influence of CoA, its biosynthetic enzymes and its thioesters in cellular metabolism and diseases and to discuss challenges and opportunities for the future.

Websites of note

Websites of note

Robert Kellogg Crane: A scientist remembers

Robert Kellogg Crane: A scientist remembers

Biotin-dependent Enzymes: the Work of Feodor Lynen

The Enzymatic Synthesis of Holotranscarboxylase from Apotranscarboxylase and (+)-Biotin. I. Purification of the Apoenzyme and Synthetase; Characteristics of the Reaction (Lane, M. D., Young, D. L., and Lynen, F. (1964)J. Biol. Chem.239, 2858–2864)

Lipmann and Anfinsen: Nobel biochemists of Beecher's anesthesia laboratory

Henry K. Beecher performed blood pH and gas analysis on patients in the 1940s, though the biochemical technology was not widely available until the 1950s. Two of Beecher's biochemist coworkers, Fritz Lipmann and Christian B. Anfinsen, went on to earn Nobel Prizes.

Bruce Merrifield's contribution to antimicrobial peptide research

Although within the scientific community at large Bruce Merrifield is and will remain celebrated for the pivotal discovery and dedicated crafting of solid phase peptide synthesis methodology, there are also other areas where his unique scientific acumen was applied to with distinctive success. Among them, those of glucagon antagonists and antimicrobial peptides are arguably the better known. Over my 25 year-long relationship with Bruce, I had occasion to work with him in both areas, but it is to the latter I will devote these brief reminiscences, as our collaboration in this fast expanding research field reached from its very dawn till relatively recently. 2006, the year of Bruce’s passing, marked the silver jubilee of antimicrobial peptide research, officially initiated with the publication of the seminal paper on the cecropins by Boman (see Figure 1) and coworkers. 1 Hans had befriended Bruce during his postdoc (1958–60) in Fritz Lipmann’s group at Rockefeller, and his logical enthusiasm over the finding of a family of eukaryotic, geneencoded peptides with remarkably potent antimicrobial activities must have been contagious for Bruce, who started to collaborate with Hans on the cecropins in late 1981. On joining Bruce’s lab in January 1982, the very first project given to me was to synthesize the putative 37-residue sequence of cecropin A, to confirm some structural assignations tentatively proposed for the C-terminal region. A previous synthetic attempt 2 had turned out an active compound, albeit nonidentical with the natural peptide. Building on that result and benefiting from several improvements emanating at the time from Bruce and Jimmy Tam’s joint research—not least the very useful high-low HF cleavage method 3 —I completed my assignment in two-and-a-half months, which at the time was regarded a reasonable time for a relative novice charged with the fully manual synthesis of a 37-residue, tritiumlabeled peptide. Our synthetic product was completely identical with the native peptide by microbiological as well as biochemical (enzyme digest + HPLC) criteria, and we were able to confirm the hitherto uncertain structure of the C-terminal end by means of plasma desorption MS, a forerunner of modern MALDI-TOF MS. In addition, our report 4 discussed the relevance of the Trp-2 residue for antimicrobial activity and thus set the basis for further analogue work. 5 In retrospect, that initial 2-year stint in the cecropin project appears as a decisive period, where Bruce’s gracious support and encouragement became the beacon blazing away the often usual angst of a nascent scientific career. A thorough and constructive draft reviewer if ever I saw one, Bruce returned each one of my versions generously endowed with pencil scribbles which, readily deciphered, brought gradual improvement to my struggling manuscripts. To Bruce I owe a great deal of any abilities I may have achieved as a (non-native) writer of English scientific texts. Those early 1980s cecropin manuscripts, first examples of the substantial contri

The nine lives of Daniel E. Koshland, Jr. (1920–2007)

Dan trained in inorganic chemistry as an undergraduate with Wendell Latimer at U.C. Berkeley and spent the war years in Chicago working on plutonium enrichment under the guidance of Glenn Seaborg for the Manhattan Project. A nascent interest in biology and Ph.D. studies with an inspiring young organic chemist, Frank Westheimer, tempted Dan away from inorganic and nuclear chemistry and into a lifelong passion for enzyme reaction mechanisms. Further training at Harvard University (Cambridge, MA) and a brief stint in Fritz Lipmann's laboratory led to Dan's first independent position at Brookhaven National Laboratory (Long Island, NY). During his work on the stereochemical specificity of enzyme reactions, Dan developed a deeper understanding of how an enzyme may adapt to a substrate, which led to his brilliant formulation of the induced-fit model of protein–ligand interaction.

Fritz Lipmann Lecture: Visualization of Chromatin Structure at High Resolution

Fritz Lipmann Lecture: Visualization of Chromatin Structure at High Resolution

Carbamyl Phosphate Biosynthesis: the Work of Mary Ellen Jones

Carbamyl Phosphate Biosynthesis: the Work of Mary Ellen Jones

Lectins: Carbohydrate-specific Reagents and Biological Recognition Molecules

Lectins: Carbohydrate-specific Reagents and Biological Recognition Molecules

Setsuro EBASHI (1922-2006)

Setsuro EBASHI (1922-2006)

Induced Fit and Wit: Celebrating the Life of Daniel E. Koshland, Jr. (1920 ‐ 2007)

On a beautiful Sunday afternoon in September, scientists, friends, and family gathered in UC Berkeley’s newly-opened Stanley Hall to celebrate the life of Daniel E. Koshland, Jr., Professor of Biochemistry at UC Berkeley, former editor of Science, and human being extraordinaire. There were hugs, laughter, and reunions of friends who had not seen each other for decades. There was also sadness – for the loss of a friend and a giant. This seemingly disparate group of people had one common thread in the tapestry of their lives: they had all been touched by a visionary biochemist. An afternoon of science – a symposium called ‘Induced Fit: The Science and Wit of Daniel E. Koshland, Jr.’ – preceded a memorial. At the symposium, students whose careers had been launched by Koshland, colleagues who had been mentored and inspired by Koshland, and the two of his children who chose careers in science (Doug Koshland, Carnegie Institution and Gail Koshland, University of Arizona) presented research talks in which the enormous influence of Dan Koshland and his incomparable humor permeated the outstanding scientific presentations. Koshland received a BSc in Chemistry from UC Berkeley in 1941. In 1949, the same year his wife, Marian (Bunny) Koshland earned her PhD in Immunology, he was awarded a PhD in inorganic chemistry, working with Wendell Latimer, from the University of Chicago. He joined the Manhattan Project, working with Glenn Seaborg in Chicago, and could have earned his reputation as an inorganic chemist. Instead, with the type of bold action that he repeated numerous times throughout his scientific career, he immersed himself in biochemistry. After two years of postdoctoral work at Harvard working in Fritz Lipmann’s laboratory, he and his wife moved to Brookhaven, where they raised their five children. He was recruited back to UC Berkeley in 1958. As he liked to explain, he told Marian that if they moved to Berkeley he would be nice to her forever, but if they stayed in Brookhaven, she would need to be nice to him forever. They moved. In 1958, in a symposium on amino acid activation, Koshland proposed a revolutionary theory that he coined ‘induced fit’ (see ‘Application of a theory of enzyme specificity to protein synthesis’ (1)). The title of the paper revealed nothing about the theory or its importance. Koshland suggested that ‘the substrate may cause an appreciable change in the three-dimensional relationship of the amino acids at the The late Daniel E. Koshland, Jr. Dr. Koshland was a founding editor of IUBMB Life (The photograph was taken by permission from the University of California at Berkeley website: http://www.berkeley.edu/news/media/download/)

Conditional deletion of Nbs1 in murine cells reveals its role in branching repair pathways of DNA double-strand breaks

NBS1 forms a complex with MRE11 and RAD50 (MRN) that is proposed to act on the upstream of two repair pathways of DNA double-strand break (DSB), homologous repair (HR) and non-homologous end joining (NHEJ). However, the function of Nbs1 in these processes has not fully been elucidated in mammals due to the lethal phenotype of cells and mice lacking Nbs1. Here, we have constructed mouse Nbs1-null embryonic fibroblasts and embryonic stem cells, through the Cre-loxP and sequential gene targeting techniques. We show that cells lacking Nbs1 display reduced HR of the single DSB in chromosomally integrated substrate, affecting both homology-directed repair (HDR) and single-stranded annealing pathways, and, surprisingly, increased NHEJ-mediated sequence deletion. Moreover, focus formation at DSBs and chromatin recruitment of the Nbs1 partners Rad50 and Mre11 as well as Rad51 and Brca1 are attenuated in these cells, whereas the NHEJ molecule Ku70 binding to chromatin is not affected. These data provide a novel insight into the function of MRN in the branching of DSB repair pathways.

James H. Schwartz

James H. Schwartz