Computational biophysics and structural biology of proteins—a Special Issue in honor of Prof. Haruki Nakamura’s 70th birthday

Receiving his initial training jointly in theoretical and applied physics at the University of Tokyo, Professor Haruki Nakamura has had a long and eventful scientific career, along the way helping to shape the way that biophysics is carried out in Japan. Concentrating his research efforts on the simulation of protein structure and function, he has, over his career arc, acted as director of the Institute for Protein Research (Osaka, Japan), director of the Protein Data Bank of Japan (PDBj), president of the Biophysical Society of Japan (BSJ), president of the Protein Science Society of Japan (PSSJ), and group leader and professor of Bioinformatics and Computational Structural Biology at Osaka University. In 2022, Prof. Haruki Nakamura turned 70 years old, and to mark this occasion, his scientific colleagues from around the world have combined their efforts to produce this Festschrift Issue of the IUPAB Biophysical Reviews journal around the theme of the computational biophysics and structural biology of proteins.

The aim of this Festschrift Issue is to both acknowledge and celebrate the scientific career and achievements of Prof. Haruki Nakamura by publishing a series of review articles contributed by his former students and colleagues in the field of computational and structural biology. In this Editorial, we first provide some background to the articles published within this Special Issue (SI) before then going on to describe some background to Professor Nakamura’s life, research science, and professional endeavors.     

History of Protein Data Bank Japan: standing at the beginning of the age of structural genomics

Prof. Haruki Nakamura, who is the former head of Protein Data Bank Japan (PDBj) and an expert in computational biology, retired from Osaka University at the end of March 2018. He founded PDBj at the Institute for Protein Research, together with other faculty members, researchers, engineers, and annotators in 2000, and subsequently established the worldwide Protein Data Bank (wwPDB) in 2003 to manage the core archive of the Protein Data Bank (PDB), collaborating with RCSB-PDB in the USA and PDBe in Europe. As the former head of PDBj and also an expert in structural bioinformatics, he has grown PDBj to become a well-known data center within the structural biology community and developed several related databases, tools and integrated with new technologies, such as the semantic web, as primary services offered by PDBj.     

The evolution of structural genomics

Structural genomics began as a global effort in the 1990s to determine the tertiary structures of all protein families as a response to large-scale genome sequencing projects. The immediate outcome was an influx of tens of thousands of protein structures, many of which had unknown functions. At the time, the value of structural genomics was controversial. However, the structures themselves were only the most obvious output. In addition, these newly solved structures motivated the emergence of huge data science and infrastructure efforts, which, together with advances in Deep Learning, have brought about a revolution in computational molecular biology. Here, we review some of the computational research carried out at the Protein Data Bank Japan (PDBj) during the Protein 3000 project under the leadership of Haruki Nakamura, much of which continues to flourish today.     

A path to the powerhouse: systems‐to‐structure approaches for studying mitochondrial proteins

The young investigator award from the Protein Society was a special honor for me because, at its essence, the goal of my laboratory is to define what obscure proteins do. Years ago, I stumbled into mitochondria as a venue for this work, and these organelles continue to define the biological theme of my laboratory. Our approaches are fairly broad, reflecting my own somewhat unorthodox training among diverse scientific fields spanning organic synthesis, chemical biology, mechanistic biochemistry, signal transduction, and systems biology. Yet, whatever the theme or the discipline, we aim to understand how proteins work—especially those that hide in the dark corners of mitochondria. Below, I recount my own path into this arena of protein science, and describe how my experiences along the way have shaped our current multi‐disciplinary efforts to define the inner workings of this complex biological system.     

Getting around

This essay is a response to a request from the Editor for a "historical reflection" relating to work on DNA repair from my laboratory. The writing has been an interesting exercise since it made me recall the people I have worked with and some of the things we found and the many we missed. In the course of the writing, an article was published in The New York Review of Books, which argued that there is a "pervasive dishonesty in the practice of science" relating to the authorship of scientific papers. It seemed to me that the events I was relating spoke to that charge and I appreciate the opportunity to comment.     

Discussion: Reply to Hitchcock

Christopher Hitchcocks discussion of my use of screening-off in analyzing the causal process of natural selection raises some interesting issues to which I am pleased to reply. The bulk of his article is devoted to some fairly general points in the theory of explanation. In particular, he questions whether or not my point that phenotype screens off genotype from reproductive success (in cases of organismic selection) supports my claim that the explanation of differential reproductive success should be in terms of phenotypic differences, not genotypic differences. I will respond to this and show why the two supposed counter-examples to my position fail.     

A career pathway in protein folding: from model peptides to postreductionist protein science

This review discusses the inherent challenge of linking "reductionist" approaches to decipher the information encoded in protein sequences with burgeoning efforts to explore protein folding in native environments-"postreductionist" approaches. Because the invitation to write this article came as a result of my selection to receive the 2010 Dorothy Hodgkin Award of the Protein Society, I use examples from my own work to illustrate the evolution from the reductionist to the postreductionist perspective. I am incredibly honored to receive the Hodgkin Award, but I want to emphasize that it is the combined effort, creativity, and talent of many students, postdoctoral fellows, and collaborators over several years that has led to any accomplishments on which this selection is based. Moreover, I do not claim to have unique insight into the topics discussed here; but this writing opportunity allows me to illustrate some threads in the evolution of protein folding research with my own experiences and to point out to those embarking on careers how the twists and turns in anyone's scientific path are influenced and enriched by the scientific context of our research. The path my own career has taken thus far has been shaped by the timing of discoveries in the field of protein science; together with our contemporaries, we become part of a knowledge evolution. In my own case, this has been an epoch of great discovery in protein folding and I feel very fortunate to have participated in it.     

My Father’s Daughter: Becoming a ‘Real’ Anthropologist among the Ubang of Southeast Nigeria

This article explores some of the complexities of fieldwork for ethnographers conducting research in the ethnographic settings of significant ‘others’. The fieldwork in question took place in the rural, geographically isolated community of Ubang, in Obudu, Nigeria, where I was following in the footsteps of my anthropologist father. Drawing on personal experience, I attempt to candidly examine the challenges inevitably faced in this situation, including acceptance by the community as a bona fide researcher, pressure to fulfill the expectations of others familiar with my father’s work, and the struggle to carve out a professional identity distinct from my father’s. An earlier version of this paper, bearing the same title, first appeared in the Anthropology Matters Journal, 2007, vol 9(1). The paper is dedicated to the memory of my father, HRH Eze (Prof.) V.C. Uchendu, whose untimely death occurred after the final editing of the article, on December 7, 2006.     

Novel eicosanoid pathways

This article reviews a lecture I was honored to present at the Leon Wolfe Symposium in Montreal on March 25, 2004. The lecture described my research career, which started with my interaction with Wolfe at the Montreal Neurological Institute as a postdoctoral fellow and research associate and was followed by additional research discoveries after I left Montreal for my first academic position at the Research Institute, The Hospital for Sick Children and University of Toronto. The article consists of two parts. The first part involves the discovery (in Wolfe’s laboratory) of a new pathway of arachidonic acid, in which a bicyclic prostanoid structure (later called prostacyclin by John Vane and his group) was described, and its further development in Toronto, which led to the discovery of the conversion of the bicyclic prostanoid into 6-keto prostaglandin F_1α. The second part deals with the hepoxilin pathway, a pathway I discovered during a sabbatical leave in Japan with Professor Shozo Yamamoto, which was followed by a stay of several months in the laboratory of Professor Bengt Samuelsson in Sweden. I deal with the historical aspects of both pathways and end with interesting novel aspects of hepoxilin stable antagonist analogs in the treatment of solid tumors in experimental animals.     

Carlo M. Croce: Seeking Truth and Beauty

Believe it or not, as a boy Carlo Croce liked to hang out in art museums, to his mother’s chagrin. There are a lot of art museums in Italy, so his mother started dropping him off and going off to the coffee bar to find more interesting company. He bought his first painting, an old master, at age 12 and that used all his savings. He didn't resume his old master collection until he was in his 30s and had saved some money from his job at the Wistar Institute in Philadelphia. He now has an exciting and growing collection.In the meantime, he received his MD degree from the University of Rome “La Sapienza” while reading textbooks and journals in English to supplement the old style medical education. He planned to join Karl Habel at Scripps Clinic in 1970 for a research fellowship just as Dr. Habel was struck in his prime by a monkey B virus infection, so Carlo was diverted from California to Philadelphia to join Hilary Koprowski's internationally known Wistar Institute of Anatomy and Biology. I was a Ph.D. student at Wistar at the time and witnessed the arrival of the quiet 25 yr. old Italian who was too shy to try out his textbook English.He began his work in somatic cell genetics and virology in a large laboratory where a number of us worked on related projects, including Barbara Knowles (now Associate Director for Research at Jackson Laboratory) and Davor Solter (now Director of Developmental Biology, Max Planck Institute, Freiburg, Germany).One of his first accomplishments was to map the very first viral integration site on chromosome 7q in an SV40 transformed fibroblast cell line, using human-mouse somatic cell hybrids that retained human chromosome 7, the SV40 T-antigen and the SV40 genome. Very recently, one of his hybrid clones was used by others to clone the SV40 genome integration site and to show that the SV40 genome had integrated into a common fragile site.Still using somatic cell hybrids, Carlo Croce and his laboratory began in the late 70s and early 80s to map genes important in cancer, such as the immunoglobulin genes that are rearranged in lymphomas, along with the MYC and BCL2 genes among others. These experiments took advantage of the leukemia/lymphoma specific translocation to walk from immunoglobulin loci, and later TCR loci, into the oncogene loci juxtaposed by translocation, the beginning of positional cloning of translocation breakpoints. These studies involved collaborations with valued colleagues, including Peter Nowell, the co-discoverer with David Hungerford, of the Philadelphia chromosome, the first reported cancer specific chromosome alteration. In the exciting decode of the 1980s, the Croce laboratory published 23 reports in Science, including the discovery of the BCL2 gene with Yoshiide Tsujimoto (now University of Osaka). They also observed that mistakes by immunoglobulin family rearrangement/recombination machinery was responsible for the type of chromosome translocations that involved the IG and TCR genes.Carlo Croce has been not only an outstanding laboratory scientist with numerous important discoveries to his credit; he has also been the Director of an NCI designated Cancer Center, first at the Fels Institute for Cancer Research, where he built a first class basic cancer research faculty from the ground up. In 1991, he moved his cancer research faculty to Jefferson Medical College, where it took the name of its benefactor, Sidney Kimmel, and became the Kimmel Cancer Center. At KCI the Croce laboratory continued to find and study genes involved in cancer development: oncogenes activated by translocation such as ALL1, involved in biphenotypic leukemias, discovered with another important collaborator, Eli Canaani and TCL1 (with Gianni Russo’s lab) activated by translocation to the TCRa locus in lymphomas of ataxia telangiectasia patients; or tumor suppressor genes, lost usually through deletions in epithelial cancers, such as FEZ1/LZTS1 at 8p22 lost in prostate, breast and other cancers and the FHIT gene at the 3p14.2 common fragile site (discovered in a collaboration with my laboratory), confirming a long held hypothesis that genes at chromosome fragile sites could contribute to cancer development through frequent chromosomal rearrangements. At the same time, Carlo Croce was living the nearly always tumultuous life of a Director of a Cancer Center, involving recruitment of faculty, constant bargaining with Deans, department chairman, University administrators, but he still manages to fit in a few skiing meetings, gossip sessions with colleagues like Web Cavenee, visits for good coffee, good food and TV appearances in his beloved Italy and most of all, he still manages to study, examine, buy, transport, restore, reframe and admire his old master paintings. I think he loves it as much as science because discovering a beautiful but misattributed painting at an obscure or even well known auction house, buying it and then proving that it is actually a painting by a Gentileschi or a Cavallino is as thrilling and elegant as discovering the connection between a specific gene alteration and its cancer.     

Interactions with John Gurdon – muscle as a mesodermal read-out and the community effect

John Gurdon has made major contributions to developmental biology in addition to his Nobel prize winning work on nuclear reprogramming. With the frog, Xenopus, as a vertebrate model, his work on mesoderm induction led him to identify a community effect required for tissue differentiation after progenitor cells have entered a specific mesodermal programme. It is in the context of this biologically important concept, with myogenesis as an example, that we have had most scientific exchanges. Here I trace my contacts with him, from an interest in histone regulation of gene expression and reprogramming, to myogenic determination factors as markers of early mesodermal induction, to the role of the community effect in the spatiotemporal control of skeletal muscle formation. I also recount some personal anecdotes from encounters in Oxford, Paris and Cambridge, to illustrate my appreciation of him as a scientist and a colleague.     

Life cycle of a giant carnivorous caddisfly, <Emphasis Type="Italic">Himalopsyche japonica</Emphasis> (Morton) (Trichoptera: Rhyacophilidae), in the mountain streams of Nagano,Central Japan

 The life cycle of a giant carnivorous caddisfly, Himalopsyche japonica (Morton), was studied in two mountain streams in Nagano Prefecture, Central Japan. Field surveys and rearing experiments in the laboratory were conducted from October 1997 to September 2001. The life cycle of H. japonica was estimated to be a complex univoltine cycle that partly includes bivoltine populations. The adults had a long flight period, from April to September, with three distinct peaks of emergence. First to third instar larvae were collected from June to February, and the last (fifth) instar larvae and pupae appeared throughout the year. In autumn, the larvae belonging to all instars were found, and younger ones overwintered in the fourth instar stage and others in the fifth instar stage. On the other hand, fifth instar larvae and pupae ceased developing in autumn even though the water temperature was higher than the developmental zero temperature. The overwintered pupae emerged as adults in April, and the overwintered fifth instar larvae pupated in May and emerged in June. The larvae which overwintered in the fourth instar stage probably emerged after June. Received: March 19, 2002 / Accepted: January 10, 2003 Present address: United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan Tel. +81-265-77-1401; Fax +81-265-74-7496 e-mail: himalo@f8.dion.ne.jp Acknowledgments The author thanks Prof. T. Yoshida, Prof. H. Nakamura, and Associate professor K. Soma, Shinshu University; Mr. T. Nozaki, Kanagawa Environmental Research Center; and Mr. N. Kubota, Environmental Assessment Center in Matsumoto laboratory for their advice and help in accomplishing this research. The author is also grateful to Prof. K. Tanida, Osaka Prefecture University; Dr. T. Ito, Hokkaido Fish Hatchery; Mr. K. Okazaki, Kutchan City Museum; and Mrs. Y. Isobe, Nara Women's University, for suggesting references. Miss. T. Ishiyama, Mr. H. Kojima, Mr. M. Yagyu, and the students of the Forest Animals Laboratory in Shinshu University kindly provided field samples. Correspondence to:T. Tsuruishi     

Developmental patterning deciphered in avian chimeras

I started my scientific carer by investigating the development of the digestive tract in the laboratory of a well-known embryologist, Etienne Wolff, then professor at the Collège de France. My animal model was the chick embryo. The investigations that I pursued on liver development together with serendipity, led me to devise a cell-marking technique based on the construction of chimeric embryos between two closely related species of birds, the Japanese quail ( Coturnix coturnix japonica ) and the chick ( Gallus gallus ).
The possibility to follow the migration and fate of the cells throughout development from early embryonic stages up to hatching and even after birth, was a breakthrough in developmental biology of higher vertebrates.
This article describes some of scientific achievements based on the use of this technique in my laboratory during the last 38 years.     

An electron microscopic observation on the cross-striated fibrils occurring in the human spermatocyte

Summary Cross-striated fibrils associated with the centriole were found in a presumed young spermatocyte of the human biopsy material. This resembles the structure in the ciliary rootlets already reported in some ciliated epithelia. Probable nature of this structure is briefly discussed.The author wishes to express his sincere thanks to Prof. T. Nonaka and Prof. K. Kurosumi The author wishes to express his sincere thanks to Prof. T. Nonaka and Prof. K. Kurosumi     

My journey into the birth of plant transgenesis and its impact on modern plant biology

I had the fortune to start my scientific carrier during the early stages of the development of plant transformation in one of the leading laboratories in the field. Here, I describe my personal experience in the laboratory of Marc van Montagu and Jeff Schell, and some important contributions that the group made to the development of the technology to produce transgenic plants. I also briefly summarize the impact of this technology on the development of modern plant biology and in plant molecular improvement.     

Hongyuan Yang: Tracking lipids,one droplet at a time

Hongyuan Yang investigates lipid trafficking and lipid droplet biogenesis.

Hongyuan Yang grew up in a small city east of Beijing, China. From his childhood, Hongyuan recalls that “food was not abundant, so I was hungry at times, but education was free and good.” Driven by his curiosity for science, after completing his undergraduate studies at Peking University Health Science Center, China, he enrolled at Columbia University, NY, for his doctoral training. Under the guidance of his advisor, Dr. Stephen Sturley, Hongyuan studied lipids in budding yeast. The laboratory’s research department fostered a strong interest in lipids and atherosclerosis, and after earning his PhD, Hongyuan obtained a faculty position at the National University of Singapore (NUS) in 1999. In 2007, he moved to the University of New South Wales (UNSW) in Sydney, Australia, to continue his scientific journey exploring lipids. We contacted Hongyuan to learn more about his career and interests.Hongyuan Robert Yang. Photo courtesy of UNSW.What interested you about lipids?My five-year doctoral study focused entirely on the enzymes Sterol O-Acyltransferases (SOAT, also known as ACAT, Acyl-CoA Cholesterol Acyltransferases), which catalyze the formation of sterol esters from sterols/cholesterol and fatty acyl CoAs (1). SOATs, integral membrane proteins of the ER, are potential therapeutic targets for heart disease and Alzheimer’s disease. Since then, I have been fascinated by two things related to SOAT: first, what happens upstream of SOAT, i.e., how exogenous cholesterol reaches SOAT/ER; and second, what happens downstream of SOAT, i.e., how its product—cholesterol esters—is stored in cells in the form of lipid droplets (LDs).These are fundamental questions in cell biology. While reading on how cholesterol arrives at the ER for esterification by SOAT/ACAT in the late 1990s, I realized that the trafficking of most lipids was poorly characterized with little molecular insight. Significant progress has been made in the last 20 years, but the lack of tools that track the movement of lipids has hampered our understanding of the selectivity, efficacy, and kinetics of lipid trafficking. Few cell biologists cared about LDs ∼20 years ago, even though LDs are prominent cellular structures in many disease conditions. Each LD comprises a hydrophobic core of storage lipids (triglycerides and sterol esters) wrapped by a monolayer of phospholipids. Largely considered inert lipid granules, LDs originate from the ER and are relatively simple cellular structures as compared with other organelles (see image). Now, we know that LDs are not that simple: their biogenesis is tightly regulated, they actively interact with other organelles, and they regulate many aspects of cellular function as well as disease progression. Astonishingly, we still have little understanding of how LDs originate from the ER. I am very much intrigued by the complexity of these two seemingly simple cellular processes, i.e., lipid trafficking and LD biogenesis.What are some of the scientific questions currently of interest in your laboratory?We are currently focusing on how LDs originate from the ER. The first significant paper from my own laboratory was the discovery of seipin as a key regulator of LD formation (2). Results from many groups have demonstrated that seipin can organize the formation of LDs; however, the exact molecular function of seipin remains mysterious. Our data suggest that seipin may directly impact the level and/or distribution of lipids such as phosphatidic acid near sites of LD biogenesis, and the effect of seipin deficiency on LD formation is secondary to changes in local lipids. We are now working hard to test this hypothesis. Moreover, data from my laboratory and others indicated that nonbilayer lipids may have a greater impact on the biogenesis of LDs than that of other ER-derived structures, such as COPII vesicles. This may result from the monolayer nature of the LD surface. We hope to dissect the dynamic changes of lipids at ER domains where LDs are born. More broadly, the ER is a fascinating organelle to me. The simple division of ER into sheets and tubules does not reflect the dynamic nature of this organelle. Dissecting the composition and organization of lipids and proteins of the ER would help answer key questions relating to LD biogenesis, and it is therefore one of our future directions.Another major focus is to understand how cholesterol and phosphatidylserine are moved between organelles. We have been working on how low-density lipoprotein (LDL)–derived cholesterol (LDL-C) reaches the ER for two decades. The release of LDL-C from lysosomes requires the Niemann Pick C1&2 proteins, whose malfunction causes lysosomal cholesterol accumulation and a lethal genetic disorder affecting young children. The Ara Parseghian Medical Research Foundation has led the way in supporting research into cholesterol trafficking, and I take this opportunity to thank their generous support. Once released from lysosomes, LDL-C is believed to reach the plasma membrane first and then the ER. We identified ORP2 as a possible carrier of LDL-C to the plasma membrane using a PI(4,5)P₂ gradient (3). There must be other carriers and/or pathways because ORP2 deficiency only causes a minor accumulation of cholesterol in lysosomes. Another interesting question is what prevents LDL-C from reaching the ER directly from lysosomes, given the close contact between lysosomes and the ER. We reported that ORP5 may bring LDL-C directly to the ER (4). However, it was later found that ORP5 binds and transfers phosphatidylserine, not cholesterol. Thus, our observed link between ORP5 and cholesterol is through some indirect yet unknown mechanism. We have been perplexed by these observations for many years, but a recent study demonstrated that phosphatidylserine is required for the trafficking of LDL-C, establishing a close link between cholesterol and phosphatidylserine (5). We are now trying to understand how the trafficking and distribution of cholesterol, phosphatidylserine, and PI(4,5)P₂ are interconnected. For a long time, I felt that it was impossible to figure out the molecular details governing the cellular trafficking of lipids due to redundant pathways and a lack of tools to track lipids. Recent progress in this field has given me hope.Lipid droplets in a HeLa cell are shown in red (BODIPY), with their surface in green. DAPI (blue) labels DNA. Image courtesy of Hongyuan Yang.What kind of approach do you bring to your work?Besides honesty and open-mindedness, we emphasize rigor and comprehensiveness. We often make our initial discoveries in cell-based screens. This approach has many advantages, but it also gives rise to artifacts and cell-line specific observations. We aim to complement our initial findings with biochemical and structural analyses in vitro as well as animal studies in vivo. To further establish the reproducibility of our data, I often ask my close friends and collaborators to independently repeat the key findings of a study before submission. It generally takes a long time for us to complete a study, but I believe the effort will pay off in the long run.What did you learn during your training that helped prepare you for being a group leader? What were you unprepared for?During my PhD at Columbia, I was most impressed with the general attitude of my mentors toward research. No matter how much they have achieved, they take every new experiment and every poster presentation seriously.As I did not have postdoctoral training, I was somewhat unprepared at the beginning of my independent career. One difficult challenge was knowing when to finish a paper and project. We often kept working and working. I have now gotten a lot better.You’ve done research on three continents throughout your career. Can you tell us about some of these transitions?During the last year of my doctoral studies at Columbia, I was offered a lecturer position by the Department of Biochemistry at NUS. It was a very hard decision to leave the United States, but I was excited by the prospect of starting my own laboratory at a top institution. Life at NUS was very good overall, despite some struggles. I had to make ∼700 slides for teaching during the first year and my start-up fund was 10,000 Singapore dollars (~6,000 USD). But the graduate students were fully supported by the university, and most of them are hard working and talented. The crucial screen that led to the discovery of seipin as a key regulator of LD formation was performed at NUS (2). I enjoyed my time at NUS, where I was promoted and tenured. However, my family and I could not get used to the heat and humidity. We looked for a place with better climate, and it happened that my current employer, UNSW, had an opening in 2006. Moving continents with two kids was very disruptive, and I had zero publications in 2007. Our work on seipin was delayed and almost got scooped. I was also very worried about funding in Australia since I hardly knew anyone and the funding system. It turned out that the Australian community was very supportive of our research from day one. I have also been very fortunate to receive generous support from the Ara Parseghian Medical Research Foundation, based in the United States, after my move to Sydney.Hongyuan’s “metabolism team” after a basketball game. Photo courtesy of Hongyuan Yang.What has been the biggest accomplishment in your career so far?While I am mostly recognized for discovering seipin’s role in lipid droplet formation, I am prouder of the work we have done on lipid trafficking and the oxysterol binding proteins. We struggled mightily for the first 15 years. At one point in 2015, I seriously considered abandoning this line of research. But we persisted and discovered their roles in regulating plasma membrane PI(4,5)P₂ and cholesterol, as well as in lipid droplet formation (3, 6).What has been the biggest challenge in your career so far?The biggest challenge has to do with the subject of my research topic: the fundamental cell biology of lipids. The sorting, distribution, and storage of cellular lipids are clearly very important topics in biology, but they are sometimes too fundamental to explain to funding agencies and new students. These days, lipid research is not as “sexy” as other topics. But there are so many unanswered questions in lipidology. I strongly believe that lipid research is going to be the next “big thing” as new techniques such as cryoEM now allow us to appreciate lipids and membrane proteins with unprecedented clarity.Who were your key influences early in your career?Besides mentors and teachers at Columbia, I really enjoyed reading and studying the works by Drs. Mike Brown and Joseph Goldstein, Ta-Yuan Chang, and Scott Emr. While they were not my teachers, their work inspired and impacted many young scientists, including me.What is the best advice you have been given?I have been given many pieces of great advice during my career. The best one in my view is “Less is more.” I was once told, “You would be better off with a lab of six than twelve.” Initially, I did not get it because I thought that a bigger group would allow me to explore more directions and be more productive. The reality is that, as a little-known junior researcher, few experienced people would join my laboratory. Funding is also a major limiting factor. Supervising a large number of students is fulfilling, but it also takes away some of my own time to think critically about the projects. I have largely kept my group under six, and this allows me to better supervise and guide the trainees. People say, “Once your team has more than 15 members, you become a manager instead of a scientist.” My own experience corroborates that statement because I struggled quite a bit when my group reached 12 at one point.What hobbies do you have?I am heavily into sports, especially basketball and tennis. I follow the NBA closely, and Jeremy Lin is my hero. I still play basketball at least twice a week. I am the captain of a basketball team comprised of scientists working on metabolism (see image). We play real, refereed basketball games against local teams during conferences. As I am getting older, I have also picked up tennis. I watch coaching videos on YouTube but still need a lot of work on my forehand. Through sports, I learned teamwork and the spirit of fighting to the last second. If I were not a scientist, I would probably run a sports-related business.What has been your biggest accomplishment outside of the laboratory?I got married and had children relatively early. Both of my kids are now in college and they appear to be decent human beings. I have been extremely lucky because my wife did most of the heavy lifting in looking after the kids. It was still a struggle for me to balance work and parental duties during the early days of my independent career. I am very proud and happy with where we are as a family right now.Any tips for a successful research career?Everyone is unique. Knowing your strengths and especially your weaknesses can be crucial to your success. My undergraduate training was in medicine and health management, and my PhD work focused on genetics and cell biology, so my understanding of physical chemistry is rather inadequate. I am also very bad at developing new methods. To alleviate these deficiencies, I constantly monitor new methods in my field and I purposefully look for collaborators with strong chemistry backgrounds. I have benefited immensely from such efforts.     

AlphaFold – A Personal Perspective on the Impact of Machine Learning

I outline how over my career as a protein scientist Machine Learning has impacted my area of science and one of my pastimes, chess, where there are some interesting parallels. In 1968, modelling of three-dimensional structures was initiated based on a known structure as a template, the problem of the pathway of protein folding was posed and bets were taken in the emerging field of Machine Learning on whether computers could outplay humans at chess. Half a century later, Machine Learning has progressed from using computational power combined with human knowledge in solving problems to playing chess without human knowledge being used, where it has produced novel strategies. Protein structures are being solved by Machine Learning based on human-derived knowledge but without templates. There is much promise that programs like AlphaFold based on Machine Learning will be powerful tools for designing entirely novel protein folds and new activities. But, will they produce novel ideas on protein folding pathways and provide new insights into the principles that govern folds?     

The history of the discovery of the nerve growth factor

The Nerve Growth Factor (NGF) is the progenitor of a family of growth factors which is still expanding. The history of its discovery is very colorful; it is a rare combination of scientific reasoning, intuition, fortuities, and good luck. In addition, I believe that the collaboration of three scientists with very different backgrounds contributed to the success: I had grown up in a laboratory of experimental embryology, Dr. Levi-Montalcini came from neurology, and Dr. Stanley Cohen was from biochemistry. The decision where to begin the history of a discovery is always arbitrary. I shall give my reasons why I begin this story with my wing bud extirpations on chick embryos and the analysis of the effects of the operation on the development of spinal nerve centers, published in 1934. Of course, I am aware of the fact that the analysis of neurogenesis had been pioneered by Dr. R. G. Harrison and his students at Yale University since the beginning of this century. It should be mentioned that their experiments had been done on amphibian embryos. My own interest in problems of neurogenesis dates back to my Ph.D. thesis in the Zoology Department of Professor H. Spemann at the University of Freiburg in (the Federal Republic of) Germany; it dealt with the influence of the nervous system on the development of limbs in frog embryos. After I had obtained some inconclusive results I did the crucial experiment of producing nerveless legs. I removed the lumbar part of the spinal cord and the spinal ganglia before the outgrowth of nerve fibers. The nerveless legs developed normally in every respect, but the muscles atrophied eventually.