50 Years of Protein Structure Determination Timeline - HTML Version - National Institute of General Medical Sciences
Structural biologists today working in the United States can trace their roots back to England, where many of the first techniques and labs to study the 3-D structures of proteins first emerged. One of these techniques—the determination of high-resolution protein structures—celebrated its 50th anniversary in 2008.
While the history of protein structure determination is rich with important discoveries, a new era of rapid advance began in 1958 when British scientists John Kendrew and Max Perutz published the very first high-resolution protein structures—first of the oxygen storage protein myoglobin and then of the related, but more complicated oxygen-transporting protein hemoglobin. For this work, which had started as early as 1937, Kendrew and Perutz shared the 1962 Nobel Prize in chemistry.
Unlike the structure of DNA that Watson and Crick had deduced five years earlier, the first determined structures revealed great irregularities. Each one was not pretty and neat like DNA, and together they revealed vastly different shapes and features. These foreshadowed the tremendous diversity in protein structure that researchers would discover over the next five decades, showing how the molecules can play so many different roles in biology.
The National Institute of General Medical Sciences (NIGMS) and other components of the National Institutes of Health (NIH) have supported many of these advances and will continue to support creative and promising research in this area.
Go back in time with us to learn more about some of the key events in the last 50 years of high-resolution protein structure determination.
(Unless noted, all scientists worked in the United States.)
Caption: The structures of myoglobin (left) and hemoglobin (right).
Courtesy of Jeremy M. Berg
Introduction: The 1960s included a flurry of new high-resolution structures and improved techniques to determine them. With these advances and others, like the discovery of the relationship between DNA sequences and protein sequences, “molecular biology” became a fully recognized field of study.
1962: The term “molecular biology” became widely used to describe a new field focused on the study of biology at the molecular level, particularly the structure and function of molecules and their interactions. Today, this field includes a branch called “structural biology.”
1962: At a lab in Cambridge, Michael Rossmann described the first use of molecular replacement, as a technique that allows scientists to use an existing structure to derive the orientation and position of a related but unknown structure.
Caption: Molecular replacement diagram. Courtesy of Ravi Basavappa
1964: Aaron Klug, working in Cambridge, showed that the principles of structure determination by X-ray diffraction could be used to develop crystallographic electron microscopy, enabling scientists to solve quite complex structures, including those of intact viruses. Klug received the 1982 Nobel Prize in chemistry for the development of this technique and his structural studies.
Caption: A beaded sculpture of a virus that infects bacteria. Courtesy of Holly Wichman
1965: David C. Phillips, working in London, determined in atomic detail the first structure of an enzyme, a type of protein that greatly accelerates and controls biochemical reactions. The structure of the enzyme lysozyme, which cleaves carbohydrate molecules, provided deep insights into how enzymes work.
Caption: A crystal of hen egg lysozyme protein. Courtesy of Alex McPherson, University of California, Irvine
1967: The first U.S. scientists—including Fred Richards, David Harker, Richard Dickerson, Joe Kraut, and William Lipscomb—published protein structures. Proteins included ribonucleases A and S, carboxypeptidase, cytochrome c, and chymotrypsin. Funded by NIH
Caption: The structures of ribonuclease A (blue), carboxypeptidase (yellow), chymotrypsin (cyan), and cytochrome c (red). Courtesy of Jeremy M. Berg
1968: Pioneering work by David Davies, Brian Matthews, and others began to reveal the 3-D structures of antibodies (also called immunoglobins), key components of the immune system. In 1973, Roberto Poljak revealed the “immunoglobulin fold,” a structural motif that recurs in antibodies and many other proteins. Funded by NIH
Caption: Drawing of an antibody based on Protein Data Bank (PDB) entry 1igt. Courtesy of David S. Goodsell and the RCSB PDB
1969: Benno P. Schoenborn demonstrated that neutron diffraction could be used to reveal the position of fixed hydrogen atoms in biological molecules.
Caption: Electron density (red) and nuclear density (blue) of a molecule. Courtesy of Benno Schoenborn
Introduction: The 1970s set many new standards for protein structure determination. The establishment of the Protein Data Bank as a global repository for 3-D protein structures revolutionized the collection and classification of proteins. Powerful new methods for structure determination emerged, allowing the list of known protein structures to keep growing.
1971: The Protein Data Bank (PDB) was established at Brookhaven National Laboratory as a repository for 3-D structural data of proteins and nucleic acids. When it was founded, the resource contained just seven structures. The PDB, now headquartered at Rutgers University and directed by Helen Berman, houses more than 50,000 structures. Funded by NIH
Caption: Annual growth of the number of structures available in the PDB archive as of July 1, 2008. Courtesy of the RCSB Protein Data Bank
1972: Paul Berg assembled the first DNA molecules that combined genes from different organisms. The experiment marked the beginning of molecular cloning, which allowed biologists to generate large quantities of protein for structural studies. Funded by NIH
Caption: Hybrid DNA produced in the lab by joining pieces of DNA from different sources.
1975: Nguyen-Huu Xuong and colleagues developed multiwire area detector technology, which allowed for high-speed data collection. Funded by NIH
Caption: Multiwire area detector. Courtesy of Ron Hamlin, Area Detector Systems Corporation
1976: Robert Langridge, credited for developing the first programs to visualize the nooks and crannies of protein structures on a computer screen, opened a computer graphics lab at the University of California, San Francisco. Funded by NIH
1976: Keith Hodgson and others demonstrated for the first time the use of synchrotron radiation in obtaining X-ray diffraction data of single protein crystals. The methods offered a number of advantages over previous techniques. Funded by NIH
Caption: The Advanced Photon Source synchrotron facility at Argonne National Lab. Courtesy of the Southeast Collaboratory for Structural Genomics
1978: Kurth Wüthrich used nuclear magnetic resonance (NMR) as a method for determining protein structures. An alternative to X-ray crystallography, NMR uses proteins in solution rather than crystallized form and can depict interactions between molecules. Wüthrich received the 2002 Nobel Prize in chemistry for this work.
Caption: Nuclear Magnetic Resonance (NMR) spectrometer. Courtesy of the Center for Eukaryotic Structural Genomics
1978: Around this time, scientists began solving the first high-resolution structures of viruses. Among the first were those of the tomato bushy stunt virus, which was determined by Stephen Harrison. This set the stage for the determination of the structures of more well-known viruses, such as the cold-causing rhinovirus determined by Michael Rossmann in 1985. Funded by NIH
Caption: Tomato bushy stunt virus. Courtesy of Jean-Yves Sgro, University of Wisconsin-Madison
Introduction: The ability to produce large amounts of proteins from cloned genes dramatically expanded the range of protein structures that could be determined in the 1980s. New methods for depicting 3-D structures enhanced our visual conception of these molecules. Protein structure determination became an accepted tool to facilitate drug discovery.
1981: Jane Richardson developed ribbon diagrams as a schematic representation of protein structure. Her diagrams, also known as Richardson diagrams, have become a standard way of visualizing proteins.
Caption: Modern-day ribbon diagram.
1981: Don Wiley determined the structure of the hemagglutinin protein from the surface of the influenza virus, leading to a deeper understanding of many processes related to viral infection. Funded by NIH
Caption: An influenza virus infects a host cell when hemagglutinin grips onto glycans on the cell surface. Image courtesy of NIGMS
1983: Jacque Dubochet, working in Germany, succeeded in producing unstained frozen-hydrated biological specimens by freezing them in vitreous ice. Vitrification, or freezing a biological sample in amorphous ice, is now key to cryoelectron microscopy.
Caption: Electron micrograph of frozen-hydrated TMV particles. Courtesy of Teresa Ruiz, University of Vermont
1985: German scientists determined in atomic detail the first integral membrane protein—a photosynthetic reaction center from a purple bacterium. For this work, Johann Deisenhofer, Robert Huber, and Hartmut Michel shared the 1988 Nobel Prize in chemistry.
Caption: Bacterial photosynthetic reaction center. Courtesy of Alisa Zapp Machalek, NIGMS
1988: Haken Hope described new methods that allowed scientists to collect data for biological macromolecules at cryogenic temperatures, greatly reducing radiation damage to the crystal.
1989: Two research teams led by Manuel Navia and Alexander Wlodawer solved the first structures of HIV protease, a key enzyme essential to the replication of HIV. These structures contributed greatly to structure-based drug design efforts that converted HIV from a nearly universally fatal disease to a potentially chronic one. Funded by NIH
Caption: Molecular model of HIV protease. Courtesy of Alisa Zapp Machalek, NIGMS
Introduction: The 1990s welcomed the beginning of structural genomics efforts to rapidly determine thousands of structures, and scientists started solving more complex structures. The development of dedicated synchrotron X-ray sources contributed greatly to these efforts.
1990: Wayne Hendrickson and colleagues demonstrated that protein crystal structures could be solved by preparing proteins containing selenomethionine (instead of the naturally occurring amino acid methionine) and then using the selenium atoms as key markers to guide structure determination. This method is called the multiwavelength anomalous diffraction (MAD) method, and it requires a synchrotron facility for data collection. MAD is now the primary technique for the solution of novel protein crystal structures. Funded by NIH
Caption: Chemical structure of selenomethionine. Courtesy of NIH’s National Center for Biotechnology Information
1996: Four times as many new crystal structures of macromolecules were published this year, as in 1990. The dramatic increase was due in large part to technologies—such as area detectors, cryogenic freezing, and MAD—that made crystallographic studies using synchrotron radiation more efficient and effective.
1998: Rod MacKinnon published the first high-resolution structure of an ion channel, a member of the class of proteins that facilitates the transport of ions through cellular membranes and thus makes nerve impulses and other key biological processes possible. This and subsequent structures have vastly broadened our understanding of neuroscience and have led to new efforts for treating and preventing diseases associated with defective ion channel functioning, such as cystic fibrosis and heart arrhythmias. For this work, MacKinnon shared the 2003 Nobel Prize in chemistry. Funded by NIH
Caption: Potassium ion channel. Courtesy of Roderick MacKinnon, Rockefeller University
1998: Advances in studying entire genomes led to efforts to study protein structures on genome-wide scales, marking the beginning of U.S. “structural genomics” efforts. This approach would require efficient techniques for all steps of protein structure determination. Funded by NIH
Caption: A scientist uses a protein purification robot. Courtesy of the Midwest Center for Structural Genomics
1999: Pioneering work led by Ada Yonath, Tom Steitz, Venki Ramakrishnan, and Harry Noller led to the determination of the first structures of the ribosome, a huge RNA and protein machine that translates RNA sequences into amino acid sequences. The advances were important steps in learning more about protein synthesis—one of life’s most fundamental processes—and could contribute to the development of new antibiotics. Funded by NIH
Caption: Ribosome. Courtesy of Catherine Lawson, Rutgers University, and the RCSB Protein Data Bank
Introduction: The 2000s ushered in new technologies that made protein structure determination faster and cheaper than ever before. The launch of the Protein Structure Initiative galvanized U.S. researchers to develop better tools and methods that have enabled researchers from across biomedical fields to study the form and function of thousands of proteins.
2000: NIGMS established the Protein Structure Initiative (PSI) to support high-throughput structure determination pipelines that would dramatically reduce the cost and time needed to solve a 3-D protein structure. As of January 2009, the PSI has led to the development of many automated tools and new methods, enabling PSI-supported scientists to generate more than 3,500 protein structures. Many of these structures are novel. Funded by NIH
Caption: PSI logo.
2001: Roger Kornberg and colleagues solved the 3-D structure of RNA polymerase, an enzyme that produces messenger RNA from DNA—the key step and a critical control point in gene expression. The work earned Kornberg the 2006 Nobel Prize in chemistry. Funded by NIH
Caption: RNA polymerase (blues and greens) reads DNA (peach) and makes a complementary strand of RNA (pink). Courtesy of David S. Goodsell, The Scripps Research Institute
2007: Brian Kobilka and colleagues overcame numerous technical challenges to solve the first structure of a human G protein-coupled receptor (GPCR). , GPCRs control critical bodily functions, several of our senses, and the action of about half of today’s pharmaceuticals. The work promises not only to speed the discovery of new and improved drugs, but also to deepen our understanding of the signaling processes that are vital to our health. Funded by NIH
Caption: Crystal structure of the beta2-adrenergic receptor protein. Courtesy of the Stevens Laboratory, The Scripps Research Institute
2008: The PSI Structural Genomics Knowledgebase, an entry point for the scientific community to easily access protein structure and production resources, launched. Funded by NIH
Caption: Visit the PSI Structure Genomics Knowledgebase at http://sbkb.org/
Future: The future holds even more promise for protein structure determination. Right now, structural biologists are developing high-throughput methods for solving more complex structures, building computational models to actually predict 3-D structures, and reaching out to the broader scientific community to explore the function and potential biomedical impact of many different protein structures. Such developments no doubt will advance our knowledge of biology and health.
Caption: In just five years, PSI scientists more than tripled the number of structures that they solved five years earlier. Imagine what scientists will achieve in the next 5, 10, or 50 years! Courtesy of the Midwest Center for Structural Genomics