Jane S. Richardson

Last updated

Jane S. Richardson
Jane S Richardson BW photo 2002.jpg
Richardson in 2002
Born (1941-01-25) January 25, 1941 (age 83)
Teaneck, New Jersey, U.S.
Alma mater Swarthmore College, Harvard University
Known for Ribbon diagram, structure validation
SpouseDavid C. Richardson
Awards MacArthur Fellowship (1985), Alexander Hollaender Award in Biophysics (2019)
Scientific career
Fields Structural biology, Biophysics
Institutions Duke University
Ribbon schematic of Triosephosphate isomerase, hand-drawn by Jane Richardson TriosePhosphateIsomerase Ribbon pastel photo mat.png
Ribbon schematic of Triosephosphate isomerase, hand-drawn by Jane Richardson
All-atom contact dots for two well-packed Ala residues All-atomContacts 1gciAlas.jpg
All-atom contact dots for two well-packed Ala residues

Jane Shelby Richardson (born January 25, 1941) [1] [2] is an American biophysicist best known for developing the Richardson diagram, or ribbon diagram, a method of representing the 3D structure of proteins. [3] Ribbon diagrams have become a standard representation of protein structures that has facilitated further investigation of protein structure and function globally. With interests in astronomy, math, physics, botany, and philosophy, Richardson took an unconventional route to establishing a science career. [4] [5] Richardson is a professor in biochemistry at Duke University. [1]

Contents

Biography

Richardson was born on January 25, 1941, and grew up in Teaneck, New Jersey. Her father was an electrical engineer and her mother was an English teacher. Her parents encouraged an interest in science and she was a member of local astronomy clubs as early as elementary school. [6] She attended Teaneck High School and in 1958 won third place in the Westinghouse Science Talent Search, the most prestigious science fair in the United States, with calculations of the satellite Sputnik's orbit from her own observations. [7] [4]

She continued her education intending to study mathematics, astronomy and physics at Swarthmore College. However, Richardson instead graduated Phi Beta Kappa with a bachelor's degree in philosophy and a minor in physics in 1962 before she pursued graduate work in philosophy at Harvard University. Meanwhile, she was able to enroll in plant taxonomy and evolution courses at Harvard that would later contribute to her big-picture approach to studying protein structure. Since Harvard's philosophy focused on modern philosophy instead of Richardson's interest, classical philosophy, Richardson left with her master's degree from Harvard in 1966. [1] [8] [9] Post-graduation, Richardson tried teaching high school, but soon realized that this career path was not for her. She subsequently rejoined the scientific world, working as a technician at Massachusetts Institute of Technology in the same laboratory as her husband, David Richardson, whom she met at Swarthmore College. [10] At MIT, David Richardson was pursuing his doctorate in Al Cotton's lab using X-ray crystallography to study the structure of staphylococcal nuclease. Jane Richardson learned the necessary technical skills and scientific background in biochemistry and biophysics through work at the lab as she worked alongside her husband, whom she still works with today. Richardson later began drawing her eponymous diagrams as a method of interpreting the structures of protein molecules. [10] Over the course of her career, Richardson has been recognized by many prestigious institutions of the scientific community. In July 1985 she was awarded a MacArthur Fellowship for her work in biochemistry. [11] She was elected to the National Academy of Sciences and the American Academy of Arts and Sciences in 1991 and to the Institute of Medicine in 2006. [5] As part of her role in the National Academy of Sciences, Richardson serves on panels that advise the White House and the Pentagon regarding nationally important scientific matters (e.g., [12] ). For the 2012-2013 year, Richardson was elected president of the Biophysical Society for the 2012-2013 year, [13] and she became a fellow of the American Crystallographic Association in 2012. [14] Richardson is currently a James B. Duke Professor of Biochemistry at Duke University. [4]

The Richardsons continue to jointly head a research group at Duke University. [10]

Richardson is a contributor to Wikipedia, where she is a prominent member of WikiProject Biophysics. [15]

Scientific work and contributions

Richardson's first forays into science were in the field of astronomy. By observing the position of Sputnik – at the time, the only artificial satellite – on two successive nights, she managed to calculate its predicted orbit. She submitted her results to the Westinghouse Science Talent Search, winning third place in 1958. [5]

Richardson joined her husband David C. Richardson, then completing his PhD work at MIT, in studying the 3-dimensional structure of the staphylococcal nuclease protein (1SNS) [16] by X-ray crystallography for his doctoral thesis. [17] [18] Staphylococcal nuclease was among the first dozen protein structures solved. [19] Classes in botany and evolution that she had taken while pursuing her degree shaped her thinking about the work she was doing in the chemistry laboratory. [4] During her crystallographic studies, Jane Richardson had come to realize that a general classification scheme can be developed from the recurring structural motifs of the proteins. [4] In the meantime, Jane and David Richardson had moved to Duke University in 1970, where they solved the first crystal structure of superoxide dismutase (2SOD). [10] [20] [21] By 1977 she published her findings on protein relatedness in Nature , with a paper entitled "β-sheet topology and the relatedness of proteins". [4] [22]

As Richardson developed the ribbon diagram to illustrate her findings over the course of her taxonomic research, her iconic images first appeared in the review journal Advances in Protein Chemistry in an article titled "The anatomy and taxonomy of protein structure" 1981, [5] [23] [24] an early hallmark publication in structural bioinformatics. The diagrams have since become a standard way of visualizing protein structure, specifically depicting beta-sheet topology and connections between amino acid sequences, or peptides, that make up proteins. The protein folding process involves four levels: primary structures, secondary structures, tertiary structures, and quaternary structures. Secondary structures result from hydrogen bond interactions between adjacent amino acids sequences to form alpha helices or beta-sheets. [25] Tertiary structures are a higher order of protein folding that depict the conformation of and connectivity between alpha-helices and beta-sheets in 3D. [25] Richardson's ribbon diagrams illustrate beta-sheet topology and connectivity in higher-order protein structures. She formalized general rules about beta-sheets linkage via "hairpin" connections or "crossover" connections. In a hairpin connection a peptide backbone stems out of and loops around to return to the same beta-sheet end from which it left. A crossover connection involves the peptide backbone extending out of one beta-sheet and looping around to enter another beta-sheet on the opposite end of the protein. [26] Her initial drawings and continual discoveries contribute to a broader understanding of protein energetics and evolution. Peter Agre, Nobel laureate and fellow Duke professor, said of the Richardsons' work: "Jane and David’s work allowed us to reveal the form of proteins, and from there it was easier to understand their function". [10]

The Richardsons' more recent work has diversified beyond classification and crystallography. In the 1980s they stretched into the fields of synthetic biochemistry and computational biology as pioneers in the de novo design of proteins, a reverse engineering approach to make and test theoretical predictions about protein folding. [27] In the 1990s the Richardsons developed the kinemage system of molecular graphics and David Richardson wrote the Mage program to display them on small computers, for the then-new journal Protein Science. [28] Additionally, they developed all-atom contact analysis (see image) to measure "goodness of fit" inside proteins and in interactions with surrounding molecules. [4] The Kinemage website offers interactive exploration of various 3D protein structures through computer displays using their Mage or KiNG graphics programs. Funded by a National Institutes of Health (NIH) grant, the website is often used as a teaching tool. Textbooks and internet sites that have sourced images from Kinemages include Introduction to Protein Structure by Branden & Tooze, [29] Fundamentals of Biochemistry by Viet, Voet & Pratt, [30] Principles of Biochemistry by Horton et al., [31] and the University of Mississippi's Kinemage Authorship Project. [32]

The Richardson Laboratory currently studies structural motifs in RNA [33] as well as proteins, as part of the RNA Ontology Consortium (ROC) [34] to better communicate RNA structure and function research findings. [35] [36] The laboratory has acted as assessors in the CASP8 structure-prediction experiment [37] (CASP), [38] is one of the four developer teams on the PHENIX software system [39] for x-ray crystallography of macromolecules, and hosts the MolProbity web service [40] for validation and accuracy improvement of protein and RNA crystal structures. MolProbity uses the KiNG program (successor to Mage) for showing 3D kinemage graphics on-line. Jane Richardson serves on the worldwide Protein Data Bank (wwPDB) X-ray Validation Task Force [41] and NMR Validation Task Force. [42] As she continues to run the Richardson laboratory alongside her husband at Duke, where they use MolProbity to validate RNA, protein, crystal structures, she also adds science-related images, images of nature, and pictures for the WikiProject Biophysics to Wikimedia Commons. [15]

Awards and honors

Notable publications

The following articles are classified as highly cited in field by Web of Science as of February 17, 2020:

Related Research Articles

<span class="mw-page-title-main">Protein structure prediction</span> Type of biological prediction

Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its secondary and tertiary structure from primary structure. Structure prediction is different from the inverse problem of protein design. Protein structure prediction is one of the most important goals pursued by computational biology; it is important in medicine and biotechnology.

<span class="mw-page-title-main">Biomolecule</span> Molecule produced by a living organism

A biomolecule or biological molecule is loosely defined as a molecule produced by a living organism and essential to one or more typically biological processes. Biomolecules include large macromolecules such as proteins, carbohydrates, lipids, and nucleic acids, as well as small molecules such as vitamins and hormones. A general name for this class of material is biological materials. Biomolecules are an important element of living organisms, those biomolecules are often endogenous, produced within the organism but organisms usually need exogenous biomolecules, for example certain nutrients, to survive.

<span class="mw-page-title-main">CASP</span> Protein structure prediction challenge

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<span class="mw-page-title-main">Kinemage</span>

A kinemage is an interactive graphic scientific illustration. It often is used to visualize molecules, especially proteins although it can also represent other types of 3-dimensional data. The kinemage system is designed to optimize ease of use, interactive performance, and the perception and communication of detailed 3D information. The kinemage information is stored in a text file, human- and machine-readable, that describes the hierarchy of display objects and their properties, and includes optional explanatory text. The kinemage format is a defined chemical MIME type of 'chemical/x-kinemage' with the file extension '.kin'.

<span class="mw-page-title-main">Ramachandran plot</span> Visual representation of allowable protein conformations

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<span class="mw-page-title-main">Frederic M. Richards</span> American biochemist and biophysicist (1925–2009)

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<span class="mw-page-title-main">Ribbon diagram</span> 3D schematic representation of protein structure

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References

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  2. ↑ "Jane Richardson Interview". Archived from the original on September 6, 2019. Retrieved September 17, 2020.
  3. ↑ Helmenstine, Anne Marie. "Famous Female Chemists and Chemical Engineers". ThoughtCo. Retrieved February 16, 2020.
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  7. ↑ United Press (March 4, 1958). "Two in same School Win Science Contest". The New York Times . The other scholarship winners are Jane Shelby, 17, of 431 Claremont Avenue, Teaneck, N. J., $5,000; Donald M. Jerina, 18, of River Grove, Ill., $4,000, and Neal L. Nininger of Larkspur, Calif., $3,000.
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  20. ↑ PDB: 2SOD ​; Tainer JA, Getzoff ED, Beem KM, Richardson JS, Richardson DC (September 1982). "Determination and analysis of the 2 A-structure of copper, zinc superoxide dismutase". Journal of Molecular Biology. 160 (2): 181–217. doi:10.1016/0022-2836(82)90174-7. PMID   7175933.
  21. ↑ Richardson J, Thomas KA, Rubin BH, Richardson DC (April 1975). "Crystal structure of bovine Cu,Zn superoxide dismutase at 3 A resolution: chain tracing and metal ligands". Proceedings of the National Academy of Sciences of the United States of America. 72 (4): 1349–53. doi: 10.1073/pnas.72.4.1349 . PMC   432531 . PMID   1055410.
  22. ↑ Richardson JS (August 1977). "beta-Sheet topology and the relatedness of proteins". Nature. 268 (5620): 495–500. Bibcode:1977Natur.268..495R. doi:10.1038/268495a0. PMID   329147. S2CID   4287690.
  23. ↑ Richardson JS, Richardson DC (2013). "Doing molecular biophysics: finding, naming, and picturing signal within complexity". Annual Review of Biophysics. 42: 1–28. doi:10.1146/annurev-biophys-083012-130353. PMC   3695750 . PMID   23451888.
  24. ↑ Richardson JS (1981). "The Anatomy and Taxonomy of Protein Structure". Advances in Protein Chemistry. 34: 167–339. doi:10.1016/s0065-3233(08)60520-3. ISBN   9780120342341. PMID   7020376. Archived from the original on February 10, 2019. Retrieved January 17, 2009.
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  26. ↑ Richardson JS (August 1977). "beta-Sheet topology and the relatedness of proteins". Nature. 268 (5620): 495–500. Bibcode:1977Natur.268..495R. doi:10.1038/268495a0. PMID   329147. S2CID   4287690.
  27. ↑ Richardson JS, Richardson DC (July 1989). "The de novo design of protein structures". Trends in Biochemical Sciences. 14 (7): 304–9. doi:10.1016/0968-0004(89)90070-4. PMID   2672455.
  28. ↑ Richardson DC, Richardson JS (January 1992). "The kinemage: a tool for scientific communication". Protein Science. 1 (1): 3–9. doi:10.1002/pro.5560010102. PMC   2142077 . PMID   1304880.
  29. ↑ Brändén CI, Tooze J (1999). Introduction to protein structure (2nd ed.). New York: Garland Publications. ISBN   0-8153-2304-2. OCLC   39508201.
  30. ↑ Voet D, Voet JG, Pratt CW (February 29, 2016). Fundamentals of Biochemistry: Life at the Molecular Level (Fifth ed.). Hoboken, NJ. ISBN   978-1-118-91840-1. OCLC   910538334.{{cite book}}: CS1 maint: location missing publisher (link)
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  34. ↑ "RNA Ontology Consortium (ROC)". ROC.bgsu.edu. Archived from the original on January 22, 2009.
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  37. ↑ Keedy DA, Williams CJ, Headd JJ, Arendall WB, Chen VB, Kapral GJ, et al. (2009). "The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models". Proteins. 77 (Suppl 9): 29–49. doi:10.1002/prot.22551. PMC   2877634 . PMID   19731372.
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  41. ↑ Read RJ, Adams PD, Arendall WB, Brunger AT, Emsley P, Joosten RP, et al. (October 2011). "A new generation of crystallographic validation tools for the protein data bank". Structure. 19 (10): 1395–412. doi:10.1016/j.str.2011.08.006. PMC   3195755 . PMID   22000512.
  42. ↑ Montelione GT, Nilges M, Bax A, Güntert P, Herrmann T, Richardson JS, et al. (September 2013). "Recommendations of the wwPDB NMR Validation Task Force". Structure. 21 (9): 1563–70. doi:10.1016/j.str.2013.07.021. PMC   3884077 . PMID   24010715.
  43. ↑ "Jane Richardson - MacArthur Foundation". www.macfound.org. Retrieved February 17, 2020.
  44. 1 2 "Society Alumni Honors | Society for Science & the Public". August 26, 2019. Retrieved February 17, 2020.
  45. 1 2 "Jane S. Richardson". www.nasonline.org. Retrieved February 17, 2020.
  46. ↑ "Membership Overview". www.nasonline.org. Retrieved February 17, 2020.
  47. ↑ "About the NAM". National Academy of Medicine. Retrieved February 17, 2020.
  48. ↑ "Member Directory". www.amercrystalassn.org. Retrieved February 7, 2020.
  49. ↑ "Fellows". www.amercrystalassn.org. Retrieved February 17, 2020.

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