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User:Cation2020/Jane S. Richardson

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Jane Shelby Richardson (born January 25, 1941) is a Jame B. Duke Professor of biochemistry at Duke University who developed 3D visual representations of proteins called ribbon diagrams, or Richardson diagrams.[1][2] With interests in astronomy, math, physics, botany, and philosophy, Richardson is an American biophysicist who took an unconventional route to establishing a science career as she approaches science with curiosity and a multidisciplinary mindset.[3]

Note to reviewers: I have written this article to parallel the existing article but with additional details and sections. I intend to later integrate the text on this page with the existing article.

Jane S Richardson
BornJanuary 25, 2941 (age 79); Teaneck, New Jersey
Alma materSwarthmore College (B.A.), Harvard University (M.A., 1966)
Known forRibbon Diagram
SpouseDave Richardson
AwardsMacArthur Fellowship, Alexander Hollaender Award
Scientific career
InstitutionsDuke University

Biography and Personal Life

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Richardson was born in Teaneck, New Jersey, where she attended a high school that allowed her to explore her passion for astronomy. Her mother, Marian E. Shelby, was a literature composition teacher and her father, Robert E. Shelby, was an electrical engineer. [4][5] Richardson has an older sister, Barbara Shelby Merello, who later worked for the US Information Service in parts of South America and Spain.[5] By 1958, at age 17, Richardson observed and calculated the orbit of Sputnik, an endeavor through which she placed third in a national and prestigious science fair called Westinghouse Science Talent Search.[4]

Richardson attended Swarthmore College for undergraduate school, where she met her husband, David Claude Richardson (Dave Richardson) in her freshman year.[5] At Swarthmore Jane Richardson majored in math, physics, and astronomy before switching her major to philosophy with a math and physics minor; she completed her degree in 1962.[5] After receiving her B.A. in philosophy then completing her master's degree in philosophy and in teaching at Harvard University in 1966,[2][3] Richardson became a technician in her husband's chemistry lab at Massachusetts Institute of Technology under Al Cotton.[3] Prior to joining her husband at MIT Richardson gained experience as a high school teacher, a career that she later decided was not for her.[4] [3]At MIT Richardson learned biochemistry and biophysics as she studied the structure of a DNA cleaving enzyme called Staphylococcal nuclease, Dave's doctoral thesis project inspired by Nobel Laureate Chris Anfinsen in 1963.[3] By 1969 the Richardsons moved to Duke University to join in biochemistry research on superoxide dismutase. After receiving the MacArthur Fellowship in 1985[6] and 1991 election to the National Academy of Sciences and Academy of Arts and Sciences, Richardson eventually received tenure at Duke University where she continues research as the James B. Duke Professor of Biochemistry at Duke University. [2][7]

Richardson and her husband have a son named Robert D. Richardson and a daughter named Claudia J. Richardson. While Robert is a Lockheed engineer in Oakland, California, Claudia is a Fearrington House baker in Durham, North Carolina.[5]

Research Contributions

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Upon joining her husband at MIT, Richardson participated in her husband's doctoral thesis study of Staphylococcal nuclease for seven years. As she began developing her ribbon diagrams collaborators including her husband Dave and Mike Carson developed her drawings into computer graphics. Focusing on structural biology at Duke University, the Richardsons used X-ray crystallography to solve the crystal structures of different proteins starting with superoxide dismutase.[8]

Richardson was one of the pioneers in closely analyzing the data of all the existing protein structures in the late 1960s.[9] Influenced by experiences in plant taxonomy and evolution, Richardson noticed patterns across the protein structures she studied such that she contributed to a taxonomy of protein structures.[3] She compared all the known protein structures at the time to devise rules, specifically on beta-sheet topology and connections between amino acid sequences, or peptides, that make up proteins. Proteins have different degrees of folding. Secondary structures result from hydrogen bond interactions between adjacent amino acids sequences to form alpha helices or beta-sheets.[10] Tertiary structures are a higher order of protein folding that depict the conformation of and connectivity between alpha-helices and beta-sheets in 3D.[11] Richardson's ribbon diagrams illustrate beta-sheet topology and connectivity in tertiary protein structures. She formalized general rules about beta-sheets linkage via "hairpin" connections or "crossover" connections.[3] 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.[12] the By 1981 Jane Richardson continued formalizing a protein structure convention that included ribbon drawings to depict 3D protein with her a publication in the journal Advances in Protein Chemistry titled "The anatomy and taxonomy of protein structure."[13][14] Her initial drawings and continual discoveries were formative in the field of structural bioinformatics and contribute to a broader understanding of protein energetics and evolution. Additionally, Richardson has researched RNA structures as a part of efforts such as the RNA Ontology Consortium to better communicate RNA structure and function research findings.[15][16] After identifying and classifying reoccurring structural motifs for proteins, Richardson extended her work to include de novo protein design, a reverse engineering approach to make and test theoretical predictions about protein folding.[3]

Today, the Richardson Laboratory's 3D Macromolecule Analysis and Kinemage website offers interactive exploration of various 3D protein structures through computer displays using their Mage or KiNG graphics programs. Funded by a National Institute of Science (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,[17] Fundamentals of Biochemistry by Viet, Voet & Pratt,[18] and Principles of Biochemistry by Horton et al.,[19] MathMol,[20] University of Mississippi's Kinemage Authorship Project.[21] Kinemage also entends to social science work in which Mage can be used to map out social networks.[22]

Since another focus of the Richardson Laboratory is protein and RNA structure validation, the Richardsons also developed a website, MolProbity, to assist other scientists in correcting their protein structures for the worldwide Protein DataBank.[23] Involved in the biophysics community Jane Richardson is a former president of the Biophysical Society and began the WikiProject on Biophysics. As Richardson 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.[24]

Honors and Award

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  • 1958: Third place in the Westinghouse Science Talent Search (currently called the Intel Science and Engineering Fair)[2]
  • 1985: MacArthur Fellowship[1][6]
  • 1991: Election to National Academy of Science[2]
  • 2012 - 2013: President of the Biophysical society[4][24]
  • 2019: Alexander Hollaender Award in Biophysics[26]

Notable Publications

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The following articles are classified as highly cited paper by Web of Science as of January 26, 2019:

  • Davis, I. W.; Leaver-Fay, A.; Chen, V. B.; Block, J. N.; Kapral, G. J.; Wang, X.; Murray, L. W.; Arendall, W. B.; Snoeyink, J.; Richardson, J. S.; et al. MolProbity: All-Atom Contacts and Structure Validation for Proteins and Nucleic Acids. Nucleic Acids Research 2007, 35 (Web Server), W375–W383. https://doi.org/10.1093/nar/gkm216.
  • Adams, P. D.; Afonine, P. V.; Bunkóczi, G.; Chen, V. B.; Davis, I. W.; Echols, N.; Headd, J. J.; Hung, L.-W.; Kapral, G. J.; Grosse-Kunstleve, R. W.; et al. PHENIX : A Comprehensive Python-Based System for Macromolecular Structure Solution. Acta Crystallogr D Biol Crystallogr 2010, 66 (2), 213–221. https://doi.org/10.1107/S0907444909052925.
  • Chen, V. B.; Arendall, W. B.; Headd, J. J.; Keedy, D. A.; Immormino, R. M.; Kapral, G. J.; Murray, L. W.; Richardson, J. S.; Richardson, D. C. MolProbity : All-Atom Structure Validation for Macromolecular Crystallography. Acta Crystallogr D Biol Crystallogr 2010, 66 (1), 12–21. https://doi.org/10.1107/S0907444909042073.
  • Adams, P. D.; Afonine, P. V.; Bunkóczi, G.; Chen, V. B.; Echols, N.; Headd, J. J.; Hung, L.-W.; Jain, S.; Kapral, G. J.; Grosse Kunstleve, R. W.; et al. The Phenix Software for Automated Determination of Macromolecular Structures. Methods 2011, 55 (1), 94–106. https://doi.org/10.1016/j.ymeth.2011.07.005.
  • Dunkle, J. A.; Wang, L.; Feldman, M. B.; Pulk, A.; Chen, V. B.; Kapral, G. J.; Noeske, J.; Richardson, J. S.; Blanchard, S. C.; Doudna Cate, J. H. Structures of the Bacterial Ribosome in Classical and Hybrid States of TRNA Binding. Science 2011, 332 (6032), 981–984. https://doi.org/10.1126/science.1202692.
  • Williams, C. J.; Headd, J. J.; Moriarty, N. W.; Prisant, M. G.; Videau, L. L.; Deis, L. N.; Verma, V.; Keedy, D. A.; Hintze, B. J.; Chen, V. B.; et al. MolProbity: More and Better Reference Data for Improved All-Atom Structure Validation. Protein Science 2018, 27 (1), 293–315. https://doi.org/10.1002/pro.3330.

References

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  1. ^ a b https://stories.duke.edu/sciences-mother-of-ribbon-diagrams-celebrates-50-years-at-duke. {{cite web}}: Missing or empty |title= (help)CS1 maint: url-status (link)
  2. ^ a b c d e "Jane S. Richardson | Chemical Heritage Foundation". web.archive.org. 2016-07-12. Retrieved 2020-01-24.
  3. ^ a b c d e f g h Bahar, Sonya. "Ribbon Diagrams and Protein Taxonomy: a profile of Jane S. Richardson". The Biological Physicist.{{cite news}}: CS1 maint: url-status (link)
  4. ^ a b c d "Jane Richardson". The Biophysical Society. Retrieved 2020-01-25.
  5. ^ a b c d e Richardson, Jane S.; Richardson, David C. (2013-05-06). "Doing Molecular Biophysics: Finding, Naming, and Picturing Signal Within Complexity". Annual Review of Biophysics. 42 (1): 1–28. doi:10.1146/annurev-biophys-083012-130353. ISSN 1936-122X. PMC 3695750. PMID 23451888.{{cite journal}}: CS1 maint: PMC format (link)
  6. ^ a b "Fellows List - July 1985 - MacArthur Foundation". web.archive.org. 2008-04-19. Retrieved 2020-01-25.
  7. ^ Christiansen, Jen. "Visualizing Protein Structures". Scientific American Blog Network. Retrieved 2020-01-24.
  8. ^ Tainer, J. A.; Getzoff, E. D.; Beem, K. M.; Richardson, J. S.; Richardson, D. C. (1982). "Determination and analysis of the 2 A-structure of copper, zinc superoxide dismutase". J.Mol.Biol. 160: 181–217. doi:10.2210/pdb2sod/pdb.
  9. ^ Richardson, Jane S. (2000-08-01). "[No title found]". Nature Structural Biology. 7 (8): 624–625. doi:10.1038/77912.
  10. ^ Nelson, David L. (David Lee), (2017). Lehninger principles of biochemistry. Cox, Michael M.,, Lehninger, Albert L. (Seventh edition ed.). New York, NY: W. H. Freeman. ISBN 978-1-4641-2611-6. OCLC 986827885. {{cite book}}: |edition= has extra text (help)CS1 maint: extra punctuation (link) CS1 maint: multiple names: authors list (link)
  11. ^ Godbey, W. T.,. An introduction to biotechnology : the science, technology and medical applications. Amsterdam. ISBN 978-1-908818-48-5. OCLC 890939491.{{cite book}}: CS1 maint: extra punctuation (link) CS1 maint: multiple names: authors list (link)
  12. ^ Richardson, Jane (August, 1977). "ß-Sheet topology and the relatedness of proteins". Nature. 268: 495–500. {{cite journal}}: Check date values in: |date= (help)
  13. ^ a b Vanderkam, Laura. "Finding Order: Jane Richardson". Scientific American. Retrieved 2020-01-25.
  14. ^ Richardson, Jane S. (2000-08-01). "Early ribbon drawings of proteins". Nature Structural Biology. 7 (8): 624–625. doi:10.1038/77912.
  15. ^ Birmingham, Amanda; Clemente, Jose C.; Desai, Narayan; Gilbert, Jack; Gonzalez, Antonio; Kyrpides, Nikos; Meyer, Folker; Nawrocki, Eric; Sterk, Peter; Stombaugh, Jesse; Weinberg, Zasha (2011-04-29). "Meeting report of the RNA Ontology Consortium January 8-9, 2011". Standards in Genomic Sciences. 4 (2): 252–256. doi:10.4056/sigs.1724282. ISSN 1944-3277. PMC 3111981. PMID 21677862.{{cite journal}}: CS1 maint: PMC format (link)
  16. ^ Leontis, N. B. (2006-02-16). "The RNA Ontology Consortium: An open invitation to the RNA community". RNA. 12 (4): 533–541. doi:10.1261/rna.2343206. ISSN 1355-8382. PMC 1421088. PMID 16484377.{{cite journal}}: CS1 maint: PMC format (link)
  17. ^ Brändén, Carl-Ivar, 1934- (1999). Introduction to protein structure. Tooze, John. (2nd ed ed.). New York: Garland Pub. ISBN 0-8153-2304-2. OCLC 39508201. {{cite book}}: |edition= has extra text (help)CS1 maint: multiple names: authors list (link) CS1 maint: numeric names: authors list (link)
  18. ^ Voet, Donald,. Fundamentals of biochemistry : life at the molecular level. Voet, Judith G.,, Pratt, Charlotte W., (Fifth edition ed.). Hoboken, NJ. ISBN 978-1-118-91840-1. OCLC 910538334. {{cite book}}: |edition= has extra text (help)CS1 maint: extra punctuation (link) CS1 maint: multiple names: authors list (link)
  19. ^ Principles of biochemistry. Horton, H. Robert, 1935- (4th ed ed.). Upper Saddle River, NJ: Pearson Prentice Hall. 2006. ISBN 0-13-145306-8. OCLC 58594968. {{cite book}}: |edition= has extra text (help)CS1 maint: others (link)
  20. ^ "Public Domain Software for Molecular Modeling". MathMol. Retrieved January 26, 2020.{{cite web}}: CS1 maint: url-status (link)
  21. ^ "NSF Award Search: Award#9980935 - Student Authorizing of Three-Dimensional Illustrations in Undergraduate Biochemistry". National Science Foundation. February 4, 2000. Retrieved January 26, 2020.{{cite web}}: CS1 maint: url-status (link)
  22. ^ Freeman, L. C.; Webster, C. M.; Kirke, D. M. (1998). "Exploring social structure using dynamic three-dimensional color images" (PDF). Social Networks. 20: 109–118.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  23. ^ Williams, Christopher J.; Headd, Jeffrey J.; Moriarty, Nigel W.; Prisant, Michael G.; Videau, Lizbeth L.; Deis, Lindsay N.; Verma, Vishal; Keedy, Daniel A.; Hintze, Bradley J.; Chen, Vincent B.; Jain, Swati (2018-01). "MolProbity: More and better reference data for improved all-atom structure validation: PROTEIN SCIENCE.ORG". Protein Science. 27 (1): 293–315. doi:10.1002/pro.3330. PMC 5734394. PMID 29067766. {{cite journal}}: Check date values in: |date= (help)CS1 maint: PMC format (link)
  24. ^ a b Lillie, Ben (2014-11-18). "What Wikipedia Taught Me About My Grandfather". The Atlantic. Retrieved 2020-01-25.
  25. ^ "Member Directory". www.amercrystalassn.org. Retrieved 2020-01-25.
  26. ^ "Jane S. Richardson". www.nasonline.org. Retrieved 2020-01-24.
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