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Guide to the Jane and David Richardson Papers, 1969-1992 (MC.0167)

Abstract

Contains the professional papers of Jane Richardson, James B. Duke professor of Biochemistry, and David Richardson, professor of Biochemistry and founding director of the Structural Biology and Biophysics Graduate Training Program at Duke University. Types of materials include correspondence, sketches, photographs, drawings, notes, computer printouts and visualizations, negatives, reprints, and clippings pertaining to the Richardson's work and research while at Duke University. Major subjects include the structure of copper, zinc superoxide dismutase, protein de novo design, the Protein Data Bank, and 1981 textbook chapter "The Anatomy and Taxonomy of Protein Structure." Materials date from 1971 to 1991.

Descriptive Summary

Call Number
MC.0167
Title
Jane and David Richardson Papers
Date
1969-1992
Creator
Richardson, Jane S.
Extent
Repository
Duke University Medical Center Archives

Collection Overview

Contains correspondence, sketches, photographs, drawings, notes, computer printouts and visualizations, negatives, reprints, and clippings pertaining to the Richardson's work and research while at Duke University. Major subjects include the structure of copper, zinc superoxide dismutase, protein de novo design, the protein data bank, and 1981 textbook chapter "The Anatomy and Taxonomy of Protein Structure." Materials date from 1971 to 1991.

Arrangement Note

Organized into the following series: Copper, Zinc Superoxide Dismutase project, 1973-1982, undated; The Anatomy and Taxonomy of Protein Structures, 1980-1981; Principles and Patterns of Protein Confirmation, 1980-1989; Other Projects, 1971-1991, undated; Personal/Biographical, 1978-1980, undated.

Restrictions on Access & Use

Some collections are stored off site and must be requested at least 48 business hours in advance for retrieval.

Access Restrictions

None.

Use Restrictions

Copyright for Official University records is held by Duke University; all other copyright is retained by the authors of items in these papers, or their descendants, as stipulated by United States copyright law.

Contents of the Collection

1. Copper, Zinc Superoxide Dismutase project, 1969-1982, undated

Series Scope and Contents: Series contains figures, sketches, photographs, and drawings pertaining to the Richardson's work on the structure of copper, zinc superoxide dismutase, an enzyme that protects all living things against the toxicity of oxygen. The Richardson's began working on this structure when they arrived at Duke the 1969. Series includes figures from the 1982 article "Determination and analysis of the 2 Å structure of copper, zinc superoxide dismutase," coauthored with John A. Tainer. Series also contains figures from the 1976 article "Similarity and Three-dimensional Structure Between the Immunoglobulin Domain and the Copper, Zinc Superoxide Dismutase Subunit." Materials date from 1973 to 1982, a significant amount being undated.

active site detail for 1978 Tainer SOD paper, 1978
Box 1
C-alpha position with backbone trace, stereos, undated
Box 3
Crystal structure of SOD graphs, undated
Box Map Folder 5
Crystallography of Superoxide Dismutase, multiple isomorphous replacement (used to solve Cu, Zn SOD structure), undated
Box 3
Cu, Zn SOD plot, Oct-82
Box 1
Determination and analysis of the 2 A structure of copper, zinc superoxide dismutase; Figure 1. Progress of the refinement represented by a plot of crystallograhic residual error versus cycle number, 1981-1982
Box 2
Determination and analysis of the 2 A structure of copper, zinc superoxide dismutase; Figure 2. Stereo drawing from plots produced by ORTEP (Johnson, 1965) showing the CA backbone of the SOD subunit viewed down the axial direction of the Cu atom from solvent., 1981-1982
Box 4
Determination and analysis of the 2 A structure of copper, zinc superoxide dismutase; Figure 3. Schematic backbone drawing of the SOD subunit viewed from the same direction as Fig. 2., 1981-1982
Box 1
Determination and analysis of the 2 A structure of copper, zinc superoxide dismutase; Figure 4. Diagram showing the SOD beta barrel and loops spread out flat and shown for the outside with the sequence given in the one-letter code., 1981-1982
Box 2
Determination and analysis of the 2 A structure of copper, zinc superoxide dismutase; Figure 5. Phi, psi plot for the co-ordinates of the Orange SOD subunit after refinement followed by manual refitting., 1981-1982
Box 2
Determination and analysis of the 2 A structure of copper, zinc superoxide dismutase; Figure 6. Stereo view from the UNC GRIP-75 molecular graphics system showing the 2F?a-F?c electron density map and the model in the disulfide region., 1981-1982
Box 1
Determination and analysis of the 2 A structure of copper, zinc superoxide dismutase; Figure 7. Stereo drawing of beta strands 1 to 4, which form the more regular side of the SOD barrel, as viewed from the protein interior, 1981-1982
Box 4
Determination and analysis of the 2 A structure of copper, zinc superoxide dismutase; Figure 8. Stereo drawing of beta strands 5 to 8, which form the more twisted side of the SOD beta barrel, viewed from the active site..., 1981-1982
Box 4
Determination and analysis of the 2 A structure of copper, zinc superoxide dismutase; Figure 9. Stereo drawing of loop 4.7 (Pro100-Gly112)., 1981-1982
Box 2
Determination and analysis of the 2 A structure of copper, zinc superoxide dismutase; Figure 10. Stereo drawing of the 14-residue disulfide region loop 6.5 (Gln47-Pro60)., 1981-1982
Box 2
Determination and analysis of the 2 A structure of copper, zinc superoxide dismutase; Figure 11. Stereo drawing of the Zn ligand region of loop 6.5 (His61-Leu82), which includes all 4 Zn ligands., 1981-1982
Box 2
Determination and analysis of the 2 A structure of copper, zinc superoxide dismutase; Figure 12. Simplified CA backbone drawings to show the similar overall arrangement of the Zn ligand region of (a) loop 6.5 and (b) loop 4.7., 1982
Box 2
Determination and analysis of the 2 A structure of copper, zinc superoxide dismutase; Figure 13. Stereo drawing of loop 7.8 (Glu119-Leu42)., 1981-1982
Box 2
Determination and analysis of the 2 A structure of copper, zinc superoxide dismutase; Figure 14. Photographed from the UNC GRIP-75 molecular graphics systems, shows the metals and their ligands after refinement with fragment difference electron density maps contoured at about 0-7 e/A3., 1981-1982
Box 1
Determination and analysis of the 2 A structure of copper, zinc superoxide dismutase; Figure 15. Photographed from the UNC GRIP-75 molecular graphics systems, stereo view along the ring plane at the His61, positioned in the continuous density from the Cu above to the Zn below., 1981-1982
Box 1
Determination and analysis of the 2 A structure of copper, zinc superoxide dismutase; Figure 16. Stereo drawing from plots produced by ORTEP (Johnson, 1965) showing the geometry of the active site metals and their ligands as viewed from the solvent., 1981-1982
Box 1
Determination and analysis of the 2 A structure of copper, zinc superoxide dismutase; Figure 17. Stereo plot showing the complex network of H-bonds stabilizing the orientations of the liganding residues for the Cu and Zn., 1981-1982
Box 1
Determination and analysis of the 2 A structure of copper, zinc superoxide dismutase; Unidentified figures, 1981-1982
Box 2
Electron Density Contours, Superoxide dismutase project, circa 1974-1978
Box 1
End-on and side views of the beta cylinder, circa 1976
Box 4
Fe superoxide dimutase ribbon diagram (related to Cu, Zn superoxide dismutase, not part of the project), undated
Box 1
Figure for Tainer paper, undated
Box 4
Figures from "Alpha-Carbon Coordinates for Bovine Cu,Zn Superoxide Dismutase" article, 1975
Box Map Folder 6
Final Cu, Zn Superoxide Dismutase figures, undated
Box 6
Handdrawn SOD versus immunoglobulin domain, showing similarities, circa 1975
Box 4
Heavy atom derivatives used to solve SOD structure, undated
Box 1
Med. Science I Stereo Pain, Impressions, 1973
Box 4
Miscellaneous figures from article, 1975
Box Map Folder 7
Photograph, CuZnSOD Stained Glass, undated
Box 1
Photograph, electron density contour model of Cu, Zn SOD, undated
Box 3
Photograph, wire bender model of Cu, Zn SOD, undated
Box 3
Preliminary early Cu,Zn SOD coordinates, undated
Box 3
Similarity and Three-dimensional Structure Between the Immunglobulin Domain and the Copper, Zinc Superoxide Dismutase Subunit; Figure 2. Topology diagrams of the beta structures of (a) an immunoglobulin variable domain and (b) a copper, zinc superoxide dismutase subunit., 1975-1976
Box 1
Similarity and Three-dimensional Structure Between the Immunglobulin Domain and the Copper, Zinc Superoxide Dismutase Subunit; Figure 4. Comparison of step-by-step build-up of backbone configuration for superoxide dismutase (down the left side) and an immunoblobulin variable domain (down the right side)., 1975-1977
Box 6
Stained glass diagram, undated
Box Map Folder 1
Stereos of four active sites, set up for Tainer paper, undated
Box 3
Stereos, set up for figures in unidentified Cu, Zn SOD article, 1981
Box 4
Superoxide dismutase, c-alpha trace, undated
Box 4
The Crystal Structure Structure of Cu, Zn Superoxide Dismutase, 1969-1973
Box 6
Worm drawing, undated
Box 4

2. Other Projects, 1970-1991, undated

Series Scope and Contents: Contains notes, clippings, sketches, photographs, computer printouts, drawings, and figures pertaining to the Richardsons' work at Duke. Materials are from a variety of projects, pertaining to the Protein Data Bank, staphylococcal nuclease, wire bender models, transfer RNA, nuclear magnetic resonance (NMR), the Output from Oak Ridge Thermal Ellipsoid Plot (ORTEP) program, and protein de novo design. Series contains materials related to the articles "De Novo Design, Expression, and Characterization of Felix: A Four-Helix Bundle Protein of Native-like Sequence" (1990), "The toxin-agglutinin fold" (1980), and "Beta sheet topology and the relatedness of proteins" (1977). Materials date from 1973 to 1982, a significant amount being undated.

A hydrophic core from carp calcium-binding protein, diagram, undated
Box 4
Beta bellin ribbon drawing, protein design project, spray paint, undated
Box 4
Beta sheet topology, unidentified publication, sketch, undated
Box 1
Computer printouts of c-alpha coordinates with reference sheet for proteins, from Byron's bender project, circa 1971
Box 4
Computer printouts related to Thermolysin, Basic Pancreatic Trypsin Inhibitor, Lactate Dehydropenase, Rubredoxin, Mar-74
Box 4
Computer printouts, Fractional Coords of A & B After Convergence of Centroid of Molecule A, undated
Box 3
Copies of Feldman computer printouts (derivative), undated
Box 1
Defraction image from Precession camera, central section of a three-dimensional defraction pattern, undated
Box 1
"De novo design, expression and characterization of Felix," clippings, Sep-90
Box 6
Diagram demonstrating protein folding, undated
Box 3
Disulfide connectivities, unidentified publication, undated
Box 4
Drawings of staphylococcal nuclease active site, undated
Box 3
Early ribbon sketch, undated
Box 1
Electron density contours, unidentified (Folder 1 of 3), undated
Box Map Folder 2
Electron density contours, unidentified (Folder 2 of 3), undated
Box 1
Electron density contours, unidentified (Folder 3 of 3), undated
Box 6
Electron density stereo, unidentified protein, undated
Box 4
Exhibit Materials (Folder 1 of 2), undated
Box 4
Exhibit Materials (Folder 2 of 2), undated
Box Map Folder 3
Figures related to "Beta sheet topology and the relatedness of proteins," published in Nature (Folder 1 of 2), undated
Box Map Folder 8
Figures related to "Beta-sheet topology and the relatedness of proteins," published in Nature (Folder 2 of 2), circa 1977
Box 4
Figures related to "The beta bulge: a common small unit of nonrepetitive protein structure" article, circa 1978
Box 4
Greek key fold, print, undated
Box 1
Handdrawn stereo and relationship on a beta barrel, undated
Box 1
"Handedness of Crossover Connections in Beta Sheets," Figure 3. Stereo alpha-carbon drawings of an assortment of actual crossover connections, each rotated into a standard position with the beta sheet in the plane of the paper and the beta strands vertical., undated
Box 3
Incredulase ribbon drawing, undated
Box 1
Incredulase, set up for Incredulase drawing, undated
Box 4
Measuring angle between adjacent carbonyls, after origami period, undated
Box 3
Metaphors for the Greek key folds, undated
Box 1
Models of unmatched DNA and RNA, photographic prints, undated
Box 3
Notes relating to "Beta sheet topology and the relatedness of proteins," published in Nature, 1977
Box 1
Nuclear magnetic resonance (NMR), 1990-1991
Box Map Folder 9
Nuclear magnetic resonance (NMR), notes on Fibronectin III, circa 1982
Box 1
Output from Oak Ridge Thermal Ellipsoid Plot (ORTEP) program, unidentified chemical, undated
Box 4
Oversized stereos, unidentified, undated
Box Map Folder 10
Packing diagram of the staphylococcal nuclease unit cell, circa 1970
Box 3
Pairs of related structures, example of an incorrect chain tracing, related to article "Interpretation of elctron density map" (1985), circa 1985
Box 4
Photograph, Rubredoxin model of Midas Muffler pipe by Byron Rubin, in Gross Chem lobby, undated
Box 1
Photographs, wire bender models, shows the backbone and side chain, brass, undated
Box 1
Photographs, wire bender models, subunit of Cu, Zn Superoxide Dismutase, gold plated, undated
Box 1
Photographs, wire bender models, TransferRNA (Byron's work), undated
Box 1
Poster, Biochemistry, Mathews and van Holde, 1989
Box 4
Protein Data Bank (Folder 1 of 2), 1981-1983
Box 1
Protein Data Bank (Folder 2 of 2), 1982-1983
Box 4
Protein Structure Coloring Book, 1979
Box 2
Protein Structure Coloring Book, notes of what was in the original coloring book, undated
Box 1
References, Protein Crystallography, undated
Box 1
Reprint, Nature, vol. 294, 1981
Box 1
Ribbon drawing guide, undated
Box Map Tube 1
Richard Feldmann's space-fill graphics, NIH, circa 1980
Box 1
rRNA, undated
Box Map Folder 4
rRNA, oversized, undated
Box Map Tube 2
Sketch of side chains on beta structures, undated
Box 3
Sketch, possibly for Nature article, undated
Box 1
Sketch, transfer RNA, undated
Box 1
Sketches and references used for drawing, possibly measuring the ends of beta strands, undated
Box 3
Sketches related to "De Novo Design, Expression, and Characterization of Felix: A Four-Helix Bundle Protein of Native-like Sequence" article, circa 1990
Box 3
Sketches, A collection of alpha-helices at varying angles to the page (Jane used to learn how to draw protein structures), undated
Box 1
Space fill images, Feldman, undated
Box 4
Spot Hb, Rotation function solution 7-81, unfinished project with Joseph Bonaventura, undated
Box 2
Staphylococcal nuclease worm drawings, undated
Box 4
Stereo pairs, identifying local motifs in structure, circa 1975
Box 4
Stereo, LAHD, undated
Box 4
The Toxin-Agglutinin Fold, reprint, 1979
Box 1
The Toxin-Agglutinin Fold; Figure 1. Schematic representation of the polypeptide backbone and disulfide bonds of one of the WGA domain's (A) and of erabutoxin (B)., 1979
Box 5
The Toxin-Agglutinin Fold; Figure 2. Stereoscopic illustration of the superposed alpha-carbon backbone of erabutoxin and the D domain of WGA., 1979
Box 5
The Toxin-Agglutinin Fold; Table 1. Alignment of half-cystine positions in four proteins, 1979
Box 3
Tyrosine corner, computer graphic, undated
Box 4
Unidentified figure, undated
Box Map Folder 11
Unidentified figures (Folder 1 of 2), undated
Box 1
Unidentified figures (Folder 2 of 2), undated
Box 6
Unidentified prints, undated
Box 3
Viral coat protein, quasi six-fold and two-fold axis, undated
Box 1
"Wire Bender for Backbone Models of Proteins," by Byron Rubin and Jane Richardson, 1971
Box 4
Worm drawing as context for hydrophobic core, undated
Box 3
Worm drawing of Rubredoxin, undated
Box 1
Worm drawing, unidentified, undated
Box 3
Worm drawings, staphylococcal nuclease structure, undated
Box 3

3. Personal/Biographical, 1978-1980, undated

Series Scope and Contents: Contains correspondence, a cartoon, a photograph, and teaching materials pertaining to the Richardsons' personal lives and the courses they taught at Duke University. Materials date from 1978 to 1980, with some material undated.

Correspondence, undated
Box 1
New Yorker Cartoon, undated
Box 1
Photograph, David and Jane Richardson, 1978
Box 1
Teaching Materials, 1979-1980
Box 1
Teaching Materials, materials for David Richardson's crystallography lectures, undated
Box 3

4. Principles and Patterns of Protein Confirmation, 1980-1989

Series Scope and Contents: This series contains the prints, drawings, and negatives of figures for the chapter "Principles and Patterns of Protein Confirmation" from the 1989 textbook "Prediction of Protein Structure and the Principles of Protein Conformation," edited by G.D. Fasman. Materials date from 1980 to 1989.

Figure 42. Examples of two proteins containing offset perpendicular helix corners:.. (b) CAP protein (GAP)., undated
Box 3
Figure 99. Simplified schematic drawing of the bacterial photosynthetic reaction center, undated
Box 2
Figure 108. Schematic drawing of gamma-crystallin (GCR) showing the two very similar domains into which it is divided., circa 1989
Box 3
Figure List, undated
Box 1
I. Constraints and. . . (Figures 1-9), 1981, undated
Box 1
II. H-bonding, a. (Figures 10-17), undated
Box 1
II. H-bonding, b. (Figures 18-27), undated
Box 1
II. H-bonding, c. (Figures 28-34), undated
Box 1
III. Tertiary Structure, a.-b. (Figures 35-42), Sep-80
Box 1
III. Tertiary Structure, c.-e. (Figures 43-56), Jan-81
Box 1
IV. Amino acids, a.-b. (Figures 57-69), undated
Box 1
IV. Amino acids, c.-e. (Figures 70-80), undated
Box 1
IV. Amino acids, f.-h. (Figures 81-91), August 1980-January 1981
Box 1
IV. Amino acids, i.-j. (Figures 92-98), undated
Box 1
Phi, psi plots for textbook, 1989
Box 3
V. Hydrophobicity. . . (Figures 99-105), undated
Box 1
VI. Handedness (Figures 106-107), undated
Box 1
VII. History (Figures 108-112), undated
Box 1

5. The Anatomy and Taxonomy of Protein Structures, 1979-1992

Series Scope and Contents: Contains sketches, drawings, photographs, notes, computer printouts and visualizations, negatives, and reprints pertaining to Jane Richardson's work on the chapter "The Anatomy and Taxonomy of Protein Structure," published in the 1981 textbook "Advances in Protein Structure." Materials date from 1980 to 1981.

C-alpha stereo of Ferradoxin, set up for a drawing with type of ligands, stereo pair, undated
Box 3
Carp muscle calcium-binding protein, worm drawing, undated
Box 5
Classic drawing, not published in "The Anatomy and Taxonomy of Protein Structure" but drawn in the same manner, undated
Box 5
Correspondence, 1992
Box 1
Early examples of pre-Anatomy and Taxonomy schematic 3D drawings, undated
Box 1
Early notes and sketches, 1979-1981
Box 1
Figure 1. Schematic drawing of the polypeptide backbone of ribonuclease S (bovine pancreatic ribonuclease A cleaved by subtilisin between residues 20 and 21)., 1980-1981
Box 5
Figure 2. Stereo drawing of all nonhydrogen atoms of basic pancreatic trypsin inhibitor., 1980-1981
Box 1
Figure 5. A key to standard nomenclature for the atoms and the more important bond angles and dihedral angles along the polypeptide backbone., 1980-1981
Box 1
Figures 7 and 8. Plots of main chain dihedral angles phi and psi, 1980-1981
Box 3
Figure 9. "Derivation diagram" showing which atomic collisions (using a hard-sphere approximation) produce the restrictions on main chain dihedral angles phi and psi., 1980-1981
Box 1
Figure 10. Diagonal plot of close Calpha-Calpha distances for an immunoglobulin light chain, diagonal plot courtsey of Michael Liebman (Folder 2 of 2), 1980-1981
Box 3
Figure 11. Drawing of a typical alpha-helix, residues 40-51 of the carp muscle calcium binding protein., 1980-1981
Box 5
Figure 12. Illustrations of the 13-atom hydrogen-bonded loop which determines the subscript in the description of the alpha-helix as a 3.613-helix., 1980-1981
Box 1
Figure 14. Schematic drawing of the backbone of an all-helical tertiary structure: domain 2 of thermolysin (also Figure 73)., 1980-1981
Box 1
Figure 15. Stereo drawing of a bent helix (glyceraldhyde-phosphate dehydrogenase residues 146-161) with an internal proline., 1980-1981
Box 5
Figure 16. An unusual interrupted helix from subtilisin (residues 62-86), in which the helical hydrogen bonds continue to a final turn that is formed by a separate piece of main chain, 1980-1981
Box 5
Figure 17. A short segment of 3?10 helix from carbonic anhydrase (residues 159-194)., 1980-1981
Box 1
Figure 18. An example of the alpha?II conformation at the end of the A helix in myoglobin (residues 8-17)., 1980-1981
Box 5
Figure 19. Examples of the two commonest types of helix-helix contact, 1980-1981
Box 1
Figure 20. An example of antiparallel beta sheet, from Cu,Zn superoxide dimutase (residues 93-98, 28-33, and 16-21)., 1980-1981
Box 5
Figure 21. An example of parallel beta sheet, from flavodoxin (residues 82-86, 49-53, and 2-6)., 1980-1981
Box 5
Figure 22. An example of a long two-stranded ribbon of antiparallel beta structure, from lactate dehydrogenase (residues 263-294)., 1980-1981
Box 1
Figure 23. Schematic drawing of the backbone of flavodoxin, a protein in which a parallel beta sheet is the dominant structural feature., 1980-1981
Box 3
Figure 24. The two major sorts of connection between beta strands, 1980-1981
Box 1
Figure 25. A topological schematic diagram of the connectivity in parallel beta sheet of flavodoxin., 1980-1981
Box 1
Figure 26. (a) A right-handed + 1x crossover connection; (b) a left-handed + 1x crossover connection., 1980-1981
Box 1
Figure 27. Examples of particular crossover connections: (a) a right-handed +1x, residues 200-242 from carboxypeptidase A; (b) a right-handed, 1980-1981
Box 3
Figure 28. Illustration of possible folding shemes which would produce the handedness of crossover connections as a consequence of (a) the handedness of twist of an initial beta ribbon, or (b) the handedness of an initial alpha-helix., 1980-1981
Box 3
Figure 29. An assortment of beta barrels, viewed down the barrel axis: (a) staphylococcal nuclease, 5-stranded; (b) soybean trypsin inhibitor, 6- stranded; (c) chymotrypsin, 6-stranded; (d) immunoglobulin (McPC603 CH1) constant domain, 7-stranded; (e) Cu,Zn superoxide dismutase, 8-stranded; (f) triosephosphate isomerase, 8-stranded; (g) immunoglobulin (McPC603 VH) variable domain, 9-stranded; (h) tomato bushy stunt virus protein domain 3, 10-stranded., 1980-1981
Box 5
Figure 30. The two major types of tight turn (I and II)., 1980-1981
Box 1
Figure 31. Stereo drawings of particular examples of type I (a), I' (b), and III (c ) turns from the known protein structures., 1980-1981
Box 1
Figure 32. Stereo drawings of particular examples of types II (a) and II' (b) turns from the known protein structures., 1980-1981
Box 1
Figure 33. Stereo drawings of particular examples of types VI a (a) and VI b (b) cis-proline turns., 1980-1981
Box 1
Figure 34. Stereo drawings of particular examples of type VII (a) and of gamma turns (b)., 1980-1981
Box 1
Figure 35. phi, psi plots of (a) position 2 and (b) position 3 of empirically observed type I and type III tight turns., 1980-1981
Box 1
Figure 36. phi, psi plot for positions 2 and 3 of tight turns type II, IIŽ, V, and VŽ., 1980-1981
Box 3
Figure 37. phi, psi plot for the cis-proline (type VI) turns from Chou and Fasman (1977), plus the two examples in the Bence-Jones protein REI., 1980-1981
Box 1
Figure 38. Stereo drawing of the polypeptide backbone of high-potential iron protein., 1980-1981
Box 3
Figure 39. An example of the effects of shifting the sequence location of a tight turn by one residue., 1980-1981
Box 1
Figure 40. A classic beta bulge: the model and electron density from refined trypsin residues Ser-214, Trp-215, and Val-227., 1980-1981
Box 1
Figure 41. Diagrammatic illustrations of various types of beta bulges, 1980-1981
Box 1
Figure 42. Five superimposed examples of classic beta bulges, in stereo: chymotrypsin Phe-41, Cys-42 opposite Val-120; and staphylococcal nuclease Ile-15, Lys-16 opposite Lys-24., 1980-1981
Box 3
Figure 43. Four superimposed examples of GI beta bulges with associated type II tight turns, 1980-1981
Box 1
Figure 44. Stereo view of the prealbumin dimer., 1980-1981
Box 1
Figure 45. The structure of L-cystine dihydrobromide, seen down the crystallographic 2-fold axis., 1980-1981
Box 1
Figure 46. A left-handed spiral disulfide from hen egg white lysozyme, viewed from a direction similar to Figure 45., 1980-1981
Box 1
Figure 47. The x1 angles observed for disulfides in protein structures., 1980-1981
Box 1
Figure 48. Plot of all five dihedral angles and Calpha-Calpha distance for the disulfides from refined, high-resolution (2A or better) protein structures., 1980-1981
Box 1
Figure 49. A left-handed spiral disulfide from ribonuclease S, viewed end-on., 1980-1981
Box 1
Figure 50. A right-handed hook disulfide from carboxypetidase A., 1980-1981
Box 1
Figure 51. Number of residues between sequence-neighbor half-cystines., 1980-1981
Box 1
Figure 52. A schematic backbone drawing of insulin, a small structure which is dependent on its disulfides for stability., 1980-1981
Box 1
Figure 53. The main chain hydrogen bonds of a basic pancreatic trypsin inhibitor, 1980-1981
Box 1
Figure 54. An asparagine side chain making a hydrogen-bond to the main chain NH of residue n + 2, an arrangement which helps, 1980-1981
Box 1
Figure 55. Two very similar 5-residue turns with a single alpha-helical hydrogen bond, 1980-1981
Box 5
Figure 56. The calcium-binding sites from carp muscle calcium-binding protein: (a) backbone of the entire "E-F"; (b) detailed view of the E-F calcium-binding site, including those side chains which are Ca ligands; (c ) detailed view of the C-D calcium-binding site, rotated to match part b., 1980-1981
Box 5
Figure 57. Model and electron density in rubredoxin after refinement at 1.2A resolution, for (a) the well-ordered ysine, Lys-46; (b) the best of the disordered lysines, Lys-3., 1980-1981
Box 1
Figure 58. Stereo drawing of the rubredoxin backbone with the iron (filled circle) and its cysteine sulfer ligands and all the water molecules (open circles) identified during refinement of the structure at 1.2 A resolution., 1980-1981
Box 5
Figure 59. Water molecules (open circles) in prealbumin, bridging between main chain groups that are too far apart to continue, 1980-1981
Box 1
Figure 60. A stereo view of one of the hydrogen-bonded networks of water molecules at the surface of the rubredoxin molecule, 1980-1981
Box 1
Figure 61. (a) The insulin hexamer; (b) the insulin monomer (from Blundell et al.)., 1980-1981
Box 1
Figure 62. A schematic drawing of the backbone of the prealbumin dimer, viewed down the 2-fold axis., 1980-1981
Box 5
Figure 63. Departures from local 2-fold symmetry, especially of side chain positions, in the beta strand dimer interaction of insulin., 1980-1981
Box 1
Figure 64. The tightly associated domains (one shown light and the other dark) of elastase., 1980-1981
Box 1
Figure 65. The "dumbbell" domain organization of phosphoglycerate kinase, with a relatively narrow neck between two well-separated domains., 1980-1981
Box 1
Figure 66. The domains of papain, which wrap "arms" around each other., 1980-1981
Box 1
Figure 67. Stereo alpha-carbon drawing of the two domains of arabinose-binding protein (viewed perpendicular to the approximate 2-fold axis between domains), with the stretch of chain shown dark which joins the end of the first domain to the beginning of the second one., 1980-1981
Box 5
Figure 68. Schematic backbone drawing of the elastase molecule, showing the similar beta barrel structures of the two domains., 1980-1981
Box 1
Figure 69. The two different positions of the hinge between domains 2 and 3 of tomato bushy stunt virus protein., 1980-1981
Box 1
Figure 70. Domains 2 (cylinders) and N-terminal tails of B- and C-type subunits around the quasi-6-fold axis in tomato bushy stunt virus., 1980-1981
Box 1
Figure 71. Examples of protein domains with different numbers of layers of backbone structure (triosephosphate isomerase)., 1980-1981
Box 1
Figure 72. Antiparallel alpha: up-and-down helix bundles, 1980-1981
Box 1
Figure 72-2. Antiparallel alpha: up-and-down helix bundles., 1980-1981
Box 2
Figure 73. Antiparallel alpha: Greek key helix bundles., 1980-1981
Box 1
Figure 74. Antiparallel alpha: miscellaneous, 1980-1981
Box 1
Figure 75. Parallel alpha/beta: singly wound parallel beta barrels., 1980-1981
Box 1
Figure 76. Parallel alpha/beta: classic doubly wound beta sheets., 1980-1981
Box 1
Figure 77. Parallel alpha/beta: doubly-wound parallel beta sheets., 1980-1981
Box 1
Figure 77-2. Parallel alpha/beta: doubly-wound parallel beta sheets., 1980-1981
Box 1
Figure 78. Parallel alpha/beta: miscellaneous, 1980-1981
Box 2
Figure 79. Antiparallel beta: up-and-down beta barrels., 1980-1981
Box 1
Figure 80. Antiparallel beta: Greek key beta barrels., 1980-1981
Box 1
Figure 81. Antiparallel beta: "jellyroll" Greek key beta barrels., 1980-1981
Box 1
Figure 82. Antiparallel beta: other, multiple, and partial barrels., 1980-1981
Box 1
Figure 83. Antiparallel beta: open-face sandwich beta sheets., 1980-1981
Box 1
Figure 83-2. Antiparallel beta: open-face sandwich beta sheets., 1980-1981
Box 1
Figure 84. Antiparallel beta: miscellaneous, 1980-1981
Box 1
Figure 85. Small disulfide-rich. (also contains Wayne Hendrickson's crambin published in Nature)., 1980-1981
Box 1
Figure 86. Small metal-rich., 1980-1981
Box 3
Figure 87. Myohemerythrin as an example of an up-and-down helix bundle (also Figure 72)., 1980-1981
Box 5
Figure 88. The dimer association of uterglobin, with one subunit shown shaded and one open., 1980-1981
Box 3
Figure 89. Hemoglobin (beta subunit) as an example of a Greek key helix bundle (also Figure 73)., 1980-1981
Box 5
Figure 90. Triosephosphate isomerase as an example of a singly wound beta barrel, 1980-1981
Box 5
Figure 91. Highly simplified sketches (viewed from the C-terminal end of beta strands) of, 1980-1981
Box 1
Figure 92. Lactate dehydrogenase domain 1 as an example of a classic doubly wound parallel beta sheet. (also Figure 96), 1980-1981
Box 5
Figure 93. Topology diagrams for the doubly wound and miscellaneous alpha/beta domains illustrated in Figs. 76 through 78., 1980-1981
Box 3
Figure 94. Carboxypeptidase A as an example of a miscellaneous alpha/beta structure (also Figure 78)., 1980-1981
Box 5
Figure 95. Papain domain 2 as an example of an up-and-down antiparallel beta barrel (also Figure 79), 1980-1981
Box 5
Figure 96. Cu,Zn superoxide dismutase as an example of a Greek key antiparallel beta barrel., 1980-1981
Box 5
Figure 97. Topology diagrams of the Greek key antiparallel beta barrels, 1980-1981
Box 2
Figure 98. Topology diagrams of the "jellyroll" Greek key beta barrels., 1980-1981
Box 2
Figure 99. A highly simplified sketch of the slightly flattened cylinder of a beta barrel, showing how the direction of flattening twists from top to bottom., 1980-1981
Box 1
Figure 100. A hypothetical folding scheme for Greek key beta barrels which could explain why essentially all of the Greek key and jellyroll beta barrels have the same handedness of topology., 1980-1981
Box 1
Figure 101. Packing of two beta barrel domains in the immunoglobulin VL dimer (from Bence-Jones REI), 1980-1981
Box 5
Figure 102. Clyceraldehyde-phosphate dehydrogenase domain 2 as an example of an open-face sandwich antiparallel beta sheet, 1980-1981
Box 5
Figure 103. Basic pancreatic trypsin inhibitor as an example of a small disulfide-rich structure. (also Figure 85), 1980-1981
Box 5
Figure 104. Cytochrome c as an example of a small metal-rich protein (also Figure 86), 1980-1981
Box 2
Figure 105. Examples of small disulfide-rich or metal-rich proteins compared with their more regular counterparts in other structural categories., 1980-1981
Box 1
Figure 106. Rhodanese domains 1 and 2 as an example of a protein with two domains which resemble each other extremely closely. (also Figure 77-2), 1980-1981
Box 1
Figure 107. Pyruvate kinase domains 1, 2, and 3 as an example of a protein whose domains show no structural resemblance whatsoever., 1980-1981
Box 1
Figure 108. Hexokinase domains 1 and 2: the proteins whose domains are least alike of all the cases that may represent gene duplications., 1989-1981
Box 1
Figure 109. Possible successive steps in the protein folding process as they might apply to a typical example of each of the four major categories of structure, 1980-1981
Box 5
Pages from the index, diagrams, 1980-1981
Box 1
pencil drawing of 20 amino acids, 1980-1981
Box 1
Potato carboxypeptidase inhibitor ribbon diagram, undated
Box 1
Reference and research, undated
Box 1
Reprint, "The Anatomy and Taxonomy of Protein Structures", 1980-1981
Box 5
RuBisCO, TIM barrel type structure, related to "The Anatomy and Taxonomy of Protein Structure", undated
Box 5
Sketch, dimer that bonds to DNA, undated
Box 1
Sketches, miscellaneous, undated
Box 1
Sketches, para-hydroxy-benzoate hydroxylase, domains 1-3, undated
Box 1
Stereo, KGPD Adolase, undated
Box 1
Stereos, some show connections between helices, 1980-1981
Box 5
Stereos, used to create ribbon drawings, 1980-1981
Box 5
Stereos, xeroxes of structures in stereo, the starting point for ribbon drawings (Folder 3 of 3), 1980-1981
Box 2
Table 1. Location of the asparagine residues are tabulated for beta sheets of at least three strands in the known protein structures., 1980-1981
Box 2
Unidentified sketches, undated
Box 3
Stereos, 2-keto-3-deoxy-6phosphgluconate aldolase (also associated with 1979 publication), 1979
Box 5
Stereos, xeroxes of structures in stereo, starting point for ribbon drawings (Folder 1 of 2), undated
Box 1
Stereos, xeroxes of structures in stereo, starting point for ribbon drawings (Folder 2 of 2), undated
Box 1

Biographical/Historical Note

Jane Shelby grew up in Teaneck, New Jersey, and received her BA in philosophy from Swarthmore College in 1962. While at Swarthmore College, Jane met David Richardson, who received a BA in chemistry in 1962. Following graduation, they married and David continued his studies at the Massachusetts Institute of Technology, pursing a PhD in chemistry while working in the laboratory of Albert F. Cotton and researching small molecule inorganic chemistry and crystallography. Meanwhile, Jane attended Harvard University to earn a MA in philosophy and master's in teaching in 1966. In 1964, Jane became a technician in the same lab where David was conducting his graduate research. The Richardson's began working to solve the structure of the staphylococcal nuclease, an enzyme that cleaves DNA and RNA. At this time, only two proteins had been solved (hemoglobin and myoglobin) and protein crystallography was in its infancy. They determined the structure of the nuclease in 1969, making it the tenth protein structure to be determined. David received his PhD from the Massachusetts Institute of Technology in 1968. The Richardsons then spent at a year at the National Institutes of Health (NIH) before coming to Duke University in 1970.

Jane Richardson was an associate in Duke University's Department of Anatomy until 1984, a medical research assistant in the Department of Biochemistry until 1988, and a medical research associate professor in the Department of Anatomy until 1991, when she became a James B. Duke Professor in the Department of Biochemistry. David Richardson was a professor in Duke University's Department of Biochemistry beginning in 1970. Upon their arrival to Duke, David and Jane Richardson established a lab and began working on the structure of copper, zinc superoxide dismutase, an enzyme that protects all living things against the toxicity of oxygen. In the 1980s the Richardsons started exploring synthetic biochemistry and computational biology and helped open up the field of protein de novo design. During the course of their work, the Richadsons designed and made synthetic proteins. These synthetic proteins reveal a great deal about how natural proteins function. In the 1990s, the Richardsons pioneered molecular graphics for personal computers by developing the kinemage system of molecular graphics and the Mage program to display them on small computers, and they developed all-atom contact analysis to measure goodness of fit inside proteins and in interactions with surrounding molecules. In the 2010s, the Richardson lab studied structural motifs in RNA and proteins as part of the RNA Ontology Consortium. The Richardson's lab also collaborated in development of the Phenix software suite for X-ray crystallography and hosted the MolProbity, a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality for proteins and nucleic acids. As of 2019, Jane is a James B. Duke professor and David a professor in Duke's Department of Biochemistry.

Jane Richardson is widely recognized for her creation of ribbon drawings to schematize protein three-dimensional structures, first published in "Advances in Protein Chemistry" in 1981. The drawings stemmed from Jane's realization that a general classification scheme could be developed from the recurring patterns of structural motifs within the "folds" of proteins. She created ribbon drawings of those folds, making a uniform set of conventions for drawing the seventy-five protein structures that had been solved at that time. The drawings have been used widely in computer adaptations, and her 1981 paper continues to be cited. Jane was awarded three honorary doctorates from Swarthmore College, the University of North Carolina at Chapel Hill, and the University of Richmond. In 1985, Jane Richardson was awarded a MacArthur Fellowship for her work in structural biology. She was elected to the National Academy of Sciences and the American Academy of Arts and Sciences in 1991, then the Institute of Medicine in 2006. In 2010, Jane was elected president of the Biophysical Society. She also is the co-recipient of the Protein Society's Amgen Award with David (1995) and the Biophysical Society's Emily M. Gray Award (2001). From 2012 to 2013 Jane Richardson was the president of the Biophysical Society, and in this capacity she began WikiProject on Biophysics to encourage society members and others to edit and improve biophysics-related Wikipedia articles. She was a fellow of the American Crystallographic Association in 2012. In 2019 Jane received the Alexander Hollaender Award in Biophysics.

David Richardson is the founding director of the Structural Biology and Biophysics Graduate Training Program at Duke University. He received numerous honors including Science Digest's 100 Best Innovations of 1985, a BioTechnology Winter Symposium Special Achievement Award (1995), and the Duke University Gordon Hammes Teaching and Mentoring Award (2009). In 2012, David was honored as the distinguished speaker of the North Carolina section of the American Chemical Society.

Subject Headings

Preferred Citation

[Identification of item], Jane and David Richardson Papers, Duke University Medical Center Archives.

Acquisitions Information

Accession A2018.024 (gift by Jane and David Richardson, May 2018), Accession A2018.027 (gift by Jane and David Richardson, May 2018)

Processing Information

Processed by Caroline Waller under the supervision of Lucy Waldrop: May 2019