Next time you see a pretty protein structural model displayed in “ribbon diagram” representation, thank Jane Richardson! She invented the ribbon representation for protein structures. You know what I’m talking about even if you have no clue what I’m talking about – it’s the way of drawing protein structures where helices are shown as ribbons and strands as flat bands with arrows. She also co-developed the highly popular and influential “MolProbity” software, which structure-solvers to help validate whether they likely got atomic positions correct in the models they’ve generated from data collected with techniques like X-ray crystallography, cryo-EM, or NMR.
note: this post is a sort of follow-up to yesterday’s post so parts might make more sense if you’ve viewed that: blog form (has figures too): https://bit.ly/crystalstructuremodels ; YouTube: https://youtu.be/YK3VkqD2o2s
And links for today’s post. blog form: http://bit.ly/jane-richardson (text adapted from May, video new) ; YouTube: https://youtu.be/IlXbYdfLwbU
As someone in the *very very!* last stages of a PhD program, one of the things I find most incredible about Jane Richardson is that she doesn’t have a PhD (although she has 3 honorary ones). She is almost purely self-taught. And she’s devoted to teaching others freely. I personally have had the privilege of learning from her in person twice at CSHL’s X-ray crystallography course. (And the second time I got over some of my fears and had conversations with her!) Her work and influence is ever-present but kinda taken for granted these days by many of us who grew up not knowing that there was a “before times” where ribbon diagrams didn’t exist. This ribbon representation didn’t just pop up out of nowhere. Instead, it was the brain-and-sweat-child of Jane Richardson.
Richardson is a true “Renaissance Woman;” born in New Jersey in 1941, her highly productive career has included work in the areas of astronomy, philosophy, biophysics, art, and computational biology (just to name a few). As a biophysicist and structural biologist, she worked with her husband, David Richardson, using X-ray crystallography to solve some of the first protein structures. By “solving structures” I mean they figured out the position of the various atoms making up the protein (proteins are folded-up strings of building blocks or “letters” called amino acids which are themselves composed of atoms).
Jane knew that these structures held key information about how the proteins worked, but the high concentration of atoms in the models made them hard for a specialist, let alone an outsider, to interpret. Therefore, she began drawing representations of these structures that highlighted just the major structural features, focusing on tracing the backbone of the protein but adding information highlighting how those backbones arranged themselves into specific motifs and showing depth. These so-called ribbon diagrams not only enabled those outside of the biophysical field to appreciate structural biology, but also allowed researchers to identify structures that were conserved between different proteins. This had major implications for understanding the function and evolution of these molecules.
She made her original diagrams by hand – it was fascinating to hear her discuss the care she took to get the details right, including wrapping mailing tubes in tape to see what helixes look like from different angles. This painstaking work has given her an unbeatable talent for moving seamlessly between 2D and 3D computer graphical representations, a talent she has graciously shared freely with the public (she uploads her work, open license, to WikiMedia Commons -search Dcrjsr) and she is proud to have convinced the RCSB PDB to make their “Molecule of the Month” graphics similarly accessible). As a Wikipedia editor myself, I was ecstatic to hear her encourage the class to contribute to the Wiki world!
Jane is still an active scientist in her lab at Duke University, where her many projects include developing software to aid in the solving of molecular structures. One such piece of software, MolProbity, uses knowledge of the biophysical properties of molecules to allow structural biologists to locate and fix problems in their models. This software is increasingly being incorporated into modeling programs and its visual representations of problems like bright pink lines where residues are too close and “clash” are joining her ribbon diagrams as a sort of universal visual language, though as she reminded us “There’s no such thing as photorealism for macromolecules – so we’re free to seek the best alternative representations.”
Lately, Richardson has been acting as a structural biology superhero, with her and her software playing a key part in the Coronavirus Structural Biology Task Force working to validate & correct any problems with the constant stream of SARS-CoV-2 structures. https://t.co/6Kas9tiz2i?amp=1
Duke University had a great exhibit of her work and they have a website for it where you can check out some pictures of some early structural models and drawings, etc. https://exhibits.library.duke.edu/exhibits/show/invisible/intro
And she (along with Dave and David Goodsell) wrote a really great piece called “Seeing the PDB” for the Journal of Biological Chemistry: https://www.jbc.org/article/S0021-9258(21)00532-9/fulltext
That article was part of a themed issue celebrating 50 years of the Protein Data Bank (PDB) I talked about last week. http://bit.ly/thepdb The PDB is a freely-accessible source to look at, analyze, and download protein structures. The default setting? Visualizing in ribbon diagrams!
While some may debate over the benefits of science versus the humanities, Jane Richardson shows that the two are not mutually exclusive – in fact, they can be quite complementary. There are never enough compliments for Jane Richardson but I hope this post helps more people know to compliment her!
here’s a great article on Jane Richardson from the Biophysical Society (she served as their president for a term in 2012-2013): here’s a great article on Jane Richardson from the Biophysical Society (she served as their president for a term in 2012-2013): https://www.biophysics.org/blog/jane-richardson
And another great one from Duke: https://stories.duke.edu/sciences-mother-of-ribbon-diagrams-celebrates-50-years-at-duke
which is where I got that photo of Jane, taken by Jared Lazarus I think
more on X-ray crystallography: http://bit.ly/xraycrystallography2
note: that structure is hAgo2 with miRNA, 4f3t
more about the PDB & structures: https://bit.ly/pdbstructures ; video: https://youtu.be/NgXwP7gGPyA
more about PyMol: https://bit.ly/pymolintro & https://bit.ly/pymolmovies
hbonds
