Twenty Years of Molecules

Celebrating the structural biology revolution

RNA polymerase (blue) stalled while unwinding a nucleosome (orange, with DNA in red). Several elongation factors are in green, and a little piece of the transcribed RNA is seen poking out in magenta.
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Every month, I feel lucky to be a scientist (and a scientific artist) at this point in history. Structural biology is in the middle of a revolution that is revealing the atom-level workings of living cells. It all started with the structure of myoglobin, and today, you can find structures for everything from actin to zika. I’m happy to report that as of this month, I’ve been exploring the PDB archive for 20 years and sharing some of what I find in these Molecule of the Month columns. Here are a few thoughts as I look back over my 20 years of molecules.

The Structural Biology Revolution

Structural biology has come a long way since the pioneering work of Kendrew, Perutz, Watson and Crick. Methods are more efficient and successful in a wider variety of systems, so scientists are increasingly empowered to explore all aspects of cellular life. The structural genomics effort streamlined crystallographic structure determination, and methods like XFEL are opening new doors on the time dimension. NMR spectroscopy provides orthogonal views of biological systems and their dynamics that are inaccessible to other techniques. CryoEM microscopy is revealing the structures of enormous assemblies that were completely intractable before, and is promising to be the go-to technique for the next decade of structural biology.

Molecular Stories

Every structure has a story to tell, giving us a new look at the inner workings of life. Some structures add a new piece to a growing puzzle, for example, filling out the entire glycolytic pathway. Other structures are a story all unto themselves. The one shown here captures a moment when RNA polymerase is transcribing RNA, and stalls when it hits a nucleosome (PDB entry 6j4y). Several elongation factors help the polymerase unwind the DNA from the nucleosome, so that it can continue. The structure shows the complex when the nucleosome is about half way unwound.

Faustovirus (left) and a tyrosine from crambin (right) showing electron density.
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Biggest and Best

When I started writing these columns, there were already 13500 entries in the PDB archive, and now, 20 years later, there are more than ten times as many. One thing you might want to do is to find the biggest and best structures in the archive. Of course, this is a tricky endeavor, because you need to find a metric to evaluate what you mean by “best.” For example, you could look to the Nobel Prize to identify subjects with high impact in the scientific community. Here, I’ve chosen two easily quantified metrics: the highest crystallographic resolution, currently for a structure of crambin (3nir), and the assembly with the largest number of chains, currently faustovirus (5j7v) with 8280 chains. To look at some other interesting features of the entire body of PDB holdings, take a look at the PDB Statistics page.

Two views of phage repressor 434 bound to its DNA operator.
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Picturing Molecules

For me, the fun really begins when I start drawing pictures of molecules. There are so many choices to make: picking a representation that highlights the features I want to show, finding the perfect view, and choosing colors that are both appealing and informative. Fortunately, there are many effective programs for molecular visualization, so I can focus my effort on getting a nice image. For this picture, I created two views of a classic DNA-protein complex showing my favorite approaches. On the left, I used NGL to get a quick, easy look at the molecule, to figure out what's where in the structure. You can do similar visualization by going to the summary page for PDB entry 2or1 and choosing "3D View: Structure." Notice that the cartoon representation nicely shows off the characteristic alpha helices that pack into the grooves of the DNA. Then I moved to my illustration program to create an picture that shows all the atoms, highlighting how the protein hugs the surface of the DNA.

Antibody Fab fragments (blue) bound to an ebola glycoprotein (orange and red).
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Global Health

Arguably the major impetus for structural biology is to discover new ways to improve our health. Biomolecular structures provide a unique resource for understanding the atomic basis of our bodies and to make targeted interventions when things go wrong. Structure-aided design is the most direct approach, for example, using structures of HIV protease to discover new drugs to fight HIV infection or using structural insights to engineer new forms of insulin to treat diabetes. Researchers are also harnessing biomolecular processes to do their bidding, for example, engineering CRISPR molecules to do specific gene-editing tasks in diseased cells. Vaccines are also one of the miracles of modern medicine, and have essentially removed the danger of polio and smallpox from the world. Researchers are now using structures of antibodies with their viral targets to attempt to extend these successes to more challenging targets such as HIV and ebola (shown here from PDB entry 6mam).

A nanoscale box made by DNA origami.
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Harnessing Biology

Biomolecules are working nanomachines, so of course researchers are interested in building their own. Many clever approaches have been successful. Some use directed evolution to tune the function of existing enzymes, creating a desired function. Others have taken a cut-and-paste approach, for example, connecting together existing proteins to build self-assembling nanocontainers. In DNA origami, bioengineers use the exquisite specificity of DNA base-pairing to build nanostructures with custom shapes, such as the little box shown here that includes single-stranded regions for use as functional tethers (PDB entry 6by7).

A kinetochore ring (yellow and red) surrounding a kinesin-microtubule complex (green and blue), and PCNA (turquoise) surrounding DNA (red, at center).
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Functional Symmetry

Biomolecules have a unique beauty that is all their own, and in the case of symmetrical biomolecules, it is beauty with a purpose. Ever since graduate school, I’ve had a fascination with biological symmetry (due, I’m certain, to my training as a crystallographer). Biomolecules provide many interesting examples of functions that rely on symmetry to build up functional assemblies from many individual modular subunits. For example, virus capsids are built with perfect symmetry, or with approximate quasisymmetries if even larger containers are needed. I have included two examples here where a ring-shaped molecules is built using cyclic symmetry, with the function of surrounding a fibrous biomolecule with helical symmetry. These include a kinetochore (6cfz) surrounding microtubule/kinesin (3j2u), and the processivity factor PCNA (1plq) surrounding DNA.

Exploring the Structure

Evolution in Action

Theodosius Dobzhansky famously said that "Nothing in biology makes sense except in the light of evolution,” and the PDB archive has many examples where you can see that connection first hand. Some evolution happens over millenia--for example, by comparing the sequences of proteins such as globins, we can discover the detailed pedigrees of related organisms. In bacterial drug resistance, we can see evolution that happens in years, as bacteria evolve new methods for evading drugs through mutation and selection of their existing biomachinery.

The structures shown here reveal evolution happening in a matter of days. Researchers subjected a culture of HIV-infected cells to an HIV protease inhibitor, and watched as increasingly resistant versions evolved through mutation and selection. The wild type enzyme at the top (PDB entry 2az8) is strongly blocked by the inhibitor. By switching a leucine to a smaller alanine, the center enzyme (PDB entry 2az9) removes a favorable interaction and is 4-fold resistant to the inhibitor. The one at the bottom (PDB entry 2azc) further tunes the activity of the enzyme with five more sites of mutation and is 30-fold resistant. To explore these structures in more detail, click on the image for an interactive JSMol.

Topics for Further Discussion

  1. What is your favorite molecule?
  2. If you're interested in reading about my goals and methods for these Molecule of the Month columns, take a look at this article in the RCSB newsletter.

References

  1. 6j4y: Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. (2019) Structural insight into nucleosome transcription by RNA polymerase II with elongation factors. Science 363: 744-747
  2. 6mam: West, B.R., Wec, A.Z., Moyer, C.L., Fusco, M.L., Ilinykh, P.A., Huang, K., Wirchnianski, A.S., James, R.M., Herbert, A.S., Hui, S., Goodwin, E., Howell, K.A., Kailasan, S., Aman, M.J., Walker, L.M., Dye, J.M., Bukreyev, A., Chandran, K., Saphire, E.O. (2019) Structural basis of broad ebolavirus neutralization by a human survivor antibody. Nat. Struct. Mol. Biol. 26: 204-212
  3. 6by7: Dong, Y., Chen, S., Zhang, S., Sodroski, J., Yang, Z., Liu, D., Mao, Y. (2018) Folding DNA into a Lipid-Conjugated Nanobarrel for Controlled Reconstitution of Membrane Proteins. Angew. Chem. Int. Ed. Engl. 57: 2072-2076
  4. 6cfz: Jenni, S., Harrison, S.C. (2018) Structure of the DASH/Dam1 complex shows its role at the yeast kinetochore-microtubule interface. Science 360: 552-558
  5. 5j7v: Klose, T., Reteno, D.G., Benamar, S., Hollerbach, A., Colson, P., La Scola, B., Rossmann, M.G. (2016) Structure of faustovirus, a large dsDNA virus. Proc.Natl.Acad.Sci.USA 113: 6206-6211
  6. 3j2u: Asenjo, A.B., Chatterjee, C., Tan, D., Depaoli, V., Rice, W.J., Diaz-Avalos, R., Silvestry, M., Sosa, H. (2013) Structural model for tubulin recognition and deformation by Kinesin-13 microtubule depolymerases. Cell Rep 3: 759-768
  7. 3nir: Schmidt, A., Teeter, M., Weckert, E., Lamzin, V.S. (2011) Crystal structure of small protein crambin at 0.48 A resolution. Acta Crystallogr.,Sect.F 67: 424-429
  8. 2az8, 2az9, 2acz: Heaslet, H., Kutilek, V., Morris, G.M., Lin, Y.-C., Elder, J.H., Torbett, B.E., Stout, C.D. (2006) Structural Insights into the Mechanisms of Drug Resistance in HIV-1 Protease NL4-3. J.Mol.Biol. 356: 967-981
  9. 1plq: Krishna, T.S., Kong, X.P., Gary, S., Burgers, P.M., Kuriyan, J. (1994) Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA. Cell 79: 1233-1243

January 2020, David Goodsell

doi:10.2210/rcsb_pdb/mom_2020_1
About Molecule of the Month
The RCSB PDB Molecule of the Month by David S. Goodsell (The Scripps Research Institute and the RCSB PDB) presents short accounts on selected molecules from the Protein Data Bank. Each installment includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details. More