Nerdy Jobs: Protein Crystallization

Watch

1. Nerdy Jobs S1E1, Exploring the Magic of Protein Crystallizationyoutu.be/siFfzoFv61I

Word of the day

Crystallography (kris-tuh-LOG-ruh-fee). The science of how crystals form and of their forms and internal structure.

• Photography means “drawing with light.”
• Cryo-, “icy cold,” comes from a Greek word related to krýstallos. Cryo-electron microscopy images proteins frozen in a thin layer of ice.

Bonus words. Protein (PROH-teen) comes from the Greek prōteîos, “primary.” Diffraction (dih-FRAK-shun) comes from the Latin diffringere, “to break into pieces.” The proteins in a crystal diffract an X-ray beam into a pattern of spots.

Predict

1. Hauptman-Woodward’s screening lab tests each protein sample against 1,536 crystallization cocktails. From 2000 to 2010, the lab tracked the samples it screened for structural genomics groups, large projects that set out to solve structures for many proteins. Make a guess before you read the paper. What percent of those samples led to a structure deposited in the Protein Data Bank (PDB)? Give your reasoning in one sentence.

   Hint. List the steps between a purified protein and a solved structure. Each step can fail.

Read the paper

Luft, Snell and DeTitta, “Lessons from high-throughput protein crystallization screening: 10 years of practical experience,” Expert Opinion on Drug Discovery, 2011. The paper is free to read.

Joseph Luft, Edward Snell and George DeTitta ran HWI’s high-throughput screening lab, the center Dr. Bowman directs today. Each sample gets 1,536 cocktails in drops of 200 nanoliters of protein plus 200 nanoliters of cocktail under oil, photographed at day 1 and at weeks 1, 2, 3, 4 and 6. Table 1 of the paper counts the samples the lab received each year. For the structural genomics samples, Table 1 also counts the structures later deposited in the PDB. The authors note that structures reach the PDB some time after a sample passes through the lab.

1. Table 1 gives the structural genomics samples and the structures they led to for each year from 2000 to 2010. The yearly rows add up to more than the paper’s printed Total row. For the total percent, use the printed Total row, 3,876 samples and 485 structures. What percent of structural genomics samples led to a structure in each year, and in total? Which year had the highest percent?

   Hint. Fill in the last column of the table first. Divide structures by structural genomics samples.

2. The authors note that structures reach the PDB some time after a sample passes through the lab, and they wrote the paper in 2011. Why might the percent for 2010 run lower than the percent those 2010 samples would reach in later years?

   Hint. List what still has to happen after a crystal hit before a structure reaches the PDB.

3. The paper reports that 269 of 823 structural genomics targets, or 32.7%, grew crystals somewhere in the screen. For those 269 targets, an average of 3.58% of the 1,536 conditions showed a crystal hit, about 55 conditions per sample. If a protein hits in only about 55 of 1,536 conditions, why does the lab test all 1,536 instead of a smaller set?

   Hint. Would the same 55 conditions work for a different protein? And what do the clear and precipitated drops tell scientists?

4. In Table 1, about one structural genomics sample in eight became a structure. In the episode, Dr. Bowman explains how structures of hemoglobin and of the main protease of SARS-CoV-2 help scientists. Given how often the path from sample to structure fails, why do scientists keep using crystallography to learn how proteins work?

   Hint. Think about what structures showed for hemoglobin’s two shapes and for drugs that block the main protease.

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