Lecture 3.1

Protein structure

Thu Oct 8Slides

Learning objectives

After this lecture, you should be able to do the following.

Read a deposited macromolecular coordinate file and state what each record and column reports about the model it stores.

1. Given one atom record, name the chain identifier, residue number, element, occupancy, and B-factor columns, and state what each one reports.
2. Identify the parts of a deposited structure file that carry the experimental metadata, the sequence of the construct that was studied, and the per-atom coordinates.
3. Explain why chain identifiers rather than residue numbers are what distinguish two copies of an identical subunit stored in one file.
4. Explain why the set of chains stored in one coordinate file need not be the biological assembly, and name where the file states which assembly is intended.
5. Classify the records in a coordinate file as macromolecule, ligand, ion, or ordered solvent, and explain why a group other than the macromolecule can come from the crystallization solution rather than from the molecule’s biology.
6. Explain why residues listed in the construct sequence can be absent from the coordinate records, and what their absence reports about the experiment rather than about the molecule.

Account for how a deposited structure is a model fitted to experimental data, and determine what its reported resolution says about the evidence behind it.

7. Define the resolution reported for a diffraction structure, and state which direction of that number means more detail.
8. Explain why a single quality statistic reported for a whole structure does not certify that any one region of the model is correct.
9. Explain what detail becomes separable in the data as resolution improves, and name one feature that is placed by chemical expectation rather than observed at ordinary resolution.
10. Explain why one set of coordinates reports an average over many copies of the molecule and over the duration of the measurement.
11. Explain why a deposited structure is a model fitted to experimental data rather than an image of one molecule.
12. Given the reported resolutions of two structures of one molecule, determine which model rests on more evidence, and state one claim the other cannot support.

Account for how a structure file reports the uncertainty in each atom position, and distinguish regions the data leave poorly determined from regions that move in the molecule itself.

13. Define the B-factor and state what a large value reports about how well the data fix that atom.
14. Define occupancy and state what a value below one reports about the atom it is assigned to.
15. Explain how a region modeled as two alternate conformations at partial occupancy differs from the same region modeled as one, and what that difference reports about the molecule.
16. Explain why a region absent from the coordinates and a region present with very high B-factors can arise from the same underlying behavior of the molecule.
17. Given the B-factors of several atoms in one model, rank them by how well the data fix their positions.
18. Predict how the displacement \(u\) that a B-factor corresponds to changes when the B-factor rises several-fold, and explain why a B-factor is not itself the distance an atom wanders.
19. Given a downstream measurement made on a structure, determine whether a region of poorly determined coordinates affects it.
20. Given per-residue B-factors together with the structure resolution and which parts of the chain contact neighboring molecules, distinguish regions that are mobile in the molecule from regions the data simply determine badly.

Account for how the function of an obligate oligomer depends on quaternary structure, and predict what follows when its subunits do not assemble.

21. Define quaternary structure and state how it differs from tertiary structure for a protein built from more than one chain.
22. Explain how an active site can be formed at the interface between two chains, with each chain supplying part of the catalytic machinery.
23. Explain why an interface required for assembly offers a mode of inhibition distinct from blocking the assembled active site.
24. Compare an obligate oligomer with a protein that functions as a single chain, and name what a deposited entry records about which one you are looking at.
25. Explain why the sequence of one chain does not reveal that the functional unit is an oligomer, and name the evidence that does.
26. Explain what a two-fold symmetry axis in a homodimer implies about the chemical environments of equivalent residues in the two chains.
27. Predict what happens to the catalytic activity of an obligate oligomer when assembly of its subunits is prevented.
28. Given a residue number and chain identifier at a site formed between two subunits, determine the equivalent residue in the second chain.

Judge whether a deposited structure is fit for a stated purpose, given what was engineered into the construct, what was bound to it, and how it disagrees with other structures of the same molecule.

29. Compare what an unliganded and a liganded structure of one molecule each report about the shape the molecule takes in the other condition.
30. Explain why an entry described as the wild-type protein can carry substitutions introduced to make the experiment work, and name where the file records them.
31. Explain why trapping an enzyme with its uncleaved substrate can require disabling the enzyme first, and what that costs the resulting model.
32. Given a deposited entry and a claim about which ligand it contains, determine from the file itself whether the claim holds.
33. Given two structures of the same unliganded molecule whose mobile regions sit in different positions, differentiate the explanations for the disagreement and state which one a further experiment could rule out.
34. Given several structures of one molecule and a stated purpose, choose the entry best suited to that purpose from what each file reports about its construct, its bound contents, and its support, and identify what that choice commits you to.
35. Given a claim about how a molecule behaves and one structure offered in support, judge whether the structure supports the claim and state what further evidence would settle it.