A3.4

Question 1 Single best answer Level 1 1 point

Two simulation frames give two sets of coordinates for one protein. What does superposing them do before they are compared, and why?

  1. It translates and rotates one onto the other, so whole-molecule motion is not counted as a difference
  2. It lines up the two sequences residue by residue, so a shift in numbering is not counted as a difference
  3. It keeps only the atoms chosen for comparison, so side-chain motion is not counted as a difference
  4. It averages the two into one structure, so frame-to-frame noise is not counted as a difference

Question 2 Single best answer Level 1 1 point

An RMSD is reported between a simulation frame and the crystal structure. What does that value tell you about the two structures?

  1. How much the two differ overall, as one length that grows as they differ more
  2. Where the two differ most, as one value taken at the region that moved farthest
  3. To what extent the frame has drifted from its start, as one rate taken along the run
  4. What kind of change separates them, as one value that tells a hinge bend from unfolding

Question 3 Single best answer Level 2 1 point

Two structures lie the same RMSD from one reference. In one, a few residues moved far; in the other, every residue moved slightly. How can such different changes give the same RMSD?

  1. It averages each atom’s motion over time into one fluctuation, and both structures fluctuate by the same amount
  2. It turns the atoms’ moves into one energy cost, and both changes cost the protein the same energy
  3. It condenses the atoms’ displacements into one length, and both changes have the same overall size
  4. It averages the atoms’ positions into one center, and both changes moved that center by the same distance

Question 4 Single best answer Level 4 1 point

A report claims that a protein’s overall fold changed during a simulation. Which RMSD plot, taken against the starting structure, would support the claim, and why?

  1. An all-atom RMSD that jumps partway through the run and then levels off higher, since all atoms track the global fold more fully
  2. An alpha-carbon RMSD that rises in the first few nanoseconds and then levels off, since alpha carbons track the global fold
  3. An alpha-carbon RMSD that jumps partway through the run and then levels off higher, since alpha carbons track the global fold
  4. An all-atom RMSD that rises in the first few nanoseconds and then levels off, since all atoms track the global fold more fully

Question 5 Single best answer Level 3 1 point

In a simulation of one protein, the alpha-carbon RMSD stays low and steady throughout. Partway through, the backbone heavy-atom RMSD for the same frames steps up to a higher plateau. What does this comparison show about the protein?

  1. The fold held, and the backbone step is noise, since a broader selection adds noise to an RMSD
  2. The fold changed, and a domain rotated partway through, since a sudden rise in the backbone RMSD marks a structural transition
  3. The fold changed, but the alpha-carbon value missed it, since the same frames should give one RMSD
  4. The fold held, but a backbone segment changed, since the rise lies in atoms beyond the alpha carbons

Question 6 Single best answer Level 3 1 point

In two superposed structures, most atoms barely moved, but a handful moved far. The RMSD is recomputed leaving out either that handful or an equal number of barely moved atoms. Which choice changes the value more, and why?

  1. Leaving out the barely moved handful, because the structures are superposed again first, which fits away the far-moved handful’s displacement
  2. Leaving out the far-moved handful, because the value is the largest single move in the selection, which their removal lowers
  3. Leaving out the barely moved handful, because the structures are superposed on the barely moved atoms, and losing some raises the other squared terms
  4. Leaving out the far-moved handful, because each one’s squared displacement adds far more to the sum

Question 7 Single best answer Level 2 1 point

Throughout a simulation, one residue stays far from its position in the reference structure but is nearly motionless. Is that residue’s RMSF large or small, and why?

  1. Small, because RMSF measures how far the residue moves from one frame to the next
  2. Small, because RMSF measures the residue’s spread about its own average over the frames
  3. Large, because RMSF measures how far the residue has moved from where the run started
  4. Large, because RMSF averages the residue’s distance from the reference structure over all the frames

Question 8 Single best answer Level 3 1 point

HIV-1 protease’s flaps rank high, and helices and strands low, in both RMSF and B-factor. One loop, the only region touching a neighboring molecule in the crystal, ranks high in RMSF but low in B-factor. Which regions move most, and why do its rankings disagree?

  1. The flaps and the loop; its crystal contact leaves the loop poorly fixed by the data, which lowers its B-factor
  2. The flaps and the loop; its crystal contact holds the loop still there, which lowers its B-factor
  3. Only the flaps; packing in the crystal makes the loop rigid, so its RMSF peak is a simulation artifact
  4. The flaps and the loop; the loop takes a different shape in different unit cells, which lowers its B-factor

Question 9 Single best answer Level 2 1 point

The potential energy along one coordinate has a narrow and a wide well of equal depth. On a free-energy surface built from frame counts along that coordinate, which well is the favored state, and why?

  1. Neither well, because the narrow well’s fewer bins each hold more frames, which makes up for the wide well’s extra bins
  2. The wide well, because the molecule spends more of the run within its range
  3. The wider well, because its greater width gives it the lower enthalpy of the two
  4. Neither, because a surface built from counts holds relative free energies, which leave the two wells unranked

Question 10 Single best answer Level 3 1 point

From one trajectory of a protein, a free-energy surface along RMSD from the starting structure shows a single basin. What does that single basin show about the protein’s states?

  1. It allows several states, since a domain rotation and a partial unfolding can give the same RMSD
  2. It shows one state, since a single basin means the frames share one structure
  3. It allows several states, since superposing each frame removes the motion of one part against another
  4. It shows one state, since RMSD takes in the protein’s atoms and so can capture its whole structure

Question 11 Single best answer Level 4 1 point

From one trajectory of a two-domain protein, a free-energy surface along a hydrogen-bond distance inside one domain shows a short-distance and a long-distance basin. A surface along the interdomain distance shows a domains-close and a domains-apart basin. Which conclusion about the protein’s states do the two surfaces support together?

  1. Two or four states; a longer run would show whether the basins pair one to one or in every combination
  2. At least two states; matching one surface’s basins to the other’s needs a surface over both distances
  3. Exactly two states, pairing the short-distance basin with the domains-close basin as one set of frames
  4. Exactly two states, since each surface from one trajectory shows two basins, so they agree

Question 12 Single best answer Level 3 1 point

Bin P of a free-energy surface holds ten times as many frames as bin Q. Which bin lies lower, and how does the free-energy difference between them change if that ratio is multiplied by ten again, or instead inverted?

  1. Q lies lower; another factor of ten multiplies the difference by ten, and inverting puts P lower by the same amount
  2. P lies lower; another factor of ten doubles the difference, and inverting puts Q lower by the same amount
  3. Q lies lower; another factor of ten doubles the difference, and inverting puts P lower by the same amount
  4. P lies lower; another factor of ten multiplies the difference by ten, and inverting puts Q lower by the same amount
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