An NOE is observed between a proton on residue 10 and a proton on residue 85. What type of structural information does this provide?
AResidues 10 and 85 are connected by a covalent bond
BResidues 10 and 85 are close in three-dimensional space (<5 Angstroms apart), even though they are far apart in the amino acid sequence — this long-range NOE constrains the protein's tertiary fold
CResidue 10 is exactly 85 Angstroms from the protein surface
DResidues 10-85 form a contiguous alpha helix
This is a long-range NOE — the most structurally informative type. It tells you that residues 10 and 85, which are 75 residues apart in the primary sequence, must be close in the folded protein's 3D structure. This constrains the global fold: it rules out all structures where these residues are far apart. A network of such long-range NOEs, combined with short-range NOEs (defining local secondary structure) and medium-range NOEs (defining helix/turn geometry), collectively determines the complete three-dimensional structure.
Question 2 True / False
NOE intensity is proportional to the inverse sixth power of the distance between two protons (1/r^6). This means NOEs can reliably measure distances up to 10 Angstroms.
TTrue
FFalse
Answer: False
The 1/r^6 dependence means that NOE intensity drops off extremely rapidly with distance. Doubling the distance reduces the intensity by a factor of 64 (2^6). In practice, NOEs are detectable only for proton pairs separated by less than about 5 Angstroms — signals from more distant pairs are too weak to distinguish from noise. This sharp distance cutoff is actually useful: it means that every observed NOE provides a reliable upper-bound distance restraint. NOEs are typically categorized into strong (<2.5 A), medium (2.5-3.5 A), and weak (3.5-5.0 A) distance bins rather than precise distance measurements, because quantitative NOE-to-distance conversion is complicated by spin diffusion, dynamics, and peak overlap.
Question 3 Short Answer
Why are long-range NOEs more important for defining the protein fold than short-range NOEs?
Think about your answer, then reveal below.
Model answer: Short-range NOEs (between residues i and i+1 to i+4) define local secondary structure — sequential backbone NOEs indicate helices, sheets, and turns. These constrain the backbone conformation locally but do not determine how secondary structure elements pack against each other in 3D space. Long-range NOEs (between residues more than 5 positions apart in sequence) constrain the relative positions of distant parts of the polypeptide chain — defining which helix packs against which sheet, which loops are close together, and how the overall fold is organized. A protein with only short-range NOEs would have defined secondary structure but unknown tertiary fold (like knowing the bricks but not the house plan). Long-range NOEs provide the blueprint for the three-dimensional architecture.
In practice, the completeness of long-range NOE assignments often determines the quality of the NMR structure. Automated NOE assignment algorithms (like CYANA's CANDID or ARIA) have greatly improved the completeness and accuracy of NOE networks, enabling routine NMR structure determination for proteins up to ~25 kDa.