NMR

Question 1

What part of proteins do we “see” with NMR?

Answer 1

Nuclei

Question 2

Which nuclei have the spin that is able to be seen with NMR?

Answer 2

H1, C13, N15, F19, P31

Question 3

What do the nuclei with the spin do in a magnetic field?

Answer 3

Behave like a magnetic dipole and align either with it or against it. The spin is detected in an absorption spectrum

Question 4

How does the local environment in a protein affect the absorption of a nearby hydrogen?

Answer 4

Local environment will shield hydrogens differently, and we can piece together the molecule

Question 5

Why do we use 2D NMR for proteins?

Answer 5

Way too many hydrogens in a protein, and way too many peaks on a 1D NMR to possibly interpret

Question 6

What are the 3 types of 2D NMR?

Answer 6

NOESY, TOCSY, HSQC

Question 7

What information do we get with a NOESY 2D NMR?

Answer 7

Distances between atoms in space

Question 8

What information do we get with a TOCSY 2D NMR?

Answer 8

The signal of H atoms connected by a system of covalent bonds

Question 9

What information do we get with a HSQC 2D NMR?

Answer 9

Connectivity between heteronuclei (H and N or C)

Question 10

What do we do with the NMR data once we’ve collected it?

Answer 10

Combine it with the ideal geometry that we know. We input bond angles and other structure constraints then compute all models that fit the constraints

Question 11

What do we get for a final structure in NMR?

Answer 11

An ensemble of structures, which is every possible structure that fits the constraints

Question 12

What are the pros of NMR?

Answer 12

Shows dynamic structures, no crystal

Question 13

What are the cons of NMR?

Answer 13

Has an upper size limit and the proteins need to be isotopically enriched ($$$)

Question 14

Why does NMR have an upper size limit?

Answer 14

The spectra starts to get really crowded and hard to interpret after about 30 kDa