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Lecture notes of 5 pages for the course Techniques For Biological And Chemical Sciences at QMUL
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NOE and protein structuresLearning objectives:
1. Recall that the magnitude of the NOE will relate directly to how close 2 H are in space
2. Apply 2D NOESY spectra to ;;;walk’’ from one aa spin system to the next
3. Distinguish types of secondary structure from patterns of NOE cross peaks
4. Illustrate the network of noes used to determine a structure
5. Describe computer algorithms used to determine and refine solution structures
6. Compare and contrast NMR solution structures with crystal structure
NOE the fundamentals
Fundamentals:
- Unlike J-coupling, which requires the prescence of a network of covalent bonds to link nuclei (through-bonds)
- The NOE works through-space
- The closer together the 2 nuclei the greater the overhauser effect
- The NOE rapidly decreases as the nuclei becomes further apart.
- Decreasing with the sixth power Of the distance
- NOE ~ 1/r6
- NOE is the main way by which structural data is obtained for molecules.
- The magnitude of the NOE tells us the distance between 2 protons
Principle of NOE
The proximity of a proton in space enables the proton to relax, this additional relaxation mechanism is known as cross-
relaxation and gives rise to the NOE phenomena
Scaling the NOE
In a NOESY spectra the closer the 2 protons are of each other, the bigger the cross peaks
The size of the cross peak is a direct measure of distance.
The distance can be scaled for all NOEs seen using standard proton-proton distances and the 1/r6 relationship.
From the volume of the cross peak a distance apart can be assigned (+/-Angstrom)
More commonly, the volume of the NOE cross peak is described as strong, medium or weak and associated distances
boundaries given. For example,
Strong NOE – less than 2.5 angstrom apart
Medium NOE - less than 3.5 angstrom apart
Weak NOE – less than 5.0 Angstrom apart
Note that it is unusual to see an NOE for 2 protons more than 5Angstrome apart.
Further apart than this and the effect is too weak to be observed
109 degrees, tetrahedral
Benzene ring; 120 degree bong angle
Use NOE as a scaling factor?
MCQ Exam Q
Q. NOE occurs between?
A. pairs of H less than 5 A apart
Spin system assignments to positions in sequence
, 2D NOESY and sequential assignments from the ‘’NOE walk’’
- The COSY and TOCSY link protons that are connected via covalent bonds, while NOESY (and ROESY) 2D spectra link
protons that are close in space
- The COSY and TOCSY link protons in each aa indicated by blue circle but can not link one aa to the next
- NOE can aid assigning indicidual aa
- No coupling between the aa as there are too many covalent bonds apart therefore link with NOE
1H NMR Assignment of protein resonance’s
Peaks in the side chain of amino acids give a characterittics spin system pattern
Use spin system pattern to work out what aa
But do not know what position he aa are in
AA spin system patterns
2D COSY spectrum
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