structure calculations using nmr...
TRANSCRIPT
![Page 1: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/1.jpg)
Structure Calculations Using NMR Data• Development began in the middle of the 1980s.
• Most of the early structures were of very small
proteins or peptides.
• You do not determine a single structure as in
crystallography, but rather an ensemble of
structures that satisfy a group of restraints.
• In general, the more experimental restraints
that are used, the better the precision of the
structures calculated.
• Advancements (new experiments, bigger
magnets, faster computers) have not only
increased the size of the molecule that can be
studied, but they have improved the quality of
the structures calculated
![Page 2: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/2.jpg)
Principles of NMR-based Structure Calculations
• The goal of all NMR structure calculation
protocols is to find the global minimum region
of a target function Etot.
Etot = Ecov + Evdw + ENMR
Ecov = covalent geometry terms for: bonds, angles
planarity and chirality.
Evdw = nonbonded contacts.
ENMR = experimental NMR restraints.
![Page 3: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/3.jpg)
Algorithms used in NMR structure calculations
• Simulated annealing (SA) in both cartesian and
torsion angle space.
• Metric matrix distance geometry (DG).
• Minimization with a variable target function in
torsion angle space.
![Page 4: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/4.jpg)
Ecov
• Depending on the algorithm used systematic
biasing may arise when calculating the
structure.
• Deviations from ideal geometry must be kept to
a minimum since the value of bond lengths,
angles, planes and chirality are known to very
high accuracy.
![Page 5: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/5.jpg)
Evdw
• This term is associated with more uncertainty.
• It may be represented as a simple van der Waalsrepulsion term.
• It may also be a complete energy function thatincludes an electrostatic and a hydrogenbonding potential.
• All structures must display good non-bondedcontacts.
• Uncertainties associated with Ecov and Evdw canintroduce errors in the range of 0.3 Å.
![Page 6: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/6.jpg)
Steps in NMR-based Structure Calculations
1) Data Input
2) Structure Determination Protocol
3) Acceptance Tests
4) Analysis of NMR structure.
![Page 7: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/7.jpg)
Types of NMR Experimental Restraints
1) Noe-derived distance restraints.
2) Torsion angle restraints.
3) Chemical shift restraints.
4) Hydrogen bond restraints.
5) Residual Dipolar Coupling Angular restraints.
![Page 8: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/8.jpg)
Outline of structure calculation protocol
![Page 9: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/9.jpg)
Nuclear Overhauser Effect (NOE)
![Page 10: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/10.jpg)
NOEs in solution structure determinations• NOEs provide the main source of geometric
information from the experimental data.
• NOEs are short in distance (~ 5Å) but they areconformationally very restrictive when they arefar apart in the primary sequence.
• At short mixing times, NOE signal isproportional to the inverse sixth power of thedistance between two protons.
• NOE intensities are converted to approximateinterproton distant restraints with lower andupper bounds.
Strong: 1.8 – 2.7 ÅMedium: 1.8 – 3.3 ÅWeak: 1.8 – 5.0 ÅVery Weak: 3.0 – 6.0 Å
![Page 11: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/11.jpg)
Types of Helices
3.10- φ= -74.0° and ϕ= --4.0°pi- φ= -57.1° and ϕ= -69.7°
![Page 12: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/12.jpg)
Short range NOEs in α-helix
![Page 13: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/13.jpg)
Anti-parallel β-sheet
![Page 14: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/14.jpg)
Parallel β-sheet
![Page 15: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/15.jpg)
Parallel vs. anti-parallel β-sheets
* Parallel sheets tend to be more regular if one examinesthe φ and ϕ angles.
* Anti-parallel sheets have H-bonds perpendicular to thestrands and alternate narrow and widely spaced pairs.
* Parallel sheets have equally spaced H-bonds that angleacross the strands.
![Page 16: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/16.jpg)
NOE patterns is β-sheet
![Page 17: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/17.jpg)
NOE patterns is β-sheet
![Page 18: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/18.jpg)
Overview of tight(β) turns* They have a succession of different φ and ϕ values for
each residue.
* They have a H-bond between the >C=0 of residue iand the >N-H of residue i+3.
* Backbone at either end of Type I or II turn is in theright position to continue an anti-parallel β-ribbon.
Type I : φ2= -60°, ϕ2= -30°, φ3= -90°, ϕ3= 0°
Type II: φ2= -60°, ϕ2= 120°, φ3= 90°, ϕ3= 0°
![Page 19: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/19.jpg)
Type I turn
![Page 20: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/20.jpg)
Type II turn
![Page 21: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/21.jpg)
Short range NOEs in β turns
![Page 22: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/22.jpg)
NOE patterns associated with 2°structure
![Page 23: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/23.jpg)
Examples of 3D NOESY Experiments
3D 15N-NOESY 3D 13C-NOESY
3D 15N/ 13C -NOESY
![Page 24: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/24.jpg)
Pictorial of NOEs in a structure
![Page 25: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/25.jpg)
Coupling constants and torsion angles
• It is possible to directly refine structures against
a HN-C!H three-bond coupling constants as
well as conformational data bases.
• There is a very good experiment to accurately
measure 3JHN! (3DHNHA)
• Although Karplus curve is symmetric about " =
-120°, other experimental data allows us to
resolve the ambiguity.
![Page 26: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/26.jpg)
Correlation between 3Jhnα and 2°Structure
Pardi et al, J. Mol. Biol 180, 741-751 1984
![Page 27: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/27.jpg)
3D- HNHA experiment for 3Jhnα
![Page 28: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/28.jpg)
TALOS* Database system for empirical prediction of phi and psi
backbone angles.
* Uses a combinations of five kinds (HA, CA, CB, CO ,N) of chemical shifts.
* Like CSI relies on fact that many secondary chemicalshifts are highly correlated with aspects to proteinsecondary structure.
* It uses triplets of amino acids to make predictions.
Reference: Cornilescu, Delaglio and Bax, J. Biomol. NMR 13, 289-302 (1999).
![Page 29: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/29.jpg)
Talos Random Coil Table
RES HA C CA CB N
A 4.32 177.8 52.3 19.0 123.8
C 4.55 174.6 56.9 28.9 118.8
C 4.71 174.6 55.4 43.7 118.6
D 4.64 176.3 54.0 40.8 120.4
E 4.35 176.6 56.4 29.7 120.2
F 4.62 175.8 58.0 39.0 120.3
G 3.96 174.9 45.1 9999. 108.8
H 4.73 173.3 54.5 27.9 118.2
I 4.17 176.4 61.3 38.0 119.9
K 4.32 176.6 56.5 32.5 120.4
L 4.34 177.6 55.1 42.3 121.8
M 4.48 176.3 55.3 32.6 119.6
N 4.74 175.2 52.8 37.9 118.7
P 4.42 177.3 63.1 31.7 135.8
Q 4.34 176.0 56.1 28.4 119.8
R 4.34 176.3 56.1 30.3 120.5
S 4.47 174.6 58.2 63.2 115.7
T 4.35 174.7 62.1 69.2 113.6
V 4.12 176.3 62.3 32.1 119.2
W 4.66 176.1 57.7 30.3 121.3
Y 4.55 175.9 58.1 38.8 120.3
![Page 30: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/30.jpg)
The TALOS triplet system
TALOS searches database for the ten best matches to agiven triplet in the target protein (Data base uses 20proteins representing 3,000 triplets).
![Page 31: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/31.jpg)
Reliability of TALOS
* makes no prediction on 20-45% of the residues in proteins.
* makes predictions for about 65% of the residues onaverage.
* in 5 of 20 proteins studied the results included no badpredictions.
* about 3% of the predictions were bad!!!
* the uncertainty for good predictions was 14 degrees for phiand 13 degrees for psi.
Web Site: http://spin.niddk.nih.gov/bax/software/TALOS/info.html
![Page 32: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/32.jpg)
Example of TALOS output
![Page 33: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/33.jpg)
Chemical shifts and 2°structure
* One can often quickly determine the 1H, 15N and 13Cchemical shifts with triple resonance experiments.
* There is a correlation between chemical shift deviations andsecondary structure elements.
* These deviations are from random coil values
* Most important ones are CO, HA and CA.
For a good recent reference on measuring chemical shift of amino acids in randomcoils see: Schwarzinger et al, J. Am. Chem. Soc 121, 2970-2978 (2001)
![Page 34: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/34.jpg)
Pattern between 2°Structure and 13C Shifts
Reference: Spera and Bax, J. Am. Chem. Soc. 113, 5490-5492 (1991)
Deviations from random coil values
![Page 35: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/35.jpg)
Chemical shift index (CSI)
* Fast, simple and reliable method to assign secondarystructure.
* It is based on a statistical analysis of chemical shifts inproteins of known structure.
* CSI=0: δ in range of random coil values* CSI= +1 or -1: δ is greater or less than random coil
chemical shift values.* Must consider at least four residues to define an element
of secondary structure.
Reference: Wishart and Yip, Biochem. and Cell Biol. 76, 153-176 (1998)
![Page 36: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/36.jpg)
CSI RANDOM COIL VALUES
RES HA C CA CB N HN
A 4.32 177.8 52.5 19.1 123.8
C 4.55 174.6 58.2 28.0 118.8
C 4.71 174.6 55.4 41.1 118.6
D 4.64 176.3 54.2 41.1 120.4
E 4.35 176.6 56.6 29.9 120.2
F 4.62 175.8 57.7 39.6 120.3
G 3.96 174.9 45.1 9999. 108.8
H 4.73 174.1 55.0 29.0 118.2
I 4.17 176.4 61.1 38.8 119.9
K 4.32 176.6 56.3 33.1 120.4
L 4.34 177.6 55.1 42.4 121.8
M 4.48 176.3 55.4 32.9 119.6
N 4.74 175.2 53.1 38.9 118.7
P 4.42 177.3 63.3 32.1 135.8
Q 4.34 176.0 55.7 29.4 119.8
R 4.34 176.3 56.0 30.9 120.5
S 4.47 174.6 58.3 63.8 115.7
T 4.35 174.7 61.8 69.8 113.6
V 4.12 176.3 62.2 32.9 119.2
W 4.66 176.1 57.5 29.6 121.3
Y 4.55 175.9 57.9 37.8 120.3
![Page 37: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/37.jpg)
CSI Scoring and 2°Structure
!-helix "-sheet
CSI (CO) +1 -1
CSI (C!) +1 -1
CSI (H!) -1 +1
CSI (C") n.a. +1
![Page 38: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/38.jpg)
Example of CSI analysisCα
CO
Residue # 10 20 30 40 50 60 70 80
![Page 39: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/39.jpg)
Secondary structure: α1 α 2 α3 β1 β2
Hα
Cons
ensu
s
Residue # 10 20 30 40 50 60 70 80
![Page 40: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/40.jpg)
• Currently, there is no experiment to directly
measure hydrogen bonds present in proteins.
• Hydrogen bonds can be modeled base on known
secondary structure elements and by measuring
slowly exchanging amide protons in deuterium
oxide.
Hydrogen bond restraints
• Direct measurement of hydrogen bonds inproteins is rare but new sequence are beingdeveloped that should be more common in thenext couple of years.
![Page 41: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/41.jpg)
Detection of slowly exchanging amide protons
![Page 42: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/42.jpg)
Hydrogen bonds is β-sheet
![Page 43: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/43.jpg)
Residual dipolar couplings
• Provide long range angular constraints
• They are not redundant with NOE constraints
• They can be used to validate structures.
• They can help provide relative orientations of
subunits within a complex.
![Page 44: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/44.jpg)
Pictorial view of RDCs � �
Prestegard, Nat. Struct. Biol. 5, 517, 1998
![Page 45: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/45.jpg)
Weak alignment media (bicelle)
DHPC/DMPC
Prestegard, Nat. Struct. Biol. 5, 517, 1998.
![Page 46: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/46.jpg)
Weak alignment media (bicelle)
DHPC/DMPCBax, Prot. Sci. 12, 1, 2003.
Isotropic 4.5% w/v 85 w/v
![Page 47: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/47.jpg)
Tunable alignment media (Phage)
Hansen et al., Nature Struct. Biol. 5, 1065, 1998.
![Page 48: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/48.jpg)
Tunable alignment media (Phage)
de Alba et al., Prog. Nucl. Mag. Res. Spec. 40, 175, 2002.
![Page 49: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/49.jpg)
Tunable alignment media (Phage)
Hansen et al., Nature Struct. Biol. 5, 1065, 1998.
-Phage + Phage
![Page 50: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/50.jpg)
Determining alignment tensor
Bax, Prot. Sci. 12, 1, 2003
![Page 51: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/51.jpg)
Measurement in multiple alignment media
Bax, Prot. Sci. 12, 1, 2003.
![Page 52: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/52.jpg)
RDCs and structure validation
Bax, Prot. Sci. 12, 1, 2003.
![Page 53: Structure Calculations Using NMR Dataesilrch1.esi.umontreal.ca/~syguschj/cours/BCM6200/bcm6200_NMR... · Structure Calculations Using NMR Data ... Coupling constants and torsion angles](https://reader031.vdocuments.site/reader031/viewer/2022030404/5a7a02f77f8b9a4b198c5512/html5/thumbnails/53.jpg)
An ensemble of structures