chemical exchange and the mcconnell equations · 2013-04-10 · intramolecular exchange – motions...
TRANSCRIPT
![Page 1: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/1.jpg)
Chemical exchangeand the
McConnell Equations
- Chapter 5, on web site: http://www.chem.ubc.ca/faculty/straus/c518_09.html
A) Derivation of the McConnell equations from the Bloch equations
B) Lineshape Analysis
1) Slow exchange2) Fast exchange
C) Exchange from 2D NMR
![Page 2: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/2.jpg)
Intramolecular exchange– Motions of sidechains in proteins– Helix-coil transitions of nucleic acids– Unfolding of proteins– Conformational equilibria
![Page 3: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/3.jpg)
Intermolecular exchange– Binding of small molecules to macromolecules– Protonation/deprotonation equilibria– Isotope exchange processes– Enzyme catalyzed reactions
Source: http://mccammon.ucsd.edu/gallery/
![Page 4: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/4.jpg)
![Page 5: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/5.jpg)
A) Derivation of the McConnell equations from the Bloch eq.
![Page 6: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/6.jpg)
Here A1 and A2 are independent... so now let’s turn on exchange:
first order kinetics
![Page 7: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/7.jpg)
B) Lineshape Analysis
![Page 8: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/8.jpg)
Recall:
![Page 9: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/9.jpg)
In lab frame:
![Page 10: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/10.jpg)
If ignore relaxation...
The solution of which is
where
![Page 11: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/11.jpg)
and
![Page 12: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/12.jpg)
Two cases: 1) Slow exchange2) Fast exchange
![Page 13: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/13.jpg)
1) Slow exchange
![Page 14: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/14.jpg)
![Page 15: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/15.jpg)
![Page 16: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/16.jpg)
![Page 17: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/17.jpg)
2) Fast exchange
![Page 18: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/18.jpg)
![Page 19: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/19.jpg)
![Page 20: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/20.jpg)
![Page 21: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/21.jpg)
In general
![Page 22: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/22.jpg)
![Page 23: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/23.jpg)
RT
Note error in othernotes (T missing)
![Page 24: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/24.jpg)
C) Using 2D NMR to investigate exchange
Perturb A1 selectively (using a 180 degree pulse), so that
![Page 25: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/25.jpg)
FT-1
∆ω
∆t
ω t
![Page 26: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/26.jpg)
![Page 27: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/27.jpg)
![Page 28: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/28.jpg)
![Page 29: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/29.jpg)
![Page 30: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/30.jpg)
And now let us use a real 2D experiment to accomplish the same thing:
![Page 31: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/31.jpg)
So at D, we have labelled the A1 and A2 states differently, according to theirprecession frequencies:
During τm, exchange can occur:
![Page 32: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/32.jpg)
i.e. during τm, the equations from before apply
![Page 33: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/33.jpg)
![Page 34: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/34.jpg)
![Page 35: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/35.jpg)
NO RELAXATION!!!!!
![Page 36: Chemical exchange and the McConnell Equations · 2013-04-10 · Intramolecular exchange – Motions of sidechains in proteins – Helix-coil transitions of nucleic acids – Unfolding](https://reader034.vdocuments.us/reader034/viewer/2022042203/5ea4cd645e76cf30b00cc96d/html5/thumbnails/36.jpg)
Why only T1? What about T2?