J-couplings..PDF

J-couplings.

Measurement and Usage in Structure

Determination

Dr. Geerten W. Vuister

Department of Biophysical Chemistry

Radboud University Nijmegen

Toernooiveld 1

6525 ED Nijmegen, The Netherlands

http://www.nmr.ru.nl

Largely based upon:

G.W. Vuister et al., “Pulse Sequences for Measuring Coupling Constants” in Biological

Magnetic Resonance, Vol. 16: Modern Techniques in Protein NMR, edited by Krishna and

Berliner, Kluwer Academic/Plenum Publishers, 1998.

Updated: August 2005

Contents

1.1 Motivations for measuring J-couplings .................................................................................. 5

2. IN-PHASE/ANTIPHASE METHODS (IPAP)................................................................... 6

3. THE E.COSY METHODS................................................................................................ 8

3.1. Explanation of the E.COSY principle. .................................................................................. 8

3.1. Explanation of the E.COSY principle. .................................................................................. 9

3.2 E.COSY 1 J and 2 J example ................................................................................................... 12

3.3 Practical outline E.COSY ..................................................................................................... 13

4. THE QUANTITATIVE J-CORRELATION METHODS. ................................................. 14

4.1. Spin-echo based quantitative J-correlation schemes. ......................................................... 14

4.1. Spin-echo based quantitative J-correlation schemes. ......................................................... 15

4.2. HMQC-based quantitative J-correlation schemes. ............................................................. 16

4.3. COSY-based quantitative J-correlation schemes................................................................ 18

4.4 Practical outline QJ............................................................................................................... 20

5. COMPARING THE MERITS OF E.COSY AND QJ-METHODS ................................... 21

6. THE BACKBONE ANGLE φ ......................................................................................... 22

6.1. J-Couplings related to φ ....................................................................................................... 22

7. THE BACKBONE ANGLE ψ ........................................................................................ 27

8. THE SIDECHAIN ANGLES χ 1 AND χ 2 ......................................................................... 29

9. EXTRACTING THE INFORMATION ............................................................................ 32

9.1. Parametrization of Karplus curves. .................................................................................... 32

9.1. Parametrization of Karplus curves. .................................................................................... 33

9.2. Analysis of J-couplings in Proteins. ..................................................................................... 34

10. CONCLUSIONS.......................................................................................................... 37

11. PRACTICAL OUTLINE............................................................................................... 37

Stage 1: Extracting initial information....................................................................................... 37

Stage 2: Extracting additional information for complete analysis............................................ 37

12. REFERENCES RELATED TO MEASUREMENT OF RDCS...................................... 38

13. REFERENCES............................................................................................................ 40

1. Introduction

It has been recognized since the early days of NMR that the J-coupling constants contain

very useful information regarding molecular conformation (Karplus, 1959, 1963; Bystrov, 1976).

For small (bio)molecules the magnitude of the J-coupling constants can often be measured directly

from the splitting of the resonances of interest. However, the accurate measurement of the

magnitude of the J-coupling constants has been problematic for larger biomolecules in which the

measurements of in-phase or antiphase splittings failed.

With the recent advent of isotope labeling techniques in proteins, RNA, and DNA molecules

interest in the measurement of J-couplings has again surged. The usage of isotope labels has

prompted the development of a series of experiments aimed at measuring a large array of both

homo- and heteronuclear coupling constants. As a result of these developments, valuable structural

information can now be obtained in a relatively straightforward way for medium-sized

biomolecules (see Vuister et al., 1998 and Griesinger et al, 1998 for reviews). Moreover, the newly

measured J-coupling data have allowed the reparametrization of the Karplus curves describing the

dependencies of the 3 J-values upon the intervening torsion angles (Vuister and Bax, 1993a, Wang

and Bax, 1995, 1996; Hu and Bax, 1996; Hu and Bax, 1997b). It is to be expected that the newly

obtained curves will be of higher accuracy compared to those derived solely on the basis of small

model compounds, in particular for the range of dihedral angles which were actually used in the

parametrization.

These new techniques can be subdivided on the basis of the underlying principle for

measuring the J-coupling. In-phase-anti-phase (IPAP) methods are well-suited for the measurement

of large- and rather uniform J-couplings (discussed in section 2). In the so-called E.COSY methods

(Griesinger et al., 1985,1986,1987) (discussed in section 3) two spins are correlated without

disturbing the energy levels of a third spin, which is J-coupled to both other spins. The resulting

E.COSY pattern then allows the measurement of a small J-coupling, provided that the second J-

coupling is large enough to allow separation of the multiplet components. E.COSY methods have

now been used to measure a large variety of 2 J and 3 J-coupling constants (Montelione et al., 1989,

Wider et al., 1989; Sörensen, 1990; Delaglio et al., 1991; Gemmecker and Fesik, 1991; Schmieder

et al., 1991; Seip et al., 1992; Vuister and Bax, 1992; Emerson and Montelione, 1992; Eggenberger

et al., 1992; Griesinger and Eggenberger, 1992; Madsen et al., 1993; Weisemann et al., 1994a;

Wang and Bax, 1995, 1996; Löhr and Rüterjans, 1995, 1997, 1999; Löhr et al., 1997).

A second class of experiments (discussed in section 4) aims to quantify the signal

modulation or attenuation resulting from the active coupling and is referred to as quantitative J-

correlation experiments (QJ) (Archer et al., 1991; Grzesiek et al., 1992; Blake et al., 1992; Billeter

et al., 1992; Vuister and Bax, 1993a,b; Vuister et al., 1993a,b; Bax et al., 1994; Vuister et al., 1994;

Kuboniwa et al., 1994; Grzesiek et al., 1995; Hu and Bax, 1996; 1997ab; Hu et al., 1997; Hennig et

al., 1997).

Alternative methods for measuring J-couplings include the so-called P-FIDS or C’-FIDS

methods (Schwalbe et al., 1994; Rexroth et al., 1995a) and the ZQ/DQ methods (Rexroth et al.,

1995b; Otting, 1997).

1.1 Motivations for measuring J-couplings

There can be several reasons for measuring J-couplings:

• J-couplings can provide structural information

• Data can provide stereo-specific assignments.

• Data can provide dynamic information.

• Data can be used for structure validation.

• The same techniques are used for measurements of residual dipolar couplings and hydrogen-

bond J couplings ( h J ).

Plik z chomika:

Inne pliki z tego folderu:

Inne foldery tego chomika: