Residual Dipolar Couplings Report on the Active Conformation of Rhodopsin-Bound Protein Fragments

Chapter
First Online:
Part of the Topics in Current Chemistry book series (TOPCURRCHEM, volume 272)

Abstract

Residual dipolar couplings (RDCs) provide unique information on the structure and dynamics of soluble biomolecules. They are easily extracted from high-resolution liquid-state NMR spectra of molecules that undergo slightly anisotropic tumbling. Options for solute alignment are discussed, followed by a summary of NMR strategies for detection of RDCs. The use of RDCs in protein structure determination and for establishing domain orientation is reviewed. Transient binding of ligand to an aligned target molecule can give rise to transferred dipolar couplings that characterize the target-bound form but are easily detected on the free form of the ligand by liquid-state NMR. There is no size limit on the target molecule. RDCs have been used to study the interaction of bound peptides with the G protein-coupled receptor rhodopsin in its natural membrane environment, with amyloid fibrils, and with lipid model membranes. Further, transient binding of small carbohydrates to soluble proteins was characterized using RDCs. A brief literature review is followed by a detailed discussion of the RDC-based structure determination of a rhodopsin-bound transducin peptide.

Ligand Membrane protein NMR Residual dipolar couplings Transient binding 

Abbreviations

A

molecular alignment tensor

Aa

magnitude of the alignment tensor

CCR

cross-correlated relaxation

CT-HSQC

constant time version of HSQC

Da

magnitude of dipolar coupling tensor [-3mm]

DBPQ

bound state dipolar coupling between nuclei P and Q [-3mm]

DFPQ

free state dipolar coupling between nuclei P and Q [-3mm]

DobsPQ

observed dipolar coupling between nuclei P and Q [-3mm]

DMPC

1,2-dimyristoyl-sn-glycero-3-phosphocholine

DHPC

1,2-dihexanoyl-sn-glycero-3-phosphocholine

Gtα

α-subunit of transducin

Gtγ

γ-subunit of transducin

HSQC

heteronuclear single quantum correlation

KD

dissociation constant

MII

metarhodopsin II state of rhodopsin

NOE

nuclear Overhauser effect

NOESY

nuclear Overhauser effect spectroscopy

PALES

prediction of alignment from structure

PAS

principal axis system

Pf1

filamentous bacteriophage

R

rhombicity of dipolar coupling tensor

RDC

residual dipolar coupling

REDCAT

residual dipolar coupling analysis tool

S

generalized order parameter

SA

simulated annealing

STD

saturation transfer difference spectroscopy

SUV

small unilamellar lipid vesicles

SVD

single value decomposition

S2

peptide with sequence IRENLKDSGLF

S3E

spin-state selective excitation

TrDC

transferred dipolar coupling

TrNOE

transferred NOE

TROSY

transverse relaxation optimized spectroscopy

2D

two-dimensional

3D

three-dimensional

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Notes

Acknowledgments

This work was supported by the Deutsche Forschungsgemeinschaft (KO2143/3-1).

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© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  1. 1.Structural Biology InstituteIBI-2, Research Center JülichJülichGermany
  2. 2.Heinrich-Heine-Universität DüsseldorfUniversitätsstrasse 1DüsseldorfGermany

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