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

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Book cover Bioactive Conformation I

Part of the book series: Topics in Current Chemistry ((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.

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Abbreviations

A :

molecular alignment tensor

A a :

magnitude of the alignment tensor

CCR:

cross-correlated relaxation

CT-HSQC:

constant time version of HSQC

D a :

magnitude of dipolar coupling tensor [-3mm]

D B PQ :

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

D F PQ :

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

D obs PQ :

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

K D :

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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Acknowledgments

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

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Authors and Affiliations

  1. Structural Biology Institute, IBI-2, Research Center Jülich, 52425, Jülich, Germany

    Bernd W. Koenig

  2. Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany

    Bernd W. Koenig

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Koenig, B.W. (2006). Residual Dipolar Couplings Report on the Active Conformation of Rhodopsin-Bound Protein Fragments. In: Peters, T. (eds) Bioactive Conformation I. Topics in Current Chemistry, vol 272. Springer, Berlin, Heidelberg . https://doi.org/10.1007/128_2006_088

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