Methods for the Determination of Torsion Angle Restraints in Biomacromolecules

Griesinger, Christian; Hennig, Mirko; Marino, John P.; Reft, B.; Richter, Christian; Schwalbe, Harald

doi:10.1007/0-306-47083-7_7

Cited by 12 publications

(20 citation statements)

References 173 publications

(121 reference statements)

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“…If this is not practicable, accurate measurement of cross-correlated relaxation rates, even of small size, can be obtained by recording several experiments with different T values and applying Eq. [3] to extract the desired rate.…”

Section: Discussionmentioning

confidence: 99%

“…[3] to be other than zero. This coefficient can assume a maximum value of 2(⌫ CЈ,CЈC␣ CSA/DD ( C )2) (equal to 0.025 for a molecule with c ϭ 4.1 ns at 600 MHz).…”

Section: Possible Inaccuracy In the Measurement Of ⌫ Cјcјc␣ Csa/ddmentioning

confidence: 95%

“…Recently, a number of liquid-state NMR experiments have been developed to derive cross-correlated relaxation rates that occur because of the interference between either two dipolar relaxation mechanisms (1)(2)(3)(4)(5) or a dipolar and a CSA relaxation mechanism (6,7) in proteins. These cross-correlated relaxation rates have been demonstrated to be a powerful tool for obtaining both motional and structural information.…”

Section: Introductionmentioning

confidence: 99%

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Errors in the Measurement of Cross-Correlated Relaxation Rates and How to Avoid Them

Carlomagno

Griesinger

2000

Journal of Magnetic Resonance

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Cross-correlated relaxation rates Gamma are commonly obtained from constant time experiments by measuring the effect of the desired cross-correlated relaxation on an appropriate coherence during the constant time T. These measurements are affected by systematic errors, which derive from undesired cross-correlated relaxation effects taking place before and after the constant time period T. In this paper we discuss the sources and the size of these errors in an example of two pulse sequences. Higher accuracy of the measured data can be obtained by recording a set of experiments with different T values. Cross-correlated relaxation rates are measured in constant time experiments either from the differential relaxation of multiple components (J-resolved Gamma experiments) or from the efficiency of magnetization transfer between two coherences (quantitative Gamma experiments). In this paper we calculate analytically the statistical errors in both J-resolved and quantitative Gamma experiments. These formulae provide the basis for the choice of the most efficient experimental approach and parameters for a given measurement time and size of the rate. The optimal constant time T for each method can be calculated and depends on the relaxation properties of the molecule under investigation. Moreover, we will show how to optimize the relative duration of cross and reference experiments in a quantitative Gamma approach.

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Section: Discussionmentioning

confidence: 99%

“…[3] to be other than zero. This coefficient can assume a maximum value of 2(⌫ CЈ,CЈC␣ CSA/DD ( C )2) (equal to 0.025 for a molecule with c ϭ 4.1 ns at 600 MHz).…”

Section: Possible Inaccuracy In the Measurement Of ⌫ Cјcјc␣ Csa/ddmentioning

confidence: 95%

Section: Introductionmentioning

confidence: 99%

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Errors in the Measurement of Cross-Correlated Relaxation Rates and How to Avoid Them

Carlomagno

Griesinger

2000

Journal of Magnetic Resonance

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“…The introduction of 13 C and 15 N labelling has greatly expanded the number of measurable J-couplings (Figure 4.5b) [35,36] and consequently enhanced the available structural information. Besides angular information, 3 J-couplings are also very useful for establishing stereo-specific assignments and for the determination of rotameric states [37].…”

Section: Dihedral Restraints Derived From J-couplingsmentioning

confidence: 99%

Measurement of Structural Restraints

Vuister

Tjandra

Shen

et al. 2011

Protein NMR Spectroscopy: Practical Techniques and Applications

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Structure determination by high-resolution NMR spectroscopy in solution has traditionally relied on the use of Nuclear Overhauser Enhancement (NOE) derived distance restraints, complemented by dihedral restraints obtained from the analysis of J-couplings [1]. This approach has proven to be very successful in solving the three-dimensional structures of proteins up to the 20-30 kDa range [2]. More recently, additional sources of structural information have become available. These include chemical shifts [3,4], reliable information about hydrogen bonding [5], residual dipolar couplings (RDCs) [6,7] and small-angle X-ray (SAXS) [8,9] or neutron scattering (SANS) data [10].The different types of data are highly complementary and their combined use has led to strongly improved NMR structures. Since the information from NOE, J-couplings and chemical shifts is inherently short-range in nature, cumulative errors from such restraints can translate into inaccurate long-range structural behaviour [11]. This is particularly the case for non-globular biomolecules, such as larger DNA-molecules or protein (complexes) made up of loosely associated modules. In contrast, RDCs and SAXS/SANS data provide long-range information by reporting on the orientation of local groups relative to an overall molecular frame and constraining the overall shape of the molecule. The combination of both types of data has opened avenues for the accurate study of a much wider range of systems, in particular large complexes, dynamic domain-domain interactions and partially or completely unfolded proteins.

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“…12) together with experimental values measured on a protein to establish unambiguously this torsional angle from a set of couplings constants measured [43].…”

Section: J Couplings As a Structural Toolmentioning

confidence: 99%

NMR Spectroscopy as a Tool for the Determination of Structure and Dynamics of Molecules

Griesinger

2001

Essays in Contemporary Chemistry

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Methods for the Determination of Torsion Angle Restraints in Biomacromolecules

Cited by 12 publications

References 173 publications

Errors in the Measurement of Cross-Correlated Relaxation Rates and How to Avoid Them

Errors in the Measurement of Cross-Correlated Relaxation Rates and How to Avoid Them

Measurement of Structural Restraints

NMR Spectroscopy as a Tool for the Determination of Structure and Dynamics of Molecules

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