General features of proton longitudinal relaxation in proteins in solution

Ishima, Rieko; Shibata, Susumu; Akasaka, Kazuyuki

doi:10.1016/0022-2364(91)90373-2

Cited by 14 publications

(19 citation statements)

References 17 publications

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“…[7], and K the kinetic matrix given above. The initial state of the A matrix, A(0), is given by the diagonal matrix: [12] where L 1F and L 2F are the free ligand concentrations, E, EL 1 , EL 2 , and EL 1 L 2 are the concentrations of the free receptor, the two binary complexes and the ternary complex.…”

Section: Theorymentioning

confidence: 99%

“…The leakage term * is generally set equal to 1 s Ϫ1 , and arises due to mobile portions of the protein which more effectively couple the magnetization to the lattice (7). In practice, it is convenient to calculate the relaxation matrix using a similarly sized interproton distance matrix, as described by Khan et al (8), with elements D ij ϭ r ij .…”

Section: Theorymentioning

confidence: 99%

“…For the ILOE calculation, the relaxation matrix is expanded to describe the free ligands L 1 and L 2 , the two binary complexes, EL 1 and EL 2 , and finally the ternary complex, EL 1 L 2 , where we have used the symbol "E" for the receptor to avoid confusion with the symbol for the relaxation matrix. We thus obtain an expanded relaxation matrix of the form: [7] where R(L 1 1F ) is the relaxation matrix calculated as described above by Eqs. [2]- [5] for ligand 1 in the free state, whose motion corresponds to a rotational correlation time 1F .…”

Section: Theorymentioning

confidence: 99%

See 2 more Smart Citations

Theoretical Analysis of the Inter-Ligand Overhauser Effect: A New Approach for Mapping Structural Relationships of Macromolecular Ligands

London

1999

Journal of Magnetic Resonance

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Section: Theorymentioning

confidence: 99%

Section: Theorymentioning

confidence: 99%

Section: Theorymentioning

confidence: 99%

See 1 more Smart Citation

Theoretical Analysis of the Inter-Ligand Overhauser Effect: A New Approach for Mapping Structural Relationships of Macromolecular Ligands

London

1999

Journal of Magnetic Resonance

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“…Thus, the effect of the large number of protons in the protein system essentially uncouples the relaxation behavior, so that a simple decay curve with a relaxation rate approximately equal to R~L, the first element of the relaxation matrix (see below), is obtained. This can be taken into account by using additional protons or, as illustrated by the dotted curve, by 265 adding a proton-relaxation sink corresponding to a rate of 1 s <, as is typically invoked for protein systems (Ishima et al, 1991). Hence, the effect of the large number of protein spins combined with rapid spin diffusion is to uncouple the fluorine spin-lattice relaxation so that approximately exponential behavior is observed.…”

mentioning

confidence: 97%

19F NMR relaxation studies on 5-fluorotryptophan- and tetradeutero-5-fluorotryptophan-labeled E. coli glucose/galactose receptor

et al. 1996

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19F NMR relaxation studies have been carried out on a fluorotryptophan-labeled E. coli periplasmic glucose/galactose receptor (GGR). The protein was derived from E. coli grown on a medium containing a 50:50 mixture of 5-fluorotryptophan and [2,4,6,7-2H4]-5-fluorotryptophan. As a result of the large gamma-isotope shift, the two labels give rise to separate resonances, allowing relaxation contributions of the substituted indole protons to be selectively monitored. Spin-lattice relaxation rates were determined at field strengths of 11.75 T and 8.5 T, and the results were analyzed using a model-free formalism. In order to evaluate the contributions of chemical shift anisotropy to the observed relaxation parameters, solid-state NMR studies were performed on [2,4,6,7-2H4]-5-fluorotryptophan. Analysis of the observed 19F powder pattern lineshape resulted in anisotropy and asymmetry parameters of delta sigma = -93.5 ppm and eta = 0.24. Theoretical analyses of the relaxation parameters are consistent with internal motion of the fluorotryptophan residues characterized by order parameters S2 of approximately 1, and by correlation times for internal motion approximately 10(-11)s. Simultaneous least squares fitting of the spin-lattice relaxation and line-width data with tau i set at 10 ps yielded a molecular correlation time of 20 ns for the glucose-complexed GGR, and a mean order parameter S2 = 0.89 for fluorotryptophan residues 183, 127, 133, and 195. By contrast, the calculated order parameter for FTrp284, located on the surface of the protein, was 0.77. Significant differences among the spin-lattice relaxation rates of the five fluorotryptophan residues of glucose-complexed GGR were also observed, with the order of relaxation rates given by: R1F183 > R1F127 approximately R1F133 approximately R1F195 > R1F284. Although such differences may reflect motional variations among these residues, the effects are largely predicted by differences in the distribution of nearby hydrogen nuclei, derived from crystal structure data. In the absence of glucose, spin-lattice relaxation rates for fluorotryptophan residues 183, 127, 133, and 195 were found to decrease by a mean of 13%, while the value for residue 284 exhibits an increase of similar magnitude relative to the liganded molecule. These changes are interpreted in terms of a slower overall correlation time for molecular motion, as well as a change in the internal mobility of FTrp284, located in the hinge region of the receptor.

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“…From theoretical calculations Ishima and coworkers deduced that methyl groups act as relaxation sinks and should therefore lower the T 1 relaxation time to approximately 1.25 s [80]. Therefore, the saturation present during the off-resonance experiment is assumed to affect the binding epitope non-homogeneously if the recycling delay is set at inappropriate values (Fig.…”

mentioning

confidence: 98%

Molecular Recognition of Ligands by Native Viruses and Virus-Like Particles as Studied by NMR Experiments

Rademacher¹,

Peters²

2008

Topics in Current Chemistry

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Viral entry into host cells is a process that in the majority of cases is not understoodin its molecular details. The first step of viral entry is the recognition of cellular receptorson host cells by viruses, and although X-ray crystallography had yielded some spectacular resultsin individual cases, in general there is little data available to unravel the principles of virus-ligandrecognition at atomic resolution. Therefore, new techniques that uncover the molecular details ofthese recognition processes are needed. The investigation of virus-ligand interactions usingligand-based NMR techniques is an emerging field with the potential to substantially contribute toa deeper understanding of the molecular aspects of viral entry into host cells. Here, we givean overview that covers some of the systems studied so far. This comprises native viruses as wellas virus-like particles (VLPs). We will not address studies that have been performed with individualproteins that are not in a native environment. It turns out that STD NMR in particular has a greatpotential to shine light on the viral entry process as this technique requires only very moderateamounts of viruses or VLPs and corresponding ligands. As a further advantage, this approachis also applicable to ligands that bind to viruses with medium to low affinity. Therefore, STD NMRis extremely well suited for development of antiviral entry inhibitors utilizing fragment-based approacheswith low molecular weight compounds.

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General features of proton longitudinal relaxation in proteins in solution

Cited by 14 publications

References 17 publications

Theoretical Analysis of the Inter-Ligand Overhauser Effect: A New Approach for Mapping Structural Relationships of Macromolecular Ligands

Theoretical Analysis of the Inter-Ligand Overhauser Effect: A New Approach for Mapping Structural Relationships of Macromolecular Ligands

19F NMR relaxation studies on 5-fluorotryptophan- and tetradeutero-5-fluorotryptophan-labeled E. coli glucose/galactose receptor

Molecular Recognition of Ligands by Native Viruses and Virus-Like Particles as Studied by NMR Experiments

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