A two-dimensional nuclear overhauser experiment with pure absorption phase in four quadrants

States, David J.; Haberkorn, R. A.; Ruben, D. J.

doi:10.1016/0022-2364(82)90279-7

Cited by 2,066 publications

(1,786 citation statements)

References 5 publications

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“…The TOCSY experiments utilized the transmitter for observation and excitation of the sample as well as presaturation of the water resonance. The phase-sensitive TOCSY data were collected with 2K points collected in t2 (16 transients per increment), a 50 ms mixing time, and 300 complex points in tl (States et al, 1982). Data were processed with zero filling to 2K points in F1 and F2 and 90" shifted sine-bell apodization used in both dimensions.…”

Section: (4)mentioning

confidence: 99%

The orientation and dynamics of substance P in lipid environments

Keire

Kobayashi

1998

Protein Science

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The membrane-associated conformation of substance P (RPKPQQFFGLM-NH2) has been previously proposed to be the NKI-receptor-active conformation. In this work, NMR methods are applied to explore the orientation and dynamics of substance P at lipid surfaces for which the peptide's three-dimensional structure had been previously determined. Here the presence of dodecylphosphocholine (DPC) or sodium dodecylsulfate (SDS) micelles has been found to cause sequence specific changes in the acid-and base-catalyzed amide proton exchange rates relative to the solution state values. On binding of substance P to SDS micelles, the FFG portion showed the largest decreases in the base-catalyzed amide exchange rates. Similar sequence-specific changes in substance P are observed in the presence of DPC micelles, albeit at much weaker levels due to fast exchange between free and bound forms of the peptide. These differences are attributed to the location of the amide protons either in the surface double layer (via electrostatic effect) or inserted into the polar head group region of the micelles (via low dielectric). The sequence-specific effects of micelle association were also observed in the homonuclear nonselective spin-lattice relaxation time; these, in combination with spin-spin relaxation times, were used to calculate correlation times for the backbone amide protons. These data combined with paramagnetic broadening observations on peptide protons in the presence of spin-labeled lipids yield a detailed model of the interaction of substance P with lipid surfaces.Keywords: amide exchange; correlation times; dodecylphosphocholine; NMR; peptide-lipid interactions; sodium dodecylsulfate; substance P; TI and T2 relaxation Substance P (SP) is a member of the tachykinin family of neuropeptides and is widely distributed in both the central and peripheral nervous system of humans. Tachykinins, which are characterized by a common C-terminal tail (F-x-GLM-NH2 where x is F or V for mammals), are of biomedical interest because they have been shown to cause hypotension, contraction of smooth muscles, salivation, transmission of pain, and inflammation (Pernow, 1983). Ligands of SP receptors have potential as a novel class of anti-inflammatory or pain medication, and as a result, interest is high in the structural elements of the peptide that may control receptor activity and selectivity.The membrane-bound conformation of SP has been proposed to be the NK1 receptor active form (Schwyzer, 1995), and the three-dimensional structure of SP in the presence of Abbreviations: DPC, dodecylphosphocholine; RMSD, root-mean-square deviation; SDS, sodium dodecylsulfate; SP, substance P; 2D TOCSY, twodimensional total correlation spectroscopy. 1996). Both structures were similar, although fast exchange between free and bound forms was observed for SP with DPC micelles and predominantly bound characteristics were found for SP with SDS micelles.The three-dimensional SP structure at these lipid-membrane mimetics may represent either a receptor-bound co...

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Section: (4)mentioning

confidence: 99%

The orientation and dynamics of substance P in lipid environments

Keire

Kobayashi

1998

Protein Science

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“…All spectra were processed with the hypercomplex method (States et al, 1982) using Varian software on a Sun Sparc Workstation. Analysis and peak picking were carried out using NMR Compass (Molecular Simulation Incorporated) on an SGI Indigo.…”

Section: Dynamics Measurementsmentioning

confidence: 99%

Contribution of the tyrosines to the structure and function of the human U1A N‐terminal RNA binding domain

Kranz

Hall

1996

Protein Science

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RNA binding domains (RBDs) are members of a large family of proteins that share minimal sequence conservation but adopt an a0 sandwich global fold. Defining the contributions of specific amino acids to RBD structure and RNA binding is critical to understanding the functions of these proteins. In these experiments with the human UlA N-terminal RNA binding domain (RBDl), the contributions from each of its four tyrosines to protein structure, stability, and RNA binding were measured. Each tyrosine was substituted with phenylalanine and one other selected residue, and the resulting proteins were characterized by chemical denaturation to measure their unfolding free energy, by binding free energies to the wild-type RNA hairpin, and by I9F NMR to probe for structural changes. Features of the protein identified in these experiments include a possible tyrosine/lysine contact in an a-helix, which may be an example of an energetically favorable aromatidamin0 side chain interaction. One long loop of the protein, which shows unusual I5N backbone and tyrosine side-chain dynamics, is implicated in protein:protein association. The diverse interactions of the four tyrosine residues in the organization of RBDl illustrate how each member of this family of proteins will have unique molecular details that contribute to function.

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“…Phase sensitive mode with quadrature detection in both dimensions was used. Nuclear Overhauser effect spectra were acquired with the procedure of States et al (1982), with a mixing time of 160 ms in all cases. Double-quantum filtered COSY (Piantini et al, 1982;Rance et al, 1983;Shaka and Freeman, 1983) were acquired with time-proportional phase incrementation of the first pulse (Redfield and Kunz, 1975;Marion and Wiithrich, 1983).…”

Section: Spectroscopymentioning

confidence: 99%

Comparison of solution structures of mutant bovine pancreatic trypsin inhibitor proteins using two‐dimensional nuclear magnetic resonance

et al. 1992

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Structural perturbations due to a series of mutations at the 30-51 disulfide bond of bovine pancreatic trypsin inhibitor have been explored using NMR. The mutants replaced cysteines at positions 30 and 51 by alanine at position 5 l and alanine, threonine, or valine at position 30. Chemical shift changes occur in residues proximate to the site of mutation. NOE assignments were made using an automated procedure, NASIGN, which used information from the wild-type crystal structure. Intensity information was utilized by a distance geometry algorithm, VEMBED, to generate a series of structures for each protein. Statistical analyses of these structures indicated larger averaged structural perturbations than would be expected from crystallographic and other information. Constrained molecular dynamics refinement using AMBER at 900 K was useful in eliminating structural movements that were not a necessary consequence of the NMR data. In most cases, statistically significant movements are shown to be those greater than approximately 1 A. Such movements do not appear to occur between wild type and A30A51, a result confirmed by crystallography (Eigenbrot, C., Randal, M., & Kossiakoff, A.A., 1990, Prorein Eng. 3 , 591-598). Structural alterations in the T30A51 or V30A51 mutant proteins near the limits of detection occur in the fl-loop (residues 25-28) or C-terminal a-helix, respectively.

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A two-dimensional nuclear overhauser experiment with pure absorption phase in four quadrants

Cited by 2,066 publications

References 5 publications

The orientation and dynamics of substance P in lipid environments

The orientation and dynamics of substance P in lipid environments

Contribution of the tyrosines to the structure and function of the human U1A N‐terminal RNA binding domain

Comparison of solution structures of mutant bovine pancreatic trypsin inhibitor proteins using two‐dimensional nuclear magnetic resonance

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