Tyrosyl motion in peptides. Deuterium NMR line shapes and spin-lattice relaxation

Rice, D.W.; Meinwald, Yvonne C.; Scheraga, Harold A.; Griffin, Robert G.

doi:10.1021/ja00240a006

Cited by 65 publications

(56 citation statements)

References 2 publications

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“…However, our experiments indicate scaled C ␦ -H ␦ and C -H dipolar interactions for the Phe ring, which are consistent with twofold flipping observed in a number of cases (48,49). The side-chain conformations of Met have slightly greater uncertainty than the backbone, largely because of the paucity of constraints on the Met S and C .…”

Section: Full Structure Searchsupporting

confidence: 89%

De novo determination of peptide structure with solid-state magic-angle spinning NMR spectroscopy

Rienstra

Tucker-Kellogg

Jaroniec

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

251

235

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The three-dimensional structure of the chemotactic peptide Nformyl-L-Met-L-Leu-L-Phe-OH was determined by using solid-state NMR (SSNMR). The set of SSNMR data consisted of 16 13 C-15 N distances and 18 torsion angle constraints (on 10 angles), recorded from uniformly 13 C, 15 N-and 15 N-labeled samples. The peptide's structure was calculated by means of simulated annealing and a newly developed protocol that ensures that all of conformational space, consistent with the structural constraints, is searched completely. The result is a high-quality structure of a molecule that has thus far not been amenable to single-crystal diffraction studies. The extensions of the SSNMR techniques and computational methods to larger systems appear promising.

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Section: Full Structure Searchsupporting

confidence: 89%

De novo determination of peptide structure with solid-state magic-angle spinning NMR spectroscopy

Rienstra

Tucker-Kellogg

Jaroniec

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

251

235

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show abstract

“…Indeed, the revised values of S zz for Trp 13 (Figure 4) and Trp 15 (Table 3), are remarkably similar to S zz of the peptide backbone itself. For Trp 9 and Trp 11 , the ring S zz of ∼0.86 ( Figure 4 and Table 3) is slightly lower than the backbone value of 0.93 (yet higher than the earlier estimate 1 of 0.80).…”

Section: Resultscontrasting

confidence: 52%

“…The best fit occurs when S zz = 0.86, an increase from S zz of 0.80 in the previous analysis without the asymmetry parameter 1 . When S zz is optimum (giving the minimum rmsd), the effect of a non-zero η on ρ 1 is negligible, representing only a change from 37.5° to 37.0° for Trp 9 . The effect on ρ 2 is larger, a change from 18°, when η is zero, to 23° when the calculated non-zero values of η are used.…”

Section: Resultsmentioning

confidence: 99%

“…It is therefore plausible that Trp indole rings on an α-helical backbone could be less contrained. Nevertheless, it seems that the interface itself places distinct constraints upon the ring motions, because the "inner pair" of Trp 9 and Trp 11 rings exhibit slightly greater motional freedom, with S zz values of 0.86 (Table 3). These "inner" rings are also bounded by bulky side chains of D-Leu and DVal, yet are marginally more distant from the interface than are Trp 13 and Trp 15 .…”

Section: Resultsmentioning

confidence: 99%

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Importance of Tensor Asymmetry for the Analysis of ²H NMR Spectra from Deuterated Aromatic Rings

et al. 2005

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We have used ab initio calculations to compute all of the tensor elements of the electric field gradient for each carbon-deuterium bond in the ring of deuterated 3-methyl-indole. Previous analyses have ignored the smaller tensor elements perpendicular to principal component V zz which is aligned with the C-2 H bond (local bond z-axis). At each ring position, the smallest element V xx is in the molecular plane and V yy is normal to the plane of the ring. The asymmetry parameter η = (|V yy |-|V xx |)/|V zz | ranges from 0.07 at C4 to 0.11 at C2. We used the perpendicular (off-bond) tensor elements, in concert with an improved understanding of the indole ring geometry 1 , to analyze prototype 2 H-NMR spectra from well-oriented, hydrated peptide/lipid samples. For each of the 4 tryptophans of membranespanning gramicidin A (gA) 2 channels, the inclusion of the perpendicular elements changes the deduced ring tilt by nearly 10° and increases the ring principal order parameter S zz for overall 'wobble' with respect to the membrane normal (molecular z-axis). With the improved analysis, the magnitude of S zz for the outermost indole rings of Trp 13 and Trp 15 is indistinguishable from that observed previously for backbone atoms (0.93 ± 0.03). For the Trp 9 and Trp 11 rings, which are slightly more buried within the membrane, S zz is slightly lower (0.86 ± 0.03). The results show that the perpendicular elements are important for the detailed analysis of 2 H-NMR spectra from aromatic ring systems.

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“…In fact, volume-conserving molecular motions have been well documented in crystalline solids. It is well known that methyl, tert-butyl, phenyl, and other highsymmetry substituents may have fast rotational dynamics in the solid state (19)(20)(21). Because of their relatively small size and high rotational symmetry, methyl groups experience ''jumps'' or dynamic ''exchange'' between sites related by a local threefold symmetry axis.…”

Section: Volume-conserving Motionsmentioning

confidence: 99%

Crystalline molecular machines: Encoding supramolecular dynamics into molecular structure

Garcia-Garibay

2005

Proc. Natl. Acad. Sci. U.S.A.

226

141

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Crystalline molecular machines represent an exciting new branch of crystal engineering and materials science with important implications to nanotechnology. Crystalline molecular machines are crystals built with molecules that are structurally programmed to respond collectively to mechanic, electric, magnetic, or photonic stimuli to fulfill specific functions. One of the main challenges in their construction derives from the picometric precision required for their mechanic operation within the close-packed, self-assembled environment of crystalline solids. In this article, we outline some of the general guidelines for their design and apply them for the construction of molecular crystals with units intended to emulate macroscopic gyroscopes and compasses. Recent advances in the preparation, crystallization, and dynamic characterization of these interesting systems offer a foothold to the possibilities and help highlight some avenues for future experimentation.crystal engineering ͉ molecular gyroscopes ͉ crystal dynamics ͉ molecular rotors T he design and construction of artificial mechanomolecular machines is one of the most interesting scientific challenges of our times (1, 2), and a deeper understanding of structure-property relations in several biological motors (3, 4) have led to considerable insights in the past few years. However, the formulation, design, and materialization of truly serviceable artificial molecular machines remains a major challenge. Whereas initial efforts have been centered on isolated molecules randomly tumbling in solution, most biomolecular systems and macroscopic machines are complex, multiple-component, densely packed assemblies, supported on membranes or within the bulk of larger structures.In this Perspective, I will describe our group's recent efforts on a quest to control the structure and dynamics of closed-packed molecular assemblies. Our thesis is based on the premise that information contained at the molecular level in the form of topology, size, shape, nonbonding interactions, electronic structure, etc. will dictate the aggregation, dynamics, actuation possibilities, and mechanical functions. One of our initial goals is to uncover the relation between supramolecular structure and intermolecular dynamics by taking advantage of dynamic stereochemistry, self-assembly, and crystal engineering. To document this relation with as high precision and certainty as possible, we have chosen the crystalline solid state as a promising model. Structural characterizations can be carried out by singlecrystal x-ray diffraction measurements, and dynamic properties can be determined over a wide range of time scales by techniques that include variabletemperature solid-state NMR, dielectric spectroscopy, and inelastic neutron scattering, among several others. From Molecular Structure Information to Self-Assembly and DynamicsA machine is defined as ''an assemblage of parts that transmits forces, motion, or energy from one to another in a predetermined manner'' (5). Not explicit in the dictionary'...

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Tyrosyl motion in peptides. Deuterium NMR line shapes and spin-lattice relaxation

Cited by 65 publications

References 2 publications

De novo determination of peptide structure with solid-state magic-angle spinning NMR spectroscopy

De novo determination of peptide structure with solid-state magic-angle spinning NMR spectroscopy

Importance of Tensor Asymmetry for the Analysis of ²H NMR Spectra from Deuterated Aromatic Rings

Crystalline molecular machines: Encoding supramolecular dynamics into molecular structure

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Tyrosyl motion in peptides. Deuterium NMR line shapes and spin-lattice relaxation

Cited by 65 publications

References 2 publications

De novo determination of peptide structure with solid-state magic-angle spinning NMR spectroscopy

De novo determination of peptide structure with solid-state magic-angle spinning NMR spectroscopy

Importance of Tensor Asymmetry for the Analysis of 2H NMR Spectra from Deuterated Aromatic Rings

Crystalline molecular machines: Encoding supramolecular dynamics into molecular structure

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Importance of Tensor Asymmetry for the Analysis of ²H NMR Spectra from Deuterated Aromatic Rings