Structural interpretation of vicinal proton-proton coupling constants 3JH alpha H beta in the basic pancreatic trypsin inhibitor measured by two-dimensional J-resolved NMR spectroscopy

Quantitative residue-specific protein backbone torsion angle dynamics from concerted measurement of 3J couplings

Three-bond (3)J(C'C') and (3)J(HNHα) couplings in peptides and proteins are functions of the intervening backbone torsion angle ϕ. In well-ordered regions, (3)J(HNHα) is tightly correlated with (3)J(C'C'), but the presence of large ϕ angle fluctuations differentially affects the two types of couplings. Assuming the ϕ angles follow a Gaussian distribution, the width of this distribution can be extracted from (3)J(C'C') and (3)J(HNHα), as demonstrated for the folded proteins ubiquitin and GB3. In intrinsically disordered proteins, slow transverse relaxation permits measurement of (3)J(C'C') and (3)J(HNH) couplings at very high precision, and impact of factors other than the intervening torsion angle on (3)J will be minimal, making these couplings exceptionally valuable structural reporters. Analysis of α-synuclein yields rather homogeneous widths of 69 ± 6° for the ϕ angle distributions and (3)J(C'C') values that agree well with those of a recent maximum entropy analysis of chemical shifts, J couplings, and (1)H-(1)H NOEs. Data are consistent with a modest (≤30%) population of the polyproline II region.

A novel detection scheme for high-resolution two-dimensional spin-echo correlated spectra in inhomogeneous fields

BACKGROUND

Two-dimensional (2D) nuclear magnetic resonance (NMR) spectroscopy is a powerful and non-invasive tool for the analysis of molecular structures, conformations, and dynamics. However, the inhomogeneity of magnetic fields experienced by samples will destroy spectral information and hinder spectral analysis. In this study, a new pulse sequence is proposed based on the modulation of distant dipolar field to recover high-resolution 2D spin-echo correlated spectroscopy (SECSY) from inhomogeneous fields.

METHOD AND MATERIAL

By using the new sequence, the correlation information between coupled spins and the J coupled information with straightforward multiplet patterns can be obtained free from inhomogeneous line broadening. In addition, the new sequence is also suitable for non-J coupled spin systems. Although three-dimensional acquisition is needed, the evolution of indirect detection dimensions is carefully designed and the ultrafast acquisition scheme is utilized to improve the acquisition efficiency. A chemical solution of butyl methacrylate (C8H14O2) in DMSO (C2H6SO) in a deshimmed magnetic field was tested to demonstrate the implementation details of the new sequence. The performance of the new sequence relative to the conventional SECSY sequence was shown by using an aqueous solution of main brain metabolites in a deshimmed magnetic field.

CONCLUSION

The results reveal that the new sequence provides an attractive way to eliminate the inhomogeneous spectral line broadening for the spin-echo correlated spectrum and is a promising tool for the study of metabolites in metabonomics, even for the applications on in vivo and in situ high-resolution 2D NMR spectroscopy.

Solution structures of the C-terminal headpiece subdomains of human villin and advillin, evaluation of headpiece F-actin-binding requirements

Headpiece (HP) is a 76-residue F-actin-binding module at the C terminus of many cytoskeletal proteins. Its 35-residue C-terminal subdomain is one of the smallest known motifs capable of autonomously adopting a stable, folded structure in the absence of any disulfide bridges, metal ligands, or unnatural amino acids. We report the three-dimensional solution structures of the C-terminal headpiece subdomains of human villin (HVcHP) and human advillin (HAcHP), determined by two-dimensional 1H-NMR. They represent the second and third structures of such C-terminal headpiece subdomains to be elucidated so far. A comparison with the structure of the chicken villin C-terminal subdomain reveals a high structural conservation. Both C-terminal subdomains bind specifically to F-actin. Mutagenesis is used to demonstrate the involvement of Trp 64 in the F-actin-binding surface. The latter residue is part of a conserved structural feature, in which the surface-exposed indole ring is stacked on the proline and lysine side chain embedded in a PXWK sequence motif. On the basis of the structural and mutational data concerning Trp 64 reported here, the results of a cysteine-scanning mutagenesis study of full headpiece, and a phage display mutational study of the 69-74 fragment, we propose a modification of the model, elaborated by Vardar and coworkers, for the binding of headpiece to F-actin.

The des(1-6)antennapedia homeodomain: comparison of the NMR solution structure and the DNA-binding affinity with the intact Antennapedia homeodomain

The nuclear magnetic resonance (NMR) solution structure of an N-terminally truncated mutant Antennapedia homeodomain, des(1-6)Antp(C39S), has been determined from 935 nuclear Overhauser effect upper distance constraints and 148 dihedral angle constraints by using the programs DIANA and OPAL. Twenty conformers representing the solution structure of des(1-6)Antp(C39S) have an average root-mean-square distance relative to the mean coordinates of 0.56 A for the backbone atoms of residues 8-59. Comparison with the intact Antp(C39S) homeodomain shows that the two proteins have identical molecular architectures. The removal of the N-terminal residues 1-6, which are flexibly disordered in the intact homeodomain, causes only strictly localized structure variations and does not noticeably affect the adjoining helix I from residues 10-21. The DNA-binding constant of des(1-6)Antp(C39S) is approximately 10-fold reduced relative to the intact Antp(C39S) homeodomain, which can now be attributed to the absence of the previously reported contacts of the N-terminal polypeptide segment of the intact Antp(C39S) homeodomain with the minor groove of the DNA duplex.

Conformational analysis of PKI(5-22)amide, the active inhibitory fragment of the inhibitor protein of the cyclic AMP-dependent protein kinase

Fourier-transform i.r. spectroscopy, 1H-n.m.r. spectroscopy and X-ray scattering were used to study the conformation and shape of the peptide PKI(5-22)amide, which contains the active site of the inhibitor protein of the cyclic AMP-dependent protein kinase [Cheng, Van Pattern, Smith & Walsh (1985) Biochem. J. 231, 655-661]. The X-ray-scattering solution studies show that the peptide has a compact structure with Rg 0.9 nm (9.0 A) and a linear maximum dimension of 2.5 nm (25A). Compatible with this, Fourier-transform i.r. and n.m.r. determinations indicate that the peptide contains approx. 26% alpha-helix located in the N-terminal one-third of the molecule. This region contains the phenylalanine residue that is one essential recognition determinant for high-affinity binding to the protein kinase catalytic site.