Ligand preference inferred from the structure of neutrophil gelatinase associated lipocalin.

Neutrophil gelatinase associated lipocalin (NGAL), a constituent of neutrophil granules, is a member of the lipocalin family of binding proteins. NGAL can also be highly induced in epithelial cells in both inflammatory and neoplastic colorectal disease. NGAL is proposed to mediate inflammatory responses by sequestering neutrophil chemoattractants, particularly N-formylated tripeptides and possibly leukotriene B(4) and platelet activating factor. The crystal structures of NGAL display a typical lipocalin fold, albeit with an unusually large and atypically polar binding site, or calyx. The fold of NGAL is most similar to the epididymal retinoic acid-binding protein, another lipocalin, though the overall architecture of the calyces are very different. The crystal structures also reveal either sulfate ions or an adventitiously copurified fatty acid bound in the binding site. Neither ligand is displaced by added N-formylated tripeptides. The size, shape, and character of the NGAL calyx, as well as the low relative affinity for N-formylated tripeptides, suggest that neither the copurified fatty acid nor any of the proposed ligands are likely to be the preferred ligand of this protein. Comparisons between the crystal structures and the recently reported solution structure of NGAL reveal significant differences, in terms of both the details of the structure and the overall flexibility of the fold.

Crystal structure of the MHC class I homolog MIC-A, a gammadelta T cell ligand.

The major histocompatibility complex (MHC) class I homolog MIC-A functions as a stress-inducible antigen that is recognized by a subset of gammadelta T cells independent of beta2-microglobulin and bound peptides. Its crystal structure reveals a dramatically altered MHC class I fold, both in detail and overall domain organization. The only remnant of a peptide-binding groove is a small cavity formed as the result of disordering a large section of one of the groove-defining helices. Loss of beta2-microglobulin binding is due to a restructuring of the interaction interfaces. Structural mapping of sequence variation suggests potential receptor binding sites on the underside of the platform on the side opposite of the surface recognized by alphabeta T cell receptors on MHC class I-peptide complexes.

Expression, purification, crystallization and crystallographic characterization of the human MHC class I related protein MICA.

Crystals of the human MHC-encoded molecule MICA, a homologue of MHC class I proteins, have been grown in hanging-drop vapor-diffusion trials using ammonium sulfate as a precipitating agent with recombinant protein expressed in a baculovirus-based system. Cryo-preserved crystals of MICA belong to the cubic space group F4132 with lattice constants a = b = c = 260.7 A and diffract to a resolution limit of 3.0 A when cryo-preserved. These crystals do not diffract when handled conventionally.

Position-dependent internal motions and effective correlation times for magnetization transfer in DNA.

An effective correlation time that accounts for position dependence of the combined local angular motions and collective twisting and bending deformations, as well as for anisotropic uniform rotation, is defined in terms of the magnetization-transfer rate and expressed in terms of molecular parameters. Application to measured magnetization-transfer rates from H6 to H5 of cytosine in cases where all other relevant data, including the uniform rotational diffusion coefficients, are known, suggests that the amplitude of local angular motion, as well as that due to collective deformations, is significantly greater for a penultimate base pair than for base pairs near the center of the molecule, and that such amplitudes might be approximately transferable from one molecule to another. Protocols are suggested for using estimated ratios of effective correlation times in the initial calibrations of internuclear distances and in the subsequent structure-refinement process.