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W A Hendrickson

Publications and source records attributed to W A Hendrickson.

At least 19 recordsLinked to original sources
PubMed1992

Structure of a C-type mannose-binding protein complexed with an oligosaccharide.

C-type (Ca(2+)-dependent) animal lectins such as mannose-binding proteins mediate many cell-surface carbohydrate-recognition events. The crystal structure at 1.7 A resolution of the carbohydrate-recognition domain of rat mannose-binding protein complexed with an oligomannose asparaginyl-oligosaccharide reveals that Ca2+ forms coordination bonds with the carbohydrate ligand. Carbohydrate specificity is determined by a network of coordination and hydrogen bonds that stabilizes the ternary complex of protein, Ca2+ and sugar. Two branches of the oligosaccharide crosslink neighbouring carbohydrate-recognition domains in the crystal, enabling multivalent binding to a single oligosaccharide chain to be visualized directly.

Acetylglucosamine↗
PubMed1992

Structure of a fibronectin type III domain from tenascin phased by MAD analysis of the selenomethionyl protein.

Fibronectin type III domains are found in many different proteins including cell surface receptors and cell adhesion molecules. The crystal structure of one such domain from the extracellular matrix protein tenascin was determined. The structure was solved by multiwavelength anomalous diffraction (MAD) phasing of the selenomethionyl protein and has been refined to 1.8 angstrom resolution. The folding topology of this domain is identical to that of the extracellular domains of the human growth hormone receptor, the second domain of CD4, and PapD. Although distinct, this topology is similar to that of immunoglobulin constant domains. An Arg-Gly-Asp (RGD) sequence that can function for cell adhesion is found in a tight turn on an exposed loop.

Amino Acid Sequence↗
PubMed1992

Structure determination and refinement of homotetrameric hemoglobin from Urechis caupo at 2.5 A resolution.

A 5 A resolution multiple isomorphous replacement solution for hemoglobin isolated from Urechis caupo revealed a previously unobserved quaternary structure for tetrameric hemoglobin [Kolatkar, Meador, Stanfield & Hackert (1988). J. Biol. Chem. 263(7), 3462-3465]. We report here the structure of Urechis hemoglobin in the cyanomet state refined to 2.5 A resolution by simulated annealing yielding R = 0.148 for reflections F greater than 3 sigma between 5.0 and 2.5 A resolution. The starting model was fitted to a map originally derived from multiple-wavelength anomalous-dispersion phases to 3 A resolution that was then subjected to cyclic twofold molecular averaging and solvent flattening. Structural analysis of the resultant model shows that the unique quaternary assemblage is possible due to several favorable interactions between subunits, including salt links, hydrophobic pockets and interactions mediated by bound water. The tetramer is stabilized by subunit-subunit interactions between the G/H turns and D helices within the crystallographic dimer, and the A/B turn regions and E helices between subunits related by a molecular twofold axis. Interestingly, each subunit has one cysteine residue (Cys21) located in the A/B turn. These twofold-related cysteinyl residues are near enough to one another to form a disulfide bridge but do not.

Animals↗
PubMed1992

Crystal structure of a soluble form of the human T cell coreceptor CD8 at 2.6 A resolution.

A secreted fragment of the extracellular portion of human CD8 alpha has been expressed in CHO cells, and a deglycosylated and proteolyzed form of this fragment has been crystallized. We report here the crystal structure of this fragment as refined at 2.6 A resolution. The structure was solved by molecular replacement using a superposition of ten variable domains from immunoglobulin light chains as the search model. Only the N-terminal 114 amino acids of CD8 alpha are visible in the electron density maps. The domain formed by these residues possesses a fold typical of immunoglobulin variable domains and associates to form Fv-like homodimers.

Amino Acid Sequence↗
PubMed1991

Identification and characterization of zinc binding sites in protein kinase C.

Metal ion coordination in the regulatory domain of protein kinase C (PKC) is suggested by the conservation of six cysteines and two histidines in two homologous regions found therein. By monitoring x-ray fluorescence from a purified sample of rat PKC beta I overexpressed in insect cells, direct evidence has been obtained that PKC beta I tightly binds four zinc ions (Zn2+) per molecule. Extended x-ray absorption fine structure (EXAFS) data are best fit by an average Zn2+ coordination of one nitrogen and three sulfur atoms. Of the plausible Zn2+ coordination models, only those featuring nonbridged Zn2+ sites accommodate the EXAFS data and all of the conserved potential ligands.

Absorptiometry, Photon↗
PubMed1991

Structure of the calcium-dependent lectin domain from a rat mannose-binding protein determined by MAD phasing.

Calcium-dependent (C-type) animal lectins participate in many cell surface recognition events mediated by protein-carbohydrate interactions. The C-type lectin family includes cell adhesion molecules, endocytic receptors, and extracellular matrix proteins. Mammalian mannose-binding proteins are C-type lectins that function in antibody-independent host defense against pathogens. The crystal structure of the carbohydrate-recognition domain of a rat mannose-binding protein, determined as the holmium-substituted complex by multiwavelength anomalous dispersion (MAD) phasing, reveals an unusual fold consisting of two distinct regions, one of which contains extensive nonregular secondary structure stabilized by two holmium ions. The structure explains the conservation of 32 residues in all C-type carbohydrate-recognition domains, suggesting that the fold seen here is common to these domains. The strong anomalous scattering observed at the Ho LIII edge demonstrates that traditional heavy atom complexes will be generally amenable to the MAD phasing method.

Acute-Phase Proteins↗
PubMed1991

Physical characterization and crystallization of the carbohydrate-recognition domain of a mannose-binding protein from rat.

A portion of rat mannose-binding protein A (MBP-A), a Ca(2+)-dependent animal lectin, has been overproduced in a bacterial expression system, biochemically characterized, and crystallized. A fragment corresponding to the COOH-terminal 115 residues of native MBP-A, produced by subtilisin digestion of the bacterially expressed protein, contains the carbohydrate-recognition domain (CRD). Gel filtration, chemical cross-linking, and crystallographic self-rotation function analyses indicate that the subtilisin fragment is a dimer, although the complete bacterially expressed fragment, containing the neck and CRD of MBP-A, is a trimer. Crystals of the minimal CRD, obtained only as a complex with a Man6GlcNAc2Asn glycopeptide, diffract to Bragg spacings of at least 1.7 A. Several trivalent lanthanide ions (Ln3+) can substitute for Ca2+, as assessed by their ability to support carbohydrate binding and to protect the CRD from proteolysis in a manner similar to that observed for Ca2+. These assays indicate that Ln2+ binds about 30 times more tightly than Ca2+ to the CRD, and that two Ca2+ or Ln3+ bind to each monomer, a result confirmed by determination of the Ho3+ positions in a Ho(3+)-containing crystal of the CRD. Crystals grown in the presence of Ln3+ belong to different space groups from those obtained with Ca2+ and are therefore not useable for traditional crystallographic phase determination methods, but are well-suited for high resolution structure determination by multiwavelength anomalous dispersion phasing.

Animals↗
PubMed1991

Determination of macromolecular structures from anomalous diffraction of synchrotron radiation.

Resonance between beams of x-ray waves and electronic transitions from bound atomic orbitals leads to a phenomenon known as anomalous scattering. This effect can be exploited in x-ray crystallographic studies on biological macromolecules by making diffraction measurements at selected wavelengths associated with a particular resonant transition. In this manner the problem of determining the three-dimensional structure of thousands of atoms is reduced to that of initially solving for a few anomalous scattering centers that can then be used as a reference for developing the entire structure. This method of multiwavelength anomalous diffraction has now been applied in a number of structure determinations. Optimal experiments require appropriate synchrotron instrumentation, careful experimental design, and sophisticated analytical procedures. There are rich opportunities for future applications.

Crystallography↗
PubMed1991

Mutational analysis of the interaction between CD4 and class II MHC: class II antigens contact CD4 on a surface opposite the gp120-binding site.

Using functional and adhesion assays, we have studied the ability of 30 human CD4 mutants to interact with class II major histocompatibility complex (MHC) molecules and also with gp120 from human immunodeficiency virus. The mutants cover the four domains (D1-D4) of CD4 and include several single-site substitutions. Analysis of the results, in the context of the CD4 crystal structure, shows that mutations that affect the interaction with class II MHC molecules are located on three exposed loops from CD4 domains 1 and 2. The specifically implicated residues, 19, 89, and 165, are separated from one another by 9 A, 24 A, and 24 A on one face of the CD4 molecule. Moreover, the class II binding site does not include residues 43 to 49 of the CD4 molecule, a region on an opposite face known to be involved in the binding of gp120.

Antibodies, Monoclonal↗
PubMed1991

Exploration of disorder in protein structures by X-ray restrained molecular dynamics.

Conformational disorder in crystal structures of ribonuclease-A and crambin is studied by including two independent structures in least-squares optimizations against X-ray data. The optimizations are carried out by X-ray restrained molecular dynamics (simulated annealing refinement) and by conventional least-squares optimization. Starting from two identical structures, the optimizations against X-ray data lead to significant deviations between the two, with rms backbone displacements of 0.45 A for refinement of ribonuclease at 1.53 A resolution, and 0.31 A for crambin at 0.945 A. More than 15 independent X-ray restrained molecular dynamics runs have been carried out for ribonuclease, and the displacements between the resulting structures are highly reproducible for most atoms. These include residues with two or more conformations with significant dihedral angle differences and alternative hydrogen bonding, as well as groups of residues that undergo displacements that are suggestive of rigid-body librations. The crystallographic R-values obtained are approximately 13%, as compared to 15.3% for a comparable refinement with a single structure. Least-squares optimization without an intervening restrained molecular dynamics stage is sufficient to reproduce most of the observed displacements. Similar results are obtained for crambin, where the higher resolution of the X-ray data allows for refinement of unconstrained individual anisotropic temperature factors. These are shown to be correlated with the displacements in the two-structure refinements.

Hydrogen Bonding↗
PubMed1991

CD4: its structure, role in immune function and AIDS pathogenesis, and potential as a pharmacological target.

CD4 is critical for the development and function of the CD4+ subset of T cells and also subserves as the receptor for the human immunodeficiency viruses. Reports in the past year clarify the role and the molecular interactions of CD4 in these events. Determination of the structure of an extracellular fragment of CD4 reveals novel variations of the immunoglobulin fold and provides an atomic framework for interpretation of its interactions with MHC class II molecules and with gp120, the external envelope glycoprotein of the human immunodeficiency virus.

Acquired Immunodeficiency Syndrome↗
PubMed1990

Effect of the anisotropy of anomalous scattering on the MAD phasing method.

The analysis of X-ray diffraction intensities is complicated by the anisotropy of anomalous scattering (AAS) that can occur due to resonance associated with transitions between core electrons and valence molecular orbitals. Substantial AAS has been observed directly in diffraction data near the K edge of selenium in selenolanthionine [Templeton & Templeton (1988). Acta Cryst. A44, 1045-1051] and in pleiochroism of X-ray absorption in selenobiotinyl streptavidin [Hendrickson, Pähler, Smith, Satow, Merritt & Phizackerley (1989). Proc. Natl Acad. Sci. USA, 86, 2190-2194]. The impact of AAS on the multiple-wavelength anomalous diffraction (MAD) method for phase determination is of particular interest in the context of this chemical state of selenium in the light of a general method that has been developed to incorporate selenomethionine into proteins for use in MAD phasing [Hendrickson, Horton & LeMaster (1990). EMBO J. 9, 1665-1672]. The first step of the MAD phasing method necessarily assumes that the anomalous-scattering factors are isotropic and our first aim here is to evaluate the effect of this approximation on initially determined phases. To obtain ultimate phases free from the effects of anisotropy, a least-squares procedure has been written in which global parameters (i.e. pertaining to the whole data set) are refined simultaneously with local parameters (i.e. pertaining to a given node h). The AAS is taken explicityly into account by considering f' and f" as tensors instead of scalars [Templeton & Templeton (1982). Acta Cryst. A38, 62-67], and the components of the f' and f" tensors are among the refinable global parameters. The effectiveness of this procedure is tested with data simulated from the refined atomic model of selenobiotinyl streptavidin. The application of this procedure to actual Photon Factory measurements is also described. The results show that AAS does not cripple the MAD method, and that phases uncorrupted by these effects can be recovered.

Bacterial Proteins↗
PubMed1990

Structure of ribonuclease H phased at 2 A resolution by MAD analysis of the selenomethionyl protein.

Ribonuclease H digests the RNA strand of duplex RNA.DNA hybrids into oligonucleotides. This activity is indispensable for retroviral infection and is involved in bacterial replication. The ribonuclease H from Escherichia coli is homologous with the retroviral proteins. The crystal structure of the E. coli enzyme reveals a distinctive alpha-beta tertiary fold. Analysis of the molecular model implicates a carboxyl triad in the catalytic mechanism and suggests a likely mode for the binding of RNA.DNA substrates. The structure was determined by the method of multiwavelength anomalous diffraction (MAD) with the use of synchrotron data from a crystal of the recombinant selenomethionyl protein.

Amino Acid Sequence↗
PubMed1990

A cooperative hemoglobin with directly communicating hemes. The Scapharca inaequivalvis homodimer.

The unique functional properties of the homodimeric hemoglobin (HbI) extracted from the Arcid blood clam Scapharca inaequivalvis are discussed in the light of the unusual assembly of this protein. At variance with vertebrate hemoglobins, in S. inaequivalvis HbI, the heme-carrying E and F helices form the subunit interface and bring the heme groups almost into direct contact. This creates a new pathway for transferring information about the ligation state of the heme from one subunit to the other which allows cooperativity in the binding of heme ligands to be displayed by a homodimer. The tight coupling between the two subunits and the two heme groups also manifests itself in other reactions that are cooperative in S. inaequivalvis HbI, but not in human hemoglobin, namely, the cleavage of the proximal histidine-heme iron bond and the modification of specific residues located at the subunit interface.

Amino Acid Sequence↗
PubMed1990

Expression, purification, and crystallization of natural and selenomethionyl recombinant ribonuclease H from Escherichia coli.

Ribonuclease H (RNase H) from Escherichia coli is an endonuclease that specifically degrades the RNAs of RNA:DNA hybrids. The enzyme is a single polypeptide chain of 155 amino acid residues, of which 4 are methionines. To solve the crystallographic three-dimensional structure of E. coli RNase H by the multi-wavelength anomalous diffraction technique, we have constructed methionine auxotrophic strains of E. coli that overexpress selenomethionyl RNase H. MIC88 yields about 10 mg of selenomethionyl RNase H per liter of culture, which is comparable to the overexpression of the natural recombinant protein. We have purified both proteins to homogeneity and crystallized them isomorphously in the presence of sulfate. These are Type I crystals of space group P2(1)2(1)2(1) with the cell parameters a = 41.8 A, b = 86.4 A, c = 36.4 A, one monomer per asymmetric unit, and approximately 36% (v/v) solvent. Crystals of both proteins diffract to beyond 2-A Bragg spacings and are relatively durable in an x-ray beam. On replacement of sulfate with NaCl, crystals of natural RNase H grow as Type I' (very similar to Type I) at pH between 7.0 and 8.0; at pH 8.8, crystals of Type II are obtained in space group P2(1)2(1)2(1) with a = 44.3 A, b = 87.3 A, and c = 35.7 A. Type II crystals can be converted to Type I by soaking in phosphate buffer. RNase H crystals of Type II have also been reported by Kanaya et al. (Kanaya, S., Kohara, A., Miyakawa, M., Matsuzaki, T., Morikawa, K., and Ikehara, M. (1989) J. Biol. Chem. 264, 11546-11549).

Chromatography, DEAE-Cellulose↗
PubMed1990

Structural transitions upon ligand binding in a cooperative dimeric hemoglobin.

Comparison of the 2.4 angstrom resolution crystal structures of dimeric clam hemoglobin in the deoxygenated and carbon-monoxide liganded states shows how radically different the structural basis for cooperative oxygen binding is from that operative in mammalian hemoglobins. Heme groups are in direct communication across a novel subunit interface formed by the E and F helices. The conformational changes at this interface that accompany ligand binding are more dramatic at a tertiary level but more subtle at a quaternary level than those in mammalian hemoglobins. These findings suggest a cooperative mechanism that links ligation at one subunit with potentiation of affinity at the second subunit.

Amino Acid Sequence↗