Biomedical subjects

M Ultsch

Publications and source records attributed to M Ultsch.

16 recordsLinked to original sources

PubMed2001

Crystal structure of human insulin-like growth factor-1: detergent binding inhibits binding protein interactions.

Despite efforts spanning considerably more than a decade, a high-resolution view of the family of proteins known as insulin-like growth factors (IGFs) has remained elusive. IGF-1 consists of three helical segments which are connected by a 12-residue linker known as the C-region. NMR studies of members of this family reveal a dynamic structure with a topology resembling insulin but little structural definition in the C-region. We have crystallized IGF-1 in the presence of the detergent deoxy big CHAPS, and determined its structure at 1.8 A resolution by multiwavelength anomalous diffraction, exploiting the anomalous scattering of a single bromide ion and six of the seven sulfur atoms of IGF-1. The structure reveals a well-defined conformation for much of the C-region, which extends away from the core of IGF-1 and has residues known to be involved in receptor binding prominently displayed in a type II beta-turn. In the crystal, these residues form a dimer interface, but analytical ultracentrifugation experiments demonstrate that at physiological concentrations IGF-1 is monomeric. A single detergent molecule contacts residues known to be important for IGF-1 binding protein (IGFBP) interactions. Biophysical and biochemical data show that the detergent binds to IGF-1 specifically and blocks binding of IGFBP-1 and IGFBP-3.

Cholic Acids↗

PubMed2001

Engineered antibodies with increased activity to recruit complement.

This manuscript describes two sites in a human IgG1 that, when mutated individually or in combination, result in a dramatic increase in C1q binding and complement-dependent cytotoxicity activity. These two residues, K326 and E333, are located at the extreme ends of the C1q binding epicenter in the C(H)2 domain of a human IgG. A mutation to tryptophan at K326 debilitates Ab-dependent cell-mediated cytotoxicity activity. In addition, substitutions of the residues E333 with serine and of K326 with tryptophan in a human IgG2 confer biological activity in the complement-dependent cytotoxicity assay in which the wild-type IgG2 is inactive. This study reveals that the residues K326 and E333 play a significant role in the control of the biological activity of an IgG molecule and can rescue the activity of an inactive IgG isotype.

Amino Acid Substitution↗

PubMed2000

Mapping of the C1q binding site on rituxan, a chimeric antibody with a human IgG1 Fc.

Rituxan (Rituximab) is a chimeric mAb with human IgG1 constant domains used in the therapy of non-Hodgkin's B cell lymphomas. This Ab targets B cells by binding to the cell-surface receptor, CD20. In our investigation of the mechanism of B cell depletion mediated by Rituximab, we first constructed mutants of Rituximab defective in complement activation but with all other effector functions intact. Our results demonstrate that the previously described C1q binding motif in murine IgG2b constituting residues E318, K320, and K322 is not applicable to a human IgG1 when challenged with either human, rabbit, or guinea pig complement. Alanine substitution at positions E318 and K320 in Rituximab had little or no effect on C1q binding and complement activation, whereas alanine substitution at positions D270, K322, P329, and P331 significantly reduced the ability of Rituximab to bind C1q and activate complement. We have also observed that concentrations of complement approaching physiological levels are able to rescue >60% of the activity of these mutant Abs with low affinity for C1q. These data localize the C1q binding epicenter on human IgG1 and suggest that there are species-specific differences in the C1q binding site of Igs.

Alanine↗

PubMed1999

Triggering cell death: the crystal structure of Apo2L/TRAIL in a complex with death receptor 5.

Formation of a complex between Apo2L (also called TRAIL) and its signaling receptors, DR4 and DR5, triggers apoptosis by inducing the oligomerization of intracellular death domains. We report the crystal structure of the complex between Apo2L and the ectodomain of DR5. The structure shows three elongated receptors snuggled into long crevices between pairs of monomers of the homotrimeric ligand. The interface is divided into two distinct patches, one near the bottom of the complex close to the receptor cell surface and one near the top. Both patches contain residues that are critical for high-affinity binding. A comparison to the structure of the lymphotoxin-receptor complex suggests general principles of binding and specificity for ligand recognition in the TNF receptor superfamily.

Amino Acid Sequence↗

PubMed1998

Crystal structure of the NK1 fragment of human hepatocyte growth factor at 2.0 A resolution.

BACKGROUND: Hepatocyte growth factor (HGF) is a mitogen for hepatocytes and has also been implicated as an epithelial morphogen in tumor invasion. HGF activates its specific cellular receptor, c-met, through an aggregation mechanism potentiated by heparan sulfate glycosaminoglycans. HGF consists of an N-terminal (N) domain, four kringle domains (the first of which carries receptor-binding determinants), and an inactive serine-protease-like domain. NK1, a naturally occurring fragment of HGF, acts as an antagonist of HGF in the absence of heparin. RESULTS: The N domain of NK1 consists of a central five-stranded antiparallel beta sheet flanked by an alpha helix and a two-stranded beta ribbon. The overall N domain structure in the context of the NK1 fragment is similar to the structure of the isolated domain; two lysines and an arginine residue coordinate a bound sulfate ion. The NK1 kringle domain is homologous to kringle 4 from plasminogen, except that the lysine-binding pocket is altered by the insertion of a glycine residue. Here, a HEPES molecule is bound in the pocket. The asymmetric unit of the crystal contains a 'head-to-tail' NK1 dimer. We use this dimer to propose a model of the NK2 fragment of HGF. CONCLUSIONS: A cluster of exposed lysine and arginine residues in or near the hairpin-loop region of the N domain might form part of the NK1 heparin-binding site. In our NK2 model, both kringle domains pack loosely against the N domain, and a long, positively charged groove lines the interface. This groove might be involved in glycosaminoglycan binding. The HGF receptor-binding determinants are clustered near the binding pocket of the first kringle domain, opposite the N domain.

Amino Acid Sequence↗

PubMed1997

Structural plasticity in a remodeled protein-protein interface.

Remodeling of the interface between human growth hormone (hGH) and the extracellular domain of its receptor was studied by deleting a critical tryptophan residue (at position 104) in the receptor, creating a large cavity, and selecting a pentamutant of hGH by phage display that fills the cavity and largely restores binding affinity. A 2.1 A resolution x-ray structure of the mutant complex showed that the receptor cavity was filled by selected hydrophobic mutations of hGH. Large structural rearrangements occurred in the interface at sites that were distant from the mutations. Such plasticity may be a means for protein-protein interfaces to adapt to mutations as they coevolve.

Carrier Proteins↗

PubMed1994

The X-ray structure of a growth hormone-prolactin receptor complex.

The human pituitary hormones, growth hormone (hGH) and prolactin (hPRL), regulate a large variety of physiological processes, among which are growth and differentiation of muscle, bone and cartilage cells, and lactation. These activities are initiated by hormone-receptor binding. The hGH and hPRL receptors (hGHR and hPRLR, respectively) are single-pass transmembrane receptors from class 1 of the haematopoietic receptor superfamily. This classification is based on sequence similarity in their extracellular domains, notably a highly conserved pentapeptide, the so-called 'WSXWS box', the function of which is controversial. All ligands in class 1 activate their respective receptors by clustering mechanisms. In the case of hGH, activation involves receptor homodimerization in a sequential process: the active ternary complex containing one ligand and two receptor molecules is formed by association of a receptor molecule to an intermediate 1:1 complex. hPRL does not bind to the hGH receptor, but hGH binds to both the hGHR and hPRLR, and mutagenesis studies have shown that the receptor-binding sites on hGH overlap. We present here the crystal structure of the 1:1 complex of hGH bound to the extracellular domain of the hPRLR. Comparisons with the hGH-hGHR complex reveal how hGH can bind to the two distinctly different receptor binding surfaces.

Amino Acid Sequence↗

PubMed1994

Comparison of the intermediate complexes of human growth hormone bound to the human growth hormone and prolactin receptors.

The crystal structures of complexes of human growth hormone (hGH) with the growth hormone and prolactin receptors (hGHR and hPRLR, respectively), together with the mutational data available for these systems, suggest that an extraordinary combination of conformational adaptability, together with finely tuned specificity, governs the molecular recognition processes operative in these systems. On the one hand, in the active 1:2 ligand-receptor complexes, 2 copies of the same receptor use the identical set of binding determinants to recognize topographically different surfaces on the hormone. On the other hand, comparing the 1:1 hGH-hGHR and hGH-hPRLR complexes, 2 distinct receptors use this same set of binding determinants to interact with the identical binding site on the ligand, even though few residues among the binding determinants are conserved. The structural evidence demonstrates that this versatility is accomplished by local conformational flexibility of the binding loops, allowing adaptation to different binding environments, together with rigid-body movements of the receptor domains, necessary for the creation of specific interactions with the same binding site.

Amino Acid Sequence↗

PubMed1993

Crystals of human growth hormone-receptor complexes. Extracellular domains of the growth hormone and prolactin receptors and a hormone mutant designed to prevent receptor dimerization.

A single-site human growth hormone mutant (hGH[G120R]), which inhibits receptor dimerization, was used to produce single crystals, suitable for high-resolution diffraction studies, of 1:1 complexes with the ligand-binding domain of the growth hormone receptor (hGHbp) and of the prolactin receptor (hPRLbp). Crystals of the hGH[G120R]-hGHbp complex are in space group P4(1)2(1)2 or P4(3)2(1)2 with a = 67.7 A, c = 228.0 A, and diffract to at least 2.2 A. Crystals of the complex between hGH[G120R] and hPRLbp are in space group P2(1)2(1)2 with a = 154.0 A, b = 68.4 A, c = 42.9 A, and diffract to at least 2.8 A. The structures of these two complexes will shed light on the early events in receptor activation, and provide the basis for an analysis of receptor specificity of growth hormone and prolactin.

Crystallization↗

PubMed1993

The molecular basis for growth hormone-receptor interactions.

High-resolution mutational and structural analyses of purified components have revealed a great deal about the molecular basis for growth hormone action. The structural and functional aspects of the interactions between hGH and its receptors have been largely elaborated. From these studies it has been possible to engineer homologues of hGH to bind to the hGH receptor and act as potential antagonists. Receptor-selective and high-affinity analogs have also been constructed based on a combination of alanine scanning and monovalent phage display. From this molecular work much has been revealed about the biology of hGH (Fig.9). Our data suggest that hGH is stored in the pituitary as a (Zn2+,hGH)2 complex. On release from somatotropic vesicles it dissociates into a monomeric form and reveals its primary receptor binding site (site 1). Free hGH can bind to the hGHbp in serum to form monomeric or dimeric complexes that slow the clearance of hGH (Moore et al., 1989). However, because the affinity for the full-length receptor is greater, hGH can bind to it preferentially. Furthermore, the constitutive levels of the hGHbp (approximately 0.5 to 1 nM) (Baumann et al., 1986; Herrington et al., 1986) are considerably below the levels of hGH after pulsatile release (approximately 2 to 5 nM) (Thompson et al., 1972). Our data indicate that hGH binds to the hGH receptor on cell membranes through site 1 and subsequently forms dimers through site 2. We believe a similar process may occur for hGH to activate the hPRL receptor, except that Zn2+ is required for site 1 association. Such receptor dimers are then activated and capable of interacting with other cellular components that may mediate the hGH "signal." Recently, based upon this proposed mechanism, we produced potent antagonists to the hGH receptor (Fuh et al., 1992) and hPRL receptor (G. Fuh, P. Colosi, W. Wood, and J. Wells, unpublished results). These antagonists bind tightly to site 1 but are blocked in their ability to bind site 2 and dimerize the receptor. We believe these methods and discoveries will be relevant to the study of signaling by other hematopoietic hormones and receptors as well as other hormones and receptors.

Amino Acid Sequence↗

PubMed1992

The structure of human lymphotoxin (tumor necrosis factor-beta) at 1.9-A resolution.

The three-dimensional structure of recombinant human lymphotoxin (residues 24-171 of the mature protein) has been determined by x-ray crystallography at 1.9-A resolution (Rcryst = 0.215 for I greater than 3 sigma (I)). Phases were derived by molecular replacement using tumor necrosis factor (TNF-alpha) as a search model. Like TNF-alpha, lymphotoxin (LT) folds to form a "jellyroll" beta-sheet sandwich. Three-fold related LT subunits form a trimer stabilized primarily by hydrophobic interactions. A cluster of 6 basic residues around the 3-fold axis may account for the acid lability of the trimer. Although the structural cores of TNF-alpha and LT are similar, insertions and deletions relative to TNF-alpha occur in loops at the "top" of the LT trimer and significantly alter the local structure and the overall shape trimer is highly conserved. The sites of two mutations (Asp-50 and Tyr-108) that abolish the cytotoxicity of LT are contained within poorly ordered loops of polypeptide chain that flank the cleft between neighboring subunits at the base of the molecule, suggesting that the receptor recognizes an intersubunit binding site.

Amino Acid Sequence↗

PubMed1992

Human growth hormone and extracellular domain of its receptor: crystal structure of the complex.

Binding of human growth hormone (hGH) to its receptor is required for regulation of normal human growth and development. Examination of the 2.8 angstrom crystal structure of the complex between the hormone and the extracellular domain of its receptor (hGHbp) showed that the complex consists of one molecule of growth hormone per two molecules of receptor. The hormone is a four-helix bundle with an unusual topology. The binding protein contains two distinct domains, similar in some respects to immunoglobulin domains. The relative orientation of these domains differs from that found between constant and variable domains in immunoglobulin Fab fragments. Both hGHbp domains contribute residues that participate in hGH binding. In the complex both receptors donate essentially the same residues to interact with the hormone, even though the two binding sites on hGH have no structural similarity. Generally, the hormone-receptor interfaces match those identified by previous mutational analyses. In addition to the hormone-receptor interfaces, there is also a substantial contact surface between the carboxyl-terminal domains of the receptors. The relative extents of the contact areas support a sequential mechanism for dimerization that may be crucial for signal transduction.

Binding Sites↗

PubMed1991

Crystals of the complex between human growth hormone and the extracellular domain of its receptor.

Single crystals suitable for high-resolution diffraction studies have been grown of the human growth hormone (hGH) complexed to the extracellular domain of its cloned receptor from the human liver (hGHbp), using the technique of repeat seeding. The crystals are in space group P2(1)2(1)2, with a = 145.8 A, b = 68.6 A, c = 76.0 A, and diffract to at least 2.7 A resolution on a rotating anode X-ray source. Analysis of the composition of these crystals showed the stoichiometry of the complex to be hGH: (hGHbp)2. This finding, coupled with biochemical data on the complex in solution, indicates that the biologically significant dimerization of the growth hormone receptor is mediated through a single hormone molecule. Structure determination of the complex is currently being completed.

Crystallization↗

PubMed1991

Dimerization of the extracellular domain of the human growth hormone receptor by a single hormone molecule.

Human growth hormone (hGH) forms a 1:2 complex with the extracellular domain of its receptor-binding protein (hGHbp) as studied by crystallization, size exclusion chromatography, calorimetry, and a previously undescribed fluorescence quenching assay. These and other experiments with protein engineered variants of hGH have led to the identification of the binding determinants for two distinct but adjacent sites on hGH for the hGHbp, and the data indicated that there are two overlapping binding sites on the hGHbp for hGH. Furthermore, the binding of hGH to the hGHbp occurred sequentially; a first hGHbp molecule bound to site 1 on hGH and then a second hGHbp bound to site 2. Hormone-induced receptor dimerization is proposed to be relevant to the signal transduction mechanism for the hGH receptor and other related cytokine receptors.

Amino Acid Sequence↗

PubMed1991

Neutron structure of subtilisin BPN': effects of chemical environment on hydrogen-bonding geometries and the pattern of hydrogen-deuterium exchange in secondary structure elements.

The neutron structure of subtilisin BPN' has been refined and analyzed at 2.0-A resolution. The structure studied was a mutant variant of subtilisin, Met222----Gln, and was used because large, uninhibited crystals could be grown, which was not the case for the native molecule. Comparison of the structure with that of the native molecule indicated that the two structures are essentially the same. Using the capability of the neutron method to locate hydrogen and deuterium atoms, the protonation states of the six histidine residues were assigned. The active site histidine, His64, was found to be neutral at the pH of the analysis (pH 6.1). This group has an unexpectedly low pKa compared to assignments made by other techniques. The altered pKa of the group could result from electrostatic effects of other molecules in the crystal lattice. The dihedral conformations of a majority of the hydroxyl rotors were assigned. The preferred orientation was trans (180 degrees) with the other two low-energy conformers (60 degrees, 300 degrees) about equally populated. For the serines, about 21% of the hydroxyls act exclusively as H-bond acceptors and 37% as H-bond donors, and in 42% the group functions as both. The experimentally observed dihedral conformations were compared to predicted conformations based on calculated energy criteria and showed a strong correspondence. Deviation from low-energy states could usually be explained by local electrostatic effects. The hydrogen exchange pattern of subtilisin identified the beta-sheet and alpha-helix secondary structure elements to be the most resistant to exchange. Fifty-five percent of the peptide amide hydrogens were fully exchanged, 15% unexchanged, and 30% partially exchanged. The largest concentration of unexchanged sites was in the seven-stranded parallel beta-sheet, in which there were 11 fully protected groups. Little correlation was found between H-bond length and angle and a peptide group's susceptibility toward exchange. Of the five alpha-helices the most protected from exchange is the one defined by residues 224-236. The pattern of exchange identifies regions in this helix where the H-bonding regularity is disrupted.

Binding Sites↗

PubMed1988

The three-dimensional structure of Bacillus amyloliquefaciens subtilisin at 1.8 A and an analysis of the structural consequences of peroxide inactivation.

The three-dimensional structure of the subtilisin from Bacillus amyloliquefaciens (BAS) has been refined to 1.8 A using the amino acid sequence deduced from the DNA coding sequence. The structure is essentially the same as the previously reported structures of subtilisin BPN' (Wright, C.S., Alden, R.A., and Kraut, J. (1969) Nature 221, 235-242) and Novo (Drenth, J., Hol, W. G. J., Jansonius, J. N., and Koekoek, R. (1972) Eur. J. Biochem. 26, 177-181) determined in different crystal forms, at 2.5 and 2.8 A resolution, respectively. The largest differences in the three crystallographic models are seen in regions where the amino acid sequence used in the fit to the electron density maps of BPN' and Novo differs from the gene sequence of BAS (Wells, J. A., Ferrari, E., Henner, D. J., Estell, D. A., and Chen, E. Y. (1983) Nucleic Acids Res. 11, 7911-7925). The refined BAS model shows new features of cation binding, hydrogen bonding, and internal solvent structure. The refined BAS model has served as a basis for the analysis of stereochemical factors involved in the peroxide inactivation of the enzyme. Methionine 222, which is adjacent to the catalytic Ser221, is quantitatively oxidized to the sulfoxide by hydrogen peroxide as had been previously shown for the related Bacillus licheniformis enzyme (Stauffer, C. E., and Etson, D. (1969) J. Biol. Chem. 244, 5333-5338). In addition to this site of modification, we observe partial to full oxidation of two of the four remaining methionines. The oxidation of the methionines does not correlate well with their solvent accessibility calculated from the x-ray structure coordinates; in addition, only one of the two possible stereoisomers of methionine sulfoxide is formed. We also detect hydrogen peroxide-induced modification of the hydroxyl groups of two tyrosines. Modeling suggests that most of the observed effect of oxidation on the enzyme's catalytic efficiency can be attributed to unfavorable interactions at the oxyanion binding site between the sulfoxide group at 222 and the carbonyl oxygen of the scissile peptide bond of the bound substrate.

Bacillus↗