Calcium coordination and pH dependence of the calcium affinity of ligand-binding repeat CR7 from the LRP. Comparison with related domains from the LRP and the LDL receptor

We have determined the X-ray crystal structure to 1.8 A resolution of the Ca(2+) complex of complement-like repeat 7 (CR7) from the low-density lipoprotein receptor-related protein (LRP) and characterized its calcium binding properties at pH 7.4 and 5. CR7 occurs in a region of the LRP that binds to the receptor-associated protein, RAP, and other protein ligands in a Ca(2+)-dependent manner. The calcium coordination is identical to that found in LB5 and consists of carboxyls from three conserved aspartates and one conserved glutamate, and the backbone carbonyls of a tryptophan and another aspartate. The overall fold of CR7 is similar to those of CR3 and CR8 from the LRP and LB5 from the LDL receptor, though the low degree of sequence homology of residues not involved in calcium coordination or in disulfide formation results in a distinct pattern of surface residues for each domain, including CR7. The thermodynamic parameters for Ca(2+) binding at both extracellular and endosomal pHs were determined by isothermal titration calorimetry for CR7 and for related complement-like repeats CR3, CR8, and LB5. Although the drop in pH resulted in a reduction in calcium affinity in each case, the changes were very variable in magnitude, being as low as a 2-fold reduction for CR3. This suggests that a pH-dependent change in calcium affinity alone cannot be responsible for the release of bound protein ligands from the LRP at the pH prevailing in the endosome, which in turn requires one or more other pH-dependent effects for regulating protein ligand release.

Role of calcium in protein folding and function of Tva, the receptor of subgroup A avian sarcoma and leukosis virus

Tva is the cellular receptor for subgroup A avian sarcoma and leukosis virus (ASLV-A). The viral receptor function of Tva is determined by a 40-residue cysteine-rich motif called the LDL-A module. In this study, we expressed and purified the wild-type (wt) Tva LDL-A module as well as several mutants and examined their in vitro folding properties. We found that, as for other LDL-A modules, correct folding and structure of the Tva LDL-A module is Ca2+ dependent. When calcium was present during in vitro protein folding, the wt module was eluted as a single peak by reverse-phase high-pressure liquid chromatography. Furthermore, two-dimensional nuclear magnetic resonance (NMR) spectroscopy gave well-dispersed spectra in the presence of calcium. In contrast, the same protein folded in vitro in the absence of calcium was eluted as multiple broad peaks and gave a poorly dispersed NMR spectrum in the presence of calcium. The calcium affinity (Kd) of the Tva LDL-A module, determined by isothermal titration calorimetry, is approximately 40 microM. Characterization of several Tva mutants provided further evidence that calcium is important in protein folding and function of Tva. Mutations of the Ca2+-binding residues (D46A and E47A) completely abrogated the Ca2+-binding ability of Tva, and the proteins were not correctly folded. Interestingly, mutations of two non-calcium-binding residues (W48A and L34A) also exerted adverse effect on Ca2+-dependent folding, albeit to a much less extent. Our results provide new insights regarding the structure and function of Tva in ASLV-A entry.

NMR solution structure of complement-like repeat CR3 from the low density lipoprotein receptor-related protein. Evidence for specific binding to the receptor binding domain of human alpha(2)-macroglobulin

We have used NMR methods to determine the structure of the calcium complex of complement-like repeat 3 (CR3) from the low density lipoprotein receptor-related protein (LRP) and to examine its specific interaction with the receptor binding domain of human alpha(2)-macroglobulin. CR3 is one of eight related repeats that constitute a major ligand binding region of LRP. The structure is very similar in overall fold to homologous complement-like repeat CR8 from LRP and complement-like repeats LB1, LB2, and LB5 from the low density lipoprotein receptor and contains a short two-strand antiparallel beta-sheet, a one turn alpha-helix, and a high affinity calcium site with coordination from four carboxyls and two backbone carbonyls. The surface electrostatics and topography are, however, quite distinct from each of these other repeats. Two-dimensional (1)H,(15)N-heteronuclear single quantum coherence spectra provide evidence for a specific, though relatively weak (K(d) approximately 140 microM), interaction between CR3 and human alpha2-macroglobulin receptor binding domain that involves a contiguous patch of surface residues in the central region of CR3. This specific interaction is consistent with a mode of LRP binding to ligands that uses contributions from more than one domain to generate a wide array of different binding sites, each with overall high affinity.

NMR solution structure of the receptor binding domain of human alpha(2)-macroglobulin

Human alpha(2)-macroglobulin-proteinase complexes bind to their receptor, the low density lipoprotein receptor-related protein (LRP), through a discrete 138-residue C-terminal receptor binding domain (RBD), which also binds to the beta-amyloid peptide. We have used NMR spectroscopy on recombinantly expressed uniformly (13)C/(15)N-labeled human RBD to determine its three-dimensional structure in solution. Human RBD is a sandwich of two antiparallel beta-sheets, one four-strand and one five-strand, and also contains one alpha-helix of 2.5 turns and an additional 1-turn helical region. The principal alpha-helix contains two lysine residues on the outer face that are known to be essential for receptor binding. A calcium binding site (K(d) approximately 11 mM) is present in the loop region at one end of the beta-sandwich. Calcium binding principally affects this loop region and does not significantly perturb the stable core structure of the domain. The structure and NMR assignments will enable us to examine in solution specific binding of RBD to domains of the receptor and to beta-amyloid peptide.

NMR solution structure of complement-like repeat CR8 from the low density lipoprotein receptor-related protein

The low density lipoprotein receptor-related protein is a member of the low density lipoprotein receptor family and contains clusters of cysteine-rich complement-like repeats of about 42 residues that are present in all members of this family of receptors. These clusters are thought to be the principal binding sites for protein ligands. We have expressed one complement-like repeat, CR8, from the cluster in lipoprotein receptor-related protein that binds certain proteinase inhibitor-proteinase complexes and used three-dimensional NMR on the 13C/15N-labeled protein to determine the structure in solution of the calcium-bound form. The structure is very similar in overall fold to repeat 5 from the low density lipoprotein receptor (LB5), with backbone root mean square deviation of 1.5 A. The calcium-binding site also appears to be homologous, with four carboxyl and two backbone carbonyl ligands. However, differences in primary structure are such that equivalent surfaces that might represent the binding interfaces are very different from one another, indicating that different domains will have very different ligand specificities.

Characterization of the calcium site in two complement-like domains from the low-density lipoprotein receptor-related protein (LRP) and comparison with a repeat from the low-density lipoprotein receptor

Calcium is required for the binding and endocytosis of protein ligands by the low-density lipoprotein receptor-related protein (LRP) and other members of the low-density lipoprotein (LDL) receptor family. Calcium binding sites are thought to be present in the complement-like repeats that occur in clusters in all members of this receptor family. We have expressed two such complement-like repeats, CR3 and CR8, from an alpha2-macroglobulin-proteinase ligand binding region of LRP, as well as repeat 1 from the LDL receptor and examined the metal binding properties and resulting structural changes of these three repeats using changes in tryptophan and terbium fluorescence and perturbation of [1H-15N]-HSQC NMR spectra of the 15N-labeled domains from LRP. We found that all three domains contain a tight calcium binding site at physiological pH and that calcium binding results in a major structural rigidification. Changes in tryptophan fluorescence and tryptophan-sensitized terbium fluorescence indicate that the calcium binding sites are located in homologous regions in all of the repeats. Differences in the details of the perturbations, as well as in the pH dependence of calcium binding, show, however, that each metal site is distinct.

Localization of basic residues required for receptor binding to the single alpha-helix of the receptor binding domain of human alpha2-macroglobulin

To better understand the structural basis for the binding of proteinase-transformed human alpha2-macroglobulin (alpha2M) to its receptor, we have used three-dimensional multinuclear NMR spectroscopy to determine the secondary structure of the receptor binding domain (RBD) of human alpha2M. Assignment of the backbone NMR resonances of RBD was made using 13C/15-N and 15N-enriched RBD expressed in Escherichia coli. The secondary structure of RBD was determined using 1H and 13C chemical shift indices and inter- and intrachain nuclear Overhauser enhancements. The secondary structure consists of eight strands in beta-conformation and one alpha-helix, which together comprise 44% of the protein. The beta-strands form three regions of antiparallel beta-sheet. The two lysines previously identified as being critical for receptor binding are located in (Lys1374), and immediately adjacent to (Lys1370) the alpha-helix, which also contains an (Arg1378). Secondary structure predictions of other alpha-macroglobulins show the conservation of this alpha-helix and suggest an important role for this helix and for basic residues within it for receptor binding.

Critical role of asparagine 1065 of human alpha2-macroglobulin in formation and reactivity of the thiol ester

It has been shown that the relative reaction preference of the C4 thiol ester toward oxygen and nitrogen nucleophiles upon activation by proteinase depends on whether residue 1106 is aspartate or histidine (Dodds, A. W., Ren, X.-D., Willis, A. C., and Law, S. K. A. (1996) Nature 379, 177-179). To determine if the equivalent residue in the related thiol ester-containing protein human alpha2-macroglobulin (alpha2M), asparagine 1065, plays a similar role, we have expressed and characterized four alpha2M variants in which this asparagine has been replaced by aspartate, alanine, histidine, or lysine. The change from asparagine resulted in an altered ability to form the thiol ester. This ranged from failure to form the thiol ester (Asn --> Asp) to a maximum extent of formation of about 50% (Asn --> Ala). For the three variants that were able to form the thiol ester, the rates of thiol ester cleavage by a given amine were found to be different from one another and slower in nearly all cases than plasma alpha2M, but with the same relative reactivity of methylamine > ethylamine > ammonia. The rate of conformational change that follows cleavage of thiol esters in a functional half-molecule was also found to differ between the variants and to be slower than plasma alpha2M. TNS emission spectra indicated that the conformations of the transformed variants differed measurably from transformed plasma alpha2M. These findings suggest that residue 1065 plays a critical role in human alpha2M, for formation of the thiol ester, for its subsequent reaction with nucleophiles, and for the conformational change induced by this reaction. By analogy with C4, where this residue influences the nucleophile preference through direct interaction with the thiol ester, residue 1065 in alpha2M is expected to be located in or very close to the thiol ester region in alpha2M.

Molecular cloning of Limulus alpha 2-macroglobulin

The American horseshoe crab Limulus polyphemus contains alpha 2-macroglobulin (alpha 2M) in the hemolymph plasma and hemocytes. alpha 2M from Limulus shows many of the typical characteristics of mammalian alpha 2M, including the presence of an internal thiol-ester, reactivity with a diversity of endopeptidases, a unique proteinase-trapping mechanism, and reactivity with the mammalian alpha 2M receptor. Additionally, Limulus alpha 2M has the unique property that it regulates the limulin-based hemolytic system of the plasma. A cDNA encoding Limulus alpha 2M has been obtained from a hemocyte cDNA library. The open reading frame encodes an N-terminal signal sequence of 25 amino acid residues and a mature protein of 1482 residues. The entire amino acid sequence is similar to those of the mammalian alpha 2Ms (28-29% identity) and contains common features found in mammalian alpha 2Ms. a bait region, an internal thiol-ester site, and a receptor-binding domain. However, the N-terminal portion (positions 24-105) has no sequence similarity with those of mammalian alpha 2Ms, and it is structurally related to that of the human complement factor C8 chain, consistent with a role for Limulus alpha 2M in host defense. The component sugar analysis of Limulus alpha 2M showed the existence of a complex type of oligosaccharide chain similar to those of mammalian alpha 2M. However, unlike mammalian alpha 2M, no sialic acid was detected in Limulus alpha 2M and it contained approximately 3 mol/mol N-acetylgalactosamine, suggesting the presence of O-linked sugar chains, which have not been found in mammalian alpha 2M. Expression of alpha 2M was detected in hemocytes, but not in hepatopancreas, heart, stomach, intestine, coxal gland, brain and skeletal muscle. Furthermore, immunoblotting of large and small granules of the hemocytes with antiserum against alpha 2M indicated the presence of the alpha 2M in large granules. Trypsin-treated Limulus alpha 2M, but not the native alpha 2M, displaced methylamine-treated human 125I-alpha 2M from the human alpha 2M receptor with a Kd of 30 nM, suggesting conservation of the proteinase-clearance mechanisms between mammalian and arthropod evolutionary lineages.

Localisation of the major reactive lysine residue involved in the self-crosslinking of proteinase-activated Limulus alpha 2-macroglobulin

When alpha 2-macroglobulin (alpha 2M) from the American horseshoe crab, Limulus polyphemus, reacts with proteinases, its thiol esters, like those of other alpha-macroglobulins, become activated, leading to the formation of covalently crosslinked species that can be detected as high molecular weight bands in reducing SDS-PAGE. While other alpha-macroglobulins extensively form crosslinks to the reacting proteinase, Limulus alpha 2M does not. It rather becomes internally crosslinked. It was found from N-terminal sequence analysis of purified [14C]carboxymethylated peptides from Limulus alpha 2M-trypsin complexes that an isopeptide bond formed in approx. 60% yield from the thiol esterified Gln-1002 specifically to Lys-254 in the opposing monomer of the disulphide bridged dimer is the main cause of the internal crosslinking.

Low resolution X-ray structure of human methylamine-treated alpha 2-macroglobulin

The structure of methylamine-treated human alpha 2-macroglobulin (alpha 2M-Ma), a 720-kDa tetrameric inactivated proteinase inhibitor from plasma, has been determined to a resolution of 10 A. Data were collected with synchrotron radiation at 120 K, and phases were calculated by multiple isomorphous replacement and solvent flattening. A novel feature of the structure of alpha 2-M is present in its proteinase-binding cavity, dividing it into two compartments. The potential sites for proteinase entrapment in these compartments are sterically restricted. The positions of the thiol groups appearing from the functional important thiol esters upon their cleavage have been determined. They are found at the walls of the compartments at the center of the structure. The overall structure of alpha 2M-MA is much more sphere-like than previously inferred from electron microscopy studies. However, several aspects of the structure are well described by recent three-dimensional reconstructions. Possible models for the monomer, the disulfide bridged dimer, and native alpha 2M are discussed.

Crystallisation and preliminary X-ray analysis of the receptor-binding domain of human and bovine alpha 2-macroglobulin

The receptor-binding domains (RBDs) of human and bovine alpha 2-macroglobulin (alpha 2M) have been isolated after limited proteolysis of methylamine-treated alpha 2M with papain. Single crystals of the RBDs have been grown by vapour diffusion. Crystals of human RBD are very thin plates unsuited for data collection. However, crystals of RBD from bovine alpha 2M give diffraction patterns suitable for X-ray analysis, and a complete dataset with a maximum resolution of 2.3 A has been collected with synchrotron radiation at cryogenic temperature. The crystals belong to spacegroup P3(1)21 or P3(2)21 with cell parameters a = b = 106.8 A, c = 72.2 A.

Crystallization of human methylamine-treated complement C3 and C3b

Human methylamine-treated complement C3 (C3-MA) and C3b (C3b-MA) have been crystallized using ammonium sulfate as precipitant. The crystals of the two compounds are morphologically indistinguishable though they belong to different space groups. We show that only minor alterations in packing are responsible for the change in space group. Crystals of C3-MA are tetragonal [P4(1(3))22, a = b = 135, c = 610 A] with two molecules per asymmetric unit. Crystals of C3b-MA are also tetragonal [P4(1(3))2(1)2, a = b = 191, c = 610 A] with four molecules per asymmetric unit. The maximum diffraction observed is 7.7 A at cryogenic temperature using synchrotron radiation.

Disulfide bridges in human complement component C3b

The disulfide bridges of human complement component C3b, derived from C3 by removal of the 77-residue C3a, have been determined. The 10 bridges are Cys537-Cys794, Cys605-Cys640, Cys851-Cys1491, Cys1079-Cys1136, Cys1336-Cys1467, Cys1367-Cys1436, Cys1484-Cys1489, Cys1496-Cys1568, Cys1515-Cys1639, and Cys1615-Cys1624. Including the 3 bridges in C3a (Cys670-Cys698, Cys672-Cys705, and Cys685-Cys706) previously determined by high-resolution X-ray crystallography [Hoppe-Seyler's Z. Physiol. Chem. 361 (1980) 1389-1399] all disulfide bridges of C3 are localized. C3 and the strongly related C4 and C5 are members of the alpha 2-macroglobulin superfamily. The predicted bridge patterns of C4 and C5 are discussed and compared with that of alpha 2-macroglobulin.