Conformations of immunoglobulin hypervariable regions

On the basis of comparative studies of known antibody structures and sequences it has been argued that there is a small repertoire of main-chain conformations for at least five of the six hypervariable regions of antibodies, and that the particular conformation adopted is determined by a few key conserved residues. These hypotheses are now supported by reasonably successful predictions of the structures of most hypervariable regions of various antibodies, as revealed by comparison with their subsequently determined structures.

Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases

HIV integrase is the enzyme responsible for inserting the viral DNA into the host chromosome; it is essential for HIV replication. The crystal structure of the catalytically active core domain (residues 50 to 212) of HIV-1 integrase was determined at 2.5 A resolution. The central feature of the structure is a five-stranded beta sheet flanked by helical regions. The overall topology reveals that this domain of integrase belongs to a superfamily of polynucleotidyl transferases that includes ribonuclease H and the Holliday junction resolvase RuvC. The active site region is identified by the position of two of the conserved carboxylate residues essential for catalysis, which are located at similar positions in ribonuclease H. In the crystal, two molecules form a dimer with a extensive solvent-inaccessible interface of 1300 A2 per monomer.

Plate Tectonics of the Red Sea and East Africa

The relative motion between the plates on each side of the East African Rift Valley can be obtained from the opening of the Red Sea and the Gulf of Aden. The calculated direction of relative motion agrees well with fault plane solutions for earthquakes north of the equator.

Phosphocholine binding immunoglobulin Fab McPC603. An X-ray diffraction study at 2.7 A

The crystal structure of the Fab of McPC603, a phosphocholine-binding mouse myeloma protein, has been refined at 2.7 A resolution by a combination of restrained least-squares refinement and molecular modeling. The overall structure remains as previously reported, with an elbow bend angle between the variable and constant modules of 133 degrees. Some adjustments have been made in the structure of the loops as a result of the refinement. The hypervariable loops are all visible in the electron density map with the exception of three residues in the first hypervariable loop of the light chain. A sulfate ion occupies the site of binding of the phosphate moiety of phosphocholine.

Interactions of protein antigens with antibodies

There are now several crystal structures of antibody Fab fragments complexed to their protein antigens. These include Fab complexes with lysozyme, two Fab complexes with influenza virus neuraminidase, and three Fab complexes with their anti-idiotype Fabs. The pattern of binding that emerges is similar to that found with other protein-protein interactions, with good shape complementarity between the interacting surfaces and reasonable juxtapositions of polar residues so as to permit hydrogen-bond formation. Water molecules have been observed in cavities within the interface and on the periphery, where they often form bridging hydrogen bonds between antibody and antigen. For the most part the antigen is bound in the middle of the antibody combining site with most of the six complementarity-determining residues involved in binding. For the most studied antigen, lysozyme, the epitopes for four antibodies occupy approximately 45% of the accessible surface area. Some conformational changes have been observed to accompany binding in both the antibody and the antigen, although most of the information on conformational change in the latter comes from studies of complexes with small antigens.

Transglutaminase is essential in receptor-mediated endocytosis of alpha 2-macroglobulin and polypeptide hormones

The receptor-mediated endocytosis of alpha 2-macroglobulin can be inhibited by a diverse group of chemical compounds all of which share the property of being inhibitors of one form of cellular transglutaminase. The present results strongly suggest that protein cross-linking may be essential for receptor-mediated endocytosis of some protein and polypeptide hormones.

Three-dimensional structure of an antibody-antigen complex

We have determined the three-dimensional structure of two crystal forms of an antilysozyme Fab-lysozyme complex by x-ray crystallography. The epitope on lysozyme consists of three sequentially separated subsites, including one long, nearly continuous, site from Gln-41 through Tyr-53 and one from Gly-67 through Pro-70. Antibody residues interacting with lysozyme occur in each of the six complementarity-determining regions and also include one framework residue. Arg-45 and Arg-68 form a ridge on the surface of lysozyme, which binds in a groove on the antibody surface. Otherwise the surface of interaction between the two proteins is relatively flat, although it curls at the edges. The surface of interaction is approximately 26 X 19 A. No water molecules are found in the interface. The positive charge on the two arginines is complemented by the negative charge of Glu-35 and Glu-50 from the heavy chain of the antibody. The backbone structure of the antigen, lysozyme, is mostly unperturbed, although there are some changes in the epitope region, most notably Pro-70. One side chain not in the epitope, Trp-63, undergoes a rotation of approximately 180 degrees about the C beta--C gamma bond. The Fab elbow bends in the two crystal forms differ by 7 degrees.

Structure of the HIV-1 integrase catalytic domain complexed with an inhibitor: a platform for antiviral drug design

HIV integrase, the enzyme that inserts the viral DNA into the host chromosome, has no mammalian counterpart, making it an attractive target for antiviral drug design. As one of the three enzymes produced by HIV, it can be expected that inhibitors of this enzyme will complement the therapeutic use of HIV protease and reverse transcriptase inhibitors. We have determined the structure of a complex of the HIV-1 integrase core domain with a novel inhibitor, 5ClTEP, 1-(5-chloroindol-3-yl)-3-hydroxy-3-(2H-tetrazol-5-yl)-pro penone, to 2.1-A resolution. The inhibitor binds centrally in the active site of the integrase and makes a number of close contacts with the protein. Only minor changes in the protein accompany inhibitor binding. This inhibitor complex will provide a platform for structure-based design of an additional class of inhibitors for antiviral therapy.

International Consensus Statement on Testing and Reporting of Antineutrophil Cytoplasmic Antibodies (ANCA)

Antineutrophil cytoplasmic antibody (ANCA) tests are used to diagnose and monitor inflammatory activity in the primary systemic small vessel vasculitides. ANCA is best demonstrated in these diseases by using a combination of indirect immunofluorescence (IIF) of normal peripheral blood neutrophils and enzyme-linked immunosorbent assays (ELISAs) that detect ANCA specific for proteinase 3 (PR3) or myeloperoxidase (MPO). For ANCA testing in "new" patients, IIF must be performed on all serum samples. Serum samples containing ANCA, any other cytoplasmic fluorescence, or an antinuclear antibody (ANA) that results in homogeneous or peripheral nuclear fluorescence then should be tested in ELISAs for PR3-ANCA and MPO-ANCA. Optimally, ELISAs for PR3-ANCA and MPO-ANCA should be performed on all serum samples. Inclusion of the most recent positive sample in the IIF or ELISA may help demonstrate a change in antibody level. Reports should use recommended terms. Any report of positive neutrophil fluorescence issued before the ELISA results are available should indicate that positive fluorescence alone is not specific for the diagnosis of Wegener granulomatosis or microscopic polyangiitis and that decisions about treatment should not be based solely on the ANCA results.

Structure of an antibody-antigen complex: crystal structure of the HyHEL-10 Fab-lysozyme complex

The crystal structure of the complex of the anti-lysozyme HyHEL-10 Fab and hen egg white lysozyme has been determined to a nominal resolution of 3.0 A. The antigenic determinant (epitope) on the lysozyme is discontinuous, consisting of residues from four different regions of the linear sequence. It consists of the exposed residues of an alpha-helix together with surrounding amino acids. The epitope crosses the active-site cleft and includes a tryptophan located within this cleft. The combining site of the antibody is mostly flat with a protuberance made up of two tyrosines that penetrate the cleft. All six complementarity-determining regions of the Fab contribute at least one residue to the binding; one residue from the framework is also in contact with the lysozyme. The contacting residues on the antibody contain a disproportionate number of aromatic side chains. The antibody-antigen contact mainly involves hydrogen bonds and van der Waals interactions; there is one ion-pair interaction but it is weak.

Crystal structure of transforming growth factor-beta 2: an unusual fold for the superfamily

The transforming growth factors-beta (TGF-beta 1 through -beta 5) are a family of homodimeric cytokines that regulate proliferation and function in many cell types. Family members have 66 to 80% sequence identity and nine strictly conserved cysteines. A crystal structure of a member of this family, TGF-beta 2, has been determined at 2.1 angstrom (A) resolution and refined to an R factor of 0.172. The monomer lacks a well-defined hydrophobic core and displays an unusual elongated nonglobular fold with dimensions of approximately 60 A by 20 A by 15 A. Eight cysteines form four intrachain disulfide bonds, which are clustered in a core region forming a network complementary to the network of hydrogen bonds. The dimer is stabilized by the ninth cysteine, which forms an interchain disulfide bond, and by two identical hydrophobic interfaces. Sequence profile analysis of other members of the TGF-beta superfamily, including the activins, inhibins, and several developmental factors, imply that they also adopt the TGF-beta fold.

Three-dimensional structure of the Tn5 synaptic complex transposition intermediate

Genomic evolution has been profoundly influenced by DNA transposition, a process whereby defined DNA segments move freely about the genome. Transposition is mediated by transposases, and similar events are catalyzed by retroviral integrases such as human immunodeficiency virus-1 (HIV-1) integrase. Understanding how these proteins interact with DNA is central to understanding the molecular basis of transposition. We report the three-dimensional structure of prokaryotic Tn5 transposase complexed with Tn5 transposon end DNA determined to 2.3 angstrom resolution. The molecular assembly is dimeric, where each double-stranded DNA molecule is bound by both protein subunits, orienting the transposon ends into the active sites. This structure provides a molecular framework for understanding many aspects of transposition, including the binding of transposon end DNA by one subunit and cleavage by a second, cleavage of two strands of DNA by a single active site via a hairpin intermediate, and strand transfer into target DNA.

Three new structures of the core domain of HIV-1 integrase: an active site that binds magnesium

HIV-1 integrase is an essential enzyme in the life cycle of the virus, responsible for catalyzing the insertion of the viral genome into the host cell chromosome; it provides an attractive target for antiviral drug design. The previously reported crystal structure of the HIV-1 integrase core domain revealed that this domain belongs to the superfamily of polynucleotidyltransferases. However, the position of the conserved catalytic carboxylic acids differed from those observed in other enzymes of the class, and attempts to crystallize in the presence of the cofactor, Mg2+, were unsuccessful. We report here three additional crystal structures of the core domain of HIV-1 integrase mutants, crystallized in the presence and absence of cacodylate, as well as complexed with Mg2+. These three crystal forms, containing between them seven independent core domain structures, demonstrate the unambiguous extension of the previously disordered helix alpha4 toward the amino terminus from residue M154 and show that the catalytic E152 points in the general direction of the two catalytic aspartates, D64 and D116. In the vicinity of the active site, the structure of the protein in the absence of cacodylate exhibits significant deviations from the previously reported structures. These differences can be attributed to the modification of C65 and C130 by cacodylate, which was an essential component of the original crystallization mixture. We also demonstrate that in the absence of cacodylate this protein will bind to Mg2+, and could provide a satisfactory platform for binding of inhibitors.

The three-dimensional structure of a phosphorylcholine-binding mouse immunoglobulin Fab and the nature of the antigen binding site

The structure of the Fab of McPC 603, a mouse myeloma protein with phosphorylcholine binding activity, has been determined to 3.1-A resoltuion. The four domains are found to be structurally similar with a well-defined double-layer structure. A large cavity exists at one end of the fragment, the walls of which are formed exclusively of hypervariable residues. Phosphorylcholine binds in this cavity and forms specific interactions with several well-defined amino-acid side chains of the protein. The hapten is bound asymmetrically and interacts more with the heavy chain than with the light chain.

Human peripheral blood contains two distinct lineages of dendritic cells

Human peripheral blood contains two populations of dendritic cells (DC) but their developmental relationship has not been established. Freshly isolated CD11c- DC possessed a lymphoid morphology, lacked myeloid markers but expressed lymphoid markers (CD4+ CD10+) whilst the CD11c+ DC were monocytoid in appearance and expressed myeloid markers. Although both populations were allostimulatory, only the CD11c+ DC were able to take up antigen. Irrespective of the culture conditions the CD11c- cells developed into CD11c- CD13- CD33- CD4+ CD1a- CD83+/- DC. In contrast, cultured CD11c+ cells developed the phenotype CD11c+ CD13+ CD33+/- CD4- CD1a+ CD83+ CD9+. Only the CD11c+ DC expressed macrophage colony-stimulating factor (M-CSF) receptor and gave rise to CD14+, esterase+, phagocytic macrophages when cultured in M-CSF. These data suggest that these two populations of DC represent distinct lineages of antigen-presenting DC.

Matrix metalloproteinase levels are elevated in inflammatory bowel disease

BACKGROUND & AIMS

The expression of matrix metalloproteinases 1, 2, 3, and 9 was examined in biopsy specimens removed from adult and pediatric patients with ulcerative colitis and Crohn's disease. The aim of this study was to determine if the expression of these enzymes was altered between areas of actively inflamed vs. noninvolved mucosa in the same patient and between patients with diseased bowel vs. a control group of patients.

METHODS

Proteolytic activity was quantified by zymography using image analysis. The identity of the matrix metalloproteinases was confirmed by using inhibitors, by comparison with purified standards, and by Western immunoblotting with specific antibodies.

RESULTS

In patients with ulcerative colitis (n = 21), a significant increase (P = 0.0051) in metalloproteinase activity was found in inflamed areas of mucosa compared with noninvolved regions. The levels of activity also were significantly greater (P < 0.001) in noninvolved areas of the bowel (n = 21) compared with levels in control patients (n = 9). In Crohn's disease (n = 8), differences between ulcerated and nonulcerated sites were not significantly different but levels of protease activity at both of these sites were significantly elevated compared with levels in control patients (P < 0.03). Of the proteases detected, matrix metalloproteinase 9 was the most abundantly expressed in the inflamed bowel; neutrophils were confirmed as the likely origin of this protease.

CONCLUSIONS

The abundance and activation of matrix metalloproteinases significantly increases in ulcerative colitis and Crohn's mucosa. Inhibitors of these proteolytic enzymes may therefore be of therapeutic value in the treatment of inflammatory bowel disease.

Methods to improve diagnostic accuracy in a community mental health setting

OBJECTIVE

This study determined the extent to which adding structured procedures improved diagnostic accuracy for outpatients with severe mental illness in a community mental health setting.

METHOD

The Structured Clinical Interview for DSM-III-R (SCID) was used to interview 200 psychiatric outpatients. A research nurse reviewed medical records and amended the SCID diagnoses accordingly. A research psychiatrist or psychologist reviewed the diagnostic data and interviewed each patient to verify or further modify the previous findings. Diagnostic outcomes at each step of the procedure were compared to determine whether adding additional data improved diagnostic accuracy. The additional time required for each element of the diagnostic procedure was also assessed.

RESULTS

Kappa comparisons of the different diagnostic levels showed that adding additional data significantly improved accuracy. Diagnoses rendered by combining the SCID and review of the medical record were the most accurate, followed by the SCID alone, and then diagnoses made by psychiatrists during routine care. In addition, the SCID alone identified five times as many current and past secondary diagnoses as were documented routinely in patients' charts.

CONCLUSIONS

Combining structured interviewing with a review of the medical record appears to produce more accurate primary diagnoses and to identify more secondary diagnoses than routine clinical methods. The patients' knowledge of their diagnoses was limited, suggesting a need for patient education in this setting. Whether use of structured interviewing in routine practice improves patient outcomes deserves further study.

Three-dimensional structure of an intact human immunoglobulin

We have examined the low-resolution structure of a complete human IgG1 using known domain coordinates from crystallographic investigations of immunoglobulin fragment structures. Our results indicate that the Fc portion of this molecule has a structure similar to that of an isolated Fc fragment, with the carbohydrate moiety playing a central role as the principal contact between the CH2 domains. Carbohydrate also forms a large part of the interface between the Fc and Fab regions. The relative orientations of the variable and constant portions of the Fab regions are intermediate between those reported previously, emphasizing the flexibility of the switch region. These data do not support a two-state allosteric model such as has been proposed for antibody effector functions.

A novel DNA-binding motif in MarA: the first structure for an AraC family transcriptional activator

A crystal structure for a member of the AraC prokaryotic transcriptional activator family, MarA, in complex with its cognate DNA-binding site is described. MarA consists of two similar subdomains, each containing a helix-turn-helix DNA-binding motif. The two recognition helices of the motifs are inserted into adjacent major groove segments on the same face of the DNA but are separated by only 27 A thereby bending the DNA by approximately 35 degrees. Extensive interactions between the recognition helices and the DNA major groove provide the sequence specificity.