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D C Wiley

Publications and source records attributed to D C Wiley.

At least 109 records · Page 6Linked to original sources
PubMed1994

Structure of influenza haemagglutinin at the pH of membrane fusion.

Low pH induces a conformational change in the influenza virus haemagglutinin, which then mediates fusion of the viral and host cell membranes. The three-dimensional structure of a fragment of the haemagglutinin in this conformation reveals a major refolding of the secondary and tertiary structure of the molecule. The apolar fusion peptide moves at least 100 A to one tip of the molecule. At the other end a helical segment unfolds, a subdomain relocates reversing the chain direction, and part of the structure becomes disordered.

Amino Acid Sequence↗
PubMed1994

MHC class II function preserved by low-affinity peptide interactions preceding stable binding.

Major histocompatibility complex class II molecules and their peptide ligands show unusual interaction kinetics, with slow association and dissociation rates that yield an apparent equilibrium constant of approximately 10(-6)-10(-8) M (refs 1-5). However, there is evidence for a specific, rapidly formed, short-lived complex. The altered migration on SDS-polyacrylamide gel electrophoresis of class II molecules upon stable peptide binding has led to the hypothesis that the two kinetically distinguishable types of class II-peptide complexes correspond to different structures. In accord with this model, we demonstrate here that insect cell-derived HLA-DR1 class II molecules show fast, almost stoichiometric occupancy with rapidly dissociating peptide while remaining sensitive to SDS-induced chain dissociation. The same DR1 molecules slowly and quantitatively form long-lived complexes resistant to SDS-induced denaturation. Surprisingly, low-affinity interaction with peptide protects class II from denaturation at physiological temperature, a finding that has implications for understanding the role of invariant chain in the intracellular behaviour of class II molecules.

Amino Acid Sequence↗
PubMed1994

Crystal structures of influenza virus hemagglutinin in complex with high-affinity receptor analogs.

BACKGROUND: The first step in influenza A virus infection involves attachment to cells through binding of viral hemagglutinin to cell-surface receptors containing alpha-5-N-acetylneuraminic acid (sialic acid). The structures of soluble hemagglutinin in isolation and in complex with several low-affinity receptor analogs have been solved previously to approximately 3A resolution. To design effective, and possibly therapeutic, inhibitors of viral attachment we have determined the structure of hemagglutinin in complex with four high-affinity (10-fold to 100-fold higher affinity) sialic acid analogs at higher resolution. RESULTS: In each crystal structure the sialic acid moiety is equivalently positioned in the receptor binding site but the substituent groups that differentiate the high-affinity analogs from each other interact with hydrophobic patches and polar residues adjacent to the binding site. Re-examination of the receptor binding site at 2.15A resolution reveals several hydrophilic pockets and an apolar channel that adjoin the receptor binding site. CONCLUSIONS: The interactions observed in the structures of soluble hemagglutinin in complex with receptor analogs suggest explanations for the observed affinities of the analogs, designs for potential sialic acid analogs with even higher affinities, and ideas both for inhibiting membrane fusion and for circumventing evasion of inhibition by antigenic variation.

Amino Acid Sequence↗
PubMed1994

Importance of peptide amino and carboxyl termini to the stability of MHC class I molecules.

An influenza virus matrix peptide in which either the charged amino or carboxyl terminus was substituted by methyl groups promoted folding of the class I human histocompatibility antigen (HLA-A2). A peptide modified at both termini did not promote stable folding. The thermal stability of HLA-A2 complexed with peptides that did not have either terminus was approximately 22 degrees C lower than that of the control peptide, whereas matrix peptide in which both anchor positions were substituted by alanines had its stability decreased by only 5.5 degrees C. Thus, the conserved major histocompatibility complex class I residues at both ends of the peptide binding site form energetically important sites for binding the termini of short peptides.

Amino Acid Sequence↗
PubMed1994

Five viral peptide-HLA-A2 co-crystals. Simultaneous space group determination and X-ray data collection.

We prepared and crystallized five complexes of the human histocompatibility molecule HLA-A2 with peptides derived from human immunodeficiency virus type 1, human T lymphotropic virus type 1, influenza A virus and hepatitis B virus proteins. Each HLA-A2 complex was refolded in vitro from insoluble proteins produced in bacteria; to crystallize, two of the complexes required seeding with microcrystals of another complex. Maintained at -160 degrees C, single co-crystals of each of the five peptide-HLA-A2 complexes yielded complete X-ray diffraction data sets to a resolution of approximately 2.5 A. After a sufficient number of diffraction peaks were acquired during data collection, the direct analysis of integrated intensities established the point group of the co-crystal, thus allowing an efficient data collection strategy to be designed. The subsequent examination of systematic absences revealed that the five peptide-HLA-A2 co-crystals formed in space groups P1, P2(1), or P2(1)2(1)2(1). Molecular replacement structure solutions yielded unambiguous protein electron density maps, thus confirming the space group determinations. The system of obtaining HLA-A2 co-crystal structures described here is applicable to other crystallographic problems where structures of several related molecules from uncharacterized single crystals are required.

Amino Acid Sequence↗
PubMed1994

Binary and ternary complexes between T-cell receptor, class II MHC and superantigen in vitro.

Superantigens are proteins that in association with class II major histocompatibility complex (MHC)-bearing cells can stimulate virtually all T cells that express particular classes of the variable beta-domains of the T-cell receptor (TCR). This mechanism of T-cell activation circumvents the usual requirement for peptide-specific MHC recognition. Staphylococcus aureus enterotoxin B (SEB) is a bacterial superantigen that causes food poisoning and shock. We have characterized the tertiary complex of SEB, a soluble T-cell receptor, and a soluble class II MHC molecule DR1, and the three binary complexes TCR-SEB, SEB-DR1, and the peptide-specific complex DR1-TCR. We report here that in each case the specificity of the interaction among the soluble molecules is the same as observed in biological assays. Native gel electrophoresis and plasmon resonance affinity measurements indicate that SEB-TCR complex can form in the absence of class II MHC and that SEB-TCR interaction increases the binding of DR1. The observation that a superantigen can form complexes with TCR in both the absence and presence of class II MHC may provide a mechanism for its ability to induce anergy in some circumstances and activation in others (reviewed in ref. 8).

Amino Acid Sequence↗
PubMed1994

Three-dimensional structure of a human class II histocompatibility molecule complexed with superantigen.

The structure of a bacterial superantigen, Staphylococcus aureus enterotoxin B, bound to a human class II histocompatibility complex molecule (HLA-DR1) has been determined by X-ray crystallography. The superantigen binds as an intact protein outside the conventional peptide antigen-binding site of the class II major histocompatibility complex (MHC) molecule. No large conformational changes occur upon complex formation in either the DR1 or the enterotoxin B molecules. The structure of the complex helps explain how different class II molecules and superantigens associate and suggests a model for ternary complex formation with the T-cell antigen receptor (TCR), in which unconventional TCR-MHC contacts are possible.

Amino Acid Sequence↗
PubMed1994

Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide.

An influenza virus peptide binds to HLA-DR1 in an extended conformation with a pronounced twist. Thirty-five per cent of the peptide surface is accessible to solvent and potentially available for interaction with the antigen receptor on T cells. Pockets in the peptide-binding site accommodate five of the thirteen side chains of the bound peptide, and explain the peptide specificity of HLA-DR1. Twelve hydrogen bonds between conserved HLA-DR1 residues and the main chain of the peptide provide a universal mode of peptide binding, distinct from the strategy used by class I histocompatibility proteins.

Amino Acid Sequence↗
PubMed1994

Crystals of a fragment of influenza haemagglutinin in the low pH induced conformation.

Fusion of the influenza viral membrane with the membrane of the host cell is preceded by a low pH induced conformation change in the viral haemagglutinin. A fragment, consisting of much of the stem domain of influenza haemagglutinin in the low pH induced conformation, has been crystallized by the vapour diffusion method. Several crystal forms have been obtained and the molecular packing in these crystals is discussed. Crystals suitable for the recording of high angle X-ray diffraction data grow in space group C222(1). Diffraction data have been recorded from crystals cooled to -170 degrees C in a cryoprotectant buffer.

Crystallization↗
PubMed1994

HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site.

A program (HOOK) is described for generating potential ligands that satisfy the chemical and steric requirements of the binding region of a macromolecule. Functional group sites with defined positions and orientations are derived from known ligand structures or the multicopy simulation search (MCSS) method (Miranker, A., Karplus, M. Proteins 11:29-34, 1991). HOOK places molecular "skeletons" from a database into the protein binding region by making bonds between sites ("hooks") on the skeleton and functional groups. The nonpolar interactions with the binding region of candidate molecules are assessed by use of a simplified van der Waals potential. The method is illustrated by constructing ligands for the sialic acid binding site of the hemagglutinin from the influenza A virus and the active site of chloramphenicol acetyltransferase. Aspects of the HOOK program that lead to a highly efficient search of 10(5) or more skeletons for binding to 10(2) or more functional group minima are outlined.

Algorithms↗
PubMed1993

The antigenic identity of peptide-MHC complexes: a comparison of the conformations of five viral peptides presented by HLA-A2.

Complexes of five peptides (from HIV-1, influenza A virus, HTLV-1, and hepatitis B virus proteins) bound to the human class I MHC molecule HLA-A2 have been studied by X-ray crystallography. While the peptide termini and their second and C-terminal anchor side chains are bound similarly in all five cases, the main chain and side chain conformations of each peptide are strikingly different in the center of the binding site, and these differences are accessible to direct TCR recognition. Each of the central peptide residues is seen to point up for some bound peptides, but down or sideways for others. Thus, although fixed at its ends, the structure of an MHC-bound peptide appears to be a highly complex function of its entire sequence, potentially sensitive to even small sequence differences. In contrast, MHC structural variation is relatively limited. These results offer a structural framework for understanding the role of nonanchor peptide side chains in both peptide-MHC binding affinity and TCR recognition.

Amino Acid Sequence↗
PubMed1993

Comparison of the P2 specificity pocket in three human histocompatibility antigens: HLA-A*6801, HLA-A*0201, and HLA-B*2705.

Coordinates from x-ray structures of HLA-A*6801, HLA-A*0201, and HLA-B*2705 were analyzed to examine the basis for their selectivity in peptide binding. The pocket that binds the side chain of the peptide's second amino acid residue (P2 residue) shows a preference for Val, Leu, and Arg in these three HLA subtypes, respectively. The Arg-specific pocket of HLA-B*2705 differs markedly from those of HLA-A*0201 and HLA-A*6801, as a result of numerous differences in the side chains that form the pocket's surface. The cause of the specificity differences between HLA-A*0201 and HLA-A*6801 is more subtle and depends both on a change in conformation of pocket residue Val-67 and on a sequence difference at residue 9. The Val-67 conformational change appears to be caused by a shift in the position of the alpha 1-domain alpha-helix relative to the beta-sheet in the cleft and may, in fact, depend on amino acid differences remote from the P2 pocket. Analysis of the stereochemistry of the P2 side chain interacting with its binding pocket permits an estimate to be made of its contribution to the free-energy change of peptide binding.

Amino Acid Sequence↗
PubMed1993

Three-dimensional structure of the human class II histocompatibility antigen HLA-DR1.

The three-dimensional structure of the class II histocompatibility glycoprotein HLA-DR1 from human B-cell membranes has been determined by X-ray crystallography and is similar to that of class I HLA. Peptides are bound in an extended conformation that projects from both ends of an 'open-ended' antigen-binding groove. A prominent non-polar pocket into which an 'anchoring' peptide side chain fits is near one end of the binding groove. A dimer of the class II alpha beta heterodimers is seen in the crystal forms of HLA-DR1, suggesting class II HLA dimerization as a mechanism for initiating the cytoplasmic signalling events in T-cell activation.

B-Lymphocytes↗
PubMed1993

A structural motif in the variant surface glycoproteins of Trypanosoma brucei.

The variable domain of the trypanosome variant surface glycoprotein (VSG) ILTat 1.24 has been shown by X-ray crystallography to resemble closely the structures of VSG MITat 1.2, despite their low sequence similarity. Specific structural features of these VSGs, including substitution of carbohydrate for an alpha-helix, can be found in other VSG sequences. Thus antigenic variation in trypanosomes is accomplished by sequence variation, not gross structural alteration; the extensive sequence differences among VSGs may be required for another reason, such as the avoidance of recognition by helper T cells. Additionally, VSG sequences are found to define families, within a VSG superfamily, which have evolved in the trypanosome genome.

Amino Acid Sequence↗
PubMed1993

How can schools help children from homeless families?

Families represent the fastest growing subgroup among the homeless in America. Most homeless families are headed by women who lack high school diplomas, have poor work skills, little job training, and are long-term users of Aid to Families with Dependent Children (AFDC). The average homeless family is comprised of two to three children, most of whom are younger than age five. These children suffer from a number of acute and chronic health problems. Once in school, these children often experience developmental and academic delays which increase the potential for school dropout. School districts must address the health and academic challenges these children bring to school. Measures include forming a community-based task force, working with homeless shelters in addressing needs of these families, increasing awareness of faculty and staff, and developing specific classroom/school environment strategies to encourage these children to succeed. Opportunities for involvement by teachers, counselors, and school nurses are noted, and seven strategies to help the homeless child in school are offered.

Child↗
PubMed1992

Different length peptides bind to HLA-Aw68 similarly at their ends but bulge out in the middle.

We report here the determination and refinement to 1.9 A resolution by X-ray cryo-crystallography the structure of HLA-Aw68. The averaged image from the collection of bound, endogenous peptides clearly shows the atomic structure at the first three and last two amino acids in the peptides but no connected electron density in between. This suggests that bound peptides, held at both ends, take alternative pathways and could be of different lengths by bulging out in the middle. Peptides eluted from HLA-Aw68 include peptides of 9, 10 and 11 amino acids, a direct indication of the length heterogeneity of tightly bound peptides. Peptide sequencing shows relatively conserved 'anchor' residues at position 2 and the carboxy-terminal residue. Conserved binding sites for the peptide N and C termini at the ends of the class I major histocompatibility complex binding groove are apparently dominant in producing the long half-lives of peptide binding and the peptide-dependent stabilization of the class I molecule's structure.

Amino Acid Sequence↗