ABSTRACT
The cytoskeletal protein alpha-catenin, which shares structural similarity with vinculin, is required for cadherin-mediated cell adhesion, and functions to modulate cell adhesive strength and to link the cadherins to the actin-based cytoskeleton. Here we describe the crystal structure of a region of alpha-catenin (residues 377-633) termed the M-fragment. The M-fragment is composed of a tandem repeat of two antiparallel four-helix bundles of virtually identical architectures that are related in structure to the dimerization domain of alpha-catenin and the tail region of vinculin. These results suggest that alpha-catenin is composed of repeating antiparallel helical domains. The region of alpha-catenin previously defined as an adhesion modulation domain corresponds to the C-terminal four-helix bundle of the M-fragment, and in the crystal lattice these domains exist as dimers. Evidence for dimerization of the M-fragment of alpha-catenin in solution was detected by chemical cross-linking experiments. The tendency of the adhesion modulation domain to form dimers may explain its biological activity of promoting cell-cell adhesiveness by inducing lateral dimerization of the associated cadherin molecule.
Subject(s)
Cell Adhesion/physiology , Cytoskeletal Proteins/physiology , Peptide Fragments/physiology , Amino Acid Sequence , Crystallography, X-Ray , Cytoskeletal Proteins/chemistry , Cytoskeletal Proteins/isolation & purification , Dimerization , Humans , Models, Molecular , Molecular Sequence Data , Peptide Fragments/chemistry , Peptide Fragments/isolation & purification , Protein Conformation , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Repetitive Sequences, Amino Acid , Sequence Homology, Amino Acid , Vinculin/chemistry , alpha CateninABSTRACT
The synthesis, crystal structure data and 1H and 13C NMR spectroscopy of methyl 3-azido-2,3-dideoxy-alpha-D-arabino-hexopyranoside (5b) is reported. This compound adopts the 4C1 conformation. Hydrogen-bonded molecules of 5b form helices around the crystallographic 4(1) axis.
Subject(s)
Azides/chemical synthesis , Carbohydrates/chemical synthesis , Glycosides/chemical synthesis , Crystallography, X-Ray , Hydrogen Bonding , Magnetic Resonance Spectroscopy , Models, MolecularABSTRACT
p97, an abundant hexameric ATPase of the AAA family, is involved in homotypic membrane fusion. It is thought to disassemble SNARE complexes formed during the process of membrane fusion. Here, we report two structures: a crystal structure of the N-terminal and D1 ATPase domains of murine p97 at 2.9 A resolution, and a cryoelectron microscopy structure of full-length rat p97 at 18 A resolution. Together, these structures show that the D1 and D2 hexamers pack in a tail-to-tail arrangement, and that the N domain is flexible. A comparison with NSF D2 (ATP complex) reveals possible conformational changes induced by ATP hydrolysis. Given the D1 and D2 packing arrangement, we propose a ratchet mechanism for p97 during its ATP hydrolysis cycle.
Subject(s)
Adenosine Triphosphatases/chemistry , Adenosine Triphosphatases/ultrastructure , Cryoelectron Microscopy , Nuclear Proteins/chemistry , Nuclear Proteins/ultrastructure , Saccharomyces cerevisiae Proteins , Vesicular Transport Proteins , Adenosine Diphosphate/metabolism , Adenosine Triphosphatases/metabolism , Adenosine Triphosphate/metabolism , Adenylyl Imidodiphosphate/metabolism , Amino Acid Sequence , Animals , Archaeal Proteins , Binding Sites , Carrier Proteins/chemistry , Crystallography, X-Ray , Fungal Proteins/chemistry , Membrane Fusion , Mice , Models, Molecular , Molecular Sequence Data , N-Ethylmaleimide-Sensitive Proteins , Nuclear Proteins/metabolism , Peptide Fragments/chemistry , Peptide Fragments/metabolism , Peptide Fragments/ultrastructure , Pliability , Protein Structure, Secondary , Protein Structure, Tertiary , Rats , Sequence Alignment , Valosin Containing ProteinABSTRACT
An analysis has been performed on the first example of a non-proline cis- peptide bond found within a complementarity determining region (CDR) of an antibody. The bond is located in CDR 3 of the heavy chain (H3) and makes substantial interactions to a peptide from a breast tumour-associated antigen. The antibody-peptide complex is compared, both in H3 length (six residues) and peptide conformation, to a number of other such complexes in the Brookhaven Data Bank (PDB). There is only one other H3 loop of the same length. Analysis of loop searches of the PDB, taken over the H3 framework of SM3, suggest that there is a limited repertoire of conformations for loops of length 6 compared to loops of length 5 and 7. It is argued that the cis-peptide bond is present because of the limited number of loop conformations of length 6, plus, the requirement of the H3 loop to contact the bound peptide. Modelling suggests that an all-trans-peptide loop conformation can replace the H3 loop and this raises the question of whether there is a trans- to cis-peptide bond isomerization upon peptide binding.
Subject(s)
Antibodies/chemistry , Immunoglobulin Variable Region/chemistry , Peptides/chemistry , Crystallography, X-Ray , Databases, Factual , Models, Molecular , Proline/chemistry , Protein ConformationABSTRACT
The anti-breast tumour antibody SM3 has a high selectivity in reacting specifically with carcinoma-associated mucin. SM3 recognises the core repeating motif (Pro-Asp-Thr-Arg-Pro) of aberrantly glycosylated epithelial mucin MUC1, and has potential as a therapeutic and diagnostic tool. Here we report the crystal structure of the Fab fragment of SM3 in complex with a 13-residue MUC1 peptide antigen (Thr1P-Ser2P-Ala3P-Pro4P-Asp5P-Thr6P -Arg7P-Pro8P-Ala9P-Pro10P-Gly11P- Ser12P-Thr13P). The SM3-MUC1 peptide structure was solved by molecular replacement, and the current model is refined at 1.95 A resolution with an R-factor of 21.3% and R-free 28.3%. The MUC1 peptide is bound both by non-polar interactions and hydrogen bonds in an elongated groove in the antibody-combining site through interactions with Complimentarity Determining Regions (CDRs), three of the light chain (L1, L2, L3) and two of the heavy chain (H1 and H3). The conformation of the peptide is mainly extended with no discernable standard secondary structure. There is a single non-proline cis-peptide bond in H3 (Val95H-Gly96H-Gln97H-Phe98H-Ala101H-Ty r102H) between Gly96H and Gln97H, which appears to play a role in SM3-peptide antigen interactions, and represents the first such example within an antibody hypervariable loop. The SM3-MUC1 peptide structure has implications for rational therapeutic and diagnostic antibody engineering.
Subject(s)
Antibodies, Neoplasm/chemistry , Breast Neoplasms/immunology , Epitopes/chemistry , Immunoglobulin Fab Fragments/chemistry , Mucins/chemistry , Peptides/chemistry , Amino Acid Sequence , Antigen-Antibody Reactions , Models, MolecularABSTRACT
PR1A3 antibody binds specifically to the tumour-associated cell-surface antigen, carcinoembryonic antigen. Crystals of the Fab fragment of the PR1A3 antibody were obtained by vapour diffusion against mother liquor containing Tris-HC1 buffer, pH 8.6, magnesium chloride and polyethylene glycol 4000 as precipitating agent. Crystals belong to the monoclinic space group P2(1) with cell dimensions a = 42.2, b = 216.7, c = 45.9 A and beta = 95.6 degrees. Two Fab fragments are proesent in the asymmetric unit. Diffracted intensities up to 2.9 A resolution have been measured from frozen crystals.
ABSTRACT
SM3 antibody binds to a tumour-associated epitope on polymorphic epithelial mucin (PEM). Crystals of the Fab fragment of SM3 in complex with a peptide antigen were obtained by vapour diffusion against mother liquor containing acetate buffer, pH 6.5, cadmium chloride and polyethylene glycol (PEG) 4000 as precipitating agent. Crystals belong to the monoclinic space group P2(1) with cell dimensions a = 42.2, b = 83.9, c = 64.5 A and beta = 93.4 degrees. One Fab-antigen complex is present in the asymmetric unit. Diffracted intensities up to 1.95 A resolution have been measured from a frozen crystal using synchrotron radiation.
