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At least 955 records · Page 53Linked to original sources
PubMed1997

Phage P22 tailspike protein: crystal structure of the head-binding domain at 2.3 A, fully refined structure of the endorhamnosidase at 1.56 A resolution, and the molecular basis of O-antigen recognition and cleavage.

The tailspike protein of Salmonella phage P22 is a viral adhesion protein with both receptor binding and destroying activities. It recognises the O-antigenic repeating units of cell surface lipopolysaccharide of serogroup A, B and D1 as receptor, but also inactivates its receptor by endoglycosidase (endorhamnosidase) activity. In the final step of bacteriophage P22 assembly six homotrimeric tailspike molecules are non-covalently attached to the DNA injection apparatus, mediated by their N-terminal, head-binding domains. We report the crystal structure of the head-binding domain of P22 tailspike protein at 2.3 A resolution, solved with a recombinant telluromethionine derivative and non-crystallographic symmetry averaging. The trimeric dome-like structure is formed by two perpendicular beta-sheets of five and three strands, respectively in each subunit and caps a three-helix bundle observed in the structure of the C-terminal receptor binding and cleaving fragment, reported here after full refinement at 1.56 A resolution. In the central part of the receptor binding fragment, three parallel beta-helices of 13 complete turns are associated side-by-side, while the three polypeptide strands merge into a single domain towards their C termini, with close interdigitation at the junction to the beta-helix part. Complex structures with receptor fragments from S. typhimurium, S. enteritidis and S. typhi253Ty determined at 1.8 A resolution are described in detail. Insertions into the beta-helix form the O-antigen binding groove, which also harbours the active site residues Asp392, Asp395 and Glu359. In the intact structure of the tailspike protein, head-binding and receptor-binding parts are probably linked by a flexible hinge whose function may be either to deal with shearing forces on the exposed, 150 A long tailspikes or to allow them to bend during the infection process.

Amino Acid Sequence↗
PubMed1995

Crystal structure of SIV matrix antigen and implications for virus assembly.

Simian immunodeficiency virus (SIV) is closely related to human immunodeficiency virus (HIV), their matrix antigens (MAs) sharing some 50% sequence identity. MA is a component of Pr55Gag, the sole protein required for assembly of the virion shell. MA targets Pr55 to the plasma membrane, and facilitates incorporation of the virus envelope protein and assembly of the Pr55Gag shell. Cleavage of Pr55 by the viral protease produces the mature protein of relative molecular mass 17-18K, which underlies the host-derived membrane and is important in both virus entry and nuclear localization of the virion core. Here we report the crystal structure of SIV MA. The molecule forms a trimer consistent with oligomerization in vitro, the observed virion architecture, and various biological properties of MA.

Amino Acid Sequence↗
PubMed2006

Synthesis of a novel glycosphingolipid from the millipede, Parafontaria laminata armigera, and the assembly of its carbohydrate moiety into multivalent structures.

A novel glycosphingolipid, beta-D-Manp-(1-->4)-[alpha-L-Fucp-(1-->3)]-beta-D-Glcp-(1-->1)-Cer, found in the millipede, Parafontaria laminata armigera, and multivalent derivatives of its carbohydrate moiety were synthesized. As the key step, the target glycolipid (1) was obtained through an inversion reaction at the 2-position of a beta-glucopyranoside residue yielding a beta-mannopyranoside. In addition, the synthesis of fluorescently labeled trimer and tetramer glycoconjugates (2, 3) was achieved by iterative amide bond formation using a monomer unit (24).

Animals↗
PubMed1995

The capsid size-determining protein Sid forms an external scaffold on phage P4 procapsids.

Although the phages P2 and P4 build their capsids from the same precursor, the product of the P2 N gene, the two capsids differ in size: P2 builds a 60 nm, T = 7 capsid from 420 subunits, whereas P4 makes a 45 nm, T = 4 capsid from 240 subunits. This difference leads to substantial changes in shell geometry and subunit interactions. Previous results have demonstrated that the P4 sid gene is responsible for the assembly of P4-sized shells. We have used cryo-electron microscopy and image reconstruction to determine the structure of a putative assembly intermediate of P4 capsids, produced in vivo from cloned genes. We demonstrate that Sid forms a P4-specific scaffold with icosahedral symmetry on the outside of the procapsid-like particles. The Sid molecules (60 or 120 copies) form lofty arches that interact with the gpN hexamers on the icosahedral 2-fold axes, and connect as trimers over the 3-fold axes, forming a continuous dodecahedrally shaped outer cage. The gpN shell inside the Sid cage is approximately 40 nm wide, consistent with the previously suggested maturational expansion. The main difference with respect to the mature P4 capsids is found in the hexamers, which appear strongly elongated and more protruding than in the mature shell. These and previous results are discussed in the light of a model for regulation of capsid size.

Amino Acid Sequence↗
PubMed1994

Oligomerization of recombinant penton base of adenovirus type 2 and its assembly with fiber in baculovirus-infected cells.

Full-length Ad2 penton base (PbFL571) and amino-terminal (PbAT69) and carboxy-terminal deletion mutants (PbCT550 and PbCT531) were expressed at high levels in recombinant baculovirus-infected insect cells. PbFL571, and with a lesser efficiency PbAT69, assembled penton base capsomers (9S pentamers), whereas pentamer assembly was abolished with the deletion of the 21 C-terminal amino acids (as in PbCT550). A discrete population of penton base capsomers in PbFL571 and PbAT69 was found to occur as 12S decamers. PbFL571 and PbAT69 penton base were able to bind to full-length (but not to N-terminal deletion mutants of) fiber trimer to form authentic penton capsomer when coexpressed in trans in double-infected cells. Penton base monomers accumulated by PbCT550 and PbCT531 were capable of interacting with both fiber trimers and monomers. This suggested that mutual binding sites exist in the fiber and penton base subunits, and that the fiber-binding domain is located between residues 70 and 531 in the penton base, with its complementary domain situated at the N-terminus of the fiber. Intranuclear inclusions of recombinant protein were observed with the three deletion mutants PbAT69, PbCT550, and PbCT531, implying the existence of karyophilic signal(s) in the central domain of penton base.

Adenoviruses, Human↗
PubMed2005

The hantavirus nucleocapsid protein recognizes specific features of the viral RNA panhandle and is altered in conformation upon RNA binding.

Hantaviruses are tripartite negative-sense RNA viruses and members of the Bunyaviridae family. The nucleocapsid (N) protein is the principal structural component of the viral capsid. N forms a stable trimer that specifically recognizes the panhandle structure formed by the viral RNA termini. We used trimeric glutathione S-transferase (GST)-N protein and small RNA panhandles to examine the requirements for specific recognition by Sin Nombre hantavirus N. Trimeric GST-N recognizes the panhandles of the three viral RNAs (S, M, and L) with high affinity, whereas the corresponding plus-strand panhandles of the complementary RNA are recognized with lower affinity. Based on analysis of nucleotide substitutions that alter either the higher-order structure of the panhandle or the primary sequence of the panhandle, both secondary structure and primary sequence are necessary for stable interaction with N. A panhandle 23 nucleotides long is necessary and sufficient for high-affinity binding by N, and stoichiometry calculations indicate that a single N trimer interacts with a single panhandle. Surprisingly, displacement of the panhandle structure away from the terminus does not eliminate recognition by N. The binding of N to the panhandle is an entropy-driven process resulting in initial stable N-RNA interaction followed by a conformational change in N. Taken together, these data provide insight into the molecular events that take place during interaction of N with the panhandle and suggest that specific high-affinity interaction between an RNA binding domain of trimeric N and the panhandle is required for encapsidation of the three viral RNAs.

Base Sequence↗
PubMed1985

Purification and characterization of gene 17 product of bacteriophage T3.

Tail fiber proteins of bacteriophage T3 are encoded by gene 17. By using in vitro complementation for phage assembly as an assay, the product of gene 17 (gp17) was purified to near homogeneity from cells infected with a double mutant of T3 defective in DNA synthesis and head assembly. The purified gp17 consists of a single polypeptide having a molecular weight of 67,000. Electron microscopy of the purified gp17 showed a fiber structure similar to the tail fiber in a virion. The subunit structure of the purified, native gp17 was analyzed by using a crosslinking agent, dimethyl suberimidate. The results indicate that native gp17 is a trimer of gp17 monomer.

Macromolecular Substances↗
PubMed2004

An icosahedral assembly of the light-harvesting chlorophyll a/b protein complex from pea chloroplast thylakoid membranes.

When the light-harvesting chlorophyll a/b protein complex (LHC-II) from pea thylakoid membranes is co-crystallized with native lipids, an octahedral crystal that exhibits no birefringence is obtained. Cryogenic electron micrographs of a crystal edge showed the crystal to be made up of hollow spherical assemblies with a diameter of 250 A. X-ray diffraction data at 9.5 A resolution revealed the spherical shell of LHC-II to have icosahedral symmetry. A T = 1 icosahedral model of LHC-II, in which the stromal surface of the protein faces outward, was constructed using the previously reported structure of the LHC-II trimer [Kühlbrandt et al. (1994), Nature (London), 367, 614-621]. The present result shows the first example of a well ordered three-dimensional crystal of icosahedral proteoliposomes.

Crystallization↗
PubMed1984

Mechanism of localization of major outer membrane lipoprotein in Escherichia coli. Studies with the OmpF-lipoprotein hybrid protein.

A chimera gene consisting of the ompF promoter, the coding regions for the signal peptide and the NH2-terminal 11 amino acid residues of outer membrane OmpF protein, and the coding region for the major outer membrane lipoprotein devoid of the NH2-terminal 7 amino acid residues was constructed. Escherichia coli carrying the cloned chimera gene produced a hybrid protein with the predicted chemical structure. The protein was localized in the periplasmic space with an interaction with the peptidoglycan layer. These results indicate that the hybrid protein was expressed, secreted across the cytoplasmic membrane, and processed for the signal peptide normally. The hybrid protein, however, was not incorporated into the outer membrane, suggesting the importance of the lipid domain in the assembly of the lipoprotein into the outer membrane. Although a larger part of the protein was extractable with sodium dodecyl sulfate, a part of the hybrid protein was covalently bound to the peptidoglycan layer as the lipoprotein is. Upon treatment with lysozyme of the envelope the hybrid protein became water soluble. The solubilized protein most probably existed as a trimer. These results most likely suggest that the major lipoprotein exists as a trimer in the periplasmic space with interactions with the peptidoglycan layer through the protein domain on one side and with the outer membrane through the lipid domain on the other side.

Amino Acid Sequence↗
PubMed1998

The role of protonation and metal chelation preferences in defining the properties of mercury-binding coiled coils.

To define the delicate interplay between metal chelation, protein folding and function in metalloproteins, a family of de novo-designed peptides was synthesized that self-assemble in aqueous solution to form two and three-stranded alpha-helical coiled coils. Each peptide contains a single Cys residue at an a or d position of the heptad repeat. Peptide association thus produces a Cys-rich coordination environment that has been used to bind Hg(II) ions. These peptides display a pH-dependent association, with trimers observed above the pKa of Glu side-chains and dimers below this value. Finite-difference Poisson-Boltzmann calculations suggest that the dimeric state decreases the unfavorable electrostatic interactions between positively charged Lys side-chains (relative to the trimer). The Cys-containing peptides bind Hg(II) in a position-dependent fashion. Cys at a positions form three-coordinate Hg complexes at high pH where the trimeric aggregation state predominates, and two-coordinate complexes at lower pH. A d position Cys, however, is only able to generate the two-coordinate complex, illustrating the difference in coordination geometry between the two positions in the coiled coil. The binding of Hg(II) was also shown to substantially increase the stability of the helical aggregates.

Amino Acid Sequence↗
PubMed2004

Molecular structure and interaction of recombinant human type XVI collagen.

Collagen XVI is a minor component of at least two different extracellular fibrillar networks of specialized regions of skin and cartilage. In skin, collagen XVI is integrated into particular fibrillin-rich microfibrils lacking an amorphous elastin core. In cartilage, collagen XVI is a component of small heterotypic D-banded fibrils, mainly occurring in the territorial matrix of chondrocytes. Here, we present the first direct evidence for the molecular structure and functional properties of these fibril-associated collagens with interrupted triple helices (FACIT). We have expressed recombinantly the full-length alpha1 chain of human collagen XVI in HEK 293 EBNA cells in large quantities using an episomal expression system. Secreted full-length recombinant collagen XVI forms stable disulfide-bonded homotrimers and is rapidly proteolytically processed to distinct fragments at specific protease sequence motifs, one resembling an aggrecanase recognition site. Limited trypsin digestion assays and thermal transition curves imply sequential thermal denaturation of individual triple helical domains of this recombinant collagen, similar to authentic collagen XVI. Molecular images of collagen XVI reveal rod-like molecules which harbor multiple sharp kinks attributing a highly flexible structure presumably introduced by non-collagenous (NC) regions. Terminally located cloverleaf-shaped nodules correspond to the large NC NC11 domain of trimeric collagen XVI. The total length of individual trimeric recombinant collagen XVI molecules constitutes about 240 nm as calculated by atomic force and negative staining electron microscopy. Recombinant collagen XVI interacts with fibrillin-1 and with fibronectin indicating multiple molecular interactions in which this ubiquitously expressed and versatile FACIT-collagen can participate. In vitro generated collagen XVI provides an indispensable tool for future determination of its function during supramolecular assembly of matrix aggregates and its role in maintenance, organization and interaction of fibrillar structures.

Amino Acid Sequence↗
PubMed2003

Analysis of the retrovirus capsid interdomain linker region.

In structural studies, the retrovirus capsid interdomain linker region has been shown as a flexible connector between the CA N-terminal domain and its C-terminal domain. To analyze the function of the linker region, we have examined the effects of three Moloney murine leukemia virus (M-MuLV) capsid linker mutations/variations in vivo, in the context of the full-length M-MuLV structural precursor protein (PrGag). Two mutations, A1SP and A5SP, respectively, inserted three and seven additional codons within the linker region to test the effects of increased linker lengths. The third variant, HIV/Mo, represented a chimeric HIV-1/M-MuLV PrGag protein, fused at the linker region. When expressed in cells, the three variants reduced the efficiency of virus particle assembly, with PrGag proteins and particles accumulating at the cellular plasma membranes. Although PrGag recognition of viral RNA was not impaired, the capsid linker variant particles were abnormal, with decreased stabilities, anomalous densities, and aberrant multiple lobed and tubular morphologies. Additionally, rather than crosslinking as PrGag dimers, particle-associated A1SP, A5SP, and HIV/Mo proteins showed an increased propensity to crosslink as trimers. Our results suggest that a wild-type retrovirus capsid linker region is required for the proper alignment of capsid protein domains.

3T3 Cells↗
PubMed2004

Light-harvesting features revealed by the structure of plant photosystem I.

Oxygenic photosynthesis is driven by two multi-subunit membrane protein complexes, Photosystem I and Photosystem II. In plants and green algae, both complexes are composed of two moieties: a reaction center (RC), where light-induced charge translocation occurs, and a peripheral antenna that absorbs light and funnels its energy to the reaction center. The peripheral antenna of PS I (LHC I) is composed of four gene products (Lhca 1-4) that are unique among the chlorophyll a/b binding proteins in their pronounced long-wavelength absorbance and in their assembly into dimers. The recently determined structure of plant Photosystem I provides the first relatively high-resolution structural model of a super-complex containing a reaction center and its peripheral antenna. We describe some of the structural features responsible for the unique properties of LHC I and discuss the advantages of the particular LHC I dimerization mode over monomeric or trimeric forms. In addition, we delineate some of the interactions between the peripheral antenna and the reaction center and discuss how they serve the purpose of dynamically altering the composition of LHC I in response to environmental pressure. Combining structural insight with spectroscopic data, we propose how altering LHC I composition may protect PS I from excessive light.

Journal Article↗
PubMed2007

Quantitation of aggregate levels in a recombinant humanized monoclonal antibody formulation by size-exclusion chromatography, asymmetrical flow field flow fractionation, and sedimentation velocity.

Size-exclusion high-performance liquid chromatography (SE-HPLC, SEC) is the long-standing biopharmaceutical industry standard for quantitation of soluble protein aggregates. Recently, sedimentation velocity analytical ultracentrifugation (SV-AUC) has emerged as a possible orthogonal technique to SEC for soluble aggregate quantitation. Moreover, asymmetrical flow field flow fractionation (AF4) has shown early promise in quantifying protein aggregates, both soluble and insoluble. We report soluble aggreg ate quantities measured by SEC, AF4, and SV-AUC analyzed by SEDFIT/c(s) for acid stressed and unstressed samples of a recombinant humanized monoclonal antibody. In equivalent antibody samples, SV-AUC, and AF4 detect markedly higher total aggregate levels than SEC. Furthermore, SEC fails to detect higher molecular weight soluble aggregates apparent in SV-AUC and AF4 analyses. Pooled fractions containing soluble dimeric aggregates were purified and re-analyzed by both SV-AUC and SEC. Reinjection of purified dimer onto the SEC column induces formation of detectable quantities of monomer and trimer. All sample types show statistically significant (p-values<0.01) antibody losses through the SEC column. This incomplete mass recovery from SEC indicates probable antibody physical adsorption to gel filtration media. Analysis of the sedimentation behavior of high molecular weight components suggests increased molecular asphericity with increasing molecular weight. We present an aggregation model based on nearly linear end-to-end assembly of monomeric subunits which is shown to be consistent with SV-AUC, SEC, AF4, and dynamic light scattering (DLS) results.

Antibodies, Monoclonal↗
PubMed1988

Collagen biosynthesis by a breast carcinoma cell strain and biopsy fragments of the primary tumour.

Collagen biosynthesis was assayed in tissue fragments and in cultured neoplastic cells derived from primary ductal infiltrating carcinoma of the human breast. Neoplastic cells "in vitro" produce 3-4% of collagen with respect to the high molecular weight protein fraction. The neosynthesized collagen is mainly composed of alpha 1 (I) chains, which may be assembled as homotrimer molecules, as indicated by their resistance to pepsin digestion. In tissue fragments, (where neoplastic and host stromal cells coexist), the collagen percentage increases up to 15-20% and more than one polypeptide chain is produced. Present data suggest that neoplastic cells "in vivo" contribute to the deposition of collagen components, actively synthesizing a certain amount of the type I-trimer, which is a significant component of the "scirrhous" stroma (Minafra et al.1984; Pucci Minafra et al, 1985). This phenomenon is interpreted as one of the numerous interrelationships occurring at the cell-matrix interface during the malignant growth.

Biopsy↗
PubMed2002

Identification of N- and C-terminal amino acids of Lhca1 and Lhca4 required for formation of the heterodimeric peripheral photosystem I antenna LHCI-730.

Apoproteins of higher plant light-harvesting complexes (LHC) share considerable amino acid sequence identity/similarity. Despite this fact, they occur in different oligomeric states (i.e., monomeric, dimeric, and trimeric). As a step toward understanding the underlying structure requirements for different oligomerization behavior, we analyzed whether amino acids at the N- and C-termini of Lhca1 and Lhca4 are involved in the formation of the heterodimeric LHCI-730. Using altered proteins produced by deletion or site-directed mutagenesis for reconstitution, we were able to identify amino acids required for the assembly of LHCI-730. At the N-terminus of Lhca1, W4 is involved in heterodimerization. This interaction probably depends on aromatic properties because only replacement of W4 by F resulted in dimer formation. Also, at the C-terminus of Lhca1, W seems to play a crucial role for interaction with Lhca4. A detailed analysis by point mutants revealed the importance of an aromatic residue at position 185. One or more other amino acid(s) located downstream of position 188 may exert additional stabilizing effects, presumably in a cooperative way. The scenario for Lhca4 is different. Dimerization broke down only after the deletion of the entire extrinsic N- or C-terminal region, demonstrating that the termini of Lhca4 are not involved in strong interactions with Lhca1 decisive for dimerization. At the N-terminus, dimerization was abolished after the removal of the same number of amino acids at which monomer formation failed. Site-specific mutagenesis of the amino acid decisive for LHC-formation in a deletion study demonstrated that its character is of no importance for dimerization and, therefore, that abolition of dimer formation may be the consequence of a loss in monomer formation. At the C-terminus of Lhca4, an even higher number of amino acids than required for monomer formation could be removed without the loss of dimerization. The decisive position is I168, located in the third transmembrane region. Because all point mutants of I168 in the full-length protein yielded dimers, failure of dimerization may be caused by either falling below a critical length of the polypeptide chain, resulting in the loss of too many weak interactions, or by too strong an impairment of Lhca4-folding. Interestingly, N- and C-terminal mutants of Lhca4 not able to form stable monomers formed stable dimers, indicating stabilization of labile monomeric complexes by the Lhca1 subunit in dimerization. Finally, the significance for dimer formation of amino acids in other parts of Lhca1 and Lhca4 which may be involved, besides the amino acids identified here in the specific assembly of the heterodimeric LHCI-730, is discussed. Their identification will result in a better understanding of structure characteristics determining the different oligomerization behavior of LHCs.

Amino Acids↗
PubMed2006

Cyclic phosphate-linked oligosaccharides: synthesis and conformational behavior of novel cyclic oligosaccharide analogues.

CyPLOS (cyclic phosphate-linked oligosaccharides), that is, novel cyclic oligosaccharide surrogates, consisting of two, three, and four phenyl-beta-D-glucopyranoside units, 4,6-linked through stable phosphodiester bonds, were prepared by a straightforward and efficient solid-phase protocol. The assembly of the linear precursors was achieved by standard phosphoramidite chemistry on an automated DNA synthesizer, using a suitably protected 4-phosphoramidite derivative of D-glucose as the building block. For the crucial cyclization step a phosphotriester methodology was exploited, followed by a mild basic treatment releasing the desired cyclic molecules in solution in a highly pure form. The cyclic dimer and trimer were also independently prepared by classical solution synthesis, basically following the same approach. The solution structural preferences of the cyclic dimer and trimer, obtained by detailed NMR analysis, are also reported.

Cytochrome P-450 Enzyme System↗
PubMed1976

Characterization of a temperature-sensitive, hexon transport mutant of type 5 adenovirus.

Infection of KB cells at 39.5 degrees C with H5ts147, a temperature-sensitive (ts) mutant of type 5 adenovirus, resulted in the cytoplasmic accumulation of hexon antigen; all other virion proteins measured, however, were normally transported into the nucleus. Immunofluorescence techniques were used to study the intracellular location of viral proteins. Genetic studies revealed that H5ts147 was the single member of a nonoverlapping complementation group and occupied a unique locus on the adenovirus genetic map, distinct from mutants that failed to produce immunologically reactive hexons at 39.5 degrees C ("hexon-minus" mutants). Sedimentation studies of extracts of H5ts147-infected cells cultured and labeled at 39.5 degrees C revealed the production of 12S hexon capsomers (the native, trimeric structures), which were immunoprecipitable to the same extent as hexons synthesized in wild type (WT)-infected cells. In contrast, only 3.4S polypeptide chains were found in extracts of cells infected with the class of mutants unable to produce immunologically reactive hexon protein at 39.5 degrees C. Hexons synthesized in H5ts147-infected cells at 39.5 degrees C were capable of being assembled into virions, to the same extent as hexons synthesized in WT-infected cells, when the temperature was shifted down to the permissive temperature, 32 degrees C. Infectious virus production was initiated within 2 to 6 h after shift-down to 32 degrees C; de novo protein synthesis was required to allow this increase in viral titer. If ts147-infected cells were shifted up to 39.5 degrees C late in the viral multiplication cycle, viral production was arrested within 1 to 2 h. The kinetics of shutoff was similar to that of a WT-infected culture treated with cycloheximide at the time of shift-up. The P-VI nonvirion polypeptide, the precursor to virion protein VI, was unstable at 39.5 degrees C, whereas the hexon polypeptide was not degraded during the chase. It appears that there is a structural requirement for the transport of hexons into the nucleus more stringent than the acquisition of immunological reactivity and folding into the 12S form.

Adenoviridae↗