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PubMed2003

Divergent signals and cytoskeletal assemblies regulate self-organizing polarity in neutrophils.

Like neutrophilic leukocytes, differentiated HL-60 cells respond to chemoattractant by adopting a polarized morphology, with F-actin in a protruding pseudopod at the leading edge and contractile actin-myosin complexes at the back and sides. Experiments with pharmacological inhibitors, toxins, and mutant proteins show that this polarity depends on divergent, opposing "frontness" and "backness" signals generated by different receptor-activated trimeric G proteins. Frontness depends upon Gi-mediated production of 3'-phosphoinositol lipids (PI3Ps), the activated form of Rac, a small GTPase, and F-actin. G12 and G13 trigger backness signals, including activation of a second GTPase (Rho), a Rho-dependent kinase, and myosin II. Functional incompatibility causes the two resulting actin assemblies to aggregate into separate domains, making the leading edge more sensitive to attractant than the back. The latter effect explains both the neutrophil's ability to polarize in uniform concentrations of chemoattractant and its response to reversal of an attractant gradient by performing a U-turn.

Cell Polarity↗
PubMed2006

Affinity of molecular interactions in the bacteriophage phi29 DNA packaging motor.

DNA packaging in the bacteriophage phi29 involves a molecular motor with protein and RNA components, including interactions between the viral connector protein and molecules of pRNA, both of which form multimeric complexes. Data are presented to demonstrate the higher order assembly of pRNA together with the affinity of pRNA:pRNA and pRNA:connector interactions, which are used to propose a model for motor function. In solution, pRNA can form dimeric and trimeric multimers in a magnesium-dependent manner, with dissociation constants for multimerization in the micromolar range. pRNA:connector binding is also facilitated by the presence of magnesium ions, with a nanomolar apparent dissociation constant for the interaction. From studies with a mutant pRNA, it appears that multimerization of pRNA is not essential for connector binding and it is likely that connector protein is involved in the stabilization of higher order RNA multimers. It is proposed that magnesium ions may promote conformational change that facilitate pRNA:connector interactions, essential for motor function.

Bacillus Phages↗
PubMedDate not supplied

Building collagen molecules, fibrils, and suprafibrillar structures.

Fibril-forming collagens are synthesized in precursor form, procollagens, with N- and C-terminal propeptide extensions. The C-propeptides direct chain association during intracellular assembly of the procollagen molecule from its three constituent polypeptide chains. Following or during secretion into the extracellular matrix, propeptides are cleaved by specific procollagen proteinases, thereby triggering fibril formation. The recent determination of the low-resolution structure of the C-propeptide trimer gives insights into the mechanism of procollagen chain association. In the extracellular matrix, the procollagen C-propeptides ensure procollagen solubility, while persistence of the N-propeptides controls fibril shape. Mechanisms for the control of fibril diameter are reviewed in terms of the radial packing model for collagen fibril structure. Finally, procollagen molecules have recently been shown to undergo liquid crystalline ordering in solution, prior to fibril assembly. This may provide an explanation for the liquid crystal-like suprafibrillar architectures of different connective tissues.

Amino Acid Sequence↗
PubMed2006

Bacteriophage T5 structure reveals similarities with HK97 and T4 suggesting evolutionary relationships.

Evolutionary relationships between viruses may be obscure by protein sequence but unmasked by structure. Analysis of bacteriophage T5 by cryo-electron microscopy and protein sequence analysis reveals analogies with HK97 and T4 that suggest a mosaic of such connections. The T5 capsid is consistent with the HK97 capsid protein fold but has a different geometry, incorporating three additional hexamers on each icosahedral facet. Similarly to HK97, the T5 major capsid protein has an N-terminal extension, or Delta-domain that is missing in the mature capsid, and by analogy with HK97, may function as an assembly or scaffold domain. This Delta-domain is predicted to be largely coiled-coil, as for that of HK97, but is approximately 70% longer correlating with the larger capsid. Thus, capsid architecture appears likely to be specified by the Delta-domain. Unlike HK97, the T5 capsid binds a decoration protein in the center of each hexamer similarly to the "hoc" protein of phage T4, suggesting a common role for these molecules. The tail-tube has unusual trimeric symmetry that may aid in the unique two-stage DNA-ejection process, and joins the tail-tip at a disk where tail fibers attach. This intriguing mix of characteristics embodied by phage T5 offers insights into virus assembly, subunit function, and the evolutionary connections between related viruses.

Amino Acid Sequence↗
PubMed2001

Chromium(III)-induced structural changes and self-assembly of collagen.

Rat tail tendon (RTT) collagen has been reacted with a homologous series of chromium(III) complexes viz., (H2O)(4)Cr(OH)(2)Cr(H2O)(4+)(4) 1 (dimer), Cr(3)(OH)(4)(H2O)(5+)(9) 2 (trimer), and Cr(4)(OH)(4)(O2)(H2O)(4+)(12) 3 (tetramer), and the structural alterations brought about by these complexes have been investigated through atomic force microscopy (AFM) and circular dichroism (CD) studies. Examination of Cr(III)-treated tendons using AFM revealed changes in the D-periodicity of collagen, which may arise due to differences in the topological distribution of various Cr(III) complexes. Evidence for organisation of monomeric collagen into quarter staggered fibrils in the presence of Cr(III) dimer, 1, has been obtained. The quaternary structural changes induced by chromium in the protein have been correlated to the conformational changes of collagen in the absence of denaturation.

Acetic Acid↗
PubMed2004

Synthetic heterotrimeric collagen peptides as mimics of cell adhesion sites of the basement membrane.

Collagen type IV forms a network in the basement membrane into which other constituents of the tissue are incorporated. It also provides cell-adhesion sites that are specifically recognized by cell-surface receptors, i.e., the integrins. Different from the ubiquitous sequential RGD adhesion motif found in most of the matrix proteins, in collagen type IV, the responsible binding sites for alpha1beta1 integrin have been identified as Asp461 of the two alpha1 chains and Arg461 of the alpha2 chain. Because of the heterotrimeric character of this collagen, the spatial geometry of the binding epitope depends not only on the triple-helical fold, but decisively even on the stagger of the chains. To investigate the effects of chain registration on the conformational properties and binding affinities of this adhesion epitope, two synthetic heterotrimeric collagen peptides consisting of the identical three chains were assembled by an artificial cystine knot in two different registers, i.e., in the most plausible alpha2alpha1alpha1' and less probable alpha1alpha2alpha1' chain alignment. A detailed conformational characterization of both trimers allowed to correlate their different binding affinities for alpha1beta1 integrin with the degree of local plasticity of the two different triple helices. Optimal local breathing of the rod-shaped collagens is apparently crucial for selective recognition by proteins interacting with these main components of the extracellular matrix.

Basement Membrane↗
PubMed2005

Human cytomegalovirus-encoded US2 and US11 target unassembled MHC class I heavy chains for degradation.

Surface MHC class I molecules serve important immune functions as ligands for both T and NK cell receptors for the elimination of infected and malignant cells. In order to reach the cell surface, MHC class I molecules have to fold properly and form trimers consisting of a heavy chain (HC), a beta2-microglobulin light chain and an 8-10-mer peptide. A panel of ER chaperones facilitates the folding and assembly process. Incorrectly assembled or folded MHC class I HCs are detected by the ER quality-control system and transported to the cytosol for degradation by proteasomes. In human cytomegalovirus-infected cells, two viral proteins are synthesized, US2 and US11, which target MHC class I HCs for proteasomal degradation. It is unknown at which stage of MHC class I folding and complex formation US2 and US11 come into play. In addition, it is unclear if the disposal takes place via the same pathway through which proteins are removed that fail to pass ER quality control. In this study, we show with a beta2m-deficient cell line that US2 and US11 both target unassembled HCs for degradation. This suggests that US2 and US11 both act at an early stage of MHC class I complex formation. In addition, our data indicate that US11-mediated degradation involves mechanisms that are similar to those normally used to remove terminally misfolded HCs.

Cytomegalovirus↗
PubMed2005

The satellite-shaped Co-15 Polyoxotungstate, [Co6(H2O)30{Co9Cl2(OH)3(H2O)9(beta-SiW8O31)3}]5-.

The 15-cobalt-substituted polyoxotungstate [Co(6)(H(2)O)(30){Co(9)Cl(2)(OH)(3)(H(2)O)(9)(beta-SiW(8)O(31))(3)}](5-) (1) has been characterized by single-crystal XRD, elemental analysis, IR, electrochemistry, magnetic measurements, and EPR. Single-crystal X-ray analysis was carried out on Na(5)[Co(6)(H(2)O)(30){Co(9)Cl(2)(OH)(3)(H(2)O)(9)(beta-SiW(8)O(31))(3)}].37H(2)O, which crystallizes in the hexagonal system, space group P6(3)/m, with a = 19.8754(17) A, b = 19.8754(17) A, c = 22.344(4) A, alpha= 90 degrees, beta = 90 degrees, gamma = 120 degrees, and Z = 2. The trimeric polyanion 1 has a core of nine Co(II) ions encapsulated by three unprecedented (beta-SiW(8)O(31)) fragments and two Cl(-) ligands. This central assembly {Co(9)Cl(2)(OH)(3)(H(2)O)(9)(beta-SiW(8)O(31))(3)}(17-) is surrounded by six antenna-like Co(II)(H(2)O)(5) groups resulting in the satellite-like structure 1. Synthesis of 1 is accomplished in a simple one-pot procedure by interaction of Co(II) ions with [gamma-SiW(10)O(36)](8-) in aqueous, acidic NaCl medium (pH 5.4). Polyanion 1 was studied by cyclic voltammetry as a function of pH. The current intensity of its Co(II) centers was compared with that of free Co(II) in solution. Our results suggest that 1 keeps its integrity in solution. Magnetic susceptibility results show the presence of both antiferro- and ferromagnetic coupling within the (Co(II))(9) core. A fully anisotropic Ising model has been employed to describe the exchange-coupling and yields g = 2.42 +/- 0.01, J(1) = 17.0 +/- 1.5 cm(-1), and J(2) = -13 +/- 1 cm(-(1). Variable frequency EPR studies reveal an anisotropic Kramer's doublet.

Journal Article↗
PubMed1997

Folding of a bacterial outer membrane protein during passage through the periplasm.

The transport of bacterial outer membrane proteins to their destination might be either a one-step process via the contact zones between the inner and outer membrane or a two-step process, implicating a periplasmic intermediate that inserts into the membrane. Furthermore, folding might precede insertion or vice versa. To address these questions, we have made use of the known 3D-structure of the trimeric porin PhoE of Escherichia coli to engineer intramolecular disulfide bridges into this protein at positions that are not exposed to the periplasm once the protein is correctly assembled. The mutations did not interfere with the biogenesis of the protein, and disulfide bond formation appeared to be dependent on the periplasmic enzyme DsbA, which catalyzes disulfide bond formation in the periplasm. This proves that the protein passes through the periplasm on its way to the outer membrane. Furthermore, since the disulfide bonds create elements of tertiary structure within the mutant proteins, it appears that these proteins are at least partially folded before they insert into the outer membrane.

Blotting, Western↗
PubMed1992

Structure and assembly of hemagglutinin mutants of fowl plague virus with impaired surface transport.

Five temperature-sensitive mutants of influenza virus A/FPV/Rostock/34 (H7N1), ts206, ts293, ts478, ts482, and ts651, displaying correct hemagglutinin (HA) insertion into the apical plasma membrane of MDCK cells at the permissive temperature but defective transport to the cell surface at the restrictive temperature, have been investigated. Nucleotide sequence analysis of the HA gene of the mutants and their revertants demonstrated that with each mutant a single amino acid change is responsible for the transport block. The amino acid substitutions were compared with those of mutants ts1 and ts227, which have been analyzed previously (W. Schuy, C. Will, K. Kuroda, C. Scholtissek, W. Garten, and H.-D. Klenk, EMBO J. 5:2831-2836, 1986). With the exception of ts206, the changed amino acids of all mutants and revertants accumulate in three distinct areas of the three-dimensional HA model: (i) at the tip of the 80-A (8-nm)-long alpha helix, (ii) at the connection between the globular region and stem, and (iii) in the basal domain of the stem. The concept that these areas are critical for HA assembly and hence for transport is supported by the finding that the mutants that are unable to leave the endoplasmic reticulum at the nonpermissive temperature do not correctly trimerize. Upon analysis by density gradient centrifugation, cross-linking, and digestion with trypsin and endoglucosaminidase H, two groups can be discriminated among these mutants: with ts1, ts227, and ts478, the HA forms large irreversible aggregates, whereas with ts206 and ts293, it is retained in the monomeric form in the endoplasmic reticulum. With a third group, comprising mutants ts482 and ts651 that enter the Golgi apparatus, trimerization was not impaired.

Amino Acid Sequence↗
PubMed1978

Studies on the oligomeric structure of yeast aldehyde dehydrogenase by cross-linking with bifunctional reagents.

The molecular w:ight of yeast aldehyde dehydrogenase determined by sucrose density gradient centrifugation was 207,000 +/- 13,000. The enzyme activity was proportional to the enzyme concentration in the range of 2 X 10(-11) M to 1 X 10(-7) M. Cross-linking patterns obtained with yeast aldehyde dehydrogenase after treatment with a series of diimidoesters of increasing chain lengths with different reaction times resulted in the appearance of tetramers as the largest cross-linked product of the enzyme subunits. The molecular weights of its monomer, dimer, trimer, and tetramer were, 57,000, 114,000, 171,000, and 228,000, respectively, as estimated from their mobilities on SDS-electrophoresis. In tetramers monomers are probably assembled in a heterologous square arrangement.

Aldehyde Oxidoreductases↗
PubMed2002

The determinants of the oligomeric structure in Hsp16.5 are encoded in the alpha-crystallin domain.

The determinants of the oligomeric assembly of Hsp16.5, a small heat-shock protein (sHSP) from Methanococcus jannaschii, were explored via site-directed truncation and site-directed spin labeling. For this purpose, subunit contacts around the two-, three- and four-fold symmetry axes were fingerprinted using patterns of proximities between nitroxide spin labels introduced at selected sites. The lack of change in this fingerprint in an N-terminal truncation of the protein demonstrates that the interactions are encoded in the alpha-crystallin domain. In contrast, the truncation of the N-terminal domain of Mycobacterium tuberculosis Hsp16.3, a bacterial sHSP with an equally short N-terminal region, results in the dissociation of the oligomer to a trimer. These results, in conjunction with those from previous truncation studies in mammalian sHSP, suggest that as the alpha-crystallin domain evolved to encode a smaller basic unit than the overall oligomer, the control of the assembly and dynamics of the oligomeric structure became encoded in the N-terminal domain.

Archaeal Proteins↗
PubMed2001

Truncation of the human adenovirus type 5 L4 33-kDa protein: evidence for an essential role of the carboxy-terminus in the viral infectious cycle.

The subgroup C human adenovirus L4 33-kDa protein is a nuclear phosphoprotein that plays a direct, but dispensable, role in virion assembly. The r-strand open reading frame (ORF) for this protein lies opposite to the 5' end of the l-strand E2 early (E2E) transcription units. To facilitate studies of regulation of E2E transcription, we wished to construct a mutant virus in which the 33-kDa ORF was truncated to serve as a background into which specific E2E mutations could be introduced without also altering the 33-kDa protein. We constructed viral DNA (vDNA) containing within the 33-kDa ORF two tandem, premature stop codons that should prevent translation of the C-terminal 47 amino acids of the protein (Delta47). We report here the unanticipated lethality of such truncation of the L4 33-kDa protein. Viral DNA harboring the Delta47 mutations did not produce infectious virus when transfected into cultured cells. In contrast, infectious virus was recovered upon transfection of revertant vDNA, indicating that the Delta47 mutations were responsible for the observed phenotype. The Delta47 mutations did not affect E2E transcription or production of the E2 DNA-binding protein. Transfected Delta47 vDNA was replicated and directed the production of early and late viral proteins, including hexon protein in the trimer conformation. However, no virus particles of any kind were produced. We propose that truncation of the adenovirus 33-kDa protein results in a lethal, late block in the infectious cycle during the assembly of progeny virions and discuss the implications of this phenotype for the mechanism of virion assembly.

Adenoviruses, Human↗
PubMed1987

Subparticles of Anabaena phycobilisomes. II. Molecular assembly of allophycocyanin cores in reference to "anchor" protein.

Entire phycobilisomes (PBS) and two derived particles, whole allophycocyanin (APC) cores and the far-red-emitting fragment of APC cores (14.5 S APC), all containing the 115-kDa polypeptide ("anchor protein"), were compared for the readiness with which the 115-kDa protein could be modified chemically, be degraded by chymotrypsin, and react with the anti-115-kDa serum. The 115 kDa in PBS and the whole APC cores were digested slightly by chymotrypsin and did not react with anti-115-kDa IgG. In contrast, the 115 kDa in 14.5 S APC was digested to 42 kDa and showed a positive reaction with anti-115-kDa IgG. Reconstitution of APC cores from 14.5 S APC and APC trimers was inhibited by the anti-115-kDa IgG, and APC particles with partly digested 115-kDa cannot reconstitute APC cores. These results imply that 115 kDa is embedded mostly inside PBS and is involved more in the maintenance of the molecular assembly of APC cores than in the "anchoring" of PBS to thylakoid. The PBS from Anabaena variabilis (M3) have an APC core larger than those of other PBS and show atypical morphology consisting of five APC discs. They have a polypeptide (115 kDa) that is significantly longer than the corresponding polypeptides (around 95 kDa) of other blue-green algae. This can be interpreted by assuming a relationship between the size of APC cores and the length of the polypeptide.

Bacterial Proteins↗
PubMed2001

Structure of c-phycocyanin from the thermophilic cyanobacterium Synechococcus vulcanus at 2.5 A: structural implications for thermal stability in phycobilisome assembly.

The crystal structure of the light-harvesting phycobiliprotein, c-phycocyanin from the thermophilic cyanobacterium Synechochoccus vulcanus has been determined by molecular replacement to 2.5 A resolution. The crystal belongs to space group R32 with cell parameters a=b=188.43 A, c=61.28 A, alpha=beta=90 degrees, gamma=120 degrees, with one (alphabeta) monomer in the asymmetric unit. The structure has been refined to a crystallographic R factor of 20.2 % (R-free factor is 24.4 %), for all data to 2.5 A. The crystals were grown from phycocyanin (alphabeta)(3) trimers that form (alphabeta)(6) hexamers in the crystals, in a fashion similar to other phycocyanins. Comparison of the primary, tertiary and quaternary structures of the S. vulcanus phycocyanin structure with phycocyanins from both the mesophilic Fremyella diplsiphon and the thermophilic Mastigocladus laminosus were performed. We show that each level of assembly of oligomeric phycocyanin, which leads to the formation of the phycobilisome structure, can be stabilized in thermophilic organisms by amino acid residue substitutions. Each substitution can form additional ionic interactions at critical positions of each association interface. In addition, a significant shift in the position of ring D of the B155 phycocyanobilin cofactor in the S. vulcanus phycocyanin, enables the formation of important polar interactions at both the (alphabeta) monomer and (alphabeta)(6) hexamer association interfaces.

Algal Proteins↗
PubMed1997

The laminin alpha chains: expression, developmental transitions, and chromosomal locations of alpha1-5, identification of heterotrimeric laminins 8-11, and cloning of a novel alpha3 isoform.

Laminin trimers composed of alpha, beta, and gamma chains are major components of basal laminae (BLs) throughout the body. To date, three alpha chains (alpha1-3) have been shown to assemble into at least seven heterotrimers (called laminins 1-7). Genes encoding two additional alpha chains (alpha4 and alpha5) have been cloned, but little is known about their expression, and their protein products have not been identified. Here we generated antisera to recombinant alpha4 and alpha5 and used them to identify authentic proteins in tissue extracts. Immunoprecipitation and immunoblotting showed that alpha4 and alpha5 assemble into four novel laminin heterotrimers (laminins 8-11: alpha4beta1gamma1, alpha4beta2gamma1, alpha5beta1gamma1, and alpha5beta2gamma1, respectively). Using a panel of nucleotide and antibody probes, we surveyed the expression of alpha1-5 in murine tissues. All five chains were expressed in both embryos and adults, but each was distributed in a distinct pattern at both RNA and protein levels. Overall, alpha4 and alpha5 exhibited the broadest patterns of expression, while expression of alpha1 was the most restricted. Immunohistochemical analysis of kidney, lung, and heart showed that the alpha chains were confined to extracellular matrix and, with few exceptions, to BLs. All developing and adult BLs examined contained at least one alpha chain, all alpha chains were present in multiple BLs, and some BLs contained two or three alpha chains. Detailed analysis of developing kidney revealed that some individual BLs, including those of the tubule and glomerulus, changed in laminin chain composition as they matured, expressing up to three different alpha chains and two different beta chains in an elaborate and dynamic progression. Interspecific backcross mapping of the five alpha chain genes revealed that they are distributed on four mouse chromosomes. Finally, we identified a novel full-length alpha3 isoform encoded by the Lama3 gene, which was previously believed to encode only truncated chains. Together, these results reveal remarkable diversity in BL composition and complexity in BL development.

Amino Acid Sequence↗
PubMed1994

Assembly, transport, and function of MHC class II molecules.

MHC class II molecules assemble in the endoplasmic reticulum in a chaperone-mediated fashion to form a nine-chain structure consisting of three alpha beta dimers associated with an invariant chain trimer. This complex is transported through the Golgi apparatus and into the endosomal system. The signal for endosomal targeting resides in the cytoplasmic tail of the invariant chain. Current evidence argues that the segregation of the class II-invariant chain complex from the constitutive pathway of membrane protein transport occurs in the trans-Golgi network. However, class II-invariant chain complexes that reach the cell surface are also rapidly internalized into endosomes. Within the endosomal system, probably in a late endosome/pre-lysosome, the invariant chain is degraded, releasing alpha beta dimers that bind peptides predominantly derived from endocytosed proteins. Evidence suggests that many of these peptides are actually generated in lysosomes. The precise mechanisms involved in forming class II-peptide complexes are unclear, although the existence of antigen-processing mutants argues that additional gene products, at least one of which is encoded in the MHC, are involved. After binding peptides, class II molecules are transported by an unknown route to the cell surface, where their primary function of presenting antigenic peptides to CD4+ T cells is carried out.

Animals↗
PubMed1981

Cyanobacterial phycobilisomes. Phycocyanin assembly in the rod substructures of anabaena variabilis phycobilisomes.

Phycocyanin complexes with "linker" polypeptides (Lundell, D. J., Williams, R. C., and Glazer, A. N. (1981) J. Biol. Chem. 256, 3580-3592) of 27 and 32.5 kilodaltons have been isolated from dissociated Anabaena variabilis phycobilisomes. In 0.05 M phosphate at pH 7.0, these "trimeric" complexes have the molar composition (alpha beta)3 . 27,000 and (alpha beta)3 . 32,500, where alpha and beta are the subunits of phycocyanin and 27,000 and 32,500 denote single copies of the linker polypeptides. The (alpha beta)3 . 27,000 and (alpha beta)3 . 32,500 complexes have lambda max at 638 and 629 nm and fluorescence emission maxima at 651 and 646 nm, respectively. In 0.6 M phosphate at pH 8.0, the (alpha beta)3 . 27,000 complex forms an (alpha beta)6 . 27,000 disc-shaped aggregate as seen in the electron microscope, whereas the (alpha beta)3 . 32,500 complex forms discs, (alpha beta)6 . 32,500, and stacked disc rods of varying lengths. The former material, containing the 27,000 polypeptide, when mixed with the (alpha beta)6 . 32,500 discs, limits their assembly into rods. The spectroscopic properties of the discs and rods assembled in vitro indicate that energy transfer in phycobilisome rod substructures proceeds from (alpha beta)6 . 32,500 discs to the (alpha beta)6 . 27,000 disc proximal to the core and thence to the core.

Circular Dichroism↗