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At least 1,045 records · Page 58Linked to original sources
PubMed2003

Biomimetic organization: Octapeptide self-assembly into nanotubes of viral capsid-like dimension.

The controlled self-assembly of complex molecules into well defined hierarchical structures is a promising route for fabricating nanostructures. These nanoscale structures can be realized by naturally occurring proteins such as tobacco mosaic virus, capsid proteins, tubulin, actin, etc. Here, we report a simple alternative method based on self-assembling nanotubes formed by a synthetic therapeutic octapeptide, Lanreotide in water. We used a multidisciplinary approach involving optical and electron microscopies, vibrational spectroscopies, and small and wide angle x-ray scattering to elucidate the hierarchy of structures exhibited by this system. The results revealed the hexagonal packing of nanotubes, and high degree of monodispersity in the tube diameter (244 A) and wall thickness (approximately equal to 18 A). Moreover, the diameter is tunable by suitable modifications in the molecular structure. The self-assembly of the nanotubes occurs through the association of beta-sheets driven by amphiphilicity and a systematic aromatic/aliphatic side chain segregation. This original and simple system is a unique example for the study of complex self-assembling processes generated by de novo molecules or amyloid peptides.

Biomimetics↗
PubMed2001

Surface organization and nanopatterning of collagen by dip-pen nanolithography.

Collagen is a key fibrous protein in biological systems, characterized by a complex structural hierarchy as well as the ability to self-assemble into liquid crystalline mesophases. The structural features of collagen influence cellular responses and material properties, with importance for a wide range of biomaterials and tissue architectures. The mechanism by which fibrillar collagen structures form from liquid crystalline mesophases is not well characterized. We report positive printing of collagen and a collagen-like peptide down to 30-50-nm line widths, using the atomic force microscopy technique of dip-pen nanolithography. The method preserved the triple-helical structure and biological activity of collagen and even fostered the formation of characteristic higher levels of structural organization. The "direct-write" capability of biologically relevant molecules, while preserving their structure and functionality, provides tremendous flexibility in future biological device applications and in proteomics arrays, as well as a new strategy to study the important hierarchical assembly processes of biological systems.

Collagen↗
PubMed1972

Identification of the proteins associated with subparticles produced by mild ribonuclease digestion of 30S ribosomal particles from Escherichia coli.

Digestion of 30S ribosomal subunits from E. coli by insoluble ribonuclease produces three subparticles. The ribosomal proteins associated with each of these particles were identified. Some of the proteins are associated with only one of the three subparticles. The protein compositions of the three particles can be arranged in an overlapping linear sequence of five groups. Furthermore, inspection of the previously determined assembly sequence of the 30S proteins indicates that proteins associated in the subparticles are interdependent in the assembly process.

Amino Acids↗
PubMed1977

In vitro assembly of pure tubulin into microtubules in the absence of microtubule-associated proteins and glycerol.

Microtubule protein from porcine cerebrum was fractionate into pure tubulin and microtubule-associated proteins by chromatography on phosphocellulose. In agreement with previous studies, pure tubulin does not form microtubules to a significant extent at 37 degrees in normal assembly buffers, which are characterized by a low concentration of Mg2+ ions. If, however, the Mg2+ concentration is raised to approximately 10 mM, rapid and extensive self-assembly of pure tubulin into microtubules is observed, provided the tubulin concentration is above 2.5 mg/ml. At a protein concentration of 3 mg/ml, the lag period is 1.5 min and the assembly process is virtually complete after 6 min at 37 degrees. These microtubules are like normal microtubules--sensitive to calcium ions, colchicine, and low temperature.

Animals↗
PubMed1979

Vp1 affects intracellular localization of Vp3 polypeptide during simian virus 40 infection.

In order to understand the functions of simian virus 40 genes, permissive cells (TC7) were infected with mutants temperature sensitive in the complementation groups A, B, C, BC, and D at permissive and nonpermissive temperatures. Cells were examined for the localization of viral polypeptide antigens by immunofluorescent staining with monospecific antibodies. The results are as follows: (i) The appearance of Vp1 antigen in cells infected by tsB, C, or BC mutants was not affected appreciably by the mutations. (ii) The appearance of Vp3 antigen was affected by the mutations in B, C, or BC. Vp3 antigen is confined to the nuclei in cells infected by wild-type virus. With mutant virus infection, Vp3 antigen is found in the cytoplasm, perinuclear region, and nucleoli. (iii) The tsD mutants and the tsA mutants did not express either Vp1 or Vp3 antigens at the nonpermissive temperature. (iv) Nucleoli seem to play an essential role in the biosynthesis and assembly of viral polypeptides. Thus, mutations in any one of complementation groups B, C, or BC, which are within the structural gene for Vp1, cause an alteration of intracellular distribution of another late gene product, Vp3. These results suggest that the amino acid sequences of Vp1 polypeptide play a role(s) in the transport of viral antigens across internal membranes or in virus assembly processes or in both.

Antigens, Viral↗
PubMed1981

Morphogenesis of phi X174: in vitro synthesis of infectious phage from purified viral components.

An in vitro system that synthesizes infectious phage phi X174 was developed. The synthesis depended on phi X174 supercoiled replicative form DNA, purified phi X174 gene A protein, gene C protein, gene J protein, prohead (phage head precursor composed of gene F, G, H, B, and D proteins), and uninfected host crude extract. The infectious phage synthesis was coupled with DNA synthesis. De novo initiation, elongation, and termination of phi X174 single-stranded DNA was observed. The phage synthesized in vitro cosedimented with in vivo phage in sucrose gradients and had the same buoyant density as in vivo phage in a CsCl gradient. Our results indicate that the in vitro system mimics the in vivo phi X174 assembly process.

Bacteriophage phi X 174↗
PubMed1985

Renaturation of skeletal muscle tropomyosin: implications for in vivo assembly.

The observation that the alpha beta heterodimer is the predominant species of tropomyosin in rabbit skeletal muscles has led to the suggestion that this species assembles preferentially. To understand the molecular basis of this assembly process, we have studied renaturation under conditions that favor heterodimer formation. When skeletal muscle tropomyosin composed of equal amounts of alpha and beta subunits is renatured either by cooling or by dialysis a distribution that favors homodimers is generated. In contrast, rapid renaturation by dilution from urea favors the heterodimer. Further analysis of this latter renaturation procedure with cysteine-cleavage fragments of tropomyosin using circular dichroic measurements shows that as few as 30 residues in the NH2-terminal third of each tropomyosin subunit are involved in the initial interaction that results in heterodimer formation. Based on the density of sequence substitutions between the alpha and beta subunits, that region probably includes residues 36-64.

Animals↗
PubMed1986

Ultrasonic absorption evidence for enhanced volume fluctuations in the tobacco mosaic virus protein helical aggregate.

The increased ultrasonic absorption brought about by self-assembly of biomolecules is analyzed for the assembly process from the 20S aggregate to the helical rod of tobacco mosaic virus protein in solution, designated here as the 20S --> P-helix transition. The analysis is based on theoretical developments in ultrasonic relaxation spectrometry presented previously and illustrates the possibility that this technique can be used for characterizing fluctuations. The analysis makes use of NMR data for the system in solution and of x-ray diffraction data for the closely related transition from the two-ring disk to the virion. These x-ray data comprise the high-resolution structures and the Debye-Waller temperature factors of the main chain atoms of both the two-ring disk in crystals and the virion in oriented gel form. First, reduced ultrasonic spectra are obtained for the 4S, 20S, and helical rod aggregates. The fluctuation-enhancement factor for the helical rod is determined independently of any deconvolution into normal modes of relaxation and is shown not to depend on the particular procedure of reduction employed. The increase of ultrasonic absorption in the 20S --> P-helix transition primarily reveals enhancement of the relaxing system's normal-mode volume fluctuations. The observed relaxations probably involve one conformational process per subunit. The normal-mode volume fluctuations are then estimated from a bimodal least-squares best fit to the data, and a lower bound for the reaction volume associated with the fast steps is obtained. Two mechanisms are considered as follows: (i) a destabilization process in which the free-energy difference between two states is reduced and (ii) an increase in reaction volumes of local conformation changes in the helical aggregate, resulting from the formation of a "carboxyl cage-like" structure and from the change in environment produced inside the cage. Increased reaction volumes would not be detected with x-ray diffraction. The possible occurrence of fluctuations at the RNA binding site raises the question of whether a quaternary structure that exhibits significant conformational fluctuations must be present for the binding of the nucleic acid.

Journal Article↗
PubMed1989

Negative transcriptional regulation in the Caulobacter flagellar hierarchy.

The Caulobacter crescentus flagellum is formed at a specific time in the cell cycle and its assembly requires the ordered expression of a large number of genes. These genes are controlled in a positive trans-acting hierarchy that reflects the order of assembly of the flagellum. Using plasmids carrying transcriptional fusions of either a neo or a lux reporter gene to the promoters of three flagellar genes representing different ranks in the hierarchy (the hook operon, a basal body gene flbN, and the flaO gene), we have measured the level of chimeric gene expression in 13 flagellar mutant backgrounds. Mutants in the hook operon or in basal body genes caused overproduction of both hook operon and basal body gene chimeric mRNAs, suggesting that negative regulation is superimposed on the positive trans-acting control for these early events in the flagellar hierarchy. Mutants in the structural genes and in genes involved in flagellar assembly had no effect on flaO expression, placing the flaO gene near the top of the hierarchy. However, flaO expression appears to be under negative control by two regulatory genes flaS and flaW. Negative control, as a response to the completion of specific steps in the assembly process, may be an important mechanism used by the cell to turn off flagellar gene expression once the gene product is no longer needed.

Bacteria↗
PubMed1992

Endoplasmic reticulum resident protein of 90 kilodaltons associates with the T- and B-cell antigen receptors and major histocompatibility complex antigens during their assembly.

In the endoplasmic reticulum (ER), newly synthesized subunits of the T-cell antigen receptor (TCR), membrane-bound immunoglobulin (mIg), and major histocompatibility complex (MHC) class I antigens must fold correctly and assemble completely into multimeric protein complexes prior to transport to the cell surface. Although folding and assembly may occur spontaneously, the concept that molecular chaperones facilitate these events is emerging. Here, an intracellular protein of 90-kDa apparent molecular mass, denoted IP90, was shown to be an ER resident protein that associated with partial complexes of the TCR, mIg, and MHC class I proteins but was absent from fully assembled complexes. We speculate that IP90 might participate in folding and assembly processes of these and other multisubunit protein complexes during their transit through the ER.

Animals↗
PubMed1992

Changing patterns in cytoskeletal mRNA expression and protein synthesis during murine erythropoiesis in vivo.

The major cytoskeletal proteins alpha-spectrin, beta-spectrin, and ankyrin are synthesized and assembled into a supportive membrane skeleton during erythroid differentiation. Information on the temporal appearance of mRNA and protein species is essential for understanding both the cytoskeletal assembly process and the function of various isoforms. We have isolated highly enriched populations of fetal erythroid cells at various stages of maturation. mRNAs for erythroid ankyrin, alpha-spectrin, and beta-spectrin were expressed at all stages but there were differences in transcript types and levels. The ratio of 9-kilobase (kb) to 7.5-kb erythroid ankyrin transcripts decreased markedly during differentiation, but there was no change in the ratio of the 10.1-kb and 9.3-kb erythroid beta-spectrin transcripts. The relative amounts of ankyrin, alpha-spectrin, and beta-spectrin mRNA increased during yolk sac cell differentiation, whereas only alpha-spectrin mRNA increased during differentiation of the fetal liver cells. The amounts of beta-spectrin mRNA exceeded the amounts of alpha-spectrin mRNA in the early precursors from both yolk sac and fetal liver; protein synthetic levels showed the same pattern. The 16-day fetal peripheral reticulocytes, on the other hand, had the adult mRNA and protein synthetic ratios with alpha/beta greater than 1. The data indicate that at least two mechanisms exist to meet changing erythroid membrane cytoskeletal requirements during development in utero: (i) stage-specific processing of the mRNA for the major cytoskeletal linker protein ankyrin and (ii) developmentally regulated alpha/beta-spectrin protein synthetic rates.

Animals↗
PubMed1992

Assembly of a hetero-oligomeric membrane protein complex.

The maltose transporter of Escherichia coli is a hetero-oligomeric complex located in the cytoplasmic membrane of the cell. The in vivo assembly of this complex has been examined by using an assay based on the proteolytic sensitivity of one of its components, MalF. Immediately after synthesis and insertion into the membrane, MalF is sensitive to exogenously added proteases. In a time- and complex assembly-dependent fashion, MalF becomes protease resistant. Using this assay, we show that MalF is inserted into the membrane independently of other components of the transport complex. The assembly of the maltose transport complex occurs subsequently from a pool of freely diffusing protein in the membrane. This assembly process is efficient and occurs with rapid kinetics.

ATP-Binding Cassette Transporters↗
PubMed1994

In vitro activation of urease apoprotein and role of UreD as a chaperone required for nickel metallocenter assembly.

The formation of active urease in Klebsiella aerogenes requires the presence of three structural genes for the apoprotein (ureA, ureB, and ureC), as well as four accessory genes (ureD, ureE, ureF, and ureG) that are involved in functional assembly of the metallocenter in this nickel-containing enzyme. Slow and partial activation of urease apoprotein was observed after addition of nickel ion to extracts of Escherichia coli cells bearing a plasmid containing the K. aerogenes urease gene cluster or derivatives of this plasmid with deletions in ureE, ureF, or ureG. In contrast, extracts of cells containing a ureD deletion derivative failed to generate active urease, thus highlighting a key role for UreD in the metallocenter assembly process. Site-directed mutagenesis methods were used to overexpress ureD in the presence of the other urease genes, and the UreD protein was found to copurify with urease. A molecule of native urease apoprotein is capable of binding 0, 1, 2, or 3 molecules of UreD, consistent with a trimeric structure of urease catalytic units. The UreD-urease apoprotein complexes are competent for activation by nickel, with the level of activity obtained being directly related to the number of UreD molecules bound per urease molecule. Activation of the UreD-urease complexes is rapid and accompanied by UreD dissociation. We propose that UreD is a chaperone protein which stabilizes a urease apoprotein conformation that is competent for nickel incorporation.

Apoenzymes↗
PubMed1996

Nucleator-dependent intercellular assembly of adhesive curli organelles in Escherichia coli.

Bacterial adhesion to other bacteria, to eukaryotic cells, and to extracellular matrix proteins is frequently mediated by cell surface-associated polymers (fimbriae) consisting of one or more subunit proteins. We have found that polymerization of curlin to fimbriae-like structures (curli) on the surface of Escherichia coli markedly differs from the prevailing model for fimbrial assembly in that it occurs extracellularly through a self-assembly process depending on a specific nucleator protein. The cell surface-bound nucleator primes the polymerization of curlin secreted by the nucleator-presenting cell or by adjacent cells. The addition of monomers to the growing filament seems to be driven by mass action and guided only by the diffusion gradient between the source of secreted monomer and the surface of monomer condensation.

Amino Acid Sequence↗
PubMed1996

Self-assembly of a heteroduplex helicate from two different ligand strands and Cu(II) cations.

Cu(II) ions have been reacted with a 1/1 mixture of two linear ligands, one containing three 2,2'- bipyridine groups and the other three 2,2':6',2"-terpyridine groups. Absorption spectroscopy and fast atom bombardment mass spectrometry indicate the formation of a trinuclear complex containing one ligand of each kind. Determination of the crystal structure of this compound has confirmed that it is indeed a linear trinuclear complex in which two different ligands are wrapped in a helical fashion around the pentacoordinated metal ions. The central coordination geometry is trigonal bipyramidal; the two lateral Cu(II) ions are in a square pyramidal environment. Thus, a heteroduplex helicate is formed by the self-assembly of two different ligand strands and three specific metal ions induced by the coordination number and geometry of the latter. The self-assembly process may be considered to result from the reading of the steric and binding information present in the two ligands by Cu(II) ions through a pentacoordination algorithm. The same ligands have been shown earlier to yield homoduplex helicates from ions of tetrahedral and octahedral coordination geometry and strands of bidentate bipyridines and tridentate terpyridines, respectively. These two types of artificial double helical species may be related on one hand to the natural homoduplex nucleic acids and on the other hand to the DNA:RNA heteroduplex.

Journal Article↗
PubMed2000

A model of fibrin formation based on crystal structures of fibrinogen and fibrin fragments complexed with synthetic peptides.

A blood clot is a meshwork of fibrin fibers built up by the systematic assembly of fibrinogen molecules proteolyzed by thrombin. Here, we describe a model of how the assembly process occurs. Five kinds of interaction are explicitly defined, including two different knob-hole interactions, an end-to-end association between gamma-chains, a lateral association between gamma-chains, and a hypothetical lateral interaction between beta-chains. The last two of these interactions are responsible for protofibril association and are predicated on intermolecular packing arrangements observed in crystal structures of fibrin double-D fragments cocrystallized with synthetic peptides corresponding to the knobs exposed by the release of the fibrinopeptides A and B.

Computer Simulation↗
PubMed1997

Folding of the glucocorticoid receptor by the reconstituted Hsp90-based chaperone machinery. The initial hsp90.p60.hsp70-dependent step is sufficient for creating the steroid binding conformation.

Rabbit reticulocyte lysate contains a multiprotein chaperone system that assembles steroid receptors into a complex with hsp90. The glucocorticoid receptor (GR) is bound to hsp90 via its hormone binding domain (HBD), which must be associated with hsp90 to have a steroid binding conformation. Recently, we have reconstituted a receptor.hsp90 heterocomplex assembly system with purified rabbit hsp90 and hsp70 and bacterially expressed human p23 and p60 (Dittmar, K. D., Hutchison, K. A., Owens-Grillo, J. K., and Pratt, W. B. (1996) J. Biol. Chem. 271, 12833-12839). In this work we show that when the GR is incubated with hsp90, hsp70, and p60, steroid binding sites are generated despite the absence of p23. In this minimal reconstituted system, the GR is incubated with the chaperones in the presence of [3H]triamcinolone acetonide ([3H]TA), which binds to the receptor as GR.hsp90 complexes are formed. When molybdate or p23 is also present during the incubation with chaperones at 30 degrees C, the formation of steroid binding sites can be assayed by incubating the washed GR with [3H]TA after heterocomplex assembly at 30 degrees C. However, in the absence of p23 or molybdate, rapid disassembly of GR.hsp90 complexes apparently occurs simultaneously with assembly, such that [3H]TA must be present during the assembly process to trap evidence of conversion of the GR HBD from a non-steroid binding to a steroid binding conformation. Mixture of purified rabbit hsp90 and hsp70 with bacterial lysate containing human p60 results in spontaneous formation of an hsp90.p60.hsp70 complex that can be adsorbed with anti-p60 antibody, and the resulting immune complex converts the GR HBD to a steroid binding state in an ATP-dependent and K+-dependent manner. When the GR is incubated with hsp90, hsp70, and p60 in the presence of the hsp90-binding antibiotic geldanamycin, GR.hsp90.p60. hsp70 complexes are formed, but they have no steroid binding activity. Our data suggest that hsp90, hsp70, and p60 work together as a chaperone complex that possesses all of the folding/unfolding activity necessary to generate the high affinity steroid binding conformation of the receptor.

Animals↗
PubMed1999

Interaction of collagen alpha1(X) containing engineered NC1 mutations with normal alpha1(X) in vitro. Implications for the molecular basis of schmid metaphyseal chondrodysplasia.

Collagen X is a short-chain homotrimeric collagen expressed in the hypertrophic zone of calcifying cartilage. The clustering of mutations in the carboxyl-terminal nonhelical NC1 domain in Schmid metaphyseal chondrodysplasia (SMCD) suggests a critical role for NC1 in collagen X structure and function. In vitro collagen X DNA expression, using T7-driven coupled transcription and translation, demonstrated that although alpha1(X) containing normal NC1 domains can form electrophoretically stable trimers, engineered SMCD NC1 missense or premature termination mutations prevented the formation of electrophoretically stable homotrimers or heterotrimers when co-expressed with normal alpha1(X). To allow the detection of more subtle interactions that may interfere with assembly but not produce SDS-stable final products, we have developed a competition-based in vitro co-expression and assembly approach. Our studies show that alpha1(X) chains containing SMCD mutations reduce the efficiency of normal alpha1(X) trimer assembly, indicating that interactions do occur between mutant and normal NC1 domains, which can impact on the formation of normal trimers. This finding has important implications for the molecular pathology of collagen X mutations in SMCD. Although we have previously demonstrated haploinsufficiency as one in vivo mechanism (Chan, D., Weng, Y. M., Hocking, A. M., Golub, S., McQuillan, D. J., and Bateman, J. F. (1998) J. Clin. Invest. 101, 1490-1499), the current study suggests dominant interference is also possible if the mutant protein is expressed in vivo. Furthermore, we establish that a conserved 13-amino acid aromatic motif (amino acids 589-601) is critical for the interaction between the NC1 domains, suggesting that this region may initiate assembly and the other NC1 mutations interfered with secondary interactions important in folding or in stabilizing the assembly process.

Base Sequence↗