Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “self-assembly”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 55 records · Page 3Linked to original sources
PubMed2026

A proteomic analysis of the PHF-forming tau fragment (tau297-391) following uptake into differentiated human neuronal SHSY5Y cells.

Tau self-assembly and intracellular deposition are associated with a group of neurodegenerative diseases called tauopathies, which include Alzheimer's disease (AD) and Pick's disease. Here, we measured the proteome response in human neuronal cells (differentiated SH-SY5Y) following the addition of a spontaneously amyloidogenic region of tau known as dGAE (tau297-391), which forms AD-like paired helical filaments in vitro, and proteomic analysis showed increased endogenous tau expression. Further interactome analysis uncovered increased association between tau and proteins associated with nuclear chromatin, the nucleolus, and the spliceosome, as well as the thiol-peroxidase, PRDX6, alongside an increase in reactive oxygen species. The present work highlights a method to identify proteome pathways that may play an important role in the development of tau pathology and reveals an oxidative stress response to dGAE.

Humans↗
PubMed1976

A molecular concept of the properdin pathway.

The sequential events of the properdin system were analyzed. Properdin-depleted serum allows the formation of a Factor B- and D-dependent C3 convertase. This enzyme, called the properdin-receptor-forming enzyme, was shown to utilize a novel serum component, the initiating factor. The protein is a beta-globulin in precursor form and is distinct from immunoglobulins. The function of the enzyme is to deposit C3b on the surface of activator particles. Apparently doublets of C3b are required for the formation of the properdin-activating principle. It consists of a complex containing surface-bound C3b and activated Factor B. properdin precursor is activated by binding to this complex without detectable change in molecular weight. The transition of properdin precursor to activated properdin is probably caused by a conformational change. The complex, consisting of bound C3b, properdin, and activated Factor B, represents the enzyme that acts on C5, thereby initiating self-assembly of the membrane attack system. Native C3 is not needed for the function of the enzyme. It is disassembled by soluble C3 or C3b and its formation is under the control of the properdin-receptor-destroying enzyme, which may be identical with the C3b inactivator.

Beta-Globulins↗
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↗
PubMed1977

Disagreement between calorimetric and van't Hoff enthalpies of assembly of protein supramolecular structures.

The effect of temperature on the extent of association of self-assembling protein polymers is expressed mathematically in terms of the van't Hoff enthalpy of polymerization, deltaHV.H. This quantity has been experimentally defined in two ways--from the respective temperature derivatives of the critical polymerization concentration and of the fractional conversion of protein into polymer. These two definitions are shown not to be identical, except in certain limits. In terms of both definitions, it is shown that deltaHV.H. depends not only upon the enthalpy changes but also upon the corresponding equilibrium constants for the various equilibria involved in polymer formation. This has two consequences: (i) large deltaHV.H. values may result from reactions having small calorimetric enthalpy changes; and (ii) deltaHV.H. can depend strongly on temperature. These considerations are applied to two systems for which there exist considerable experimental data--namely, hemoglobin S and tubulin. The large discrepancy between the calorimetric and van't Hoff enthalpies for the polymerization of tubulin is shown to be explicable in terms of these considerations.

Calorimetry↗
PubMed1978

A gene on human chromosome 6 functions in assembly of tissue-specific adenosine deaminase isozymes.

In human tissues, adenosine deaminase (ADA) (adenosine aminohydrolase; EC 3.5.4.4) activity can be separated by gel electrophoresis into several isozymes. A structural gene (ADA) on chromosome 20 codes for the "erythrocyte" isozyme, ADA-1, which is also expressed in some nonerythroid tissues. Nonerythroid cells also differentially express five ADA "tissue isozymes" of a greater molecular weight than ADA-1. Each ADA tissue isozyme has a characteristic electrophoretic mobility and tissue distribution. It has been suggested that these ADA tissue isozymes are composed of ADA-1 and other components. We report that the expression of one of these tissue isozymes, ADA-d, is dependent upon ADA on chromosome 20 and another gene on chromosome 6 which functions in the assembly of the ADA tissue isozymes. In human-mouse hybrids segregating human chromosomes, chromosome 6(+),20(+) hybrids express both ADA-1 and ADA-d; chromosome 6(-),20(+) hybrids express only ADA-1; while 6(+),20(-) hybrids have no human ADA activity. ADA-d formation also occurs in vitro by self-assembly when an extract of human erythrocytes or chromosome 6(-),20(+) hybrids is mixed with a homogenate of chromosome 6(+),20(-) hybrids. The gene on chromosome 6, designated ADCP, codes for an adenosine deaminase complexing protein. The product of ADCP presumably combines with ADA-1 to form the ADA tissue isozymes. The data are consistent with the hypothesis that the distribution of enzymatic activity between ADA-1 and the tissue isozymes depends on the expression of the gene for ADA complexing protein, while the differences in the electrophoretic mobilities of the ADA isozymes, except ADA-1, are generated, as suggested by others, by the degree of glycosylation of the complexing protein.

Adenosine Deaminase↗
PubMed1976

The microsporidian spore invasion tube. The ultrastructure, isolation, and characterization of the protein comprising the tube.

The extrusion apparatus of the microsporidian parasitic protozoan Nosema michaelis discharges an invasion (or polar) tube with a velocity suitalbe for piercing cells and injecting infective sporoplasm. The tube is composed of a polar tube protein (PTP) which consists of a single, low molecular weight polypeptide slightly smaller than chymotrypsinogen-A. Assembled PTP tubes resist dissociation in sodium dodecyl sulfate and brief exposures in media at extreme ends of the pH range; however, the tubes are reduced by mercaptoethanol and dithiothreitol. When acidified, mercaptoethanol-reduced PTP self-assembles into plastic, two-dimensional monolayers. Dithiothreitol-reduced PTP will not reassemble when acidified. Evidence is presented which indicates that PTP is assembled as a tube within the spore; that the ejected tube has plasticity during sporoplasm passage; and, finally, that the subunits within the tube polymer are bound together, in part, by interprotein disulfide linkages.

Amino Acids↗
PubMed1979

Chick brain actin and myosin. Isolation and characterization.

Brain actin extracted from an acetone powder of chick brains was purified by a cycle of polymerization-depolymerization followed by molecular sieve chromatography. The brain actin had a subunit molecular weight of 42,000 daltons as determined by co-electrophoresis with muscle actin. It underwent salt-dependent g to f transformation to form double helical actin filaments which could be "decorated" by muscle myosin subfragment 1. A critical concentration for polymerization of 1.3 microM was determined by measuring either the change in viscosity or absorbance at 232 nm. Brain actin was also capable of stimulating the ATPase activity of muscle myosin. Brain myosin was isolated from whole chick brain by a procedure involving high salt extraction, ammonium sulfate fractionation and molecular sieve chromatography. The purified myosin was composed of a 200,000-dalton heavy chain and three lower molecular weight light chains. In 0.6 M KCl the brain myosin had ATPase activity which was inhibited by Mg++, stimulated by Ca++, and maximally activated by EDTA. When dialyzed against 0.1 M KCl, the brain myosin self-assembled into short bipolar filaments. The bipolar filaments associated with each other to form long concatamers, and this association was enhanced by high concentrations of Mg++ ion. The brain myosin did not interact with chicken skeletal muscle myosin to form hybrid filaments. Furthermore, antibody recognition studies demonstrated that myosins from chicken brain, skeletal muscle, and smooth muscle were unique.

Actins↗
PubMed2025

Transcriptome-wide analysis reveals sequence selection to avoid mRNA aggregation in E. coli.

The stability of RNA base pairing and its limited four-letter code create an intrinsic potential for promiscuous RNA-RNA interactions. In vitro, such interactions drive RNA to self-assemble into aggregates. This raises a fundamental unanswered question: within a confined cellular volume at physiological mRNA abundances, how much aggregation would arise from sequence-encoded chemistry alone? Here, we establish this baseline with large-scale kinetic simulations of the E. coli transcriptome. Our simulations reveal that sequence-encoded base-pairing energetics is sufficient to generate a dynamic network of large aggregates, organized by long, multivalent mRNA hubs. Strikingly, evolutionary analysis shows that native E. coli sequences exhibit clear signatures of selection to counteract this propensity: they fold more stably, minimize unstructured regions, and form weaker intermolecular contacts than dinucleotide-preserving controls. These findings demonstrate that maintaining transcriptome solubility has been a significant, previously unrecognized constraint shaping genome evolution, and provide a new lens to interpret cellular RNA management.

Biological Sciences (Biophysics and Computational ↗
PubMed1977

Purification of protected syntheic peptides by preparative high performance liquid chromatography on silica gel 60.

A simple preparative system is described for rapid and efficient purification of protected synthetic peptides on a gram scale by high performance liquid chromatography on prepacked silica gel 60 columns. A variety of protected peptides up to tetradecapeptides have been chromatographed at pressures of 50 to 150 psi and obtained in analytically pure from within 2 to 4 h. With such commonly used protecting groups as N-benzyloxycarbonyl (Z), N-2-(p-biphenylyl)-2-propyloxycarbonyl (Bpoc), N-t-butyloxycarbonyl (Boc), O- and S-t-butyl (But), and S-acetamidomethyl (Acm), compounds were sufficiently soluble in chloroform, alcohols, acetic acid, or mixtures of these solvents for column loading. Dimethylformamide was also used as a solvent for loading. Solvent systems for column elution in isocratic, stepwise, or gradient modes were composed of chloroform, isopropanol, ethanol, or methanol and acetic acid in ratios that differed for each protected peptide depending on Rf values on t.l.c. plates. A simple chromatography is described which was self-assembled using standard instruments commonly in use in most laboratories. A shut-off valve was designed to prevent loss of material between fractions.

Chromatography, Liquid↗
PubMed1979

Specific interaction of the tetragonally arrayed protein layer of Bacillus sphaericus with its peptidoglycan sacculus.

Tetragonal layer protein (T-layer) isolated from Bacillus sphaericus NTCC 9602 (wild type) or 9602 Lmw (variant) bonded specifically to the sacculi (peptidoglycan) of either cell type. Only uncleaved T-layer subunits were capable of specific recognition of the B. sphaericus sacculi; other Bacillus strains and gram-positive bacterial sacculi would not adsorb B. sphaericus strain 9602 T-layer. The peptidogylcan did not function as a template since isolated T-layer subunits self-assembled into characteristic pattern. Upon reassociation with sacculi, T-layer assemblies were randomly oriented patches compared with more continuous strictly oriented pattern on cells or fresh cell walls. T-layer associated with the sacculus was less susceptible to conditions that dissociated in vitro-assembled T-layer. Mild proteolysis of both wild-type and variant T-layer subunits by a variety of enzymes reduced the molecular weight by 18,000 in all cases, indicating that one region of the molecule was particularly susceptible to cleavage. Subunits from which the minor fragment had been cleaved upon aging retained the capacity to assemble in vitro, but would no longer adsorb to sacculi. Thus, the ability of T-layer to form networks was separate from its ability to bind cell walls, and the 18,000-dalton piece of the T-layer polypeptide was necessary for attachment to the cell wall.

Bacillus↗
PubMed2025

IgStrand: A universal residue numbering scheme for the immunoglobulin-fold (Ig-fold) to study Ig-proteomes and Ig-interactomes.

The Immunoglobulin fold (Ig-fold) is found in proteins from all domains of life and represents the most populous fold in the human genome, with current estimates ranging from 2 to 3% of protein coding regions. That proportion is much higher in the surfaceome where Ig and Ig-like domains orchestrate cell-cell recognition, adhesion and signaling. The ability of Ig-domains to reliably fold and self-assemble through highly specific interfaces represents a remarkable property of these domains, making them key elements of molecular interaction systems: the immune system, the nervous system, the vascular system and the muscular system. We define a universal residue numbering scheme, common to all domains sharing the Ig-fold in order to study the wide spectrum of Ig-domain variants constituting the Ig-proteome and Ig-Ig interactomes at the heart of these systems. The "IgStrand numbering scheme" enables the identification of Ig structural proteomes and interactomes in and between any species, and comparative structural, functional, and evolutionary analyses. We review how Ig-domains are classified today as topological and structural variants and highlight the "Ig-fold irreducible structural signature" shared by all of them. The IgStrand numbering scheme lays the foundation for the systematic annotation of structural proteomes by detecting and accurately labeling Ig-, Ig-like and Ig-extended domains in proteins, which are poorly annotated in current databases and opens the door to accurate machine learning. Importantly, it sheds light on the robust Ig protein folding algorithm used by nature to form beta sandwich supersecondary structures. The numbering scheme powers an algorithm implemented in the interactive structural analysis software iCn3D to systematically recognize Ig-domains, annotate them and perform detailed analyses comparing any domain sharing the Ig-fold in sequence, topology and structure, regardless of their diverse topologies or origin. The scheme provides a robust fold detection and labeling mechanism that reveals unsuspected structural homologies among protein structures beyond currently identified Ig- and Ig-like domain variants. Indeed, multiple folds classified independently contain a common structural signature, in particular jelly-rolls. Examples of folds that harbor an "Ig-extended" architecture are given. Applications in protein engineering around the Ig-architecture are straightforward based on the universal numbering.

Humans↗
PubMed2026

Metal-Organic Framework-Based and Metal-Organic Framework-Derived Nanomaterials for Cancer Theranostics and Antibacterial Applications: Advances, Challenges, and Perspectives.

Metal-organic frameworks (MOFs), constructed through coordination-driven self-assembly of metal ions/clusters and organic linkers, have emerged as a uniquely versatile class of porous nanomaterials with broad biomedical potential. Despite substantial clinical progress, both oncological treatment and antimicrobial intervention remain constrained by inadequate tumor-targeting selectivity, multidrug resistance, immunosuppressive tumor microenvironments, and the global proliferation of antibiotic-resistant pathogens, limitations that conventional nanocarrier platforms have addressed only in part. MOF-based and MOF-derived nanomaterials, distinguished by tunable pore architecture, structurally and compositionally adaptable metal nodes, high surface areas, and stimulus-responsive degradability, offer a rational framework for overcoming these barriers. This review systematically examines the synthetic strategies underlying MOF-based and MOF-derived nanomaterials, including pyrolysis, chemical etching, composite modification, and functional group introduction, and their structural determinants of performance. In cancer theranostics, we critically evaluate their roles as multimodal imaging contrast agents, stimulus-responsive drug delivery carriers, and platforms for combination therapies encompassing photodynamic, photothermal, chemodynamic, and immunomodulatory modalities. In antibacterial applications, we analyze the mechanistic basis of MOF-based and MOF-derived activity, including physical membrane disruption, reactive oxygen species-mediated oxidative stress, and sustained metal ion release, alongside strategies targeting biofilm formation and antibiotic resistance. Multifunctional platforms that concurrently integrate cancer theranostic and antibacterial capabilities are further discussed. This review also addresses the principal barriers to clinical translation, encompassing large-scale manufacturing, long-term biosafety, and regulatory approval, and proposes future directions incorporating artificial intelligence-assisted design and materials genomics, underscoring the transformative potential of MOF-based and MOF-derived nanomaterials as next-generation precision nanomedicines. This review establishes a unified mechanistic framework grounded in the intrinsic physicochemical properties of MOF-derived nanomaterials, systematically integrating their applications in cancer theranostics and antibacterial therapy. Critically, it bridges fundamental advances with translational reality by incorporating a rigorous assessment of regulatory pathways, scalable manufacturing constraints, and clinical implementation barriers, and offers a comprehensive, practice-oriented reference for the rational design and responsible translation of MOF-based and MOF-derived nanomaterials.

Theranostic Nanomedicine↗
PubMedDate not supplied

[Role of phospholipids in the generation of membrane potentials by proteoliposomes].

Closed protein-phospholipid particles (proteoliposomes), obtained by self-assembly method, are capable to generate and to maintain the membrane potential in the case if their protein complex is represented by: a) a complex of mitochondrial ATPase; b) a complex of cytochrome oxidase and cytochrome c and c) bacteriorhodopsin from Halobacterium halobium; and their phospholipid component is represented by phosphatidylethanolamine or by a mixture of mitochondrial phospholipids. Only cytochromoxidase and bacteriorhodopsin (but not ATPase) proteoliposomes with phosphatidylserine are active. Cardiolipin also is not active in experiments with ATPase. Phosphatidylcholine produces in all the cases proteoliposomes incapable of maintaining the membrane potential. It is concluded that the inefficiency of phosphatidylcholine in the formation of proteoliposomes, generating the membrane potential, is due to the impossibility of obtaining closed membrane forms with a high electric resistance. The inefficiency of phosphatidylserine and cardiolipine, in the case of ATPase protein component of proteoliposomes, may be due to a specific requirement of this generator of the membrane potential in phosphatidylethanolamine.

Adenosine Triphosphatases↗
PubMed1978

Protein-lipid interactions and the role of water.

The rigidity of the three-dimensional structure of a native protein is dependent on the network of hydrogen-bonded groups which provide the scaffolding for the other interactions. The structure is stabilized by the hydrophobic interactions of the nonpolar side chains. The latter are formed by the very unfavorable entropy change that occurs in water but not in less-polar solvents. It is unlikely that any solvent other than water can produce the same folding of a polypeptide chain to form the active native structure. Water plays a unique role, since it alone is responsible for the heat capacity changes observed when nonpolar groups are transferred from an aqueous to a nonaqueous environment, as exists in the interior of a protein. The need to juxtapose like groups and to avoid making contact among unlike groups imposes severe restrictions on the binding of small or large molecules to proteins. Consequently there must be proper pairing of polarities as well as close fitting of ligands for strong binding to occur. This is clearly evident from the x-ray studies of proteins containing subunits or prosthetic groups. The thermodynamic parameters observed in the most complex protein reactions--i.e., self-assembly systems--resemble rather well those observed in micelle association reactions or even in the solution of nonpolar gases in water. This interaction--hydrophobic--can be looked upon as the controlling reaction which stabilized the organized structures of most cellular entities aside from nucleic acids--i.e., membranes and organelles.

Butanes↗
PubMedDate not supplied

[Cooperative interaction of serum albumin with quaternized poly-4-vinyl pyridine and structure of the complexes].

Interaction of bovine serum albumin (BSA) with quaternized poly-4-vinyl pyridine (PE) in aqueous solutions at pH 7 was studied. It was shown that in a wide range of the ratios of the components (nBSA/nPE) soluble stable cooperative complexes were formed. At the same time a certain critical content of the protein exists at which the system loses its homogeneity. Complex formation is not accompanied by protein denaturation. At smaller nBSA/nPE ratios non-homogeneous distribution of protein globulas among polyelectrolite macromolecules was found; this corresponded to the "all or none" principle. Using ultracentrifugation technique viscosimetric measurements and electron microscopy it was shown that the soluble complexes exist in the form of rode-like particles consisting of protein globules stabilized by polycation chains. Such particle can be considered as a model of nucleoprotein complex. At certain crytical nBSA/nPE rations the rod-like particles aggregate with additional number of BSA-molecules and form more complicate soluble and insoluble cooperative complexes. Possible structural models of the complexes described were suggested and the thermodinamic and kinetic cryteria of their self-assembly were discussed.

Drug Stability↗
PubMed1977

[Quaternary structure of oligomeric immunoglobulin A forms from human blood serum].

A character of forces stabilyzing quaternary structure of dimer and more high molecular human immunoglobulin A oligomers is found to be different. Quaternary structure of IgA dimer is formed when joining subunits with disulfide bonds and is stabilized by non-covalent interactions between them. Disulfide bonds play a main part in the formation of trimers and tetramers. Dimer IgA reconstructs by 40% from subunits with intact interchain S--S bonds. The addition of exogenous J-chain does not significantly affect the process of dimer self-assembling from subunits with recovered and intact interchain disulfide bonds.

Chemical Phenomena↗
PubMed1979

The binding of ribosomal protein S4 does not change the gross conformation of the 16 S RNA.

The binding of ribosomal protein S4 to the 16 S RNA does not result in a large shape or conformational change in the 16 S RNA under the conditions of reconstitution. The sedimentation coefficient, frictional coefficient ratio, and effective hydrodynamic radius of the 16 S RNA.protein S4 complex are very similar to those obtained for the 16 S RNA free in solution. Only subtle conformational differences were obtained in the comparison of the complex and free 16 S RNA by circular dichroism. Thus, extensive organization of the 16 S RNA by ribosomal protein S4 is not a step in the process of self-assembly of the 30 S subunit.

Circular Dichroism↗
PubMedDate not supplied

[Spectrum differentiation as a method of studying protein preparations with a high turbidity level].

The studies on a model of a mixture of fibrin-monomer with glycogen and of fibrin gels of different turbidity show that in the first and second derivatives of the absorption spectra the contribution of turbidity is several orders lower. The derivative spectra are shown to be valuable technique to study the phenomena that are accompanied by substantial changes in turbidity: protein association and self-assembly of supermolecular structure.

Fibrin↗