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Adaptations to high hydrostatic pressure.

The importance of adaptation to high pressure has long been implicit in the findings of studies in which 1 atm-adapted species were subjected to elevated pressures. Recent comparative studies have shown that pressure sensitivities of enzymes, structural proteins, and membrane-based systems differ markedly between shallow- and deep-living species. These studies allow operational definition of what constitutes high pressures for different biological structures and processes. These are the habitat (adaptation) pressures at which a given type of system first exhibits reduced perturbation by pressure. These threshold pressures vary among physiological systems, but are similar for a given system among different species. Dehydrogenase enzymes and adenylyl cyclases exhibit threshold perturbation pressures of only 50-100 atm; the Na(+)-K(+)-ATPase of teleost gills appears to have a pressure perturbation threshold near 200 atm, and a similar threshold was found for actin self-assembly. Even this limited sample of physiological processes indicates that the terms deep and high pressure begin to apply at depths of only 500 m or less--and processes yet to be examined in comparative analysis may yield even lower pressure thresholds. The differences in sensitivity to pressure of homologous systems in shallow- and deep-living organisms have implications at several levels of biological organization. The vertical distribution patterns of species in aquatic habitats may be established, in part, by interspecific differences in resistance to pressure. High pressures may restrict the depths to which shallow-living species can penetrate, and the obligately barophilic systems found in deep-living organisms may limit their upper distribution limits. The similarities noted among the adaptations of deep-sea species with different shallow-water ancestors reflect a high degree of convergent evolution in pressure adaptation. It will be interesting to learn if the similarities in pressure-resistance of function among diverse deep-sea species are the result of similar or identical changes at the molecular level, e.g. in protein sequence. Acclimation to pressure may be of widespread occurrence among species that undergo large changes in depth, e.g. during ontogeny. Pressure acclimation may require pressure-regulation of gene expression. Lastly, comparisons of species from the cold deep sea with those from hydrothermal vents have shown that adaptations to both temperature and pressure play critical roles in determining the distribution patterns of deep-living species.

Adaptation, Physiological↗

Levels and reduction.

This paper addresses the problem of reconciling pluralism with reductionism, i.e., acknowledging both the variety of the world and the need and possibility to explain it. First the various kinds of monism and pluralism that litter the scientific and philosophical literature are examined cursorily. Then certain maligned notions are examined, mainly those of novelty, self-assembly, level, and levels "hierarchy." They are shown to be amenable to analysis and even mathematization. Then the logic of reduction is analyzed. Two kinds of reduction are distinguished: full or straight, and partial or roundabout. And three stands on reduction are examined: anti-, radical, and moderate reductionism. The former is dismissed for being obscurantist and the second for being quixotic. Moderate reductionism, aiming at the (partial) reduction of higher levels to lower ones without skipping any intermediate levels, is adopted. Finally moderate reductionism is found to be consistent with a certain variety of pluralism, characterized as naturalistic.

Logic↗

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↗

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↗

Review: Casein micelle structure; an examination of models.

The casein micelle system of bovine milk is unique in that protein aggregates of similar spherical shape but extreme variability of size are formed by the self-assembly of three major nonidentical subunits. The monomeric subunits appear to be approximately the same size and shape with similar amphiphilic natures, the chief difference in properties being in the carbohydrate-containing kappa-casein which acts to stabilize the system against precipitation by calcium ion. Micelle models with kappa-casein exclusively in the interior lack a stabilization mechanism and can be eliminated. Statistical considerations of a chain polymer model also lead to its rejection. Electron microscopy reveals spherical submicellar aggregates which at present can be accounted for by only three models. Of these three, the experimental data are predicted only by one in which, alphas 1-, beta-, and kappa-casein subunits are associated into spherical soap micelle-like particles with the kappa-casein segregated into one portion, giving these submicelles an amphiphilic nature. The alphas 1- and beta-caseins are hydrophobic while the kappa-casein portion of the submicelle surface is hydrophilic. Of particular interest is the ability of this micelle model to explain the formation of a minimum micelle which is larger than a submicellar particle.

Amino Acid Sequence↗

The matrix of the optic vesicle-presumptive lens interface during induction of the lens in the chicken embryo.

The cell coats of the presumptive lens cells and the extracellular interface between the lens rudiment and optic vesicle were investigated in the chicken embryo throughout the period during which lens induction is presumed to take place. Histochemical methods showed that the cell coats contained both glycoproteins and glycosaminoglycans. Autoradiography after [3H]glucosamine injection indicated incorporation of the precursor with subsequent localization primarily at the cell surface. No obvious changes in the properties of the coat were noted with the progression of early lens morphogenesis. The extracellular matrix at the interface between ectoderm and optic vesicle also contained glycoprotein and glycosaminoglycan. There was a heavy concentration of [3H]glucosamine-containing macromolecules in the area. Electron microscopy revealed that the interface consisted of the basement membrane systems of lens and optic vesicle, fused with their external fibrillar layers. In contrast to the findings on cell coats the density of the interfacial matrix increases appreciably during the lens induction period. Evidence suggests that the cells of the two ocular epithelia are themselves the source of the matrix materials. It is proposed that the macromolecules excreted by the epithelial cells into the interface interact at different concentrations to form aggregates of various structure by a process of self-assembly. This may be reflected in the different ultrastructure of the layers of the interfacial matrix. Quantitative changes in the density of the matrix, leading to increased adhesion between lens rudiment and optic vesicle, may restrict the lateral spreading of the lens cells and so fix the basal area of the lens rudiment. This, together with continued cell replication, may produce the cell crowding, placode formation and invagination characteristic of lens morphogenesis.

Amylases↗

[Interaction of the components of the cytochrome P-450 monooxygenase system from liver microsomes. I. Immobilization of the solubilized and partially purified protein components].

The method of matrix fixation has been used to study the interaction between the components of the cytochrome P-450 monooxygenases from rat liver microsomes. The solubilized, isolated protein components were covalently bound to BrCN-activated. Sepharose in different ways and subsequently the N-demethylase activity was determined. It has been proved that in each case of fixation a certain amount of activity could be determined. However the degree of activity varied in dependence on the sequence and number of bound components. The activity compared with the reconstituted soluble system decreased in the following sequence: single fixation of NADPH-cytochrome P-450 reductase (40%), of cytochrome P-450 (23%); sequential fixation: first component cytochrome P-450 (33%), first component NADPH-cytochrome P-450 reductase (8%). Simultaneous fixation of both components yielded a lower activity. From the results it was concluded that the activity is influenced by some kind of self-assembly.

Animals↗

Polymerization of pNcollagen I and copolymerization of pNcollagen I with collagen I. A kinetic, thermodynamic, and morphologic study.

Previous observations established that pNcollagen III copolymerized with collagen I and decreased the diameter of the fibrils formed (Romanic, A.M., Adachi, E., Kadler, K.E., Hojima, Y., and Prockop, D.J. (1991) J. Biol. Chem. 266, 12703-12709). Here, procollagen I alone or mixtures of procollagen I and pCcollagen I were incubated with procollagen C-proteinase to generate pNcollagen I or mixtures of pNcollagen I and collagen I. The results confirmed previous reports that pNcollagen I assembles into sheet-like structures. They also demonstrated that polymerization of pNcollagen I exhibits a lag period and propagation phase similar to those seen with other protein self-assembly systems. In addition, the results demonstrated that pNcollagen I formed true copolymers with collagen I in that the presence of pNcollagen I increased the lag time, decreased the propagation rate, and increased the concentration of collagen I in solution at equilibrium. Copolymerization of pNcollagen I with collagen I, however, differed in two features from copolymerization of pNcollagen III with collagen I. One was that, in confirmation of previous work, copolymerization of pNcollagen I with collagen I markedly altered the circularity of the fibrils formed. The second difference was that the copolymerization increased the concentration in solution at equilibrium of pNcollagen I whereas copolymerization with collagen I was previously shown to decrease the concentration in solution of pNcollagen III. The increase in concentration in solution of pNcollagen I was explicable either by the assembly of soluble oligomers of pNcollagen I and collagen I, or by subtle changes in the activities of pNcollagen I and collagen I in the solid-phase. Comparison with previous data with pNcollagen III indicated that although pNcollagen I and pNcollagen III copolymerize with collagen I, there are marked differences in the two kinds of copolymers.

Collagen↗

Epitope mapping of anti-recA protein IgGs by region specified polymerase chain reaction mutagenesis.

Monoclonal IgGs were shown to be useful for the specific inhibition of a set of activities of the recA protein, a key protein in homologous genetic recombination. The mapping of the epitopes for these IgGs and site-directed mutagenesis based on the mapping will facilitate location of the functionally active sites on the tertiary structure of the protein, which is being solved by means of physicochemical techniques. We developed a novel technique for region-specified mutagenesis and applied the technique to epitope mapping. Using the polymerase chain reaction in the presence of deoxyinosine triphosphate, we introduced random base substitutions specifically into a region of the recA gene defined by a pair of primers. RecA mutants exhibiting altered antigenicity were selected, in plaque-immunoblotting experiments, from libraries of mutagenized recA genes constructed on the lambda gt11 expression vector. Mutant recA genes were obtained at the frequency of about 10(-2) among the plaques expressing fused recA genes and then each one was expressed as a whole protein, which was characterized by enzyme-linked immunosorbent assay. Analyzing the DNA sequences of the mutant recA genes, we located at the amino acid sequence level the epitopes for two anti-recA IgGs which could not be located in previous studies. One of the antibodies was shown to prevent self-assembly of the recA protein and the other was suggested to inhibit the binding of double-stranded DNA. Thus, the active sites involved in these functions would be located in the space around or near the relevant epitope.

Amino Acid Sequence↗

Copolymerization of normal type I collagen with three mutated type I collagens containing substitutions of cysteine at different glycine positions in the alpha 1 (I) chain.

Previous observations with type I collagen from a proband with lethal osteogenesis imperfecta demonstrated that type I collagen containing a substitution of cysteine for glycine alpha 1-748 copolymerized with normal type I collagen (Kadler, K. E., Torre-Blanco, A., Adachi, E., Vogel, B. E., Hojima, Y., and Prockop, D. J. (1991) Biochemistry 30, 5081-5088). Here, three preparations containing normal type I procollagen and type I procollagen with a substitution of cysteine for glycine alpha 1-175, glycine alpha 1-691, or glycine alpha 1-988 were purified from cultured skin fibroblasts from probands with osteogenesis imperfecta. The procollagens were then used as substrates in a system for assaying the self-assembly of type I collagen into fibrils. The cysteine-substituted collagens in all three preparations were incorporated into fibrils. The cysteine alpha 1-175 and cysteine alpha 1-691 collagens were shown to increase the lag time and decrease the propagation rate constant for fibril assembly. All three preparations containing cysteine-substituted collagens formed fibrils with diameters that were two to four times the diameter of fibrils formed under the same conditions by normal type I collagen. Also, the three preparations containing cysteine substituted collagens had higher solubilities than normal type I collagen. The results, therefore, demonstrated that the three cysteine-substituted collagens copolymerized with normal type I collagen. The effects of the mutated collagens on fibril assembly can be understood in terms of a recently proposed model of fibril growth from symmetrical tips by assuming that the mutated monomers partially inhibit tip growth but not lateral growth of the fibrils. Of special interest was the observation that the Cys alpha 1-175 collagen from a proband with a non-lethal variant of osteogenesis imperfecta had quantitatively less effect on several parameters of fibril assembly at 37 degrees C than cysteine-substituted collagens from three probands with lethal variants of the disease.

Adult↗

The roles of fibrinogen and fibrin in hemostasis and thrombosis.

Proteolytic conversion of fibrinogen to fibrin results in self-assembly to form a clot matrix that subsequently becomes cross-linked by fXIIIa to form the main structural element of the thrombus in vivo. Fibrin formation and assembly lead to new properties that regulate the rate and extent of clotting, cross-linking, and fibrinolysis. These are brought about by the ability of fibrin (1) to bind thrombin at a nonsubstrate site, thus limiting its diffusability but at the same time preserving its catalytic potential; (2) to bind fXIII, regulate its activation to fXIIIa, and limit further activation of fXIII once fibrin cross-linking has occurred; and (3) to bind alpha 2-PI, t-PA, and plasminogen and regulate the initiation and propagation of fibrinolysis. Fibrinogen and fibrin contain several potential platelet binding sites that interact with platelet GPIIb/IIIa receptors, and thus promote their participation in the hemostatic process. Additional, less well-defined interactions, not covered in detail here, such as those between fibrinogen or fibrin and other plasma proteins, cells, or tissue matrix components, suggest other functions that, along with those detailed above, will further define its multiple roles in modulating hemostasis, inflammation, and the wound healing process.

Amino Acid Sequence↗

Assembly of progesterone receptor with heat shock proteins and receptor activation are ATP mediated events.

To better understand assembly mechanisms of progesterone receptor (PR) complexes, we have developed a cell-free system for studying PR interactions with the 90- and 70-kDa heat shock proteins (hsp90 and hsp70), and we have used this system to examine requirements for hsp90 binding to PR. Purified chick PR, free of hsp90 and immobilized on an antibody affinity resin, will rebind hsp90 in rabbit reticulocyte lysate when several conditions are met. These include: 1) absence of progesterone, 2) elevated temperature (30 degrees C), 3) presence of ATP, and 4) presence of Mg2+. We have obtained maximal hsp90 binding to receptor when lysate is supplemented with 3 mM MgCl2 and an ATP-regenerating system. ATP depletion of lysate by dialysis or by enzymatic means blocks hsp90 binding to PR; likewise, addition of EDTA to lysate blocks hsp90 binding, but binding is restored by the addition of excess Mg2+. Addition to lysate of monoclonal antibody against hsp70 inhibits hsp90 binding to PR and destabilizes preformed complexes. Stabilization of hsp90-receptor complexes also requires ATP, indicating that ATP and hsp70 are needed to form and to maintain hsp90 complexes. Hormone-dependent activation of reconstituted receptor complexes was also examined. The addition of progesterone to the reticulocyte lysate promotes dissociation of hsp90 and hsp70 from the receptor. This also appears to require ATP and dissociation is most efficient in the presence of an ATP-regenerating system. In conclusion, these studies indicate that PR-hsp90 complexes do not self-assemble; instead, assembly is probably a multistep process requiring ATP and other cellular factors.

Adenosine Triphosphate↗

[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↗

[Anticoagulants of the nondialyzed fractions of the ammonia extract of the herb Pulmonaria mollissima].

T-100 anticoagulants non-dialyzed through cellophane are isolated from ammonia extract of herb Pulmonaria mollissima. Their effect is mainly realized at the stage of coagulation conversions of fibrinogen, first of all at the stage of fibrin self-assembly. One of these anticoagulants is a peptide, another one is a glycopeptide which contains glucose residues like carbohydrate. Peptide components of the both anticoagulants are characterized by the high level of amino acids, their radicals are capable to ionization under physiological conditions. In contrast to animal-origin analogs, glycopeptide in nontoxic doses causes stable hypocoagulemia in animals. It is expedient to study Pulmonaria mollissima extracts as a source of direct anticoagulants.

Amino Acids↗

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↗

[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↗

[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↗

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↗