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PubMed1995

A visual data flow environment for macromolecular crystallographic computing.

This article describes the integration of programs from the widely used CCP4 macromolecular crystallography package into a modern data flow visualization environment (application visualization system [AVS]), which provides a simple graphical user interface, a visual programming paradigm, and a variety of 1-, 2-, and 3-D data visualization tools for the display of graphical information and the results of crystallographic calculations, such as electron density and Patterson maps. The CCP4 suite comprises a number of separate Fortran 77 programs, which communicate via common file formats. Each program is encapsulated into an AVS macro module, and may be linked to others in a data flow network, reflecting the nature of many crystallographic calculations. Named pipes are used to pass input parameters from a graphical user interface to the program module, and also to intercept line printer output, which can be filtered to extract graphical information and significant numerical parameters. These may be passed to downstream modules, permitting calculations to be automated if no user interaction is required, or giving the user the opportunity to make selections in an interactive manner.

Base Sequence↗
PubMed1996

Construction, purification and immunogenicity of antigen-antibody-LTB complexes.

An oligonucleotide, encoding a short epitope peptide tag, termed Pk, was inserted at the 3'-end of the gene coding B-subunit of Escherichia coli heat-labile enterotoxin (LTB). The presence of the Pk epitope on LTB-Pk was used to construct novel macromolecular assemblies comprising LTB-Pk, an anti-Pk mAb, (mAb SV5-P-k) and Pk-linked recombinant SIV proteins. The 1:1:1 stoichiometry of such complexes was ensured by binding LTB-Pk to one arm of mAb SV5-P-k and an SIV-Pk antigen to the other arm of the antibody. Such SIV-mAb-LTB macromolecular complexes bound to GM1-ganglioside in vitro, and when immunized systemically into mice were highly immunogenic, inducing both humoral and cell-mediated responses to the recombinant SIV antigens.

Amino Acid Sequence↗
PubMed1994

The oxidative inactivation of cytochrome P450 in monooxygenase reactions.

Possible mechanisms of cytochrome P450 self-inactivation during catalytic turnover have been considered. Two ways of hemoprotein inactivation are so far known. The first, studied extensively by many authors, is the formation of active substrate intermediates, capable of modifying heme and apoenzyme. The second way, revealed quite recently and resulting from uncoupled cytochrome P450-catalyzed monooxygenase reactions, is yet to be clarified. Briefly, it involves formation of hydrogen peroxide in the hemoprotein active center, which interacts with the enzyme associated Fe2+, thereby generating hydroxyl radicals that bleach the heme and modify the apoenzyme. This mechanism operates with substrates and cytochrome P450 forms with partially coupled monooxygenase reactions, thus causing the formation of hydrogen peroxide as a byproduct.

Animals↗
PubMed1995

Potential energy functions.

When energy is a critical quantity, accurate biomolecular simulations rest in substantial part on accurate potential energy functions (force fields). Improvements in methodology for determining parameters--particularly, in the systematic use of computational data obtained from quantum chemical calculations--and enhancements in functional form are leading to better potential energy functions. New calculations have been developed for water (including calculations that incorporate electronic polarizability to take account of the degree to which a molecule can be polarized), proteins, nucleic acids, carbohydrates, lipids, and general organic molecules. Most notably, two new biomolecular force fields have recently been derived and significant redeterminations of the parameters of two existing biomolecular force fields have been carried out. Some progress has also been made in incorporating polarizability into potential energy functions for molecules in general and in improving the treatment of metal-ligand interactions in systems of biomolecular interest.

Electrochemistry↗
PubMed2005

Liquid chromatography of polymers under limiting conditions of adsorption. IV. Sample recovery.

The high performance liquid chromatography of polymers under limiting conditions of adsorption (LC LCA) separates macromolecules, either according to their chemical structure or physical architecture, while molar mass effect is suppressed. A polymer sample is injected into an adsorption-active column flushed with an adsorption promoting eluent. The sample solvent is a strong solvent which prevents sample adsorption. As a result, macromolecules of sample elute within the zone of their original solvent to be discriminated from other, non-adsorbing polymer species, which elute in the exclusion mode. LC LCA sample recovery has been studied in detail for poly (methyl methacrylate)s using a bare silica gel column and an eluent comprised toluene (adsorli) and tetrahydrofuran (desorli). Sample solvent was tetrahydrofuran. It was found that a large part of injected sample may be fully retained within the LC LCA columns. The amount of retained polymer increases with decreasing packing pore size and with higher sample molar masses and, likely, also with the column diameter. The extent of full retention of sample does not depend of sample volume. An additional portion of the injected desorli sample solvent (a tandem injection) does not fully eliminate full retention of the sample fraction and the reduced recovery associated with it. The injected sample is retained along the entire LC LCA column. The reduced sample recovery restricts applicability of many LC LCA systems to oligomers and to discrimination of the non-adsorbing minor macromolecular components of complex polymer mixtures from the adsorbing major component(s). The full retention of sample molecules within columns may also complicate the application of other liquid chromatographic methods, which combine entropic and enthalpic retention mechanisms for separation of macromolecules.

Adsorption↗
PubMed1986

Evidence of binary complex formations between cytochrome P-450, cytochrome b5, and NADPH-cytochrome P-450 reductase of hepatic microsomes.

Water-soluble carbodiimide-catalyzed cross-linking of purified cytochrome P-450 LM2, cytochrome b5, and NADPH-cytochrome P-450 reductase was used to identify stable complexes formed between these proteins. High yields of P-450-b5 and P-450 reductase-b5 dimers, and lower yields of P-450 reductase-LM2 dimers were obtained. Substitution of native b5 and P-450 reductase with fully amidinated derivatives showed that LM2 and b5 were cross-linked exclusively through their respective amino and carboxyl groups. However, there appeared to be two complexation sites on the reductase which cross-link to b5 through amino groups and to LM2 through carboxyl groups respectively. A heterotrimer could not be identified following incubation of all three proteins together with EDC.

Animals↗
PubMed1994

Molecular models and structural comparisons of native and mutant class I filamentous bacteriophages Ff (fd, f1, M13), If1 and IKe.

The filamentous bacteriophages are flexible rods about 1 to 2 microns long and 6 nm in diameter, with a helical shell of protein subunits surrounding a DNA core. The approximately 50-residue coat protein subunit is largely alpha-helix and the axis of the alpha-helix makes a small angle with the axis of the virion. The protein shell can be considered in three sections: the outer surface, occupied by the N-terminal region of the subunit, rich in acidic residues that interact with the surrounding solvent and give the virion a low isoelectric point; the interior of the shell, including a 19-residue stretch of apolar side-chains, where protein subunits interact mainly with each other; and the inner surface, occupied by the C-terminal region of the subunit, rich in basic residues that interact with the DNA core. The fact that virtually all protein side-chain interactions are between different subunits in the coat protein array, rather than within subunits, makes this a useful model system for studies of interactions between alpha-helix subunits in a macromolecular assembly. We describe molecular models of the class I filamentous bacteriophages. This class includes strains fd, f1, M13 (these 3 very similar strains are members of the Ff group), If1 and IKe. Our model of fd has been refined to fit quantitative X-ray fibre diffraction data to 30 A resolution in the meridional direction and 7 A resolution in the equatorial direction. A simulated 3.3 A resolution diffraction pattern from this model has the same general distribution of intensity as the experimental diffraction pattern. The observed diffraction data at 7 A resolution are fitted much better by the calculated diffraction pattern of our molecular model than by that of a model in which the alpha-helix subunit is represented by a rod of uniform density. The fact that our fd model explains the fd diffraction data is only part of our structure analysis. The atomic details of the model are supported by non-diffraction data, in part previously published and in part newly reported here. These data include information about permitted or forbidden side-chain replacements, about the effect of chemical modification, and about spectroscopic experiments.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1985

Changes in the sedimentation properties of cytosolic androgen receptors associated with activation in vitro and in vivo.

In cell-free systems androgen receptor (AR) labeled with (3H)DHT at 0 degrees C in the presence of 50mM molybdate remains unactivated (less than 3% binding to nuclei) and untransformed (7-8S on sucrose density gradients containing 0.4M KCl and 50mM molybdate). In the absence of molybdate, however, these complexes undergo activation and transformation even at 0 degrees C, albeit, very slowly. Incubation of unactivated, untransformed AR complexes at 18 degrees C, or at 0 degrees C in the presence of 0.4M KCl, greatly accelerated both activation and transformation. Activation and transformation are also associated with formation of high affinity (3H)DHT-receptor complexes as indicated by decreased rates of (3H)DHT dissociation from the receptor. Cytosolic AR complexes labeled with (3H)DHT in tissue slices at 37 degrees C, or in vivo, undergo rapid activation, transformation and nuclear translocation. The data suggest that activation and transformation of cytosolic AR in cell-free systems is associated with changes in the physicochemical properties of AR similar to those occurring upon hormone binding in intact cells and in vivo.

Animals↗
PubMed1983

Biosynthesis of acetylcholine receptor in vitro.

Torpedo acetylcholine receptor is accessible to analysis by cell-free protein synthesis, like other membrane proteins studied previously. The factors deserving particular attention in this system are the small amounts of messenger RNA contained in electroplax tissue, the inherent complexity of an oligomeric membrane protein (necessitating the use of subunit-specific antibodies), the anomalous electrophoretic behavior of the primary translation products (attributable in part to the high--SH content of sAChRs), and the multiple glycosylated forms that appear upon processing by microsomal membranes. Although not all these complexities can be satisfactorily explained, they have been empirically characterized and can be well controlled if the appropriate procedures are followed.

Animals↗
PubMed2001

The hydration problem in solution biophysics: an introduction.

The background and purpose of the British Biophysical Society Discussion meeting, The Hydration Problem in Solution Biophysics, held at the University of Glasgow, 12 September 2000, is described, particularly in relation to previous meetings in this field. Whereas a study of the nature and dynamic properties of water associated with a molecule is an important topic by itself, the collection of papers based on this meeting focus mainly on its affect in interpreting biophysical data in terms of macromolecular shape in a solution environment, particularly under dilute and very dilute systems. The techniques considered are largely hydrodynamically or thermodynamically based and supplemented by molecular modeling strategies; but in the context of how these could be used in conjunction with techniques like X-ray crystallography, NMR and neutron scattering.

Biophysics↗
PubMed1978

[Modifications of genetic markers during malignant blood disease].

Genetic marker changes in malignancy are related to an acquired disfunction of the genetic material in stem cells. This disfunction always leads to the lack of antigen; whenever we evidenced a new specificity it was an unconverted substrate. In malignant states modifications are multiple, polyclonal and independent. This least feature explains the extent of the process giving that disfunction. The evidence of a genetic defect is supported by the simultaneous decrease of the primary gene product: the glycosyl-transferase (ABO locus). In some other malignant carcinoma, blood group specificities were observed, their meaning is not well explained. Blood group specificities associated to carcino embryogenic antigen (CEA) or to some mucins could be related to the structure of macromolecular carriers.

ABO Blood-Group System↗
PubMedDate not supplied

Oligonucleotide structure influences the interactions between cationic polymers and oligonucleotides.

We examined the effect of oligodeoxynucleotide (ODN) structure on the interactions between cationic polymers and ODNs. Unstructured and hairpin structured ODNs were used to form complexes with the model cationic polymer, poly-L-lysine (pLL), and the characteristics of these polymer-ODN interactions were subsequently examined. We found that hairpin structured ODNs formed complexes with pLL at slightly lower pLL:ODN charge ratios as compared to unstructured ODNs and that, at high charge ratios, greater fractions of the hairpin ODNs were complexed, as measured by dye exclusion. The dissociation of pLL-ODN interactions was tested further by challenge with heparin, which induced complex disruption. Both the kinetics and heparin dose response of ODN release were determined. The absolute amount and the kinetic rate of ODN release from the complexes of pLL and unstructured ODN were greater, as compared to hairpin ODNs. Our results therefore highlight the role of ODN structure on the association-dissociation behavior of polymer-ODN complexes. These findings have implications for the selection of ODN sequences and design of polymeric carriers used for cellular delivery of ODNs.

Biocompatible Materials↗
PubMedDate not supplied

Organo hydrogel hybrids. Formation of reservoirs for protein delivery.

A biodegradable organo hydrogel hybrid material is presented, which is formed through the water uptake of a phosphoryl choline zwitterionomer (PC ionomer). The water uptake and subsequent swelling is induced by the phosphoryl choline (PC) end group functionality. The nonfunctional poly(trimethylene carbonate) is hydrophobic and as such does not absorb any water. Disks of the PC ionomer showed significant water uptake, typically above 90 wt % when fully swollen. This high water uptake triggered us to utilize the material for drug and protein loading and subsequent release. Fluorescein and fluorescein-labeled proteins were used as simple models for the loading and release characteristics of the material which was studied by fluorescence spectroscopy. The rate of release of the loaded molecules was compared, and it was shown that the release rate was similar for FITC and insulin but slightly slower for albumin. These results suggest that the PC ionomer may be used as a biodegradable and low elastic modulus material with an additional drug and/or protein release capacity. Such materials are of particular interest for use in a variety of applications in vivo, for example as drug eluting stents.

Albumins↗
PubMedDate not supplied

DNA-responsive hydrogels that can shrink or swell.

Molecule-responsive hydrogels are reputed to be smart materials because of their unique properties. We recently reported that hydrogels containing directly grafted single-stranded (ss) DNA or ssDNA-polyacrylamide conjugate in a semi-interpenetrating network (semi-IPN) manner that "only shrunk" by the addition of ssDNA samples. To date, however, no DNA-responsive hydrogels have been reported capable of "swelling" in response to specific DNAs. Smart materials capable of both shrinking and swelling in response to specific DNAs would be very useful in biochemical and biomedical applications. Here, we show a novel "shrinking or swelling" DNA-responsive mechanism. Novel hybrid hydrogels containing rationally designed ssDNA as the cross-linker were capable of shrinking or swelling in response to ssDNA samples and recognizing a single base difference in the samples. On the basis of the results presented in this paper, it is envisioned that these novel hybrid hydrogels could function and have potential in applications such as DNA-sensing devices and DNA-triggered actuators.

Acrylic Resins↗
PubMed2006

Dendrimers: novel polymeric nanoarchitectures for solubility enhancement.

Poor solubility and hydrophobicity of drugs/bioactives limit their possible applications in drug delivery and formulation development. Apart from conventional methods of solubility enhancement, there are some novel methods which can be used in solubilization. Dendrimers represent a novel type of polymeric material that has generated much interest in many diverse areas due to their unique structure and properties. Dendrimer-mediated solubility enhancement mainly depends on factors such as generation size, dendrimer concentration, pH, core, temperature, and terminal functionality. Added advantage in solubilization can be achieved considering these factors. Available literature suggests that ionic interaction, hydrogen bonding, and hydrophobic interactions are the possible mechanisms by which a dendrimer exerts its solubilizing property. This review presents various mechanisms and reports relating to solubility enhancement using dendrimers. Also, micellar behavior and future possibilities in relation to solubilization via dendrimers are included.

Dendrimers↗
PubMed2006

Phosphorylcholine-based pH-responsive diblock copolymer micelles as drug delivery vehicles: light scattering, electron microscopy, and fluorescence experiments.

The micellization behavior of a diblock copolymer comprising a highly hydrophilic and biocompatible poly(2-methacryloyloxyethyl phosphorylcholine) (PMPC) corona-forming block and a pH-sensitive poly(2-(diisopropylamino)ethyl methacrylate) (PDPA) core-forming block (PMPC-b-PDPA) has been studied by static and dynamic light scattering (SDLS), transmission electron microscopy (TEM), and potentiometry. Self-assembly of PMPC-b-PDPA copolymers with two different DPA volume fractions (phi(DPA)) leads to narrowly distributed and structurally distinct spherical micelles, as evidenced by their molecular weight (M(w,mic)), aggregation number (N(agg)), hydrodynamic radius (R(H)), corona width (W), and core radius (R(c)). The excellent potential of these pH-responsive micelles as nanosized drug delivery vehicles was illustrated by the encapsulation of dipyridamole (DIP), a model hydrophobic drug that dissolves in acid solutions and becomes insoluble above pH 5.8, which is comparable to the pK(a) of the PDPA block. The influence of micelle structure (namely M(w,mic), N(agg), R(H), W, and R(c)) on drug loading content, drug loading efficiency, partition coefficient, and release kinetics was investigated and confirmed by fluorescence spectroscopy studies. The maximum dipyridamole loadings within PMPC(30)-b-PDPA(30) (R(H) = 14.0 nm; W = 4.8 nm; R(c) = 9.2 nm) and PMPC(30)-b-PDPA(60) (R(H) = 27.1 nm; W = 11.0 nm; R(c) = 16.1 nm) micelles were 7 and 12% w/w(p), respectively. This preferential solubilization of DIP into micelles formed by copolymer chains having longer core-forming blocks (i.e., possessing larger core volumes) reflects the larger partition coefficient (K(V)) of DIP between the aqueous phase and PMPC(30)-b-PDPA(60) micelles (K(V) = 5.7 x 10(4)) compared to PMPC(30)-b-PDPA(30) micelles (K(V) = 1.1 x 10(4)). This enhanced ability of PMPC(30)-b-PDPA(60) aggregates to entrap/stabilize small hydrophobic molecules also produces slower release kinetics. Rapid release can be triggered by lowering the pH to induce micellar dissociation.

Dipyridamole↗