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PubMed1996

Overview lecture. Hydration processes in biological and macromolecular systems.

I discuss several themes arising from the papers presented at this Faraday Discussion that are, in my view, particularly interesting and/or important. With respect to model systems, recent progress in understanding structural aspects of the hydrophobic interaction, and of through-solvent interactions in general, is highlighted, together with the need to continue to develop more sophisticated (theoretical and computational) interpretational techniques if we are to exploit to the full the power of present-day experimental techniques. The current state of our knowledge of hydration effects on the structure and dynamics of biomolecules is discussed, and the importance of being able to see how molecular-level structural effects control behaviour at the important mesoscopic level is underlined. Issues relating to recent progress in characterising solvent effects in more complex systems and processes, including those of industrial interest, are raised, and the necessity of using a range of appropriate experimental techniques when tackling such complex problems is stressed. Progress since the 1975 Royal Society Discussion is highlighted, and interesting issues ripe for fruitful discussion at this meeting are raised. A strong case can now be made that our under-standing of both the structure and dynamics of water as a function of its local environment is now sufficiently good to enable us to use water as a probe of complex system behaviour, rather than, as heretofore, an objects of study in itself.

Animals↗
PubMed2005

Polaron delocalization in ladder macromolecular systems.

Organic macromolecules with conjugated building blocks have been the focus of extensive research that is motivated, in part, by the potential to create optical and electronic devices. We have shown that palladium-catalyzed amination can assemble triarylamine ladder materials with extended structures. Two ladder macromolecules have been prepared in high yields by a series of twelve or sixteen C-N coupling reactions. Studies of the electronic and optical properties of neutral and oxidized forms of the ladder structures were conducted. The optical and electronic properties of the ladder systems are compared to those of the linear tetra-phenyl-p-phenylenediamine as well as the tetra-p-anisyl-p-tetraazacyclophane. The electrochemistry of the ladder systems consists of a multiwave voltammogram with a relatively low first oxidation potential. Electron paramagnetic resonance spectroscopy of the ladder systems suggests the presence of a large density of delocalized polarons. Linear absorption measurements of the chemically oxidized ladders revealed both polaron and intervalence absorption bands. Steady-state and time-resolved fluorescence measurements were also carried out to characterize the dynamics in these novel systems.

Amines↗
PubMed1975

Rapid semiquantitative testing of antibiotic susceptibility: use of a multicell disk elution system.

Semiquantitative data regarding antibiotic susceptibility of bacteria were obtained by measuring the growth of bacteria in several different compartments ("cells") of a plastic module. Each compartment contained an inoculum of the organism and various concentrations of antibiotics in broth, achieved by elution of antibiotic from paper disks placed into the individual cells. Growth of the organisms was measured using an automated monitor to detect the scattering of light. Susceptibility of 300 strains of gram-negative bacilli to multiple concentrations of nine antibiotics was determined by this disk elution system, and the results (expressed in terms of four clinical susceptibility groupings) were compared with those obtained by a quantitative agar dilution method. Results obtained by the two methods agreed completely in 78% of the 2,700 determinations. In evaluating whether individual strains would be susceptible to systemic therapy or not, results obtained by the two systems agreed in all except 149 of the tests. Results of testing by the disk elution method were available on the same day that testing was begun. A system of this type may prove useful, for it provides information of a semiquantitative nature and decreases the time between isolation of a bacterial pathogen and availability of susceptibility data to the clinician.

Anti-Bacterial Agents↗
PubMed1989

Distance estimation from NOE data in macromolecular systems: a quadratic approach.

A new procedure has been suggested for the estimation of interproton distances from Nuclear Overhauser Enhancement (NOE) data in biological macromolecules. A critical assessment of the errors and advantages has been made vis a vis the commonly used initial rate approximation. Experimental data supporting the theoretical ideas have been presented.

Biopolymers↗
PubMed1976

Statistical interpretation of fluorescence energy transfer measurements in macromolecular systems.

A statistical method is presented for the interpretation of intramolecular distance measurements by the fluorescence energy transfer technique in systems for which the detailed geometries of the donor-acceptor pairs are unknown. This method enables calculation of the probability that a specified distance range corresponds to the actual distance to be measured. It makes use of the numerically calculated probability density function for the distance of interest. The two general systems considered are the single donor-acceptor pair and the multi-donor-single-acceptor transfer. In both systems, the statistical method incorporates the uncertainty in the orientation of the donor and acceptor dipoles. In addition, it can take into account the rotational mobility of the donor dipoles determined by time-dependent emission anisotropy measurements. When more than one donor is involved in the transfer process, the uncertainties associated with the number and location of individual donors and the size and shape of the donor distribution are also incorporated in calculating the distance ranges. Application of the method was demonstrated for a wide range of transfer efficiency and Ro values for the single donor-acceptor system. Specific examples are also presented for interpretation of both single donor-acceptor and multi-donor-single-acceptor energy transfer measurements performed in order to reveal the spatial relationship of the sigma subunit and the rifampicin binding site in the Escherichia coli RNA polymerase (see Wu, C.-W., Yarbrough, L. R., Wu, F. Y.-H., and Hillel, Z. (1976), Biochemistry, preceding paper in this issue). Analysis of these energy transfer data by methods which use average values of the unknown geometrical parameters of the system yielded results similar to those obtained by the statistical method. However, the statistical method represents a more realistic approach to the interpretation of energy transfer measurements since it provides information concerning the entire range of possible distances and their relative likelihood.

Energy Transfer↗
PubMed1989

Cytochrome c at charged interfaces. 2. Complexes with negatively charged macromolecular systems studied by resonance Raman spectroscopy.

We have analyzed the structure of cytochrome c (cyt c) bound in a variety of complexes in which negatively charged molecular groups interact with the positively charged binding domain around the heme crevice of cyt c. Using resonance Raman spectroscopy, we could demonstrate that these interactions induce the same conformational changes as they were observed in the surface-enhanced resonance Raman experiments of cyt c adsorbed on the Ag electrode [Hildebrandt & Stockburger (1989) Biochemistry (preceding paper in this issue)]. When cyt c is bound to (As4W40O140)27-, state II is stabilized, whereas in complexes with phosvitin and cytochrome b5 state I is formed. The complexes with phospholipid vesicles and inverted micelles reveal a mixture of both states. It is suggested that these systems as well as cyt c adsorbed on the Ag electrode may be regarded as model systems for the physiological complexes of cyt c with cytochrome oxidase and cytochrome reductase. On the basis of our findings it is proposed that the biological electron-transfer reactions are controlled by electric field induced conformational transitions of cyt c upon complex formation with its physiological redox partners.

Animals↗
PubMed1999

Non-Boltzmann thermodynamic integration (NBTI) for macromolecular systems: relative free energy of binding of trypsin to benzamidine and benzylamine.

The relative free energies of binding of trypsin to two amine inhibitors, benzamidine (BZD) and benzylamine (BZA), were calculated using non-Boltzmann thermodynamic integration (NBTI). Comparison of the simulations with the crystal structures of both complexes, trypsin-BZD and trypsin-BZA, shows that NBTI simulations better sample conformational space relative to thermodynamic integration (TI) simulations. The relative binding free energy calculated using NBTI was much closer to the experimentally determined value than that obtained using TI. The error in the TI simulation was found to be primarily due to incorrect sampling of BZA's conformation in the binding pocket. In contrast, NBTI produces a smooth mutation from BZD to BZA using a surrogate potential, resulting in a much closer agreement between the inhibitors' conformations and the omit electron density maps. This superior agreement between experiment and simulation, of both relative binding free energy differences and conformational sampling, demonstrates NBTI's usefulness for free energy calculations in macromolecular simulations.

Benzamidines↗
PubMed1985

Solubilization from rat pancreatic plasma membranes of a cholecystokinin (CCK) agonist-receptor complex interacting with guanine nucleotide regulatory proteins coexisting in the same macromolecular system.

Using the non-denaturing detergent 3-[(3-cholamidopropyl)dimethylammonio]-2-hydroxy-1-propane sulfonate (Chaps), cholecystokinin (CCK) receptors were solubilized from rat pancreatic membranes as a reversible complex with the CCK 31-39 nonapeptide 125I-labelled by the Bolton and Hunter reagent. Bound ligand dissociation from this soluble complex was similar to that from the membranous receptors of origin and the marked increase in the rate of dissociation induced by GTP was preserved in the soluble state, indicating that the solubilized CCK receptors remained functionally coupled with the guanine nucleotide regulatory site modulating the affinity for CCK. In fact, two guanine nucleotide regulatory proteins, Ns and Ni, coexisted in the soluble complex as established by identifying the 42-kDa subunit of Ns and the 40-kDa subunit of Ni, after ADP-ribosylation by cholera toxin and Bordetella pertussis toxin, respectively.

Animals↗
PubMed1976

Investigation of biological macromolecular systems with a pulsed neutron source--a review.

The conclusion that can be drawn on the basis of the above considerations is that investigation of biological macromolecules and crystalline structures by SAS and diffraction of neutrons with the TOF method is feasible. The main difficulties of the TOF method (the wavelength dependence of the incident beam, resolution power, and detector efficiency; the need for their determination and up-to-date values) are compensated for by its advantages. Both methods allow a high data accumulation rate and optimal employment of the incident neutron spectrum. The latter has been achieved by utilizing a dominant part of the Maxwellian spectrum and by a more uniform distribution of statistical accuracy over the most informative measuring range. Another advantage is the high degree of monochronatization of the incident neutron beam by the TOF method. The rigid requirements concerning the data accumulation rate and the capacity of the on-line system computer memory are technical problems but not basic ones.

Collagen↗
PubMed2003

Synthetic artificial peptidases and nucleases using macromolecular catalytic systems.

Effective artificial enzymes have been designed by adopting macromolecular systems for catalyst-substrate complexes. Artificial active sites comprising two or more organic functional groups were built on macromolecular backbones, leading to several types of organic artificial proteases. The activity of metal centers for peptide or DNA hydrolysis was greatly enhanced by attachment to polystyrene, leading to artificial metallopeptidases with substrate selectivity as well as artificial metallonucleases with high catalytic activity for double stranded DNA. A small artificial protease selective for a macromolecular target protein was synthesized. Target-specific artificial proteases can be used as protein-cleaving catalytic drugs.

Catalysis↗