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PubMed2001

Delayed luminescence of biological systems arising from correlated many-soliton states.

The kinetics of the delayed luminescence arising from correlated coherent many-soliton states in low-dimensional macromolecular systems, is calculated and shown to be different from the one arising from independent soliton states. The correlation between coherent electron states is essential at relatively high levels of excitation in the presence of very long macromolecules in a system. These conditions can be fulfilled in such biological systems, like algae Acetabularia Acetabulum. The cytoskeleton of this unicellular alga contains macromolecular structures (actin filaments, microtubules, etc.) of the length of several hundreds angstroms and more, in which many-soliton coherent states can exist. Indeed, the correlated coherent model is shown to give better fit of the experimental data for this type of algae in a wide range of intensities of the stimulating light, as compared with the model of noncorrelated solitons. The nonlinearity of the dependence of delayed luminescence intensity on the level of excitation increases with the increase of correlation between solitons.

Acetabularia↗

PubMed1977

On the existence of a steady state in a biological system.

This paper deals with the existence, uniqueness, and stability of a critical point (steady state) in the case of a macromolecular system, such as an allosteric or polysteric protein, for which the first-order kinetic equations are nonlinear. It presents a brief outline of a rigorous proof (to be given in full elsewhere) that, in a restricted but not unrepresentative system of this kind, there always exists one and only one positive critical point and that this point is asymptotically stable in the large: no matter what its starting point, the system will always approach this point by some kind of relaxation process, however complex.

Kinetics↗

PubMed1991

Comparison of agarose and cross-linked protein gels as magnetic resonance imaging phantoms.

Measurements of the magnetic field dependence of spin-lattice relaxation rates and the response of the water-proton signal intensity to off-resonance radio frequency fields show that the commonly used agarose phantom provides a less faithful representation for the magnetic response of tissue than does a cross-linked protein system. The origin of these differences lies in the structure and intramolecular dynamics of the macromolecular system used to make the gel. These distinctions will also cause differences in the magnetic response of the water spin system when paramagnetic relaxation agents or contrast agents are incorporated. Use of a thermally cross-linked bovine serum albumin phantom is suggested.

Animals↗

PubMed1970

Fluorescent probes of biological membranes.

FLUORESCENT AND PHOSPHORESCENT PROBES THAT HAVE READILY INTERPRETABLE EMISSION PROPERTIES CAN BE SPECIFICALLY INSERTED INTO BIOLOGICAL MACROMOLECULES TO REVEAL FACETS OF THEIR STRUCTURE AND DYNAMICS: (1) Proximity. Singlet-singlet and triplet-singlet energy transfer can serve as spectroscopic rulers in the 10-65 A range, whereas triplet-triplet transfer can be used to show that two groups are less than about 12 A apart. (2) Rotational mobility. Nanosecond fluorescence polarization measurements can reveal whether a macromolecular system has any modes of flexibility in times of nanoseconds. (3) Polarity. The presence of mobile dipoles in the environment of certain chromophores is reflected in their fluorescence quantum yield and emission spectrum. We have synthesized a number of new fluorescent probes for biological membranes. Anthroyl stearic acid (I), dansyl phosphatidyl ethanolamine (II), and octadecyl naphthylamine sulfonic acid (III) are readily incorporated into bilayer vesicles composed of phosphatidyl choline. The emission spectra of these probes in the vesicles indicate that the chromophore of I is located in the hydrocarbon region, that of II is located in the glycerol layer, and that of III is located at the aqueous interface of the bilayer. Thus, fluorescent chromophores can be selectively placed in different transverse regions of a model membrane system.

Anthracenes↗

PubMed2004

Analysis of protein-protein interactions by simulation of small-zone gel filtration chromatography.

Small-zone gel filtration chromatography, combined with analytical-scale columns and fast run times, provides a useful system for the study of protein-protein interactions. A computer simulation (SCIMMS, or Simulated Chromatography of Interactive MacroMolecular Systems) that replicates the small-zone behavior of interacting proteins has been developed. The simulation involves an iterative sequence of transport, equilibration, and diffusion steps. This chapter illustrates the use of the simulation to study the homodimerization of rapidly equilibrating immunoglobulin light chain proteins and for determination of association constants. The simulation can also be used to study heterogeneous interactions, kinetically controlled interactions, and higher-order oligomerization, and it can replicate large-zone and Hummel-Dreyer conditions.

Chromatography, Gel↗

PubMed1981

Fluorescence photobleaching recovery in solutions of labeled actin.

We have demonstrated that the technique of fluorescence photobleaching recovery (FPR) can be used to examine the state of a single component in complex self-assembling macromolecular systems. Polymerization of actin, initiated by addition of salt or Mg+2 to a low-ionic-strength solution of G-actin, has been observed by sequential measurement of FPR with the aid of fluorescein-labeled actin. Solutions of actin which had been labeled using 5-iodoacetamido fluorescein (5-IAF) showed anomalous recovery of fluorescence above the initial value, which indicates a photoinduced increase in local polymerization. No such anomaly was observed with actin that had been labeled with fluorescein isothiocyanate (FITC). The FPR data are directly interpretable in terms of the fraction of labeled protein that is immobilized in the supramolecular assembly and in terms of the average diffusion coefficient of the mobile fraction. Our data are consistent with the "treadmill" model of actin polymerization, in that they show that actin is present under polymerizing conditions either as a high polymer or as monomer or low oligomer. We believe that the FPR technique can be applied to the study of many types of reconstituted motile or cytoskeletal systems in vitro or in vivo.

Actins↗

PubMed1997

Effect of periodic box size on aqueous molecular dynamics simulation of a DNA dodecamer with particle-mesh Ewald method.

The particle-mesh Ewald (PME) method is considered to be both efficient and accurate for the evaluation of long-range electrostatic interactions in large macromolecular systems being studied by molecular dynamics simulations. This method assumes "infinite" periodic boundary conditions resembling the symmetry of a crystal environment. Can such a "solid-state" method accurately portray a macromolecular solute such as DNA in solution? To address this issue, we have performed three 1500-ps PME molecular dynamics (MD) simulations, each with a different box size, on the d(CGCGA6CG)-(CGT6CGCG) DNA dodecamer. The smallest box had the DNA solvated by a layer of water molecules of at least 5 A along each orthogonal direction. The intermediate size box and the largest box had the DNA solvated by a layer of water molecules of at least 10 A and 15 A, respectively, along each orthogonal direction. The intermediate size box in the present study is similar to the box size currently chosen by most workers in the field. Based on a comparison of RMSDs and curvature for this single DNA dodecamer sequence, the larger two box sizes do not appear to afford any extra benefit over the smallest box. The implications of this finding are briefly discussed.

Base Sequence↗

PubMed1991

Electrostatic screening in molecular dynamics simulations.

The screened Coulombic potential has been shown to describe satisfactorily equilibrium properties like pK shifts, the effects of charged groups on redox potentials and binding constants of metal ions. To test how well the screening of the electrostatic potential describes the dynamical trajectory of a macromolecular system, a series of comparative simulations have been carried out on a protein system which explicitly included water molecules and a system in vacuo. For the system without solvent the results of using (i) the standard potential form were compared with results of (ii) the potential where the Coulomb term was modified by the inclusion of a distance dependent dielectric, epsilon (r), to model the screening effect of bulk water, and (iii) standard potential modified by reducing the charge on ionized residue side chains. All molecular dynamics simulations have been carried out on bovine pancreatic trypsin inhibitor. Comparisons between the resulting trajectories, averaged structures, hydrogen bonding patterns and properties such as solvent accessible surface area and radius of gyration are described. The results show that the dynamical behaviour of the protein calculated with a screened electrostatic term compares more favourably with the time-dependent structural changes of the full system with explicitly included water than the standard vacuum simulation.

Animals↗

PubMed1992

Increased thermal stability of proteins in the presence of naturally occurring osmolytes.

Organisms and cellular systems which have adapted to stresses such as high temperature, desiccation, and urea-concentrating environments have responded by concentrating particular organic solutes known as osmolytes. These osmolytes are believed to confer protection to enzyme and other macromolecular systems against such denaturing stresses. Differential scanning calorimetric (DSC) experiments were performed on ribonuclease A and hen egg white lysozyme in the presence of varying concentrations of the osmolytes glycine, sarcosine, N,N-dimethylglycine, and betaine. Solutions containing up to several molar concentrations of these solutes were found to result in considerable increases in the thermal unfolding transition temperature (Tm) for these proteins. DSC scans of ribonuclease A in the presence of up to 8.2 M sarcosine resulted in reversible two-state unfolding transitions with Tm increases of up to 22 degrees C and unfolding enthalpy changes which were independent of Tm. On the basis of the thermodynamic parameters observed, 8.2 M sarcosine results in a stabilization free energy increase of 7.2 kcal/mol for ribonuclease A at 65 degrees C. This translates into more than a 45,000-fold increase in stability of the native form of ribonuclease A over that in the absence of sarcosine at this temperature. Catalytic activity measurements in the presence of 4 M sarcosine give kcat and Km values that are largely unchanged from those in the absence of sarcosine. DSC of lysozyme unfolding in the presence of these osmolytes also results in Tm increases of up to 23 degrees C; however, significant irreversibly occurs with this protein.(ABSTRACT TRUNCATED AT 250 WORDS)

Betaine↗

PubMed1987

Nesting: hierarchies of allosteric interactions.

A generalization of the allosteric model is presented that incorporates a hierarchy of conformational equilibria. Such a formulation draws upon structural organization already seen in many large macromolecular systems. The functional binding properties of the macromolecule reflect conformational equilibria at each structural level. Appropriate "nested" models are used to interpret structural features and functional aspects of two hemocyanin systems with a large number (12 and 24) of binding sites.

Allosteric Regulation↗

PubMed2001

Pulsed electron paramagnetic resonance methods for macromolecular structure determination.

Pulsed electron paramagnetic resonance (EPR) distance measurement techniques target macromolecular structure elucidation at both the local and global level. Recent developments in pulse microwave technology and high-field EPR have led to the development of a variety of pulsed EPR distance measurement techniques. These methods have emerged as powerful tools for the determination of structure/function relationships in macromolecular systems. In this review article, we discuss recent applications of long-range and short-range EPR distance measurements.

Animals↗

PubMed2000

TROSY and CRINEPT: NMR with large molecular and supramolecular structures in solution.

TROSY and CRINEPT are new techniques for solution NMR studies of molecular and supramolecular structures. They allow the collection of high-resolution spectra of structures with molecular weights >100 kDa, significantly extending the range of macromolecular systems that can be studied by NMR in solution. TROSY has already been used to map protein-protein interfaces, to conduct structural studies on membrane proteins and to study nucleic acid conformations in multimolecular assemblies. These techniques will help us to investigate the conformational states of individual macromolecular components and will support de novo protein structure determination in large supramolecular structures.

Aldehyde-Lyases↗

PubMed2002

On the calculation of absolute macromolecular binding free energies.

The standard framework for calculating the absolute binding free energy of a macromolecular association reaction A + B --> AB with an association constant K(AB) is to equate chemical potentials of the species on the left- and right-hand sides of this reaction and evaluate the chemical potentials from theory. This theory involves (usually hidden) assumptions about what constitutes the bound species, AB, and where the contribution of the solvent appears. We present here an alternative derivation that can be traced back to Bjerrum, in which the expectation value of K(AB) is obtained directly through the statistical mechanical method of evaluating its ensemble (Boltzmann-weighted) average. The generalized Bjerrum approach more clearly delineates: (i) the different contributions to binding; (ii) the origin of the much-discussed and somewhat controversial association entropy term; and (iii) where the solvent contribution appears. This approach also allows approximations required for practical evaluation of the binding constant in complex macromolecular systems, to be introduced in a well defined way. We provide an example, with application to test cases that illustrate a range of binding behavior.

Energy Transfer↗

PubMed2002

New directions for fluorescent speckle microscopy.

Fluorescent Speckle Microscopy (FSM) is a technology for analyzing cytoskeleton dynamics, giving novel insight into their roles in living cells. New applications of FSM, together with the development of computer-based FSM image analysis, will make FSM the first microscopy-based method to deliver quantitative kinetic readouts at high spatial and temporal resolution for a wide variety of macromolecular systems. Here, we review the most recent applications and developments and give a glimpse of future directions and potentials of FSM.

Actins↗

PubMed2005

Synthesis and antioxidant efficiency of a new copolymer containing phosphorylated myo-inositol.

New data are constantly gathered to show the role of oxidative stress and the involvement of reactive oxygen species in the pathogenesis of degenerative diseases. InsP6 is able to coordinate iron metal in order to prevent iron-catalyzed free radical formation. The aim of the present paper is to describe a new synthetic strategy in order to prepare a polymeric structure containing chemical functions able to coordinate iron ions. Here, we report the synthesis of a copolymer containing phosphorylated myo-inositol groups and we evaluate its antioxidant efficiency. Such a system was synthesized by binding chemical groups susceptible of radical polymerization to myo-inositol. The synthesized monomer was copolymerized with N,N-dimethylacrylamide (DMAA) (molar ratio 1:3) and submitted to exhaustive phosphorylation. The reaction was proved by an assay specific for phosphate groups. Finally, we evaluated the copolymer's ability in inhibiting lipid peroxidation in rat liver microsomal membranes. This study showed that the designed macromolecular system is particularly effective as antioxidant.

Acrylamides↗

PubMedDate not supplied

Modeling large macromolecular structures using promolecular densities.

A procedure to easily construct fitted density functions is presented. This methodology, based on the promolecule approach, is able to handle large macromolecular systems, such as proteins. The usual procedure dealing with fitted densities has been improved by adding some restrictions, which allow faster calculations. As a main application example, molecular isodensity contours (MIDCOs) are constructed for two proteins, one of them composed of more than 50 000 atoms. MIDCOs, as a visual representation of the molecular density function, and thus an important descriptor of the molecular charge distribution, constitute a powerful tool in the understanding of molecular systems. MIDCOs are presented for both proteins, allowing exploration of their surfaces, as well as analysis of their shapes. Also, as a quantum mechanical calculation example, molecular quantum self-similarity measures are calculated for several proteins.

Computer Simulation↗

PubMed1982

A simple test for macromolecular heterogeneity in the analytical ultracentrifuge.

A simple check for the presence of heterogeneity in a macromolecular system is proposed, employing comparison of Rayleigh sedimentation-equilibrium patterns for two solutions of the same fringe concentration but differing absolute concentrations. The method is illustrated by application to a bronchial glycoprotein from a cystic-fibrosis patient.

Glycoproteins↗

PubMedDate not supplied

Autocatalysis, information and coding.

Autocatalytic self-construction in macromolecular systems requires the existence of a reflexive relationship between structural components and the functional operations they perform to synthesise themselves. The possibility of reflexivity depends on formal, semiotic features of the catalytic structure-function relationship, that is, the embedding of catalytic functions in the space of polymeric structures. Reflexivity is a semiotic property of some genetic sequences. Such sequences may serve as the basis for the evolution of coding as a result of autocatalytic self-organisation in a population of assignment catalysts. Autocatalytic selection is a mechanism whereby matter becomes differentiated in primitive biochemical systems. In the case of coding self-organisation, it corresponds to the creation of symbolic information. Prions are present-day entities whose replication through autocatalysis reflects aspects of biological semiotics less obvious than genetic coding.

Biological Evolution↗