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At least 19 recordsLinked to original sources
PubMed1984

Self-organization in macromolecular systems: the notion of adaptive value.

Self-organization in macromolecular systems refers to the transition from a random assembly of interacting oligomers to a system of stable heteropolymers. The concept of adaptive value describes the correlation between environmental variability and the variability in replication and mutation rates of the interacting oligomers. This paper describes a model of self-organization in macromolecular systems based on the concept of adaptive value. The equilibrium states of a set of interacting polymers are described by states that maximize the adaptive value. The analytic basis for this notion of equilibrium, which is called the adaptive value principle, is given and this principle is invoked to explain two examples of macromolecular self-assembly.

Base Sequence↗
PubMed2001

Application of promolecular ASA densities to graphical representation of density functions of macromolecular systems.

In this article we report the application of the Promolecular Atomic Shell Approximation (Promolecular ASA) to the graphical representation of the density function (DF) of large macromolecular systems. Promolecular ASA DF, constructed from previously computed and fitted atomic densities, provides a fast and practical representation of Molecular IsoDensity Contours (MIDCOs). These representations can be extended to macromolecular systems composed by > 1000 atoms easily and with low computational costs, allowing the visualization of protein DF. The method is at first presented with a small molecule (2,4,6-trinitrophenol), comparing the resulting ASA MIDCOs with direct ab initio contours. For macromolecular tests the Promolecular ASA densities are also applied to the generation of macromolecular density surfaces of two proteins: myoglobin (2541 atoms) and gene V protein (1362 atoms).

Computer Graphics↗
PubMed1988

Chemical oscillations in closed macromolecular systems.

A cycle of irreversible, first-order, autocatalytic reactions among different states of a polyfunctional macromolecule, subject to the conservation of mass, can display stable chemical oscillations. This introduces a class of nonlinear dynamic models for energy transduction in closed macromolecular systems.

Chemical Phenomena↗
PubMed1988

Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis.

In this report we describe an accurate numerical method for calculating the total electrostatic energy of molecules of arbitrary shape and charge distribution, accounting for both Coulombic and solvent polarization terms. In addition to the solvation energies of individual molecules, the method can be used to calculate the electrostatic energy associated with conformational changes in proteins as well as changes in solvation energy that accompany the binding of charged substrates. The validity of the method is examined by calculating the hydration energies of acetate, methyl ammonium, ammonium, and methanol. The method is then used to study the relationship between the depth of a charge within a protein and its interaction with the solvent. Calculations of the relative electrostatic energies of crystal and misfolded conformations of Themiste dyscritum hemerythrin and the VL domain of an antibody are also presented. The results indicate that electrostatic charge-solvent interactions strongly favor the crystal structures. More generally, it is found that charge-solvent interactions, which are frequently neglected in protein structure analysis, can make large contributions to the total energy of a macromolecular system.

Binding, Competitive↗
PubMed1983

Selection and evolution in macromolecular systems.

The notion of a quasi-species represents the ensemble of macromolecular sequences derived by the mechanism of mutation and replication from a single wild type. In Eigen (1971) and Eigen & Schuster (1979), the deterministic evolution of this ensemble under constant environmental conditions is given in terms of continuous models which describe the dynamics of the distribution of polynucleotides. This paper starts from a discrete model of macromolecular evolution and introduces the notion of a genealogy in order to study the dynamics of the quasi-species in constant and variable environments. We introduce, in terms of these genealogies, the notions of entropy and adaptive value of a quasi-species and the notion of capacity of the environment. We discuss the significance of these indices as measures of selective value and we analyse the conditions under which these measures coincide with the growth rate of the quasi-species.

Base Sequence↗
PubMed1988

Velocity of linear crystallization of ice in macromolecular systems.

The velocity of ice crystallization in gelled systems was compared with that in solutions of similar macromolecular materials. Neither the constituting material nor the dimensions of the tubes in which the measurements were made influenced the results. The velocity of linear crystallization of ice was slowed in macromolecular solutions and gels, and this decrease was not associated with changes in dynamic or thermodynamic properties of water. It was probably the consequence of a mechanical effect of the macromolecules directly on ice crystal growth.

Crystallization↗
PubMed2002

The effects of osmotic and hydrostatic pressures on macromolecular systems.

Osmotic pressure and hydrostatic pressure can be used effectively to probe the behavior of biologically important macromolecules and their complexes. Using the two techniques requires a theoretical framework as well as knowledge of the more common pitfalls. Both are discussed in this review in the context of several examples.

Animals↗
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↗