Electrostatic potentials of tumour promoters

Molecular-modelling studies and quantum-chemical calculations have been undertaken on a variety of structurally unrelated tumour promoters. The modelling studies reveal some broad areas of agreement in the associated electrostatic potentials for the molecules TPA, teleocidin, aplysiatoxin and ingenol. Azulene-type derivatives were used as models for inactive and active tumour promoters in the quantum chemical studies. The results obtained from these calculations of the electrostatic potentials show very little difference between active and inactive compounds, thus suggesting that other factors are of importance in these systems.     

Program for the visualization of inorganic crystals

A program has been developed to manipulate images of inorganic structures and organic molecules on ALLIANT VFX/40 using the PHIGS + standard. This article reviews algorithms for representing spheres, ellipsoids and various polyhedrons involved in inorganic chemistry. The program also supports the display and manipulation of animated frames from dynamics simulations. Many graphical facilities have been implemented and we discuss their interest in the field of molecular graphics.     

Electrostatic potentials in membrane systems

A membrane with an arbitrary distribution of fixed charges inside and on its surfaces is considered. A procedure for calculating the local electrostatic potential at an arbitrary point of the system is described and its validity discussed. This procedure is based on the linearization of the 3-dimensional Poisson-Boltzmann equation around an exact 1-dimensional solution.     

Electrostatic potentials of E.coli genome DNA

Distribution of electrostatic potential of the complete sequence of E. coli genome was calculated. Comparative analysis of electrostatic patterns for 359 promoter and nonpromoter nucleotide sequences was carried out. It is found that nonpromoter regions are characterized by more homogeneous distribution of electrostatic potential with no common specific elements. Electrostatic patterns of promoter DNAs can be specified due to the presence of some distinctive motifs which may be involved as promoter signal elements in RNA-polymerase-promoter recognition.     

Electrostatic potentials of the alpha helix dipole and of elastase

Molecular graphics has been used to display the electrostatic potentials of the α-helix dipole and that of elastase calculated using atomic charges obtained by a new, simple method^1–3. Calculations on the α-helix dipole support the simple dipole model in which the helix is represented by single, half integral charges at the helix termini. The potentials of elastase show some interesting features which may be related to the binding processes.     

Electrostatic potential comparison and molecular metric spaces

A possible definition of a metric associated with a set of electrostatic molecular potentials is analyzed. Examples of its application to formaldehyde and analogous structures, and to MAO substrates are presented.     

Quantitative analysis of molecular surfaces: areas, volumes, electrostatic potentials and average local ionization energies

We describe a procedure for performing quantitative analyses of fields f(r) on molecular surfaces, including statistical quantities and locating and evaluating their local extrema. Our approach avoids the need for explicit mathematical representation of the surface and can be implemented easily in existing graphical software, as it is based on the very popular representation of a surface as collection of polygons. We discuss applications involving the volumes, surface areas and molecular surface electrostatic potentials, and local ionization energies of a group of 11 molecules.

Generation of molecular surfaces for graphic display

A procedure is described for the generation of a variety of molecular surfaces using a ‘bit’ lattice, and avoiding the computational load imposed by geometric techniques. The procedure is well suited to minicomputers used to host calligraphic displays, and is flexible in terms of resolution and size of surface, and permits several styles of display. The procedure may be used as a standalone program, or as part of a real-time molecular manipulation system.     

Approximation and characterization of molecular surfaces

The representation and characterization of molecular surfaces are important in many areas of molecular modeling. Parametric representations of protein molecular surfaces are a compact way to describe a surface, and are useful for the evaluation of surface properties such as the normal vector, principal curvatures, and principal curvature directions. Simplified representations of molecular surfaces are useful for efficient rendering and for the display of large-scale surface features. Several techniques for representing surfaces by expansions of spherical harmonic functions have been reported, but these techniques require that the radius function is single valued, that is, each ray from an origin inside the surface intersects the surface at one and only one point. A new technique is described that removes this limitation and can be used to compute surface shape properties. © 1993 John Wiley & Sons, Inc.     

Degradation of poliovirus by adsorption on inorganic surfaces

Alteration of the specific infectivity of 3H-labeled ribonucleic acid and 14C-protein labeled poliovirus type 1 by adsorption on inorganic surfaces is investigated by application of kinetic theory to data obtained from sequential extractions of adsorbed virus. Some surfaces, e.g., SiO2, appear to have no significant effect. On the other hand, CuO substantially decreases the specific infectivity of adsorbed preparations. Differences in kinetic plots between 3H-labeled ribonucleic acid and 14C-labeled protein suggest that the inactivation observed involves physical disruption of virions. Van der Waals interactions between solid surfaces and virus are suspected to induce spontaneous virion disassembly. Surface catalyzed disassembly in aquatic and soil environments is implicated as an important mechanism controlling enterovirus dissemination. Methods developed here to evaluate complete recovery of adsorbed virus have potenital application to other degradation studied and problems concerning virus recovery from adsorbents used in virus concentrators.     

Fuzzy molecular surfaces.

Surface area of a macromolecule, accessible to a solvent, is defined and calculated, taking into account the probabilistic character of atomic positions due to the high frequency atomic vibrations. For a given a space point, we consider a probability of the event, that this point is covered by a macromolecule. A volume is defined as a space integral of this probability field. The envelope, accessible to a solvent molecule center, becomes fuzzy, existing only in a probabilistic sense. The accessible area is defined as a derivative of the envelope volume with respect to the probe size.     

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.     

Computer representation of molecular surfaces

The simplest and earliest drawings of molecules had a line segment for each bond and could be modified in real time¹. However, to understand the interaction of an enzyme with a substrate or inhibitor, or a drug or hormone with a receptor site, we must know the location of the molecular surface. Because the surfaces are so important, computer drawings have long been a useful tool in our understanding of the 3D structure of molecules.This article reviews various algorithms for representing these surfaces, either as unions of spheres or as other smoothed surfaces.     

RMS: programs for generating raster molecular surfaces

RMS (Raster Molecular Surfaces) is a package of programs that offer the researcher a number of solid modeling techniques for presenting a macromolecular structure. The programs use a mapping algorithm, calculating the shading parameters only once, to reduce computation time. A simple linear approximation is used for antialiasing of atomic edges, shadows and surface intersections. I have implemented two major advances: depth cueing using an opaque “fog” and z-clipping to show detailed interactions in the interior of molecules. Spherical atoms and cylindrical bonds are also available.