The molecular surface package

The Molecular Surface Package is a reimplementation, in C, of a set of earlier FORTRAN programs for computing analytical molecular surfaces, areas, volumes, polyhedral molecular surfaces, and surface curvatures. The software does not do interactive molecular graphics, but it will produce pixel maps of smooth molecular surfaces. The polyhedral molecular surfaces are suited to display on graphics systems with real-time rendering of polyhedra.     

SDS-PAGE comparative studies on the polyhedral and viral polypeptides of the nuclear polyhedrosis viruses of Mamestra brassicae, Autographa californica, and Lymantria dispar

After solubilization of polyhedra of Autographa californica, Lymantria dispar, and Mamestra brassicae nuclear polyhedrosis viruses, PAGE showed at least eight distinct polyhedral polypeptide bands. Whereas the molecular weights of the major polypeptide were similar for the three NPVs (28.0–30.0 kdalton), characteristic differences between the species were found for the minor polypeptides having molecular weights in the range from 12.4 to 62.0 kdalton. It is assumed that these polypeptides are not generated by polyhedral alkaline protease since they are detected after protease inactivation. The data demonstrate that different baculoviruses can be distinguished from each other by SDS-PAGE of their polyhedral polypeptides.     

A simple method to display molecular orbitals with computer graphics

A computer program named LOBE was developed to draw molecular orbitals as lobes on a graphic display. With this program, any molecular orbital of large molecules can be displayed quickly. This program is suitable not only for general-purpose computers but also for microcomputers. A sample application is used to illustrate the program.     

Computer-assisted DNA length measurements from electron micrographs with special reference to partial denaturation mapping

A convenient semi-automatic procedure is described for the measurement, manipulation and display of electron microscopic partial denaturation data. Preliminary work on a completely automatic system is also discussed.     

Auxin structure/activity relationships: Aryloxyacetic acids

The results of self-consistent field molecular orbital calculations on auxins of the aryloxyacetic acid type do not support the ‘charge separation’     

Bridging the gap in RNA structure prediction

The field of RNA structure prediction has experienced significant advances in the past several years, thanks to the availability of new experimental data and improved computational methodologies. These methods determine RNA secondary structures and pseudoknots from sequence alignments, thermodynamics-based dynamic programming algorithms, genetic algorithms and combined approaches. Computational RNA three-dimensional modeling uses this information in conjunction with manual manipulation, constraint satisfaction methods, molecular mechanics and molecular dynamics. The ultimate goal of automatically producing RNA three-dimensional models from given secondary and tertiary structure data, however, is still not fully realized. Recent developments in the computational prediction of RNA structure have helped bridge the gap between RNA secondary structure prediction, including pseudoknots, and three-dimensional modeling of RNA.     

Polyhedral organelles compartmenting bacterial metabolic processes

Bacterial polyhedral organelles are extremely large macromolecular complexes consisting of metabolic enzymes encased within a multiprotein shell that is somewhat reminiscent of a viral capsid. Recent investigations suggest that polyhedral organelles are widely used by bacteria for optimizing metabolic processes. The distribution and diversity of these unique structures has been underestimated because many are not formed during growth on standard laboratory media and because electron microscopy is required for their observation. However, recent physiological studies and genomic analyses tentatively indicate seven functionally distinct organelles distributed among over 40 genera of bacteria. Functional studies conducted thus far are consistent with the idea that polyhedral organelles act as microcompartments that enhance metabolic processes by selectively concentrating specific metabolites. Relatively little is known about how this is achieved at the molecular level. Possible mechanisms include regulation of enzyme activity or efficiency, substrate channeling, a selectively permeable protein shell, and/or differential solubility of metabolites within the organelle. Given their complexity and distinctive structure, it would not be surprising if aspects of their biochemical mechanism are unique. Therefore, the unusual structure of polyhedral organelles raises intriguing questions about their assembly, turnover, and molecular evolution, very little of which is understood.     

Topological Analysis of Enzymatic Actions on DNA Polyhedral Links

Current synthetic biology has witnessed a revolution that natural DNA molecule steps onto a broad scientific area by assembling a large variety of three-dimensional structures with the connectivity of polyhedra. A mathematical model of these biomolecules is crucial to clarify the biological self-assembly principle, and unravel a first-step understanding of biological regulation and controlling mechanisms. In this paper, mechanisms of two different enzymatic actions on DNA polyhedra are elucidated through theoretical models of polyhedral links: (1) topoisomerase that untangles DNA polyhedral links produces separated single-stranded DNA circles through the crossing change operation; (2) recombinase generates a class of polyhedral circular paths or polyhedral knots by applying the crossing smoothing operation. Furthermore, we also discuss the possibility of applying two theoretical operations in molecular design of DNA polyhedra. Thus, our research provides a new sight of how geometry and topology of DNA polyhedra can be manipulated and controlled by enzymes, as well as has implications for molecular design and structural analysis of structural genome organization.     

Molecular surface comparison: Application to drug design

An interactive system for the display and manipulation of molecular surface properties is presented. The property at the molecular surface is mapped onto the sphere by gnomonic projection. This representation allows direct comparison of the surface properties of pairs of molecules.The system allows the user to explore the similarities between a pair of molecules in an interactive manner, and provides extensive visual (color-coded field and field difference maps) and numerical (rms difference value) aids to complement the user's chemical intuition. Examples of the use of the system to study beta-lactam compounds and phosphodiesterase inhibitors are presented.     

Genquire: genome annotation browser/editor

We present a software package, Genquire, that allows visualization, querying, hand editing, and de novo markup of complete or partially annotated genomes. The system is written in Perl/Tk and uses, where possible, existing BioPerl data models and methods for representation and manipulation of the sequence and annotation objects. An adaptor API is provided to allow Genquire to display a wide range of databases and flat files, and a plugins API provides an interface to other sequence analysis software. AVAILABILITY: Genquire v3.03 is open-source software. The code is available for download and/or contribution at http://www.bioinformatics.org/Genquire     

<Emphasis Type="Italic">Ab initio</Emphasis> Hartree-Fock calculations on linear and second-order nonlinear optical properties of new acridine-benzothiazolylamine chromophores

The calculation of optimized molecular structure and molecular hyperpolarizability of four new acridine-benzothiazolylamine chromophores (1–4) [2-nitro-6-(piperid-1-yl) acridine (1), 6-(benzothiazol-2-yl-amino)-2-nitro-acridine (2), 6-(6-ethylcarboxylate-benzothiazol-2-yl-amino)-2-nitroacridine (3), 6-(6-(β-hydroxyethyl-benzothiazol-2-yl-amino)-2-nitroacridine (4)] have been investigated using ab initio methods. Ab initio optimization were performed at the Hartree–Fock level using STO-3G basis set. The first hyperpolarizabilities have been calculated at the Hartree–Fock method with 6–31G and 6–311G basis sets using Gaussian 98W. In general, the first hyperpolarizability is dependent on the choice of method and basis set. To understand this phenomenon in the context of molecular orbital picture, we examined the frontier molecular orbital energies of all the molecules by using HF/6–31G, 6–311G levels. The polarizability, anisotropy of polarizability and ground state dipole moment of all the molecules have also been calculated. These acridine-benzothiazolylamine chromophores display significant second–order molecular nonlinearity, β (60.2–137.0 × 10⁻³⁰ esu) and provide the basis for future design of efficient nonlinear optical materials having the acridine-benzothiazolylamine core.     

EzMol: A Web Server Wizard for the Rapid Visualization and Image Production of Protein and Nucleic Acid Structures

EzMol is a molecular visualization Web server in the form of a software wizard, located at http://www.sbg.bio.ic.ac.uk/ezmol/. It is designed for easy and rapid image manipulation and display of protein molecules, and is intended for users who need to quickly produce high-resolution images of protein molecules but do not have the time or inclination to use a software molecular visualization system. EzMol allows the upload of molecular structure files in PDB format to generate a Web page including a representation of the structure that the user can manipulate. EzMol provides intuitive options for chain display, adjusting the color/transparency of residues, side chains and protein surfaces, and for adding labels to residues. The final adjusted protein image can then be downloaded as a high-resolution image. There are a range of applications for rapid protein display, including the illustration of specific areas of a protein structure and the rapid prototyping of images.     

Creating Eclipses: Using Scale Models to Explore How Eclipses Happen

The importance of using proportional scaled models in teaching about eclipses to elementary- and middle-level students is presented in this article. The authors illustrate how using creative models to display the basic concepts of shadows, scale, and perspective can foster a deeper understanding of how eclipses occur. Three innovative, easy-to-construct, scaled models are described as effective tools to enhance students’ understanding of eclipses. The models include space perspective on cast shadows, Earth perspective on solar eclipses, and the Moon's orbital plane around Earth.     

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.     

MOLMOL: A program for display and analysis of macromolecular structures

MOLMOL is a molecular graphics program for display, analysis, and manipulation of three-dimensional structures of biological macromolecules, with special emphasis on nuclear magnetic resonance (NMR) solution structures of proteins and nucleic acids. MOLMOL has a graphical user interface with menus, dialog boxes, and on-line help. The display possibilities include conventional presentation, as well as novel schematic drawings, with the option of combining different presentations in one view of a molecule. Covalent molecular structures can be modified by addition or removal of individual atoms and bonds, and three-dimensional structures can be manipulated by interactive rotation about individual bonds. Special efforts were made to allow for appropriate display and analysis of the sets of typically 20–40 conformers that are conventionally used to represent the result of an NMR structure determination, using functions for superimposing sets of conformers, calculation of root mean square distance (RMSD) values, identification of hydrogen bonds, checking and displaying violations of NMR constraints, and identification and listing of short distances between pairs of hydrogen atoms.     

Molecular biology in living cells by means of digital optical microscopy

The intention of this review is to introduce to microscopists some of the fundamental limits as well as the advances made in digital optical microscopy techniques, also to show their potentialities in the field of molecular cell biology. Several items within the wide field of this subject will be discussed, such as geometric and photometric features, photophysics, statistics of photon flux and detection, spatial and intensity characteristics of digital images, their manipulation and display, fluorescent probes, and measuring techniques.     

MAXAMIZE. A DNA sequencing strategy advisor.

The MAXAMIZE advisory system determines from user-provided restriction maps an optimal strategy to do nucleotide sequencing by methods involving end-labeled fragments. The maps may be either simple linear restriction maps of fragments or complex circular maps including restriction sites of a vector. The whole system is interactive and is written in the Genetic English language provided by the GENESIS System, a molecular genetics knowledge representation and manipulation package. In addition, MAXAMIZE provides bookkeeping facilities for sequencing and offers advise on how to verify the newly obtained sequence data.     

Purification of ribulose 1,5-bisphosphate carboxylase/oxygenase and of carboxysomes from Thiobacillus thyasiris the putative symbiont of Thyasira flexuosa (Montagu)

The bacterial symbionts of many marine invertebrates contain ribulose 1,5-bisphosphate (RuBP) carboxylase but apparently no carboxysomes, polyhedral bodies containing RuBP carboxylase. In the few cases where polyhedral bodies have been observed they have not been characterised enzymatically. Polyhedral bodies, 50–90 nm in diameter, were observed in thin cell sections of Thiobacillus thyasiris the putative symbiont of Thyasira flexuosa and RuBP carboxylase activity was detected in both soluble and particulate fractions after centrifugation of cell-free extracts. RuBP carboxylase purified 90-fold from the soluble fraction was of high molecular weight and consisted of large and small subunits, with molecular weights of 53,110 and 11,100 respectively. Particulate RuBP carboxylase activity was associated with polyhedral bodies 50–100 nm in diameter, as revealed by density gradient centrifugation and electron microscopy. Therefore, the polyhedral bodies were inferred to be carboxysomes. Native electrophoresis of isolated carboxysomes demonstrated a major band which comigrated with the purified RuBP carboxylase and three minor bands of lower molecular weight. Sodium dodecyl-sulphate (SDS) gel electrophoresis of SDS-dissociated carboxysomes demonstrated nine major polypeptides two of which were the large and small subunits of RuBP carboxylase. The RuBP carboxylase subunits represented 21% of the total carboxysomal protein. The most abundant polypeptide had a molecular weight of 40,500. Knowledge of carboxysome composition is necessary to provide an understanding of carboxysome function.Abbreviations FPLC fast performance liquid chromatography - IB isolation buffer - PAGE polyacrylamide gel electrophoresis - RuBP carboxylase - ribulose 1,5-bisphosphate carboxylase/oxygenase - SDS sodium dodecyl-sulphate