Plotting protein surfaces

This paper presents two methods for drawing solvent-accessible surfaces of proteins on a plotter. One method draws a stack of contours and the other draws a triangulated polyhedral surface. Both methods perform hidden-line elimination. These methods should be very useful in laboratories which do not possess vector or raster colour graphics equipment.     

Polyhedral approximation approach to molecular orbital graphics

Interactive molecular orbital display and manipulation system is developed under the concept of polyhedral approximation of equivalued surfaces of orbital and density functions. Two new methods for generating polyhedral data, lscell-based’ and ‘propagation’ methods, are presented. The use of stored polyhedral data largely simplifies the shaded-image synthesis, direct manipulation, and animation display of molecular orbitals. Manual overlay of frontier orbitais is useful to estimate the geometries of chemically reacting molecules.     

SURFNET: A program for visualizing molecular surfaces,cavities, and intermolecular interactions

The SURFNET program generates molecular surfaces and gaps between surfaces from 3D coordinates supplied in a PDB-format file. The gap regions can correspond to the voids between two or more molecules, or to the internal cavities and surface grooves within a single molecule. The program is particularly useful in clearly delineating the regions of the active site of a protein. It can also generate 3D contour surfaces of the density distributions of any set of 3D data points. All output surfaces can be viewed interactively, along with the molecules or data points in question, using some of the best-known molecular modeling packages. In addition, PostScript output is available, and the generated surfaces can be rendered using various other graphics packages.     

A molecular model for the retinol binding protein-transthyretin complex

A three-dimensional model for the complex between human serum retinol binding protein and transthyretin (formerly named prealbumin) is presented. The model was obtained by interactive rigid-body computer graphics docking and the characterization of the molecular surfaces in terms of fractal dimension. Available experimental data, as well as results from molecular dynamics calculations, support the proposed model.     

DNurbs: DNA modeled with NURBS

DNurbs (dee-in-urbs) are a small number of bicubic patches wrapping each base pair in complementary DNA. NURBS, the nonuniform rational B-spline surfaces now popular in computer graphics, are employed for the patches. Control points for the surface patches are generated from the molecular surface based on canonical base pairs.     

Personal computer-based visualization of three-dimensional scalar and vector fields: An application to molecular graphics

A desktop PC-based graphics package, UNIVIS, for visualization of three-dimensional numerical data is described. Apart from routine molecular model visualization, the package provides for a host of other features such as extraction of various surfaces, planar cross-sections of the three-dimensional data, and property texturing. Fast rendering and transparency are the strengths of the present package. These features are comprehensively discussed. The salient features of UNIVIS are presented in the form of visualization of a variety of molecular properties, which are of immense importance in understanding molecular structure and reactivity patterns.     

Surface fractality as a guide for studying protein-protein interactions

The concept of fractal dimension is applied to protein surfaces. Satellite tobacco necrosis virus, prealhumin, retinol binding protein and lysozyme have been studied. A residue fractal index has been defined, which provides a suitable colour code when using computer graphics for visualizing surfaces. Some provisions are made that render the MS algorithm useful to calculate protein surface fractal dimensions. It has been found that a correlation exists between regions of high fractal dimension and those involved in protein-protein interactions. The usefulness of surface fractality in this context is demonstrated by a molecular docking experiment.     

Rendering volumetric data in molecular systems

A raster-based computer graphics method of imaging volumetric data (data sampled on a three-dimensional grid) has been added to an existing molecular rendering program. Any molecular property expressed as a 3D grid of scalar data values can be displayed around and inside of the molecular van der Waals surface as a collection of colored clouds and transparent surfaces. Different antical properties, such as color and opacity, are assigned to ranges of the molecular property and are rendered by a ray-tracing technique simulating the shading and shadowing of real objects, making the final images highly eadable. We have found useful applications in the visualization of crystallographic electron density, electrostatic potentials and protein active sites.     

Texture mapping: A new tool for molecular graphics

The real-time texture mapping capabilities of modern graphics workstations are explored with respect to their applications in a variety of relevant scenarios in interactive molecular modeling techniques. The common usage of texture mapping to reduce geometric complexity while enhancing realism is extended, opening new ways to visualize large amounts of molecular data in a comprehensive fashion. Thus, texture mapping may be employed to (1) display and filter multichannel information of structural properties on molecular surfaces, (2) improve the quality and accuracy of highly complex isodensity contours, (3) increase the rendering speed of space-filling atomic representations by two orders of magnitude and (4) apply volume-rendering techniques to large, three-dimensional density distributions in real time. Implementation of these novel techniques requires only moderate modifications or extensions to existing molecular modeling applications.     

Getting in Touch with the Clathrin Terminal Domain

The N‐terminal domain (TD) of the clathrin heavy chain is folded into a seven‐bladed β‐propeller that projects inward from the polyhedral outer clathrin coat. As the most membrane‐proximal portion of assembled clathrin, the TD is a major protein–protein interaction node. Contact with the TD β‐propeller occurs through short peptide sequences typically located within intrinsically disordered segments of coat components that usually are elements of the membrane‐apposed, inner ‘adaptor’ coat layer. A huge variation in TD‐binding motifs is known and now four spatially discrete interaction surfaces upon the β‐propeller have been delineated. An important operational feature of the TD interaction sites in vivo is functional redundancy. The recent discovery that ‘pitstop’ chemical inhibitors apparently occupy only one of the four TD interaction surfaces, but potently block clathrin‐mediated endocytosis, warrants careful consideration of the underlying molecular basis for this inhibition.     

Protein structure databases with new web services for structural biology and biomedical research

The Protein Data Bank Japan (PDBj) curates, edits and distributes protein structural data as a member of the worldwide Protein Data Bank (wwPDB) and currently processes approximately 25-30% of all deposited data in the world. Structural information is enhanced by the addition of biological and biochemical functional data as well as experimental details extracted from the literature and other databases. Several applications have been developed at PDBj for structural biology and biomedical studies: (i) a Java-based molecular graphics viewer, jV; (ii) display of electron density maps for the evaluation of structure quality; (iii) an extensive database of molecular surfaces for functional sites, eF-site, as well as a search service for similar molecular surfaces, eF-seek; (iv) identification of sequence and structural neighbors; (v) a graphical user interface to all known protein folds with links to the above applications, Protein Globe. Recent examples are shown that highlight the utility of these tools in recognizing remote homologies between pairs of protein structures and in assigning putative biochemical functions to newly determined targets from structural genomics projects.     

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.     

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.     

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.     

Cooperative interactions of the gene 5 protein

Using the refined molecular structure of the Gene 5 DNA Binding Protein (G5BP) and the mechanism of DNA binding deduced from a variety of experimental techniques (G. D. Brayer and A. McPherson, J. Mol. Biol. 169, 565, 1983; G. D. Brayer and A. McPherson, Biochemistry 23, 340, 1984), we have modeled the contiguous, linear aggregation of G5BP dimers along two opposing single strands of DNA. Using both automated graphics systems and systematic calculations of intermolecular contacts between adjacent units, we have optimized the fit of complementary protein surfaces in the presence of DNA. We propose that a minor conformational change involving residues 38-43, triggered by the binding of nucleic acid, relieves several critical steric contacts and permits otherwise extensively complementary surfaces to form an interface. The bonding between surfaces on adjacent G5BP units is the primary source of the cooperativity of binding observed for G5BP. The interacting amino acid residues at the interface are described.     

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     

A technique for identifying atoms from a screen image

Improving the interfaces in molecular graphics applications, making them more natural and easy to use, is an important task, given the current complexity of the displayed objects and of modeling operations. Clicking near an atom center is the usual method of atom selection. However, this method has certain disadvantages when working with images composed of different atomic representations such as sticks, CPK, or dotted surfaces. We propose another technique allowing the user to obtain the correct answer when he or she clicks on any element of the atom image.     

Tek FRODO: A new version of FRODO for Tektronix graphics stations

A new version of the molecular graphics program FRODO was developed to allow the range of Tektronix graphics stations to be used for molecular modeling and crystallographic applications. The work was divided into two parts: first, the universal molecular modeling graphic package (Tek_MMGP) was written to enable basic modeling operations for Tektronix stations. Second, all routines of FRODO involving computer graphics were modified to fit the new hardware environment, and linked with Tek_MMGP. The resulting package, Tek_FRODO, has been used successfully for crystallographic refinement in several projects. The program, written in FORTRAN, is ready to be ported to any of Tektronix 3D graphics stations; it is available from the authors on request.     

Cooperative Interactions of the Gene 5 Protein

Abstract

Using the refined molecular structure of the Gene 5 DNA Binding Protein (G5BP) and the mechanism of DNA binding deduced from a variety of experimental techniques (G. D. Brayer and A. McPherson, J. Mol. Biol. 169, 565, 1983; G. D. Brayer and A. McPherson, Biochemistry 23, 340, 1984), we have modeled the contiguous, linear aggregation of G5BP dimers along two opposing single strands of DNA. Using both automated graphics systems and systematic calculations of intermolecular contacts between adjacent units, we have optimized the fit of complementary protein surfaces in the presence of DNA. We propose that a minor conformational change involving residues 38–43, triggered by the binding of nucleic acid, relieves several critical steric contacts and permits otherwise extensively complementary surfaces to form an interface. The bonding between surfaces on adjacent G5BP units is the primary source of the cooperativity of binding observed for G5BP. The interacting amino acid residues at the interface are described.