Biomedical subjects

B V Prasad

Publications and source records attributed to B V Prasad.

9 recordsLinked to original sources

PubMed1992

Method for calculating 3-D coordinates from molecular stereograms.

The three-dimensional coordinates for the alpha-carbon atoms of crambin and basic pancreatic trypsin inhibitor (BPTI) were determined from the respective alpha-carbon trace stereograms using an improved Simplex algorithm. This algorithm was used in a two-step process to estimate the z-coordinate values. In one approach, an average interatomic distance value, an approximate viewing angle, and a table of digitized values for xleft, yleft and xright, yright are provided in the first step. In the second step, the z-coordinate values are derived by varying z to minimize the bond distance error (Rossmann and Argos, 1980). In another approach, only a reference bond distance table is provided along with the table of xleft, yleft and xright, yright digitized values. In the first step, the viewing angle (phi), a combined scale and viewing distance parameter (q), a rotational angular distortion from digitizing and/or photocopying (z), and translational distortion factors (xerr and yerr) are calculated. In the second step, the z-coordinate values are varied to minimize the bond distance error. RMS difference values of less than 1.5 A were obtained for both crambin and BPTI alpha-carbon atoms.

Algorithms↗

PubMed1992

Visualization and characterization of tobacco mosaic virus movement protein binding to single-stranded nucleic acids.

Cell-to-cell spread of tobacco mosaic virus (TMV) is presumed to occur through plant intercellular connections, the plasmodesmata. Viral movement is an active process mediated by a specific virus-encoded P30 protein. P30 has at least two functions, to cooperatively bind single-stranded nucleic acids and to increase plasmodesmatal permeability. Here, we visualized P30 complexes with single-stranded DNA and RNA. These complexes are long, unfolded, and very thin (1.5 to 2.0 nm in diameter). Unlike TMV virions (300 x 18 nm), the complexes are compatible in size with the P30-induced increase in plasmodesmatal permeability (2.4 to 3.1 nm), making them likely candidates for the structures involved in the cell-to-cell movement of TMV. Mutational analysis using single and double deletion mutants of P30 revealed three regions potentially important for the protein function. Amino acid residues 65 to 86 possibly are required for correct folding of the active protein, and the regions between amino acid residues 112 to 185 and 185 to 268 potentially contain two independently active single-stranded nucleic acid binding domains designated binding domains A and B, respectively.

Amino Acid Sequence↗

PubMed1992

Three-dimensional structure of single-shelled bluetongue virus.

The three-dimensional structure of single-shelled bluetongue virus has been determined to a resolution of 3 nm by using electron cryomicroscopy and image-processing techniques. The single-shelled virion has a diameter of 69 nm. The three-dimensional structure of the virion has icosahedral symmetry with a triangulation number of 13 in a left-handed configuration. The three-dimensional structure can be described in terms of two concentric layers of density surrounding a central core density. Two distinctive features of the outer layer are the 260 knobby capsomeres located at all the local and strict threefold axes and the aqueous channels located at all the five- and six-coordinated positions. These protrusions extend outward from an inner radius of 28 nm. They are interconnected out to a radius of 30 nm by saddle-shaped densities across the local and strict twofold axes. The aqueous channels surrounded by these capsomeres are about 8 nm wide at the outer surface and 8 nm deep. Some of these channels extend inward, penetrating the inner layer. These channels may provide pathways for transporting the metabolites and mRNA during the transcriptase activity of the particles. The inner layer is a featureless smooth bed of density except for the indentations in register with the channels of the outer layer. We propose that the 260 capsomeres in the outer layer are made up of trimers of the major protein, VP7, and that the inner layer is composed of the second major protein, VP3. The density in the central portion of the structure at a radius of less than 21 nm is likely due to the minor proteins and the genomic RNA.

Bluetongue virus↗

PubMed1990

Localization of VP4 neutralization sites in rotavirus by three-dimensional cryo-electron microscopy.

Three-dimensional structures of several spherical viruses have been determined by electron microscopy and X-ray crystallography. We report here the first three-dimensional structure of the complex between an intact virus and Fab fragments of a neutralizing monoclonal antibody. The antibody is against VP4, one of the two outer capsid proteins of rotaviruses. These large icosahedral viruses cause gastroenteritis in children and young animals and account for over a million human deaths annually. VP4 in these viruses has been implicated in several important functions such as cell penetration, haemagglutination, neutralization and virulence. Here we demonstrate that the surface spikes on rotavirus particles are made up of VP4. Antigenic sites are located near the distal ends of the spikes and two Fab fragments bind to each of the sixty spikes. The mass of the spike indicates that it is a dimer of VP4. The bilobed structure at the distal end of the spike may be involved in both the attachment to the cell and in viral penetration. A novel feature in the virus-Fab complex is the structural difference between the two chemically equivalent Fab fragments on each spike, which could be indicative of variations in the Fab elbow angles.

Antibodies, Monoclonal↗

PubMed1990

Estimation of allowable errors for tilt parameter determination in protein electron crystallography.

A three-dimensional reconstruction of a thin protein crystal requires an accurate assignment of amplitudes and phases in the three-dimensional reciprocal space. This assignment depends upon the tilt parameters which are experimentally determined. A theoretical estimate is made of the tolerable error in the determination of tilt parameters as a function of resolution and crystal thickness.

Crystallization↗

PubMed1989

Three-dimensional structure of the HSV1 nucleocapsid.

The three-dimensional structures of full and empty capsids of HSV1 were determined by computer analysis of low dose cryo-electron images of ice embedded capsids. The full capsid structure is organized into outer, intermediate, and inner structural layers. The empty capsid structure has only one layer which is indistinguishable from the outer layer of the full capsids. This layer is arranged according to T = 16 icosahedral symmetry. The intermediate layer of full capsids appears to lie on a T = 4 icosahedral lattice. The genomic DNA is located inside the T = 4 shell and is the component of the innermost layer of the full capsids. The outer and intermediate layers interact in such a way that the channels along their icosahedral two-fold axis coincide and form a direct pathway between the DNA and the environment outside the capsid.

Capsid↗

PubMed1988

Three-dimensional structure of rotavirus.

The three-dimensional structures of double and single-shelled simian rotavirus have been determined to a resolution of 40 A by image processing electron micrographs of unstained, unfixed virus particles embedded in vitreous ice. This study demonstrates that the icosahedral surface lattices in these structures have a triangulation number of 13 in a left-handed configuration. The double-shelled virion has a smooth outer surface with 60 slender spikes. The single-shelled virion, in contrast, exhibits a bristly surface. On the basis of these structures, the locations and number of copies of outer and inner shell proteins have been deduced. The spikes likely correspond to VP3, a hemagglutinin, while the rest of the mass density in the outer shell represents 780 molecules of VP7, a neutralization antigen. The 260 morphological units, located on all the local and strict 3-fold axes of the single-shelled virion are proposed to represent 260 trimers of VP6, which is a subgroup antigen. The regions of closed contact between the outer and the inner shells are located mainly near the local and strict 3-fold axes. A distinctive feature in the rotavirus structure is the presence of 132 large channels spanning across both the shells at all 5 and 6-co-ordinated positions linking the outermost surface with the inner core. In the transcriptionally active single-shelled virion, these channels may provide pathways for importing the metabolites required for the viral RNA transcription and exporting the newly synthesized RNA molecules for subsequent viral replication processes.

Capsid↗

PubMed1987

Sequence comparison of single-stranded DNA binding proteins and its structural implications.

The primary sequences were compared among several proteins: gene product 5 protein (GP5) from phage M13; PIKE from phage Ike; gene product 32 protein (GP32) from phage T4; RecA, SSB and SSF from Escherichia coli. These proteins bind strongly and cooperatively to single-stranded DNA with no sequence specificity. GP5 is the smallest in this group and its three-dimensional structure is well-characterized. Using the entire sequence of GP5 as a template we searched for the regions in other single-stranded DNA binding proteins yielding the best alignment of aromatic and basic residues. The identified domains show alignment of five aromatic and four charged residues in these proteins. The domains in PIKE, GP32 and RecA exhibit statistically significant sequence homology with GP5. These observations strongly favor the hypothesis that the protein-single-stranded DNA complex in this class of proteins is stabilized by the stacking interaction of the aromatic residues with the bases of the DNA, and by the electrostatic interaction of the basic residues with the phosphate groups of the DNA. We also find that the DNA binding domains of these proteins have similar secondary structural preferences, mainly beta structures. The triple-stranded beta-sheet may be a common motif in the DNA binding domains of these proteins.

Amino Acid Sequence↗

PubMed1977

Conformation of polypeptide chains containing both L- and D-residues. II. Double-helical structures of poly-LD-peptides.

Polypeptides with alternating L- and D-amino acid residues can take up stereo-chemically satisfactory coaxial double-helical structures, both antiparallel and parallel, which are stabilized by systematic interchain NH...O hydrogen bonds. Semiempirical energy calculations over allowed regions of conformational space have yielded the characteristics of these double-helices. There are four possible types of antiparallel double-helices - A3, A4, A5 and A6, with n, the number of LD peptide units per turn, around 2.8, 3.6, 4.5 and 5.5 respectively, while for the parallel double-helices there are two types, P3 and P4, having similar helical parameters as in A3 and A4. The hydrogen-bonding scheme restricts the pitch in all the models to the narrow range of 10.0 to 11.5 A. All these helices have large central cores whose radii increase proportionately with n. In this respect, A3 and A4 are suitable models for the structure of gramicidin A. In terms of their relative energies, antiparallel double-helices are marginally more stable than those with parallel strands. Our results indicate that the energy differences amongst the members in the antiparallel family are not significant and thus provide an explanation for the polymorphism reported for poly (gamma-benzyl-LD-glutamate).

Amino Acids↗