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Vijay S Reddy

Publications and source records attributed to Vijay S Reddy.

9 recordsLinked to original sources
PubMed2006

Presence of a surface-exposed loop facilitates trypsinization of particles of Sinsiro virus, a genogroup II.3 norovirus.

Noroviruses (NoVs) are the causative agents of nonbacterial acute gastroenteritis in humans. NoVs that belong to genogroup II (GII) are quite prevalent and prone to undergo recombination, and their three-dimensional structure is not yet known. Protein homology modeling of Sinsiro virus (SV), a member of the GII.3 NoVs, revealed the presence of a surface-exposed 20-amino-acid (aa) insertion in the P2 domain of the capsid protein (CP) relative to the Norwalk virus (NV) CP, which is a well known hot spot for mutations to counter the host immunological response. To further characterize the role of the long insertion in SV, the capsid protein gene was expressed using the recombinant baculovirus system. Trypsinization of the resultant virus-like particles yielded two predominant bands (31.7 and 26.1 kDa) in sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot analysis. N-terminal sequencing and analysis of the mass spectroscopic data indicated that these fragments correspond to residues 1 to 292 (26.1 kDa) and 307 to 544 (31.7 kDa). In addition, the above data taken together with the comparative modeling studies indicated that the trypsin cleavage sites of the Sinsiro virus CP, Arg292 and Arg307, are located at the beginning of and within the 20-aa insertion in the P2 domain, respectively. This study demonstrates that the presence of the surface-exposed loop in the GII.3 NoVs facilitates the trypsinization of the capsid protein in the assembled form. The SV particles remain intact even after trypsin digestion and retain the suggested receptor binding linear epitope of residues 325 to 334. The above results are distinct from those obtained from the trypsinization studies performed earlier on the NV (GI) and VA387 (GII) viruses, both of which lack the large surface insertion and associated basic residues. These new observations may have implications for host receptor binding, cell entry, and norovirus infection in general.

Animals↗
PubMed2006

Characterization of polymorphism displayed by the coat protein mutants of tomato bushy stunt virus.

Expression of full-length and N-terminal deletion mutants of the coat protein (CP) of tomato bushy stunt virus (TBSV) using the recombinant baculovirus system resulted in spontaneously assembled virus-like particles (VLPs). Deletion of the majority of the R-domain sequence of the CP, residues 1-52 (CP-NDelta52) and 1-62 (CP-NDelta62), produced capsids similar to wild-type VLPs. Interestingly, the CP-NDelta62 mutant that retains the last 3 residues of R-domain is capable of forming both the T = 1 and T = 3 particles. However, between the two types of VLPs, formation of the T = 1 capsids appears to be preferred. Another mutant, CP-NDelta72, in which R-domain (residues 1-65) was completely removed but contains most of the beta-annulus and extended arm (betaA) regions exclusively formed T = 1 particles. These results suggest that as few as 3 residues (63-65) of the R-domain, which includes 2 basic amino acids together with the arm (betaA) and beta-annulus regions, may be sufficient for the formation of T = 3 particles. However, anywhere between 4 to 13 residues of the R-domain may be required for proper positioning of betaA and beta-annulus structural elements of the C-type subunits to facilitate an error free assembly of T = 3 capsids.

Amino Acid Sequence↗
PubMed2006

VIPERdb: a relational database for structural virology.

VIPERdb (http://viperdb.scripps.edu) is a database for icosahedral virus capsid structures. Our aim is to provide a comprehensive resource specific to the needs of the structural virology community, with an emphasis on the description and comparison of derived data from structural and energetic analyses of capsids. A relational database implementation based on a schema for macromolecular structure makes the data highly accessible to the user, allowing detailed queries at the atomic level. Together with curation practices that maintain data uniformity, this will facilitate structural bioinformatics studies of virus capsids. User friendly search, visualization and educational tools on the website allow both structural and derived data to be examined easily and extensively. Links to relevant literature, sequence and taxonomy databases are provided for each entry.

Capsid↗
PubMed2005

Extent of protein-protein interactions and quasi-equivalence in viral capsids.

Viral capsids are composed of multiple copies of one or a few gene products that self-assemble on their own or in the presence of the viral genome and/or auxiliary proteins into closed shells (capsids). We have analyzed 75 high-resolution virus capsid structures by calculating the average fraction of the solvent-accessible surface area of the coat protein subunits buried in the viral capsids. This fraction ranges from 0 to 1 and represents a normalized protein-protein interaction (PPI) index and is a measure of the extent of protein-protein interactions. The PPI indices were used to compare the extent of association of subunits among different capsids. We further examined the variation of the PPI indices as a function of the molecular weight of the coat protein subunit and the capsid diameter. Our results suggest that the PPI indices in T=1 and pseudo-T=3 capsids vary linearly with the molecular weight of the subunit and capsid size. This is in contrast to quasi-equivalent capsids with T>or=3, where the extent of protein-protein interactions is relatively independent of the subunit and capsid sizes. The striking outcome of this analysis is the distinctive clustering of the "T=2" capsids, which are distinguished by higher subunit molecular weights and a much lower degree of protein-protein interactions. Furthermore, the calculated residual (R(sym)) of the fraction buried surface areas of the structurally unique subunits in capsids with T>1 was used to calculate the quasi-equivalence of different subunit environments.

Binding Sites↗
PubMed2005

Exploring icosahedral virus structures with VIPER.

Virus structures are megadalton nucleoprotein complexes with an exceptional variety of protein-protein and protein-nucleic-acid interactions. Three-dimensional crystal structures of over 70 virus capsids, from more than 20 families and 30 different genera of viruses, have been solved to near-atomic resolution. The enormous amount of information contained in these structures is difficult to access, even for scientists trained in structural biology. Virus Particle Explorer (VIPER) is a web-based catalogue of structural information that describes the icosahedral virus particles. In addition to high-resolution crystal structures, VIPER has expanded to include virus structures obtained by cryo-electron microscopy (EM) techniques. The VIPER database is a powerful resource for virologists, microbiologists, virus crystallographers and EM researchers. This review describes how to use VIPER, using several examples to show the power of this resource for research and educational purposes.

Capsid↗
PubMed2003

Busulfan, cyclophosphamide, and etoposide as conditioning for autologous stem cell transplantation in multiple myeloma.

Autologous stem cell transplantation (ASCT) has enabled the use of high-dose alkylating agents either as a single agent or in combination with other cytotoxic agents and/or total body irradiation (TBI) for the treatment of multiple myeloma. Despite improved complete remission rates, relapse and regimen-related toxicities remain challenging. In an effort to increase event-free survival and decrease the high incidence of regimen-related toxicity, we have studied the use of etoposide in combination with reduced-dose busulfan and cyclophosphamide as a conditioning regimen for ASCT in a group of 26 patients with advanced multiple myeloma. Median follow-up for the group was 30 months. There was no early treatment-related mortality. The main toxicity was mucositis. Otherwise, there was 1 case of reversible, clinically diagnosed hepatic veno-occlusive disease. Post-engraftment, 10 patients (38%) achieved CR, 15 (58%) patients achieved PR or SD, and 1 patient developed progressive disease (4%). Five patients in PR and 1 with progressive disease before transplant attained a CR post-transplant. The median times for event-free survival and overall survival after transplantation were 24 and 43 months, respectively. In conclusion, conditioning with busulfan, cyclophosphamide, and etoposide followed by ASCT is a safe regimen with comparable effectiveness to other previously used preparative regimens, thus providing another approach of non-TBI containing high-dose chemotherapy for patients with multiple myeloma.

Adult↗
PubMed2002

A general method to quantify quasi-equivalence in icosahedral viruses.

A quantitative, atom-based, method is described for comparing protein subunit interfaces in icosahedral virus capsids with quasi-equivalent surface lattices. An integrated, normalized value (between 0 and 1) based on equivalent residue contacts (Q-score) is computed for every pair of subunit interactions and scores that are significantly above zero readily identify interfaces that are quasi-equivalent to each other. The method was applied to all quasi-equivalent capsid structures (T=3, 4, 7 and 13) in the Protein Data Bank and the Q-scores were interpreted in terms of their structural underpinnings. The analysis allowed classification of T=3 structures into three groups with architectures that resemble different polyhedra with icosahedral symmetry. The preference of subunits to form dimers in the T=4 human Hepatitis B virus capsid (HBV) was clearly reflected in high Q-scores of quasi-equivalent dimers. Interesting differences between the classical T=7 capsid and polyoma-like capsids were also identified. Application of the method to the outer-shell of the T=13 Blue tongue virus core (BTVC) highlighted the modest distortion between the interfaces of the general trimers and the strict trimers of VP7 subunits. Furthermore, the method identified the quasi 2-fold symmetry in the inner capsids of the BTV and reovirus cores. The results show that the Q-scores of various quasi-symmetries represent a "fingerprint" for a particular virus capsid architecture allowing particle classification into groups based on their underlying structural and geometric features.

Amino Acid Sequence↗
PubMed2002

The architecture of a water-selective pore in the lipid bilayer visualized by electron crystallography in vitreous ice.

The water-selective pathway through aquaporin 1 (AQP1) membrane channel has been visualized by fitting an atomic model to a 3.7 A resolution three-dimensional density map. This map was determined by analysing images and electron diffraction patterns of lipid-reconstituted two-dimensional crystals of AQP1 preserved in vitrified buffer in the absence of any additive. The aqueous pathway in a monomer is characterized by a size-selective, to approximately 4.0 +/- 0.5 A wide pore that spans a length of to approximately 18 and bends by to approximately 25 degrees as it traverses the bilayer. This narrow pore is connected by wide, funnel-shaped openings at the extracellular and cytoplasmic faces, and is outlined mostly by hydrophobic residues interspersed with short stretches of polar amino acids, which results in relatively inert pathway conducive to diffusion-limited water flow. Although not visible at the current resolution, the 3D structure suggests putative binding sites for water molecules in the size-selective pore.

Amino Acid Sequence↗