Biomedical subjects

Ganapathy Rajaseger

Publications and source records attributed to Ganapathy Rajaseger.

5 recordsLinked to original sources

PubMed2006

Profiling of hepatocellular proteins by 1D PAGE-MALDI/MS/MS in a rat heat stress model.

Heat induced complications cause an increase in a large number of proteins which play a role in diverse pathways during heat shock. A detailed characterization of these proteins is essential for understanding the molecular mechanisms involved in heat stroke. In this report, the proteins present in rat liver were compared at 37 degrees C (control) and at core temperature (Tc) 42 degrees C (heat stress) by 1D PAGE and MALDI/MS/MS. Among proteins identified in the sample after heat stress are dimethyglycine dehydrogenase, transketolase, carboxylic ester hydrolase, pyruvate kinase, L-type pyruvate kinase, arginosuccinate synthetase; fumarylacetoacetate hydrolase and peptidylpropyl isomerase A. These findings show that analysis of large scale proteins by MALDI/MS/MS provides a better understanding of the molecular mechanisms associated with heat shock. The resolution of proteins examined by 1D-PAGE was less than that obtained with 2D-PAGE. More specifically, 2D-PAGE allows better identification of low molecular weight proteins that can not be resolved by 1D-PAGE.

Animals↗

PubMed2005

A framework to sub-type HLA supertypes.

The human leukocyte antigen (HLA) alleles are extremely polymorphic among ethnic population and the peptide binding specificity varies for different alleles in a combinatorial manner. However, it has been suggested that majority of alleles can be covered within few HLA supertypes, where different members of a supertype bind similar peptides, yet exhibiting distinct repertoires. Since the overlap between different members of a supertype appears to be extensive, it is crucial to develop a framework for grouping alleles into supertypes just from sequence information. In this report, we define sub supertypes, where members show functional overlap with identical repertoire, and describe a strategy to group HLA-A, B and C alleles into different categories of sub supertypes. The strategy grouped 47% of 295 A alleles, 44% of 540 B alleles and 35% of 156 C alleles to just 36, 71 and 18 groups, respectively. The grouping is moderately validated using available binding data. However, the validation is limited due to lack of binding data. Hence, the data presented in this article serve as a framework to test specific functional overlap between alleles. The grouping of HLA alleles into different categories of sub supertypes has profound use in the understanding of antigenic peptide selection, degeneration and discrimination during T-cell mediated immune response. A complete knowledge of this phenomenon finds utility in epitope design for the development of HLA based vaccines and immuno-therapeutics.

Alleles↗

PubMed2003

Crystallization and preliminary X-ray analysis of candoxin, a novel reversible neurotoxin from the Malayan krait Bungarus candidus.

Candoxin, a novel three-finger toxin from Bungarus candidus, is a reversible antagonist of muscle (alphabetagammadelta) but a poorly reversible antagonist of neuronal alpha7 nicotinic acetylcholine receptors. It has a molecular weight of 7344 Da, with 66 amino-acid residues including ten half-cystines. The fifth disulfide bridge is located at the tip of loop I (Cys6-Cys11) instead of in loop II as found in other alpha-neurotoxins. Interestingly, candoxin lacks the segment cyclized by the fifth disulfide bridge at the tip of the middle loop of long-chain neurotoxins, which was reported to be critical for binding to alpha7 receptors. As a first step to determining its three-dimensional structure, candoxin was crystallized by the hanging-drop vapour-diffusion technique in conditions around 1.5 M sodium chloride, 10%(v/v) ethanol. The crystals formed belonged to the hexagonal system, space group P6(2)22, with unit-cell parameters a = 54.88, b = 54.88, c = 75.54 A, alpha = beta = 90, gamma = 120 degrees, and diffract to a resolution of 1.80 A. The crystallographic asymmetric unit contains one molecule of candoxin, with an estimated solvent content of 44.6%. Attempts to solve these structures by molecular-replacement methods have not been successful and a heavy-atom derivative search has been initiated.

Animals↗

PubMed2003

A novel MHCp binding prediction model.

Many statistical and molecular mechanics models have been developed and tested for major histocompatibility complex peptide (MHCp) binding predictions during the last decade. The statistical model prediction using pooled peptide sequence data and three-dimensional modeling prediction by molecular mechanics calculations have been assessed for efficiency and human leukocyte antigen diversity coverage. We describe a novel predictive model using information gleaned from 29 human MHCp crystal structures. The validation for the new model is performed using four different sets of data: (1) MHCp crystal structures, (2) peptides with known IC(50) binding values, (3) peptides tested positive by tetramer staining, (4) peptides with known binding information at the MHCBN database. The model produces high prediction efficiencies (average 60 %) with good sensitivity (approximately 50%-73%) and specificity (52%-58%) values. The average positive predictive value of the model is 89%, while the average negative predictive value is only 18%. The efficiency is very high in predicting binders and very low in predicting nonbinders. This model is superior to many existing methods because of its potential application to any given MHC allele whose sequence is clearly defined.

Amino Acid Sequence↗

PubMed2002

Types of inter-atomic interactions at the MHC-peptide interface: identifying commonality from accumulated data.

BACKGROUND: Quantitative information on the types of inter-atomic interactions at the MHC-peptide interface will provide insights to backbone/sidechain atom preference during binding. Qualitative descriptions of such interactions in each complex have been documented by protein crystallographers. However, no comprehensive report is available to account for the common types of inter-atomic interactions in a set of MHC-peptide complexes characterized by variation in MHC allele and peptide sequence. The available x-ray crystallography data for these complexes in the Protein Databank (PDB) provides an opportunity to identify the prevalent types of such interactions at the binding interface. RESULTS: We calculated the percentage distributions of four types of interactions at varying inter-atomic distances. The mean percentage distribution for these interactions and their standard deviation about the mean distribution is presented. The prevalence of SS and SB interactions at the MHC-peptide interface is shown in this study. SB is clearly dominant at an inter-atomic distance of 3A. CONCLUSION: The prevalently dominant SB interactions at the interface suggest the importance of peptide backbone conformation during MHC-peptide binding. Currently, available algorithms are developed for protein sidechain prediction upon fixed backbone template. This study shows the preference of backbone atoms in MHC-peptide binding and hence emphasizes the need for accurate peptide backbone prediction in quantitative MHC-peptide binding calculations.

Binding Sites↗