In silico CD4+, CD8+ & humoral immunity associated antigenic epitope prediction and HLA distribution analysis of HTLV-I.

PURPOSE: The linkage of human T-cell leukemia virus type 1 (HTLV-1) to fatal diseases is a well known fact for many years. However, there has been no significant progress in the field of the treatment that can lead to the development of a successful vaccine. Furthermore, there are no means of assessing the risk of disease and its prognosis in the infected people. METHODS: The current study has taken the cognizance of the importance of host's immune response in reducing the risk of infectious diseases to carry out immunoinformatics driven epitope screening strategy of vaccine candidates against HTLV-1. In this study, a genetic variability and HLA distribution analysis among the documented HTLV-1 genotypes I, II, III, IV, V & VI was performed to ensure the coverage of the vast majority of population, where vaccine would be employed. The meticulous screening of effective dominant immunogens was done with the help of ABCPred and Immune Epitope Database. RESULTS: The results showed that the identified epitopes might be protective immunogens with high conservancy and potential of inducing both protective neutralizing antibodies and T-cell responses. The peptides "PSQLPPTAPPLLPHSNLDHI", "PCPNLVAYSSYHATY", and "YHATYSLYLF", were 100% conserved among different isolates from far and wide separated countries, suggesting negligible antigenic drift in HTLV-1. CONCLUSIONS: Overall, the mentioned epitopes are soluble, non-toxic suitable candidates for the development of vaccine against HTLV-1 and warrant further investigation and experimental validation.

INTERACTION PATTERN OF FULLERENES (C20-C180) AND CARBON NANOTUBES WITH DIFFERENT FORMS OF DNA: A COMPUTATIONAL BIOLOGY APPROACH.

Recently, the venues of exposure to nanoparticles have increased significantly owing to their increased deliberate production. In this study the interaction of fullerenes with DNA was analyzed along with various factors affecting this interaction like mol. wt. of fullerenes (C20 to C180), the form of DNA i.e., A, B and Z, and sequences of DNA, and was compared with the DNA binding of CNTs. Increase in the molecular weight of the fullerene showed increase in the binding score with A & B-form of DNA, but no regular affect was seen on binding with Z-form of DNA. Although the binding of all fullerenes was best with A form. While CNTs bind with all forms of DNA, but best scores were with B form, which were comparable with those of fullerene C80 and C84 with A form. The interaction of both fullerenes and CNTs were not affected by the sequence of DNA. The number of interacting base pairs increased from 1 base-pair to 4, as the molecular size of fullerene increases in all A & B-and Z form of DNA. Whereas CNTs interact with 5 bases in A and B form, and 3 bases in Z form. The groove where binding occurs depended on the form of DNA. Smaller (< C48) fullerenes bind in minor groove of B-DNA, and larger fullerenes bind in major groove. While in A form of DNA, fullerenes of all sizes bind in major groove. The binding was random and not size dependent in Z form of DNA. Whereas, CNTs bind to major groove of DNA in a parallel fashion in A and B form of DNA, and in minor groove attached perpendicularly in Z form.

Interaction pattern for the complex of B-DNA Fullerene compounds with a set of known replication proteins using docking study.

Fullerenes have attracted considerable attention due to their unique chemical structure and potential applications which has opened wide venues for possible human exposure to various fullerene types. Therefore, in depth knowledge of how fullerene may interfere with various cellular processes becomes quite imperative. The present study was designed to investigate how the presence of fullerene affect the binding of DNA with different enzymes involved in replication process. Different fullerenes were first docked with DNA and then binding scores of different enzymes was analyzed with fullerene docked DNA. C30, C40 & C50 once docked with DNA, reduced the binding score of primase, whereas no significant change in the binding score was observed with the helicase, ssb protein, dna pol δ, dna pol ε, ligase, DNA clamp, and topoisomerases. On the contrast, the binding score of RPA14 decreases in fluctuating manner while interacting with increasing molecular weight of fullerene bound single-stranded DNA complex. The study revealed the affect of fullerene family interacting with DNA on the binding pattern of enzymes involved in replication process. Study suggests that the presence of most of fullerenes may not affect the activity of these enzymes necessary for replication process whereas C30, C40 & C50 may disrupt the activity of primase, (strating point for DNA polymerase) its docking score decreases from 13820 to 10702.