Biochemistry and Microbial Sciences-Research Publications
http://kr.cup.edu.in/handle/32116/157
2024-03-28T10:25:25ZBioinformatics insights into CENP-T and CENP-W protein-protein interaction disruptive amino acid substitution in the CENP-T-W complex
http://kr.cup.edu.in/handle/32116/2956
Bioinformatics insights into CENP-T and CENP-W protein-protein interaction disruptive amino acid substitution in the CENP-T-W complex
Mohanty, Suryakanta; Bhadane, Rajendra; Kumar, Shashank
Kinetochores are multi-protein assemblies present at the centromere of the human chromosome and play a crucial role in cellular mitosis. The CENP-T and CENP-W chains form a heterodimer, which is an integral part of the inner kinetochore, interacting with the linker DNA on one side and the outer kinetochore on the other. Additionally, the CENP-T-W dimer interacts with other regulatory proteins involved in forming inner kinetochores. The specific roles of different amino acids in the CENP-W at the protein-protein interaction (PPI) interface during the CENP-T-W dimer formation remain incompletely understood. Since cell division goes awry in diseases like cancer, this CENP-T-W partnership is a potential target for new drugs that could restore healthy cell division. We employed molecular docking, binding free energy calculations, and molecular dynamics (MD) simulations to investigate the disruptive effects of amino acids substitutions in the CENP-W chain on CENP-T-W dimer formation. By conducting a molecular docking study and analysing hydrogen bonding interactions, we identified key residues in CENP-W (ASN-46, ARG-53, LEU-83, SER-86, ARG-87, and GLY-88) for further investigation. Through site-directed mutagenesis and subsequent binding free energy calculations, we refined the selection of mutant. We chose four mutants (N46K, R53K, L83K, and R87E) of CENP-W to assess their comparative potential in forming CENP-T-W dimer. Our analysis from 250 ns long revealed that the substitution of LEU83 and ARG53 residues in CENP-W with the LYS significantly disrupts the formation of CENP-T-W dimer. In conclusion, LEU83 and ARG53 play a critical role in CENP-T and CENP-W dimerization which is ultimately required for cellular mitosis. Our findings not only deepen our understanding of cell division but also hint at exciting drug-target possibilities. � 2023 The Authors. Journal of Cellular Biochemistry published by Wiley Periodicals LLC.
2023-11-09T00:00:00ZImmunodominant conserved moieties on spike protein of SARS-CoV-2 renders virulence factor for the design of epitope-based peptide vaccines
http://kr.cup.edu.in/handle/32116/2957
Immunodominant conserved moieties on spike protein of SARS-CoV-2 renders virulence factor for the design of epitope-based peptide vaccines
Mohapatra, Subhashree; Kumar, Santosh; Kumar, Shashank; Singh, Atul Kumar; Nayak, Bismita
The outbreak of novel SARS-CoV-2 virion has wreaked havoc with a high prevalence of respiratory illness and high transmission due to a vague understanding of the viral antigenicity, augmenting the dire challenge to public health globally. This viral member necessitates the expansion of diagnostic and therapeutic tools to track its transmission and confront it through vaccine development. Therefore, prophylactic strategies are mandatory. Virulent spike proteins can be the most desirable candidate for the computational design of vaccines targeting SARS-CoV-2, followed by the meteoric development of immune epitopes. Spike protein was characterized using existing bioinformatics tools with a unique roadmap related to the immunological profile of SARS-CoV-2 to predict immunogenic virulence epitopes based on antigenicity, allergenicity, toxicity, immunogenicity, and population coverage. Applying in silico approaches, a set of twenty-four B lymphocyte-based epitopes and forty-six T lymphocyte-based epitopes were selected. The predicted epitopes were evaluated for their intrinsic properties. The physico-chemical characterization of epitopes qualifies them for further in vitro and in vivo analysis and pre-requisite vaccine development. This study presents a set of screened epitopes that bind to HLA-specific allelic proteins and can be employed for designing a peptide vaccine construct against SARS-CoV-2 that will confer vaccine-induced protective immunity due to its structural stability. � 2023, The Author(s), under exclusive licence to Indian Virological Society.
2023-11-23T00:00:00ZCombing of picogram level DNA equivalent to genomic DNA present in single human cell by self propelled droplet motion over a stable gradient surface
http://kr.cup.edu.in/handle/32116/2955
Combing of picogram level DNA equivalent to genomic DNA present in single human cell by self propelled droplet motion over a stable gradient surface
Yadav, Hemendra; Algaonkar, Prashant S.; Chakraborty, Sudip; Ramakrishna, Wusirika
DNA combing is a powerful technique for studying replication profile, fork-directionality and fork velocity. At present, there is requirement of a methodology to comb DNA present in a single human cell for studying replication dynamics at early embryonic stage. In our study, a surface having dual characteristics i.e., affinity towards negatively charged single DNA molecules and a hydrophobic gradient for self propelled droplet motion of combing solution was developed. The surface was made by coating of TCOS (trichloro-octylsilane) by vapor diffusion on APTES (Aminopropyl-triethoxysilane) coated glass slides. A gradient surface having high deposition efficiency (DE) was developed on which 5 picogram DNA equivalent to genomic DNA present in one single human cell can be combed. The gradient surface was thermostable in nature having the ability to sustain boiling temperature for two hours and sustain anisotropy in 70 % ethanol for 80 h. Applicability for multiple runs was enhanced such that the surface can be used for 13�14 times. Factors associated with gradient surface are unidirectional movement of combing solution droplet over the gradient surface for combing straight DNA molecules and a longer gradient surface of more than 1 cm such that long size DNA molecules can be combed. Ellipsometry and contact angle hysteresis confirmed the presence of hydrophobic gradient. XPS (X-ray photoelectron spectroscopy) and FTIR (Fourier Transform Infrared Spectroscopy) confirmed the presence of characteristic affinity towards negatively charged DNA molecules on the gradient surface. Combing solution was optimized for increasing deposition efficiency and for increasing the applicability of gradient surface for multiple runs. High temperature of combing solution was found to increase Deposition Efficiency. Combing solution was also optimized for combing single DNA molecules over the gradient surface. Single DNA molecules were combed by reducing pH and lowering concentration of triton-X in the combing solution. Dye: bp ratio was optimized for high fluorescent intensity and low surface background. � 2023 Elsevier Inc.
2023-11-08T00:00:00ZGenome-wide identification of NAC transcription factors in Avena sativa under salinity stress
http://kr.cup.edu.in/handle/32116/2954
Genome-wide identification of NAC transcription factors in Avena sativa under salinity stress
Bokolia, Muskan; Singh, Baljinder; Kumar, Avneesh; Goyal, Nandni; Singh, Kashmir; Chhabra, Ravindresh
Background: NAC (NAM, ATAF1/2, and CUC2) is one of the most prominent family of plant-specific transcription factors that play diverse roles in plant growth and development as well as in abiotic stress responses in plants. The members of this family are recognized by presence of typical conserved NAC domain at the N-terminal and diverse C-terminal region. Results: In this study, we have identified 101 Avena sativa NAC (AsNAC) genes from the available Avena genome database. Genes were analyzed for their physicochemical properties, conserved motifs, gene structure, chromosomal localization, phylogenetic relationship, and cis-acting elements. The phylogenetic analysis illustrated that there were 15 subgroups in both Avena sativa and Arabidopsis thaliana. Mainly four types of cis-acting regulatory elements were present in the promoter regions of NAC genes, including hormone-responsive, light-responsive, stress-responsive and growth and developmental responsive elements. The chromosomal mapping analysis concluded that 101 NAC genes of Avena sativa were unevenly distributed on 21 chromosomes. Expression analysis identified 27 Avena NAC genes that respond to salt stress based on transcriptomic data analysis available on the NCBI SRA database. Significance: The genome-wide identification and molecular analysis of NAC TFs involved in environmental stress responses have the ability to overcome the limitations that came across in producing the transgenic crops with superior quality and improved production under abiotic stressed conditions. Future prospectives: These NAC genes may be considered as potential candidates for further explorations of functional analysis and could be used to develop stress tolerant lines in Avena sativa. � 2023 The Author(s)
2023-10-29T00:00:00Z