arXiv subjects

Suman K. Banik

Publications and source records attributed to Suman K. Banik.

5 recordsLinked to original sources

arXiv2016

Information theoretical study of cross-talk mediated signal transduction in MAPK pathways

Biochemical networks related to similar functional pathways are often correlated due to cross-talk among the homologous proteins in the different networks. Using a stochastic framework, we address the functional significance of the cross-talk between two pathways. Our theoretical analysis on generic MAPK pathways reveals cross-talk is responsible for developing coordinated fluctuations between the pathways. The extent of correlation evaluated in terms of the information theoretic measure provides directionality to net information propagation. Stochastic time series and scattered plot suggest that the cross-talk generates synchronization within a cell as well as in a cellular population. Depending on the number of input and output, we identify signal integration and signal bifurcation motif that arise due to inter-pathway connectivity in the composite network. Analysis using partial information decomposition quantifies the net synergy in the information propagation through these branched pathways.

q-bio.MN↗

arXiv2014

Role of relaxation time scale in noisy signal transduction

Intracellular fluctuations, mainly triggered by gene expression, are an inevitable phenomenon observed in living cells. It influences generation of phenotypic diversity in genetically identical cells. Such variation of cellular components is beneficial in some contexts but detrimental in others. To quantify the fluctuations in a gene product, we undertake an analytical scheme for studying few naturally abundant linear as well as branched chain network motifs. We solve the Langevin equations associated with each motif under the purview of linear noise approximation and quantify Fano factor and mutual information. Both quantifiable expressions exclusively depend on the relaxation time (decay rate constant) and steady state population of the network components. We investigate the effect of relaxation time constraints on Fano factor and mutual information to indentify a time scale domain where a network can recognize the fluctuations associated with the input signal more reliably. We also show how input population affects both quantities. We extend our calculation to long chain linear motif and show that with increasing chain length, the Fano factor value increases but the mutual information processing capability decreases. In this type of motif, the intermediate components are shown to act as a noise filter that tune up input fluctuations and maintain optimum fluctuations in the output. For branched chain motifs, both quantities vary within a large scale due to their network architecture and facilitate survival of living system in diverse environmental conditions.

q-bio.MN↗

arXiv2012

Positive feedback and temperature mediated molecular switch controls differential gene regulation in Bordetella pertussis

Based on the phosphorelay kinetics operative within BvgAS two component system we propose a mathematical framework for signal transduction and gene regulation of phenotypic phases in Bordetella pertussis. The proposed model identifies a novel mechanism of transcriptional interference between two promoters present in the bvg locus. To understand the system behavior under elevated temperature, the developed model has been studied in two different ways. First, a quasi-steady state analysis has been carried out for the two component system, comprising of sensor BvgS and response regulator BvgA. The quasi-steady state analysis reveals temperature induced sharp molecular switch, leading to amplification in the output of BvgA. Accumulation of a large pool of BvgA thus results into differential regulation of the downstream genes, including the gene encoding toxin. Numerical integration of the full network kinetics is then carried out to explore time dependent behavior of different system components, that qualitatively capture the essential features of experimental results performed in vivo. Furthermore, the developed model has been utilized to study mutants that are impaired in their ability to phosphorylate the transcription factor, BvgA, of the signaling network.

q-bio.MN↗

arXiv2006

Breathing dynamics in heteropolymer DNA

While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule spectroscopy. The dynamical opening of DNA bubbles (DNA breathing) is supposedly crucial for biological functioning during, for instance, transcription initiation and DNA's interaction with selectively single-stranded DNA binding proteins. Motivated by this, we consider the bubble breathing dynamics in a heteropolymer DNA based on a (2+1)-variable master equation and complementary stochastic Gillespie simulations, providing the bubble size and the position of the bubble along the sequence as a function of time. We utilize new experimental data that independently obtain stacking and hydrogen bonding contributions to DNA stability. We calculate the spectrum of relaxation times and the experimentally measurable autocorrelation function of a fluorophore-quencher tagged base-pair, and demonstrate good agreement with fluorescence correlation experiments. A significant dependence of opening probability and waiting time between bubble events on the local DNA sequence is revealed and quantified for a promoter sequence of the T7 phage. The strong dependence on sequence, temperature and salt concentration for the breathing dynamics of DNA found here points at a good potential for nanosensing applications by utilizing short fluorophore-quencher dressed DNA constructs.

q-bio.BM↗

arXiv2006

Sequence sensitivity of breathing dynamics in heteropolymer DNA

We study the fluctuation dynamics of localized denaturation bubbles in heteropolymer DNA with a master equation and complementary stochastic simulation based on novel DNA stability data. A significant dependence of opening probability and waiting time between bubble events on the local DNA sequence is revealed and quantified for a biological sequence of the T7 bacteriophage. Quantitative agreement with data from fluorescence correlation spectroscopy (FCS) is demonstrated.

q-bio.BM↗