Proceedings of the 2019 6th International Conference on Bioinformatics Research and Applications, 2019
A simulation of the kinetics of the sodium-glucose transporters has been reported using a model w... more A simulation of the kinetics of the sodium-glucose transporters has been reported using a model widely used in literature. However, the various kinetic constants of the transporter have been replaced by 1 (as they are not available in the literature). We have also studied the effect of the membrane potential on glucose transport. The used model is leaky, i.e., sodium transport can take place independently of glucose transport. Although the results can be considered only semi-quantitative, we find that glucose transport is rather energy-intensive, because around 15 sodium ions needed to be transported for each glucose molecule carried inside. However, the process is powerful, in the sense that the final glucose concentration outside can fall almost to zero.
We have explored the region around the splice sites of the human intron and exons from the exon-i... more We have explored the region around the splice sites of the human intron and exons from the exon-intron database (EID) and located a number of short 6-nucleotide and 7-nucleotide sequences that are relatively common in the regions. These short sequences, we expect play an important role in the selection of the appropriate splicing process. We propose that the external signals via short recognition sequences play the deterministic role in the actual splicing process. We have obtained 50 such sequences each from the exon and intron from the beginning and from the ending and noted a number of common features.
Glutathione (L-gamma-glutamyl-L-cysteinyl-L-glycine; GSH) forms a surface monolayer on gold nanop... more Glutathione (L-gamma-glutamyl-L-cysteinyl-L-glycine; GSH) forms a surface monolayer on gold nanoparticles by tethering via sulfur bonds (Au:GSH). In the present study, glucose oxidase (GOx; EC 1.1.3.4) was immobilized by covalent chemical coupling reactions on to Au:GSH nanoparticles and the enzyme coupled nanoparticles formed a stable colloid (stable for several weeks) in water. The immobilized enzyme was investigated for electrochemical characteristics to monitor the FAD (prosthetic group of the GOx) redox potentials. Various concentrations of substrate (glucose) were added to check the oxidation characteristics. It was observed that with increase in substrate concentrations, the oxidation rate increased proportionally with the current. The present study demonstrated that GOx was effectively coupled to the gold nanoparticle (Au:GSH). The coupled nanoparticle system could be used in a potential biosensor application. Similarly, other enzymes (e.g., horseradish peroxidase) could be ...
Toll-like receptors (TLRs) are proteins that play key role in the innate immune system. In the pr... more Toll-like receptors (TLRs) are proteins that play key role in the innate immune system. In the present study, -1000 base pairs upstream are taken from the transcription start site of the various TLR genes (10 known) in human. About 40 microRNAs have been identified that share 12-19 nucleotide sequence similarity with the promoter regions of 10 TLRs. It is proposed that the microRNA performs potential role in identification of promoter sequence and initiation of transcription.
In this report, we have modelled a secondary active co-transporter (symport and antiport), based ... more In this report, we have modelled a secondary active co-transporter (symport and antiport), based on the classical kinetics model. Michaelis-Menten model of enzyme kinetics for a single substrate, single intermediate enzyme catalyzed reaction was proposed more than a hundred years ago. However, no single model for the kinetics of co-transport of molecules across a membrane is available in the literature We have made several simplifying assumptions and have followed the basic Michaelis-Menten approach. The results have been simulated using GNU Octave. The results will be useful in general kinetic simulations and modelling.
We have studied the direct electrochemistry of horseradish peroxidase (HRP) coupled to gold nanop... more We have studied the direct electrochemistry of horseradish peroxidase (HRP) coupled to gold nanoparticles (AuNP) using electrochemical techniques, which provide some insight in the application of biosensors as tools for diagnostics because HRP is widely used in clinical diagnostics kits. AuNP capped with (i) glutathione and (ii) lipoic acid was covalently linked to HRP. The immobilized HRP/AuNP conjugate showed characteristic redox peaks at a gold electrode. It displayed good electrocatalytic response to the reduction of H2O2, with good sensitivity and without any electron mediator. The covalent linking of HRP and AuNP did not affect the activity of the enzyme significantly. The response of the electrode towards the different concentrations of H2O2 showed the characteristics of Michaelis Menten enzyme kinetics with an optimum pH between 7.0 to 8.0. The preparation of the sensor involves single layer of enzyme, which can be carried out efficiently and is also highly reproducible when...
We have studied the presence of long-range correlations in the complete genomes of ten different ... more We have studied the presence of long-range correlations in the complete genomes of ten different dsDNA viruses and Saccharomyces cerevisiae (bakers' yeast) chromosome I. We have also studied the correlation between the distribution of the gene length and the domain of "1/f region" of their genomes. Linear regression analysis was done for the power-law region of these organisms and the slope values obtained were approximately -1, which signify the existence of "1/f noise" in the low and medium (intermediate) frequency regions. This suggests the presence of long-range correlations in their genomes. The presence of 1/f noise in a given frequency interval indicates the existence of a fractal (self-similar) structure in the corresponding range of wavelengths. The results of our study suggest that genes have correlations within themselves, and the correlations appear to be related with the scaling exponent alpha.
SummaryWe have carried out a comparative analysis of the sub-sequences of size six| ten at the (d... more SummaryWe have carried out a comparative analysis of the sub-sequences of size six| ten at the (donor| acceptor) splice site regions of five different organisms. The frequency analysis of the unique sub-sequences at the donor and acceptor regions suggests that the distribution of their occurrence is approximately exponential. We have observed that the number of unique sub-sequences (occurring with different frequencies) at the donor region are less than at the acceptor, suggesting that the sub-sequences at the acceptor region are more variable. The sub-sequences with high percentage of occurrence (uniqueness) are considered to be highly involved in splicing. Our analysis suggests that sub-sequences of length ~6-8 nucleotides (nt) at the splice sites – with six bases in intron (including the two central, conserved dinucleotides) and two bases in exon are optimal for the efficient assembly and binding of the spliceosomal complex during the process of splicing. The score pattern obtain...
SummaryA new look at the transcription start is presented in which we can see transcription facto... more SummaryA new look at the transcription start is presented in which we can see transcription factors binding to both sides of the TSS as an essential requirement. Naturally the factor binding to the downstream region must be removed so that transcription process can continue. The presence of a number of distinct transcription factors also can be used to explain selective activation of various genes. The transcription start site by itself plays only a minor role in the whole process. We also suggest that mutations close to the TSS on the coding side can be fatal even if preserves the codon table.
SummaryMicroRNAs (miRNAs) are short noncoding RNA sequences ~22 nucleotides in length that play a... more SummaryMicroRNAs (miRNAs) are short noncoding RNA sequences ~22 nucleotides in length that play an important role in gene regulation-transcription and translation. The processing of these miRNAs takes place in both the nucleus and the cytoplasm while the final maturation occurs in the cytoplasm. Some mature miRNAs with nuclear localisation signals (NLS) are transported back to the nucleus and some remain in the cytoplasm. The functional roles of these miRNAs are seen in both the nucleus and the cytoplasm. In the nucleus, miRNAs regulate gene expression by binding to the targeted promoter sequences and affect either the transcriptional gene silencing (TGS) or transcriptional gene activation (TGA). In the cytoplasm, targeted mRNAs are translationally repressed or cleaved based on the complementarity between the two sequences at the seed region of miRNA and mRNA. The selective transport of mature miRNAs to the nucleus follows the classical nuclear import mechanism. The classical nuclea...
Indian Journal of Biochemistry Biophysics, Feb 1, 2011
Bacterial organophosphate hydrolases (OPH) have been shown to hydrolyze structurally diverse grou... more Bacterial organophosphate hydrolases (OPH) have been shown to hydrolyze structurally diverse group of organophosphate (OP) compounds and nerve agents. Due to broad substrate range and unusual catalytic properties, the OPH has successfully been used to develop eco-friendly strategies for detection and decontamination of OP compounds. However, their usage has failed to gain necessary acceptance, due to short half-life of the enzyme and loss of activity during process development. In the present study, we report a simple procedure for immobilization of OPH on biocompatible gelatin pads. The covalent coupling of OPH using glutaraldehyde spacer has been found to dramatically improve the enzyme stability. There is no apparent loss of OPH activity in OPH-gelatin pads stored at room temperature for more than six months. As revealed by a number of kinetic parameters, the catalytic properties of immobilized enzyme are found to be comparable to the free enzyme. Further, the OPH-gelatin pads effectively eliminate OP insecticide methyl parathion and nerve agent sarin.
In this report we have used gold nanoparticles (AuNPs) to covalently attach an antibody (Ab(1)) u... more In this report we have used gold nanoparticles (AuNPs) to covalently attach an antibody (Ab(1)) using a spacer arm. The AuNPs/Ab(1) modified gold electrode was used for a sandwich electrochemical immunoassay. The detection was done using cyclic voltammetry and impedance measurements using Horse Radish Peroxidase (HRP) as enzyme label on secondary antibody (Ab(2)) and 3,3', 5,5'-tertramethyl benzidine (TMB) as an electroactive dye. The cyclic voltammetric experiments showed three clear peaks at potentials 154 mV, -33 mV and -156 mV. There was an increase in the both anodic and cathodic current values for the peak at potential -33 mV, when H2O2 was added and the other peaks observed at potential 154 mV and -156 mV resulted due to the oxidation and reduction of TMB. The detection limit of this electrode was 2 ng/mL or 10 pg/5 microL of the analyte. The electrochemical impedance spectroscopy studies demonstrate that the formation of antigen-antibody complexes increases the series resistance and thus confirms the assembly on the electrode. This study showed that AuNPs was efficient in preserving the activity and orientation of the antibody and it can form a major platform in many clinical immunoassays.
Http Dx Doi Org 10 1080 07391102 2012 762723, Mar 25, 2013
The Krebs cycle and oxidative phosphorylation are the two most important sets of reactions in a e... more The Krebs cycle and oxidative phosphorylation are the two most important sets of reactions in a eukaryotic cell that meet the major part of the total energy demands of a cell. In this paper, we present a computer simulation of the coupled reactions using open source tools for simulation. We also show that it is possible to model the Krebs cycle with a simple black box with a few inputs and outputs. However, the kinetics of the internal processes has been modelled using numerical tools. We also show that the Krebs cycle and oxidative phosphorylation together can be combined in a similar fashion - a black box with a few inputs and outputs. The Octave script is flexible and customisable for any chosen set-up for this model. In several cases, we had no explicit idea of the underlying reaction mechanism and the rate determining steps involved, and we have used the stoichiometric equations that can be easily changed as and when more detailed information is obtained. The script includes the feedback regulation of the various enzymes of the Krebs cycle. For the electron transport chain, the pH gradient across the membrane is an essential regulator of the kinetics and this has been modelled empirically but fully consistent with experimental results. The initial conditions can be very easily changed and the simulation is potentially very useful in a number of cases of clinical importance.
Electrochemical and fluorometric studies on a few selected phenazine and phenoxazine dyes has bee... more Electrochemical and fluorometric studies on a few selected phenazine and phenoxazine dyes has been carried out in free conditions and when covalently attached to a protein. The dyes have been coupled using the conventional coupling agent carbodiimide (derivative). Neutral Red and Nile Blue A, show significant shifts in their emission peaks to shorter wavelengths on binding to bovine serum albumin
Proceedings of the 2019 6th International Conference on Bioinformatics Research and Applications, 2019
A simulation of the kinetics of the sodium-glucose transporters has been reported using a model w... more A simulation of the kinetics of the sodium-glucose transporters has been reported using a model widely used in literature. However, the various kinetic constants of the transporter have been replaced by 1 (as they are not available in the literature). We have also studied the effect of the membrane potential on glucose transport. The used model is leaky, i.e., sodium transport can take place independently of glucose transport. Although the results can be considered only semi-quantitative, we find that glucose transport is rather energy-intensive, because around 15 sodium ions needed to be transported for each glucose molecule carried inside. However, the process is powerful, in the sense that the final glucose concentration outside can fall almost to zero.
We have explored the region around the splice sites of the human intron and exons from the exon-i... more We have explored the region around the splice sites of the human intron and exons from the exon-intron database (EID) and located a number of short 6-nucleotide and 7-nucleotide sequences that are relatively common in the regions. These short sequences, we expect play an important role in the selection of the appropriate splicing process. We propose that the external signals via short recognition sequences play the deterministic role in the actual splicing process. We have obtained 50 such sequences each from the exon and intron from the beginning and from the ending and noted a number of common features.
Glutathione (L-gamma-glutamyl-L-cysteinyl-L-glycine; GSH) forms a surface monolayer on gold nanop... more Glutathione (L-gamma-glutamyl-L-cysteinyl-L-glycine; GSH) forms a surface monolayer on gold nanoparticles by tethering via sulfur bonds (Au:GSH). In the present study, glucose oxidase (GOx; EC 1.1.3.4) was immobilized by covalent chemical coupling reactions on to Au:GSH nanoparticles and the enzyme coupled nanoparticles formed a stable colloid (stable for several weeks) in water. The immobilized enzyme was investigated for electrochemical characteristics to monitor the FAD (prosthetic group of the GOx) redox potentials. Various concentrations of substrate (glucose) were added to check the oxidation characteristics. It was observed that with increase in substrate concentrations, the oxidation rate increased proportionally with the current. The present study demonstrated that GOx was effectively coupled to the gold nanoparticle (Au:GSH). The coupled nanoparticle system could be used in a potential biosensor application. Similarly, other enzymes (e.g., horseradish peroxidase) could be ...
Toll-like receptors (TLRs) are proteins that play key role in the innate immune system. In the pr... more Toll-like receptors (TLRs) are proteins that play key role in the innate immune system. In the present study, -1000 base pairs upstream are taken from the transcription start site of the various TLR genes (10 known) in human. About 40 microRNAs have been identified that share 12-19 nucleotide sequence similarity with the promoter regions of 10 TLRs. It is proposed that the microRNA performs potential role in identification of promoter sequence and initiation of transcription.
In this report, we have modelled a secondary active co-transporter (symport and antiport), based ... more In this report, we have modelled a secondary active co-transporter (symport and antiport), based on the classical kinetics model. Michaelis-Menten model of enzyme kinetics for a single substrate, single intermediate enzyme catalyzed reaction was proposed more than a hundred years ago. However, no single model for the kinetics of co-transport of molecules across a membrane is available in the literature We have made several simplifying assumptions and have followed the basic Michaelis-Menten approach. The results have been simulated using GNU Octave. The results will be useful in general kinetic simulations and modelling.
We have studied the direct electrochemistry of horseradish peroxidase (HRP) coupled to gold nanop... more We have studied the direct electrochemistry of horseradish peroxidase (HRP) coupled to gold nanoparticles (AuNP) using electrochemical techniques, which provide some insight in the application of biosensors as tools for diagnostics because HRP is widely used in clinical diagnostics kits. AuNP capped with (i) glutathione and (ii) lipoic acid was covalently linked to HRP. The immobilized HRP/AuNP conjugate showed characteristic redox peaks at a gold electrode. It displayed good electrocatalytic response to the reduction of H2O2, with good sensitivity and without any electron mediator. The covalent linking of HRP and AuNP did not affect the activity of the enzyme significantly. The response of the electrode towards the different concentrations of H2O2 showed the characteristics of Michaelis Menten enzyme kinetics with an optimum pH between 7.0 to 8.0. The preparation of the sensor involves single layer of enzyme, which can be carried out efficiently and is also highly reproducible when...
We have studied the presence of long-range correlations in the complete genomes of ten different ... more We have studied the presence of long-range correlations in the complete genomes of ten different dsDNA viruses and Saccharomyces cerevisiae (bakers' yeast) chromosome I. We have also studied the correlation between the distribution of the gene length and the domain of "1/f region" of their genomes. Linear regression analysis was done for the power-law region of these organisms and the slope values obtained were approximately -1, which signify the existence of "1/f noise" in the low and medium (intermediate) frequency regions. This suggests the presence of long-range correlations in their genomes. The presence of 1/f noise in a given frequency interval indicates the existence of a fractal (self-similar) structure in the corresponding range of wavelengths. The results of our study suggest that genes have correlations within themselves, and the correlations appear to be related with the scaling exponent alpha.
SummaryWe have carried out a comparative analysis of the sub-sequences of size six| ten at the (d... more SummaryWe have carried out a comparative analysis of the sub-sequences of size six| ten at the (donor| acceptor) splice site regions of five different organisms. The frequency analysis of the unique sub-sequences at the donor and acceptor regions suggests that the distribution of their occurrence is approximately exponential. We have observed that the number of unique sub-sequences (occurring with different frequencies) at the donor region are less than at the acceptor, suggesting that the sub-sequences at the acceptor region are more variable. The sub-sequences with high percentage of occurrence (uniqueness) are considered to be highly involved in splicing. Our analysis suggests that sub-sequences of length ~6-8 nucleotides (nt) at the splice sites – with six bases in intron (including the two central, conserved dinucleotides) and two bases in exon are optimal for the efficient assembly and binding of the spliceosomal complex during the process of splicing. The score pattern obtain...
SummaryA new look at the transcription start is presented in which we can see transcription facto... more SummaryA new look at the transcription start is presented in which we can see transcription factors binding to both sides of the TSS as an essential requirement. Naturally the factor binding to the downstream region must be removed so that transcription process can continue. The presence of a number of distinct transcription factors also can be used to explain selective activation of various genes. The transcription start site by itself plays only a minor role in the whole process. We also suggest that mutations close to the TSS on the coding side can be fatal even if preserves the codon table.
SummaryMicroRNAs (miRNAs) are short noncoding RNA sequences ~22 nucleotides in length that play a... more SummaryMicroRNAs (miRNAs) are short noncoding RNA sequences ~22 nucleotides in length that play an important role in gene regulation-transcription and translation. The processing of these miRNAs takes place in both the nucleus and the cytoplasm while the final maturation occurs in the cytoplasm. Some mature miRNAs with nuclear localisation signals (NLS) are transported back to the nucleus and some remain in the cytoplasm. The functional roles of these miRNAs are seen in both the nucleus and the cytoplasm. In the nucleus, miRNAs regulate gene expression by binding to the targeted promoter sequences and affect either the transcriptional gene silencing (TGS) or transcriptional gene activation (TGA). In the cytoplasm, targeted mRNAs are translationally repressed or cleaved based on the complementarity between the two sequences at the seed region of miRNA and mRNA. The selective transport of mature miRNAs to the nucleus follows the classical nuclear import mechanism. The classical nuclea...
Indian Journal of Biochemistry Biophysics, Feb 1, 2011
Bacterial organophosphate hydrolases (OPH) have been shown to hydrolyze structurally diverse grou... more Bacterial organophosphate hydrolases (OPH) have been shown to hydrolyze structurally diverse group of organophosphate (OP) compounds and nerve agents. Due to broad substrate range and unusual catalytic properties, the OPH has successfully been used to develop eco-friendly strategies for detection and decontamination of OP compounds. However, their usage has failed to gain necessary acceptance, due to short half-life of the enzyme and loss of activity during process development. In the present study, we report a simple procedure for immobilization of OPH on biocompatible gelatin pads. The covalent coupling of OPH using glutaraldehyde spacer has been found to dramatically improve the enzyme stability. There is no apparent loss of OPH activity in OPH-gelatin pads stored at room temperature for more than six months. As revealed by a number of kinetic parameters, the catalytic properties of immobilized enzyme are found to be comparable to the free enzyme. Further, the OPH-gelatin pads effectively eliminate OP insecticide methyl parathion and nerve agent sarin.
In this report we have used gold nanoparticles (AuNPs) to covalently attach an antibody (Ab(1)) u... more In this report we have used gold nanoparticles (AuNPs) to covalently attach an antibody (Ab(1)) using a spacer arm. The AuNPs/Ab(1) modified gold electrode was used for a sandwich electrochemical immunoassay. The detection was done using cyclic voltammetry and impedance measurements using Horse Radish Peroxidase (HRP) as enzyme label on secondary antibody (Ab(2)) and 3,3', 5,5'-tertramethyl benzidine (TMB) as an electroactive dye. The cyclic voltammetric experiments showed three clear peaks at potentials 154 mV, -33 mV and -156 mV. There was an increase in the both anodic and cathodic current values for the peak at potential -33 mV, when H2O2 was added and the other peaks observed at potential 154 mV and -156 mV resulted due to the oxidation and reduction of TMB. The detection limit of this electrode was 2 ng/mL or 10 pg/5 microL of the analyte. The electrochemical impedance spectroscopy studies demonstrate that the formation of antigen-antibody complexes increases the series resistance and thus confirms the assembly on the electrode. This study showed that AuNPs was efficient in preserving the activity and orientation of the antibody and it can form a major platform in many clinical immunoassays.
Http Dx Doi Org 10 1080 07391102 2012 762723, Mar 25, 2013
The Krebs cycle and oxidative phosphorylation are the two most important sets of reactions in a e... more The Krebs cycle and oxidative phosphorylation are the two most important sets of reactions in a eukaryotic cell that meet the major part of the total energy demands of a cell. In this paper, we present a computer simulation of the coupled reactions using open source tools for simulation. We also show that it is possible to model the Krebs cycle with a simple black box with a few inputs and outputs. However, the kinetics of the internal processes has been modelled using numerical tools. We also show that the Krebs cycle and oxidative phosphorylation together can be combined in a similar fashion - a black box with a few inputs and outputs. The Octave script is flexible and customisable for any chosen set-up for this model. In several cases, we had no explicit idea of the underlying reaction mechanism and the rate determining steps involved, and we have used the stoichiometric equations that can be easily changed as and when more detailed information is obtained. The script includes the feedback regulation of the various enzymes of the Krebs cycle. For the electron transport chain, the pH gradient across the membrane is an essential regulator of the kinetics and this has been modelled empirically but fully consistent with experimental results. The initial conditions can be very easily changed and the simulation is potentially very useful in a number of cases of clinical importance.
Electrochemical and fluorometric studies on a few selected phenazine and phenoxazine dyes has bee... more Electrochemical and fluorometric studies on a few selected phenazine and phenoxazine dyes has been carried out in free conditions and when covalently attached to a protein. The dyes have been coupled using the conventional coupling agent carbodiimide (derivative). Neutral Red and Nile Blue A, show significant shifts in their emission peaks to shorter wavelengths on binding to bovine serum albumin
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Papers by Chanchal Mitra