Nearest-neighbour parametrization of DNA single, double and triple mismatches at low sodium concentration
Biophys Chem. 2023 Dec 22;306:107156. doi: 10.1016/j.bpc.2023.107156. Online ahead of print.ABSTRACTDNA mismatches, that is, base pairs different from the canonical AT and CG, are involved in numerous biological processes and can be a problem for technological applications such as PCR amplification. The nearest-neighbour (NN) model is the standard approach for predicting melting temperatures and is used in methods of secondary structure predictions and modelling of hybridization kinetics. However, despite its biological and technological importance, existing NN parameters that include DNA mismatches are incomplete, and tho...
Source: Biophysical Chemistry - December 29, 2023 Category: Chemistry Authors: Erik de Oliveira Martins Gerald Weber Source Type: research

Nearest-neighbour parametrization of DNA single, double and triple mismatches at low sodium concentration
Biophys Chem. 2023 Dec 22;306:107156. doi: 10.1016/j.bpc.2023.107156. Online ahead of print.ABSTRACTDNA mismatches, that is, base pairs different from the canonical AT and CG, are involved in numerous biological processes and can be a problem for technological applications such as PCR amplification. The nearest-neighbour (NN) model is the standard approach for predicting melting temperatures and is used in methods of secondary structure predictions and modelling of hybridization kinetics. However, despite its biological and technological importance, existing NN parameters that include DNA mismatches are incomplete, and tho...
Source: Biophysical Chemistry - December 29, 2023 Category: Chemistry Authors: Erik de Oliveira Martins Gerald Weber Source Type: research

Nearest-neighbour parametrization of DNA single, double and triple mismatches at low sodium concentration
Biophys Chem. 2023 Dec 22;306:107156. doi: 10.1016/j.bpc.2023.107156. Online ahead of print.ABSTRACTDNA mismatches, that is, base pairs different from the canonical AT and CG, are involved in numerous biological processes and can be a problem for technological applications such as PCR amplification. The nearest-neighbour (NN) model is the standard approach for predicting melting temperatures and is used in methods of secondary structure predictions and modelling of hybridization kinetics. However, despite its biological and technological importance, existing NN parameters that include DNA mismatches are incomplete, and tho...
Source: Biophysical Chemistry - December 29, 2023 Category: Chemistry Authors: Erik de Oliveira Martins Gerald Weber Source Type: research

Exploring solubility and energetics: Dissolution of biologically important l-threonine in diverse aqueous organic mixtures across the temperature range of 288.15  K to 308.15 K
Biophys Chem. 2023 Dec 19;306:107154. doi: 10.1016/j.bpc.2023.107154. Online ahead of print.ABSTRACTThis research provides a thorough investigation into the solubility behavior and solution thermodynamics of l-threonine in significant organic solvent systems. The work was done on measuring the actual solubility and subsequently calculating overall transfer solvation free energetics (∆Genergetic0i) and transfer entropies (∆St0i) at a temperature of 298.15 K. These measurements were performed as l-threonine transitioned from water to different water-organic mixed solvents systems. The saturated solubilities of l-threonin...
Source: Biophysical Chemistry - December 24, 2023 Category: Chemistry Authors: Nilam Sing Kalachand Mahali Pratima Mondal Jit Chakraborty A M A Henaish Jahangeer Ahmed Afzal Hussain Sanjay Roy Source Type: research

Exploring solubility and energetics: Dissolution of biologically important l-threonine in diverse aqueous organic mixtures across the temperature range of 288.15  K to 308.15 K
Biophys Chem. 2023 Dec 19;306:107154. doi: 10.1016/j.bpc.2023.107154. Online ahead of print.ABSTRACTThis research provides a thorough investigation into the solubility behavior and solution thermodynamics of l-threonine in significant organic solvent systems. The work was done on measuring the actual solubility and subsequently calculating overall transfer solvation free energetics (∆Genergetic0i) and transfer entropies (∆St0i) at a temperature of 298.15 K. These measurements were performed as l-threonine transitioned from water to different water-organic mixed solvents systems. The saturated solubilities of l-threonin...
Source: Biophysical Chemistry - December 24, 2023 Category: Chemistry Authors: Nilam Sing Kalachand Mahali Pratima Mondal Jit Chakraborty A M A Henaish Jahangeer Ahmed Afzal Hussain Sanjay Roy Source Type: research

Exploring solubility and energetics: Dissolution of biologically important l-threonine in diverse aqueous organic mixtures across the temperature range of 288.15  K to 308.15 K
Biophys Chem. 2023 Dec 19;306:107154. doi: 10.1016/j.bpc.2023.107154. Online ahead of print.ABSTRACTThis research provides a thorough investigation into the solubility behavior and solution thermodynamics of l-threonine in significant organic solvent systems. The work was done on measuring the actual solubility and subsequently calculating overall transfer solvation free energetics (∆Genergetic0i) and transfer entropies (∆St0i) at a temperature of 298.15 K. These measurements were performed as l-threonine transitioned from water to different water-organic mixed solvents systems. The saturated solubilities of l-threonin...
Source: Biophysical Chemistry - December 24, 2023 Category: Chemistry Authors: Nilam Sing Kalachand Mahali Pratima Mondal Jit Chakraborty A M A Henaish Jahangeer Ahmed Afzal Hussain Sanjay Roy Source Type: research

Exploring solubility and energetics: Dissolution of biologically important l-threonine in diverse aqueous organic mixtures across the temperature range of 288.15  K to 308.15 K
Biophys Chem. 2023 Dec 19;306:107154. doi: 10.1016/j.bpc.2023.107154. Online ahead of print.ABSTRACTThis research provides a thorough investigation into the solubility behavior and solution thermodynamics of l-threonine in significant organic solvent systems. The work was done on measuring the actual solubility and subsequently calculating overall transfer solvation free energetics (∆Genergetic0i) and transfer entropies (∆St0i) at a temperature of 298.15 K. These measurements were performed as l-threonine transitioned from water to different water-organic mixed solvents systems. The saturated solubilities of l-threonin...
Source: Biophysical Chemistry - December 24, 2023 Category: Chemistry Authors: Nilam Sing Kalachand Mahali Pratima Mondal Jit Chakraborty A M A Henaish Jahangeer Ahmed Afzal Hussain Sanjay Roy Source Type: research

Exploring solubility and energetics: Dissolution of biologically important l-threonine in diverse aqueous organic mixtures across the temperature range of 288.15  K to 308.15 K
Biophys Chem. 2023 Dec 19;306:107154. doi: 10.1016/j.bpc.2023.107154. Online ahead of print.ABSTRACTThis research provides a thorough investigation into the solubility behavior and solution thermodynamics of l-threonine in significant organic solvent systems. The work was done on measuring the actual solubility and subsequently calculating overall transfer solvation free energetics (∆Genergetic0i) and transfer entropies (∆St0i) at a temperature of 298.15 K. These measurements were performed as l-threonine transitioned from water to different water-organic mixed solvents systems. The saturated solubilities of l-threonin...
Source: Biophysical Chemistry - December 24, 2023 Category: Chemistry Authors: Nilam Sing Kalachand Mahali Pratima Mondal Jit Chakraborty A M A Henaish Jahangeer Ahmed Afzal Hussain Sanjay Roy Source Type: research

Exploring solubility and energetics: Dissolution of biologically important l-threonine in diverse aqueous organic mixtures across the temperature range of 288.15  K to 308.15 K
Biophys Chem. 2023 Dec 19;306:107154. doi: 10.1016/j.bpc.2023.107154. Online ahead of print.ABSTRACTThis research provides a thorough investigation into the solubility behavior and solution thermodynamics of l-threonine in significant organic solvent systems. The work was done on measuring the actual solubility and subsequently calculating overall transfer solvation free energetics (∆Genergetic0i) and transfer entropies (∆St0i) at a temperature of 298.15 K. These measurements were performed as l-threonine transitioned from water to different water-organic mixed solvents systems. The saturated solubilities of l-threonin...
Source: Biophysical Chemistry - December 24, 2023 Category: Chemistry Authors: Nilam Sing Kalachand Mahali Pratima Mondal Jit Chakraborty A M A Henaish Jahangeer Ahmed Afzal Hussain Sanjay Roy Source Type: research

Exploring solubility and energetics: Dissolution of biologically important l-threonine in diverse aqueous organic mixtures across the temperature range of 288.15  K to 308.15 K
Biophys Chem. 2023 Dec 19;306:107154. doi: 10.1016/j.bpc.2023.107154. Online ahead of print.ABSTRACTThis research provides a thorough investigation into the solubility behavior and solution thermodynamics of l-threonine in significant organic solvent systems. The work was done on measuring the actual solubility and subsequently calculating overall transfer solvation free energetics (∆Genergetic0i) and transfer entropies (∆St0i) at a temperature of 298.15 K. These measurements were performed as l-threonine transitioned from water to different water-organic mixed solvents systems. The saturated solubilities of l-threonin...
Source: Biophysical Chemistry - December 24, 2023 Category: Chemistry Authors: Nilam Sing Kalachand Mahali Pratima Mondal Jit Chakraborty A M A Henaish Jahangeer Ahmed Afzal Hussain Sanjay Roy Source Type: research

Interaction mechanism of a cysteine protease inhibitor, odanacatib, with human serum albumin: In vitro and bioinformatics studies
Biophys Chem. 2023 Nov 10;305:107140. doi: 10.1016/j.bpc.2023.107140. Online ahead of print.ABSTRACTOdanacatib (ODN) is a selective cathepsin K inhibitor that acts as an anti-resorptive agent to treat osteoporosis. ODN is also found effective in reducing the effect of severe periodontitis. The interaction between ODN and human serum albumin (HSA) was investigated using spectroscopic, microscopic, and in silico approaches to characterize their binding. The fluorescence intensity of HSA increased upon the addition of increasing concentrations of ODN accompanied by blueshift in the fluorescence spectrum, which suggested hydro...
Source: Biophysical Chemistry - December 20, 2023 Category: Chemistry Authors: Nurul Jannah Mohd Asngari Khairul Azreena Bakar Shevin Rizal Feroz Fathilah Abdul Razak Adyani Azizah Abd Halim Source Type: research

Interaction mechanism of a cysteine protease inhibitor, odanacatib, with human serum albumin: In vitro and bioinformatics studies
Biophys Chem. 2023 Nov 10;305:107140. doi: 10.1016/j.bpc.2023.107140. Online ahead of print.ABSTRACTOdanacatib (ODN) is a selective cathepsin K inhibitor that acts as an anti-resorptive agent to treat osteoporosis. ODN is also found effective in reducing the effect of severe periodontitis. The interaction between ODN and human serum albumin (HSA) was investigated using spectroscopic, microscopic, and in silico approaches to characterize their binding. The fluorescence intensity of HSA increased upon the addition of increasing concentrations of ODN accompanied by blueshift in the fluorescence spectrum, which suggested hydro...
Source: Biophysical Chemistry - December 20, 2023 Category: Chemistry Authors: Nurul Jannah Mohd Asngari Khairul Azreena Bakar Shevin Rizal Feroz Fathilah Abdul Razak Adyani Azizah Abd Halim Source Type: research

Interaction mechanism of a cysteine protease inhibitor, odanacatib, with human serum albumin: In vitro and bioinformatics studies
Biophys Chem. 2023 Nov 10;305:107140. doi: 10.1016/j.bpc.2023.107140. Online ahead of print.ABSTRACTOdanacatib (ODN) is a selective cathepsin K inhibitor that acts as an anti-resorptive agent to treat osteoporosis. ODN is also found effective in reducing the effect of severe periodontitis. The interaction between ODN and human serum albumin (HSA) was investigated using spectroscopic, microscopic, and in silico approaches to characterize their binding. The fluorescence intensity of HSA increased upon the addition of increasing concentrations of ODN accompanied by blueshift in the fluorescence spectrum, which suggested hydro...
Source: Biophysical Chemistry - December 20, 2023 Category: Chemistry Authors: Nurul Jannah Mohd Asngari Khairul Azreena Bakar Shevin Rizal Feroz Fathilah Abdul Razak Adyani Azizah Abd Halim Source Type: research

Interaction mechanism of a cysteine protease inhibitor, odanacatib, with human serum albumin: In vitro and bioinformatics studies
Biophys Chem. 2023 Nov 10;305:107140. doi: 10.1016/j.bpc.2023.107140. Online ahead of print.ABSTRACTOdanacatib (ODN) is a selective cathepsin K inhibitor that acts as an anti-resorptive agent to treat osteoporosis. ODN is also found effective in reducing the effect of severe periodontitis. The interaction between ODN and human serum albumin (HSA) was investigated using spectroscopic, microscopic, and in silico approaches to characterize their binding. The fluorescence intensity of HSA increased upon the addition of increasing concentrations of ODN accompanied by blueshift in the fluorescence spectrum, which suggested hydro...
Source: Biophysical Chemistry - December 20, 2023 Category: Chemistry Authors: Nurul Jannah Mohd Asngari Khairul Azreena Bakar Shevin Rizal Feroz Fathilah Abdul Razak Adyani Azizah Abd Halim Source Type: research

Structure and energetics guide dynamic behaviour in a T  = 3 icosahedral virus capsid
Biophys Chem. 2023 Dec 8;305:107152. doi: 10.1016/j.bpc.2023.107152. Online ahead of print.ABSTRACTAlthough virus capsids appear as rigid, symmetric particles in experimentally determined structures; biochemical studies suggest a significant degree of structural flexibility in the particles. We carried out all-atom simulations on the icosahedral capsid of an insect virus, Flock House Virus, which show intriguing differences in the degree of flexibility of quasi-equivalent capsid subunits consistent with previously described biological behaviour. The flexibility of all the β and γ subunits of the protein and RNA fragments...
Source: Biophysical Chemistry - December 19, 2023 Category: Chemistry Authors: Gourav Shrivastav Subhomoi Borkotoky Debajit Dey Bhumika Singh Nidhi Malhotra Kimi Azad B Jayaram Manish Agarwal Manidipa Banerjee Source Type: research