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Publications (14)
The use of enzymes in non-aqueous solvents expands the use of biocatalysts to hydrophobic substrates, with the ability to tune selectivity of reactions through solvent selection. Non-aqueous enzymology also allows for fundamental studies on the role of water and other solvents in enzyme structure, dynamics, and function. Molecular dynamics simulati...
The enzyme Candida Antarctica lipase B (CALB) serves here as a model for understanding connections among hydration layer dynamics, solvation shell structure, and protein surface structure. The structure and dynamics of water molecules in the hydration layer were characterized for regions of the CALB surface, divided around each α-helix, β-sheet, an...
Solvation is critical for protein structural dynamics. Spectroscopic studies have indicated relationships between protein and solvent dynamics, and rates of gas binding to heme proteins in aqueous solution were previously observed to depend inversely on solution viscosity. In this work, the solvent-compatible enzyme Candida antarctica lipase B, whi...
Protein dynamics is strongly influenced by its surrounding environment and physiological conditions. Here we employ broad-band megahertz-to-terahertz spectroscopy to explore the dynamics of water and myoglobin protein on an extended time-scale from femto- to nanosecond. The dielectric spectra reveal
several relaxations corresponding to orientationa...
This study is focused on the SARS-CoV-2 virus by in silico screening of phytochemicals contained in ‘Paspanguwa’ water extract, targeting ACE2 receptors using molecular docking. Phytochemicals of the five herbal ingredients contained in ‘Paspanguwa’ were extracted into water and were identified based on the literature reviews. Ligands geometries we...
Chronic kidney disease of unknown etiology (CKDu) has been recognized as a global non-communicable health issue. There are many proposed risk factors for CKDu and the exact reason is yet to be discovered. Understanding the inhibition or manipulation of vital renal enzymes by pesticides can play a key role in understanding the link between CKDu and...
The solvation layer surrounding a protein is clearly an intrinsic part of protein structure-dynamics-function, and our understanding of how hydration dynamics influence protein function is emerging. We have recently reported simulations indicating a correlation between regional hydration dynamics and the structure of the solvation layer around diff...
Fluorine NMR spectroscopy has diverse applications, including characterization of chemical reaction mechanisms, protein structure-function studies, and solid-state NMR characterization of crystalline, amorphous, and soft materials. Computational methods have aided in assigning and interpreting chemical shifts, with wide use in solid-state NMR spect...
Questions
Question (1)
I used GROMACS to use solvent accessible surface area. My command was g_sas -f run.xtc -s ions.gro -o -or. At the beginning of the calculation I saw a message saying that all the atoms of my protein were classified as hydrophobic (it cannot be). At the end of calculation, looking at the .xvg file with xmgrace -nxy, I saw total SASA is hydrophobic SASA, whereas the hydrophilic area is 0 for all the time. Does anyone have a solution?
