Browsing by Author "Dahanayake, Jayangika Niroshani"
Now showing items 1-9 of 9
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Analysis of enzyme and solvent dynamics of Candida antarctica lipase B in non-aqueous solvents using molecular dynamics simulations
Dahanayake, Jayangika Niroshani; Mitchell-Koch, Katie R. (American Chemical Society, 2014-08-10)Solvents play a major role in changing biomolecule structure, dynamics and functions. The main objective of this project is to use molecular dynamics simulations to shed light on enzyme-solvent interactions between Candida ... -
Entropy connects water structure and dynamics in protein hydration layer
Dahanayake, Jayangika Niroshani; Mitchell-Koch, Katie R. (Royal Society of Chemistry, 2018-07-03)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 ... -
Evaluating electronic structure methods for accurate calculation of F-19 chemical shifts in fluorinated amino acids
Dahanayake, Jayangika Niroshani; Kasireddy, Chandana; Ellis, Jonathan M.; Hildebrandt, Derek; Hull, Olivia A.; Karnes, Joseph P.; Morlan, Dylan; Mitchell-Koch, Katie R. (Wiley, 2017-11-15)The ability of electronic structure methods (11 density functionals, HF, and MP2 calculations; two basis sets and two solvation models) to accurately calculate the F-19 chemical shifts of 31 structures of fluorinated amino ... -
Heterogeneous solvation shell dynamics around candida antarctica lipase b enzyme using molecular dynamics simulations: relationships with solvent structure, enzyme structure and enzyme dynamics
Dahanayake, Jayangika Niroshani (Wichita State University, 2017-12)Solvent-compatible enzymes (those that function in organic solvents) are an important field of research. Understanding the relationship between solvent dynamics and protein dynamics will improve applications of proteins ... -
How does solvation layer mobility affect protein structural dynamics?
Dahanayake, Jayangika Niroshani; Mitchell-Koch, Katie R. (Frontiers Media S.A., 2018-07-13)Salvation 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 ... -
Kinetics of prepreg epoxy resin curing for aircraft body repair
Dahanayake, Jayangika Niroshani (Wichita State University. Graduate School, 2014-04-25)Curing is the cross-linking of polymer chains, which results in toughening of polymer material and it is widely used in bonded composite repair for aerospace components. The main objective of this project is to analyze ... -
Progress in Our Understanding of 19F Chemical Shifts
Dahanayake, Jayangika Niroshani; Kasireddy, Chandana; Karnes, Joseph P.; Verma, Rajni; Steinert, Ryan M.; Hildebrandt, Derek; Hull, Olivia A.; Ellis, Jonathan M.; Mitchell-Koch, Katie R. (Elsevier, 2018)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 ... -
Protein solvent shell structure provides rapid analysis of hydration dynamics
Dahanayake, Jayangika Niroshani; Shahryari, Elaheh; Roberts, Kirsten M.; Heikes, Micah E.; Kasireddy, Chandana; Mitchell-Koch, Katie R. (American Chemical Society, 2019-03-13)The solvation layer surrounding a protein is clearly an intrinsic part of protein structure-dynamics-function, and our understanding of how the hydration dynamics influences protein function is emerging. We have recently ... -
To keep or not to keep? the question of crystallographic waters for enzyme simulations in organic solvent
Dahanayake, Jayangika Niroshani; Gautam, Devaki N.; Verma, Rajni; Mitchell-Koch, Katie R. (Taylor & Francis Group, 2016)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 ...