Molecular dynamics investigation of the ionic liquid/enzyme interface: application to engineering enzyme surface charge.

Molecular simulations of the enzymes Candida rugosa lipase and Bos taurus α-chymotrypsin in aqueous ionic liquids 1-butyl-3-methylimidazolium chloride and 1-ethyl-3-methylimidazolium ethyl sulfate were used to study the change in enzyme-solvent interactions induced by modification of the enzyme surface charge. The enzymes were altered by randomly mutating lysine surface residues to glutamate, effectively decreasing the net surface charge by two for each mutation. These mutations resemble succinylation of the enzyme by chemical modification, which has been shown to enhance the stability of both enzymes in ILs.

Structural effects of methionine oxidation on isolated subdomains of human fibrin D and αC regions.

Oxidation of key methionine residues on fibrin leads to altered fibrin polymerization producing severely altered fibrin gel structure and function. This is important because fibrinogen and its modification by oxidative stress have been implicated as key contributors to both pathological thrombotic and hemorrhagic diseases ranging from cardiovascular thrombosis to the acute coagulopathy of trauma. However, how oxidation leads to altered fibrin polymerization remains poorly understood at the molecular level.

Structural and dynamic features of Candida rugosa lipase 1 in water, octane, toluene, and ionic liquids BMIM-PF6 and BMIM-NO3.

Ionic liquids (ILs) and organic chemicals can be used as solvents in biochemical reactions to influence the structural and dynamic features of the enzyme, sometimes detrimentally. In this work we report the results for molecular dynamics simulations of Candida rugosa lipase (CRL) in ILs BMIM-PF6 and BMIM-NO3, as well as organic solvents toluene and octane in an effort to explore the role of solvent on the structure and dynamics of an enzyme known to be active in many nonaqueous media. Simulations of CRL in water were also included for comparison, bringing the aggregate simulation time to over 2.

A novel approach to high accuracy of video-based microrheology.

Video-based particle tracking monitors the microscopic movement of labeled biomolecules and fluorescent probes within a complex cellular environment. Information gained from this technique enables us to extract the dynamic behavior of biomolecules and the local mechanical properties inside the cell from a tracked particle's mean-square displacement (MSD). However, MSD measurements are highly susceptible to static error introduced by noise in the image acquisition process that leads to an incorrect positioning of the particle.