Microscopic modes and free energies of 3-phosphoinositide-dependent kinase-1(PDK1) binding with celecoxib and other inhibitors

Article Abstract:

An extensive molecular docking and combined molecular dynamics (MD) simulations and molecular mechanics/Poisson-Boltzmann surface area binding free energy calculations are performed on eight representative PDK1 inhibitors to understand the binding effect of PDK1 with celecoxib and its derivatives. Based on the determined most stable binding structures, the calculated binding free energies are all in good agreement with the corresponding experimental data, thus revealing that the biological activity data available for celecoxib and its derivatives can be determined.

Protein kinases, Celecoxib, Phosphoinositides, Chemical properties, Phosphatidylinositols, Report

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Binding constant measurement by hyper-Rayleigh scattering: Bilirubin-human serum albumin binding as a case study

Article Abstract:

A new application of the hyper-Rayleigh scattering technique in determining multiple binding constants of a small molecule like bilirubin to a macromolecule like the protein human serum albumin is demonstrated. Human serum albumin has two binding sites for bilirubin, and the binding constants are measured by carrying out a second harmonic titration of the protein against bilirubin and vice versa.

Rayleigh scattering, Bilirubin

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Protein environment facilitates [O.sub.2] binding in non-heme iron enzyme

Article Abstract:

The binding of dioxygen to a non-heme enzyme which was modeled by using the ONIOM combined quantum mechanical/molecular mechanical (QM/MM) method is reported.

Analysis, Quantum theory, Quantum mechanics, Hemoproteins

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