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Simulation of the Ligand-leaving Process of the Human Heat Shock Protein by Yi-Xiao Hu; Jun-wen Fei; Li-Hua Bie; Jun Gao is a Chemistry article available to read on EtoBox.

What is Simulation of the Ligand-leaving Process of the Human Heat Shock Protein about?

The human heat shock protein plays a critical role in various diseases and is an important target for pharmacological modulation. Simulation of conformational changes and free energy profiles of the human heat shock protein derived by the ligand-leaving process is a challenging issue. In this work, steered molecular dynamics simulation was adopted to simulate the ligand-leaving process. Two composite systems of heat shock protein NHSP90 and small molecules 6FJ and 6G7 are selected as research objects. The free energy during the leaving of ligand small molecules is calculated using conventional molecular dynamics simulation, steered molecular dynamics simulation (SMD), and the umbrella sampling method. We found that the a slower pulling velocity (0.001 nm ns À1 ) will result in 2.19 kcal mol À1 , and the umbrella sampling method gives a value of 3.26 kcal mol À1 for the free energy difference for the two systems, which reasonably agrees with experimental results. A faster-pulling velocity (0.01 nm ns À1 ) leads to a large overestimation of free energy. At the same time, the conformational analysis indicated that the faster pulling velocity may lead to the conformational change of NH

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Author

Yi-Xiao Hu; Jun-wen Fei; Li-Hua Bie; Jun Gao

Publisher

Royal Society of Chemistry (RSC)

Published

2023

Language

EN

Field

Chemistry (Physical Sciences)