Atomic force microscopy is one of the experimental techniques that helps to decipher the free energy of a protein along a specific pulling coordinate. This method is especially useful when trying to find the conformational changes in proteins as a result of mechanical forces. A similar stretching can be performed in silico using a Steered Molecular Dynamics (SMD). The major problem with the implementation of SMD is that the time scale of the pull is shorter by a few orders of magnitude than in an AFM experiment. This fast numerical pull often over estimates the energetics.In this work we describe an approach that reduces the computational effort of an SMD numerical experiment in explicit water.We used this method to perform a high accuracy SMD experiment on an IG27 domain of titin. We were able to recover the experimental results and obtained new insights about the pathway.

Optimization of steered molecular dynamics for the stretching of large proteins

248th National Meeting (2014)

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