I have been studying the conformational changes and stability of proteins in different solvents using MolecularDynamic Simulations. Wonder whether changes in activity of enzymes could also be analysed using MDS.
Yes, it is possible to employ molecular dynamics simulations for exploring alternative reaction mechanisms, for quantifying the reaction rate, and for assessing the effect of mutations on the reaction mechanism and the reaction rate: free energy perturbation (FEP), empirical valence bond (EVB), linear response approximation (LRA), and linear interaction energy (LIE), and their combinations.
Hi Vidya
I don't know about your protein. Still you can predict some functions of your protein based on the motion, free energy calculations etc. from MDS. You can see the interactions of substrates of the enzyme. I'll suggest please follow literatures. There are other methods to predict activity. Like I'm attaching few for your references.
https://www.nature.com/articles/srep10804
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2254328/
Yes, it is possible to employ molecular dynamics simulations for exploring alternative reaction mechanisms, for quantifying the reaction rate, and for assessing the effect of mutations on the reaction mechanism and the reaction rate: free energy perturbation (FEP), empirical valence bond (EVB), linear response approximation (LRA), and linear interaction energy (LIE), and their combinations.
If you mean changes in enzymatic activity as a function of, for example, small changes of the substrate structure or enzyme mutations, the probably yes. Activity of an enzyme definitely depends on its structure and dynamics. So, you should choose some quantitative metrics, which is expected to correlate with the enzyme's catalytic activity. These can be affinity to the substrate or co-factor, or net force upon the leaving group, or energy of a transition state. You can then monitor these parameters while simulating your systems of interest.
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