These equations demonstrate that it is possible to estimate a drug's free energy of binding, an indirect measurement of drug potency, by running two simulations, one in which the receptor-bound ligand disappears, and one in which the solvated ligand disappears.
It has been suggested that the direct effect of the mutation was on nucleotide binding and that the loss of α-ketoglutarate binding reflected an indirect effect of the mutation (16).
Our findings differ in that we identified two independent means of CHIP binding to LRRK2: an indirect interaction between the TPR domain of CHIP and the ARM domain of LRRK2, likely via Hsp90, and an interaction between the charged domain of CHIP and the ROC domain of LRRK2, which is either direct or indirect via a common adaptor protein.
To assess whether this increase in promoter activity was specific to the MTF-1 binding site or an indirect effect of MTF-1 over-expression, we abolished the MRE binding site in β-Syn −1.1/−0.6 kb by site-directed mutagenesis.
These are fuelled by the lack of reproducibility between the various assays using VWF multimers or collagen binding, which provide an indirect measure of ADAMTS13 (Studt et al, 2003).
Here we identify TCF-4, a transcriptional regulator and β-catenin binding partner as an indirect target of the VDR pathway.
However, this may be due to an indirect effect, such as improved binding of a protein with which MUC7 forms cross-links.
These techniques detect methylation sequences by sequence-specific binding of primers, which is an indirect method and only detects a limited number of methylation sites.
3) Increased p53 binding upon loss of G9a may be an indirect consequence of the defect in enhancer repression, perhaps resulting in the increased enhancer accessibility- did the authors consider looking at chromatin accessibility measurements such as ATAC, DNase or FAIRE?
Thus it will be important to determine the fraction of co-regulated genes whose expression is regulated by direct binding of NR3C1 versus other indirect mechanisms of regulation.
