In sequence from CHIP seq Analysis, it is possible to identify the interaction between the gene and transcription factor. In structural biology,please explain me the steps?
Which transcription factor are you working with? You must have noticed that a large number of transcription factors have long stretches of disordered regions. A good way to probe DNA binding and modulation by transcription factors is through NMR spectroscopy, which will allow you work with these IDRs. Prepare 15N and 13C labelled protein constructs and assign the HSQC pattern. Titrate that with DNA and observe the change in chemical shift for the amino acid residues participating in DNA binding. You could also calculate T1, T2 and NOE for your construct to investigate protein flexibility on a residue-wise basis. Depending on the size of your construct and level of orderness you can also solve the solution state ensemble of structures using NMR.
Do you already know the K-mer target of the transcription factor?
As pointed out by Aditya Jyoti Basak NMR is the way to go for proteins smaller than 35 kDa. Assuming you can express and concentrate the protein to the required amounts.
Alternatively you can try hydrogen-deuterium exchange MS/MS, there you need very little protein in terms of amounts.
Can I use Bioinformatics to model the Gene and transcription factor and try to dock it?
Making a model of your transcription factor and your consensus DNA and then docking it alone would not be enough without any experimental data to validate it.
The association between TF-DNA were already verified using CHIP Seq.
I meant experimental structural data obtained either by NMR or X Ray crystallography. Just only modelling and docking could generate any type of result you want. Alone it is not reliable .
