protein footprinting

larry goldstein lgoldstein at UCSD.EDU
Fri Nov 4 17:06:47 EST 1994

their are also methods based on chemical protection, i.e., one assays
modification of cysteines or methionines by NCS (reportedly oxidizes
solvent exposed residues faster than buried residues) in the presence of
some binding protein.  modification is assessed by cleavage with NTCB or
CnBr.  the catch for all of these methods is whether one is looking at
residues buried in a binding interface or residues in a region of protein
that changes conformation upon binding.  anybody manage to distinguish
these two possibilities without a crystal structure?
larry goldstein
>> Dear protein experts,
>> has anyone ever heard of protein -protein footprinting??
>>  pl send me your replies at iyer at
>> thanks a lot
>> N.iyer
>Yes, Michael Carey at UCLA has been working to optimize this technology. 
>The theory is similar to DNAase I footprinting.  Protein is radiolabelled
>with a kinase, and subjected to limited proteolysis while complexed with a
>second, interacting protein.  Regions of the protein involved in direct
>protein-protein contact will be protected from proteolytic clipping.  The
>reaction is run on SDS-PAGE next to a control digest of the radiolabelled
>protein alone, and the two patterns compared.  Michael was able to
>correctly identify the domain of TFIIB that is directly contacted by the
>transcription activation of herpes VP16 protein.  
>Marian Waterman
>Microbiology and Molecular Genetics
>UC Irvine
>mlwaterm at

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