of a protein and the
> surrounding proteins are considered in the calculation?
>
> I hope not too disturbing you.
>
> Danilo
>
> On Thu, 9 Aug 2012 10:05:19 -0400, "Dr. Lorenzo Finci"
> wrote:
> > Danilo,
> >
> > The protein cavity can be ana
Danilo,
The protein cavity can be analyzed utilizing the program Voidoo ( Kleywegt GJ,
1994). This program uses an atomic-flattening algorithm based on a
3-dimensional grid to locate and delineate different cavities. A Van Der Waals
cavity can further be generated with a probe radius with a co
Dear Colleagues,
I have a question for all of you bioinformatics oriented structural biologists:
How do I predict the sites of protein-protein interactions between two
receptors that have been proven to interact biochemically but lack specific
details regarding proximity. This is not a straigh
Dr. Lorenzo Finci wrote:
Anita, In terms of the basics:Thermodynamic stability of a protein is related
to Gibbs Free Energy of unfolding. The Gibbs Free Energy is made of
temperature, enthalpy and entropy (Delta G = Delta H - T Delta S). At Delta G
equivalent to zero, the concentration of folded protein is equivalent
Jan,
I agree that the DTNB assay (Ellman's Reagent) can be used to quantify exposed
Cysteines. Alternatively, you could do site directed mutagenesis and mutate
significant amino acids responsible for the conformational change from the open
to the closed state, with hopes to lock the protein in
