Indeed! If the B factors are rather large compared to the globular protein
core (assuming there is a globular core being that the protein
crystallized), one can make the assumption, especially within a loop
region, that this is an indirect measurement of flexibility. However,
as Jürgen pointed out, it IS imperative to take a close look at the crystal
packing in the unit cell. For instance, if the loop region were to make
hydrogen bond or electrostatic interactions with a symmetry mate, you must
be careful in your conclusion.
Might I recommend a paper that uses B factors as a direct correlation with
heteronuclear NOEs to compare two almost identical structures (both of
which contain disordered regions?
Wang, Y., Fisher, J.C., Assem, M., Matthew, R., Sublet, J, Xiao, L.,
Roussel, M.F., and Kriwacki, R.W. (2011). Structural basis for the diverse
cell cycle regulatory functions of the intrinsically disordered protein, p21
Cip1. Nature Chemical Biology, 7, 214-221.
You can always confirm disordered or flexible loop segments using limited
proteolysis.
Best,
John
John Fisher, M.D./PhD
St. Jude Children's Research Hospital
Department of Structural Biology
Department of Oncology
On Sun, Mar 3, 2013 at 3:52 PM, Bosch, Juergen jubo...@jhsph.edu wrote:
yes - but keep in mind your protein is in the context of the crystal
lattice, so flexible regions in solution are likely to be stabilized in the
crystal lattice. So if you color by B also look at the symmetry mates.
And you should also submit both structures to the TLSMD server and look at
those results.
http://skuld.bmsc.washington.edu/~tlsmd/
Jürgen
On Mar 3, 2013, at 4:35 PM, Faisal Tarique wrote:
Dear all
Can B factor in the crystal structure be the criteria to look into the
flexibility of a region or domain.? Also if two structures are at
different resolutions.
Faisal
--
..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab: +1-410-614-4894
Fax: +1-410-955-2926
http://lupo.jhsph.edu
