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 <[email protected]> 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 >
