RE: [ccp4bb]: B factors

["Salam Al-Karadaghi" <salam.al-karadaghi@mbfys.lu.se>]

***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***


Sorry, I missed the beginning of this discussion, may be somebody has
already mentioned this paper:

Halle, B.
Flexibility and packing in proteins
  PNAS 2002 99: 1274-1279;

The basic idea is that B-factors reflect packing within the protein and
nothing else. I include here the abstract of the paper:

Structural flexibility is an essential attribute, without which few proteins
could carry out their biological functions. Much information about protein
flexibility has come from x-ray crystallography, in the form of atomic
mean-square displacements (AMSDs) or B factors. Profiles showing the AMSD
variation along the polypeptide chain are usually interpreted in dynamical
terms but are ultimately governed by the local features of a highly complex
energy landscape. Here, we bypass this complexity by showing that the AMSD
profile is essentially determined by spatial variations in local packing
density. On the basis of elementary statistical mechanics and generic
features of atomic distributions in proteins, we predict a direct inverse
proportionality between the AMSD and the contact density, i.e., the number
of noncovalent neighbor atoms within a local region of ~1.5 nm3 volume.
Testing this local density model against a set of high-quality crystal
structures of 38 nonhomologous proteins, we find that it accurately and
consistently reproduces the prominent peaks in the AMSD profile and even
captures minor features, such as the periodic AMSD variation within
helices. The predicted rigidifying effect of crystal contacts also agrees
with experimental data. With regard to accuracy and computational
efficiency, the model is clearly superior to its predecessors. The
quantitative link between flexibility and packing density found here implies
that AMSDs provide little independent information beyond that contained in
the mean atomic coordinates.

Salam