The Amounts of Thermal Vibrations and Static Disorder in Protein X-ray
Crystallographic B-factors
Abstract
Crystallographic B-factors provide direct dynamical information on the
internal mobility of proteins that is closely linked to function, and
are also widely used as a benchmark in assessing elastic network models.
A significant question in the field is: what is the exact amount of
thermal vibrations in protein crystallographic B-factors? This work sets
out to answer this question. First, we carry out a thorough,
statistically sound analysis of crystallographic B-factors of over
10,000 structures. Second, by employing a highly accurate all-atom model
with the well-known CHARMM force field, we obtain computationally the
magnitudes of thermal vibrations of nearly 1,000 structures. Our key
findings are: (i) the magnitude of thermal vibrations, surprisingly, is
nearly protein-independent, as a corollary to the universality in
vibrational spectra of globular proteins established earlier; (ii) the
magnitude of thermal vibrations is small, less than 0.1
Å2 at 100 K; (iii) the percentage of thermal
vibrations in B-factors is the lowest at low resolution and low
temperature (<10%) but increases to as high as 60% for
structures determined at high resolution and at room temperature. The
significance of this work is that it provides for the first time, using
an extremely large dataset, a thorough analysis of B-factors and their
thermal and static disorder components. The results clearly demonstrate
that structures determined at high resolution and at room temperature
have the richest dynamics information. Since such structures are
relatively rare in the PDB database, the work naturally calls for more
such structures to be determined experimentally.