Temperature factor analysis of outer membrane beta-stranded porins

component of the biophysical efforts put forth to understand protein
structure and function, due to the diversity and complexity of their
structure. Outer membrane proteins form a diverse and complex set of
proteins. Of these, porins that allow passage of molecules across the
membrane interface have been analyzed here from a biophysical and
structural perspective. The objective of this study is to analyze the
structural organization of porins using atomic temperature factor as a
parameter. Generally atomic temperature factors of molecules from crystal
structures indicate the degree of mobility or disorder seen in the crystal
structure. As good crystal structures have lesser possibilities of errors
so there is lesser chance that errors are playing roles in temperature
factors. Structures of six porins (Four 16-stranded beta barrel porins and
two 8-stranded beta barrel porins) were taken from the PDB for the
analysis based on resolution and R-factor. Programs and scripts were
written for extracting the temperature factors for the beta strands, loops
and turns so that the analysis could be done for different atom-types and
residue-types. The residue distribution and mobility distribution was
found to be characteristic of each of the porins. The mobility and residue
distribution amongst the secondary structural elements were found to
follow the level of homology at the sequence and structural level. The
loops that had defined functional roles in structural terms were found to
have lower temperature factors than the other loops. The turn regions that
are thought to face the periplasmic region in the cell, showed higher
temperature factors. For both the 16 stranded and the 8-stranded barrels
it was found one part of the barrel (the lower wall or 'inner' wall
comprising the trimer interface in the case of the 16-stranded barrels)
was more rigid and the other half of the barrel (the higher or 'outer'
wall) showed more mobility as seen from the temperature factors. This
seems to be an intrinsic structural component of the beta barrels.