Department of Biochemistry and Molecular Biology, University College, London, England.
Proteins 17: 232-51 (1993)
Abstract
A study is presented of the conformational characteristics of
NMR-derived protein structures in the Protein Data Bank compared to
X-ray structures. Both ensemble and energy-minimized average structures
are analyzed. We have addressed the problem using the methods developed
for crystal structures by examining the distribution of phi, psi, and
chi angles as indicators of global conformational irregularity. All
these features in NMR structures occur to varying degrees in multiple
conformational states. Some measures of local geometry are very tightly
constrained by the methods used to generate the structure, e.g., proline
phi angles, alpha-helix phi,psi angles, omega angles, and C alpha
chirality. The more lightly restrained torsion angles do show increased
clustering as the number of overall experimental observations increases.
phi, psi, and chi 1 angle conformational heterogeneity is strongly
correlated with accessibility but shows additional differences which
reflect the differing number of observations possible in NMR for the
various side chains (e.g., many for Trp, few for Ser). In general, we
find that the core is defined to a notional resolution of 2.0 to 2.3 A.
Of real interest is the behavior of surface residues and in particular
the side chains where multiple rotameric states in different structures
can vary from 10% to 88%. Later generation structures show a much
tighter definition which correlates with increasing use of J-coupling
information, stereospecific assignments, and heteronuclear techniques. A
suite of programs is being developed to address the special needs of
NMR-derived structures which will take into account the existence of
increased mobility in solution.
Mesh Headings
Unique Identifier: 94097785
Chemical Identifiers (Names)