Conformational analysis of protein structures derived from NMR data

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 ϕ, Ψ, and χ 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 ϕ angles, α‐helix ϕ, Ψ angles, ω angles, and C_α chirality. The more lightly restrained torsion angles do show increasead clustering as the number of overall experimental observations increases. ϕ, Ψ, and χ₁ 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 Å. 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 heteronumclear 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.