Protein structure calculation with data imputation: the use of substitute restraints

Abstract

The amount of experimental restraints e.g., NOEs is often too small for calculating high quality threedimensional structures by restrained molecular dynamics. Considering this as a typical missing value problem we propose here a model based data imputation technique that should lead to an improved estimation of the correct structure. The novel automated method implemented in AUREMOL makes a more efficient use of the experimental information to obtain NMR structures with higher accuracy. It creates a large set of substitute restraints that are used either alone or together with the experimental restraints. The new approach was successfully tested on three examples: firstly, the Ras-binding domain of Byr2 from Schizosaccharomyces pombe, the mutant HPr (H15A) from Staphylococcus aureus, and a X-ray structure of human ubiquitin. In all three examples, the quality of the resulting final bundles was improved considerably by the use of additional substitute restraints, as assessed quantitatively by the calculation of RMSD values to the ''true'' structure and NMR R-factors directly calculated from the original NOESY spectra or the published diffraction data.

Structural transitions in full-length human prion protein detected by xenon as probe and spin labeling of the N-terminal domain

“…An upper distance limit for the xenon-proton distances of 0.54 nm and a lower distance limit of 0.34 nm was selected. Modeling of the (90–230) Q212 fragment of hu PrP was done using the substitute restraint method as described by Cano et al 65. along with the pseudo distance restraints generated for Xenon atoms positioned into the cavities.…”

PSCD Domains of Pleuralin-1 from the Diatom Cylindrotheca fusiformis : NMR Structures and Interactions with Other Biosilica-Associated Proteins

“…The PERMOL routine (Mö glich et al, 2005) was used to obtain 1,069 additional substitute restraints (Table S2) from the simulated structure of the PSCD4 domain. The generation of the substitute restraints (Cano et al, 2009) is described in Experimental Procedures and leads to the definition of 132 dihedral angles, 13 hydrogen bonds, and 919 NOE distances (Table S2). Figure 3 shows the lowest-energy structure of the PSCD4 domain (from E16 to P102) as yielded from a combination of experimental and substitute restraints.…”

“…Distance restraints for degenerated resonances were corrected according to Kalbitzer and Hengstenberg (1993). Additional substitute restraints (Cano et al, 2009) were generated by PERMOL (Mö glich et al, 2005).…”

“…The 3D structures were determined using the standard simulated annealing protocol of the CNS 1.21 program for extended-strand starting structures (Brü nger and Nilges, 1998). The structures were refined according to the protocol proposed by Cano et al (2009), using substitute restraints; finally, the structures were refined in explicit water (Linge et al, 2003).…”

“…The ten lowest-energy structures were refined in explicit water using the CNS protocol re_h2o.inp. From these structures additional substitute restraints were created (Cano et al, 2009), and the protocol was repeated including the experimental restraints and the substitute restraints.…”