Untitled

Abstract

Residual dipolar couplings provide significant structural information for proteins in the solution state, which makes them attractive for the rapid determination of protein structures. While dipolar couplings contain inherent structural ambiguities, these can be reduced via an overlap similarity measure that insists that protein fragments assigned to overlapping regions of the sequence must have self-consistent structures. This allows us to determine a backbone fold (including the correct Calpha-Cbeta bond orientations) using only residual dipolar coupling data from one ordering medium. The resulting backbone structures are of sufficient quality to allow for modeling of sidechain rotamer states using a rotamer prediction algorithm and a force field employing the Surface Generalized Born continuum solvation model. We demonstrate the applicability of the method using experimental data for ubiquitin. These results illustrate the synergies that are possible between protein structural database and molecular modeling methods and NMR spectroscopy, and we expect that the further development of these methods will lead to the extraction of high resolution structural information from minimal NMR data.

Determination of regulatory phosphorylation sites in nanogram amounts of a synthetic fragment of ZAP‐70 using microprobe NMR and on‐line coupled capillary HPLC–NMR

“…5 and provides H-C correlations via 1 J CH for the assignment of the 13 C signals via the known 1 H assignments. It is important to point out a construction feature of the microprobe that effects 13 C measurements. The copper detection coil is surrounded by a fluid that is similar to the susceptibility of the copper in order to decrease field inhomogeneities.…”

“…This fluid, FC-43, shows resonance signals between 80 and 115 ppm. Therefore, this range of the 13 C chemical shifts is not available for direct observation, but the limitation is irrelevant for the current studies since the peptides of interest do not have 13 C resonances in the inaccessible range. The resolved 1 H signals for the methyl groups L(υ a , L(υ b , and T( correlate with resolved 13 C chemical shifts, while the three alanine methyl groups resolved in 1 H could not be resolved in 13 C.…”

“…11 Thus, NMR is widely used for determining peptide and protein structures, 12 and one of the principle steps is the sequential assignment of side chain proton resonances. 13 This task is considerably more difficult and time consuming than the sequential assignment of chemical shifts for H˛and NH protons along the peptide backbone, for which relatively robust automated methods already exist. The secondary backbone structure is normally elucidated from the pattern of nuclear Overhauser effects, from vicinal coupling constants and from observation of slowly exchanging amino hydrogens.…”

Wie verlässlich sind aktuelle Docking‐Ansätze für strukturbasiertes Wirkstoffdesign? – Fallstudie zur Aldose‐Reduktase

“…Die dargestellten Ergebnisse wurden mit der 1us0-Struktur erhalten. Glide wurde im "Induced-Fit-Docking"-Modus verwendet, das Seitenkettenflexibilität unter Verwendung von Prime 1.5 [17] berück-sichtigt. Der Glide-SP-Docking-Modus wurde für ein initiales Docking verwendet, wogegen das XP-Scoringschema für die finalen DockingSchritte genutzt wurde.…”

How Reliable Are Current Docking Approaches for Structure‐Based Drug Design? Lessons from Aldose Reductase

“…The illustrated docking positions were obtained with the 1us0 structure. Glide was used in the "induced-fit docking" mode, [15] which allows for side-chain flexibility by using Prime 1.5 [17] for side-chain modeling. The Glide SP docking mode was applied during initial docking, whereas the XP scoring scheme was used for the final docking steps.…”