Comparison of the accuracy of protein solution structures derived from conventional and network‐edited NOESY data

Abstract

Network-editing experiments are variants of the basic NOESY experiment that allow more accurate direct measurement of interproton distances in macromolecules by defeating specific spin-diffusion pathways. Two network-editing approaches, block-decoupled NOESY and complementary-block-decoupled-NOESY, were applied as three-dimensional, heteronuclear-edited experiments to distance measurement in a small protein, turkey ovomucoid third domain (OMTKY3). Two-hundred and twelve of the original 655 distance constraints observed in this molecule (Krezel AM et al., 1994, JMol Biol242:203-214) were improved by their replacement by distances derived from networkedited spectra, and distance geometryhimulated annealing solution structure calculations were performed from both the unimproved and improved distance sets. The resulting two families of structures were found to differ significantly, the most important differences being the hinge angle of a 0-turn and an expansion of the sampled conformation space in the region of the reactive-site loop. The structures calculated from network-editing data are interpreted as a more accurate model of the solution conformation of OMTKY3.Keywords: BD-NOESY-HSQC; CBD-NOESY-HSQC; cross relaxation; network editing; "N NMR assignments; NOESY; nuclear magnetic resonance; protein structure; spin diffusionThe accuracy and reliability of structural models derived by NMR is a key issue in the methodology of structure determination. In the context of a drug-development study, for example, a relatively minor structural distortion can lead to a tremendous amount of wasted effort on the part of synthetic chemists. NMR data directly determine only short-range constraints, and those with relatively low precision, but yield those constraints in great abundance such that converged and apparently highly precise structures are obtained. Therefore, the extent to which the accuracy and precision of distance measurements will affect the quality of derived structural models has been a source of controversy for some time.Two different approaches can be taken in improving the accuracy of distance measurements derived from NMR data. One approach makes use of a model structure in the analysis of the full relaxation matrix (Boelens et al

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“…The chimeras included SjAPI-M1 from the Ascaris -type peptide AMCI-1 [18], SjAPI-M2 from the Ascaris -type peptide ATI [27], SjAPI-M3 from the Ascaris -type peptide C/E-1 [16], SjAPI-M4 from the Kazal-type peptide OMTKY3 [31], SjAPI-M5 from the potato I family peptide CMTI-V [32], and SjAPI-M6 from the potato I family peptide CI-2 [33] (Fig. 7A).…”

Underuse of colorectal cancer screening in a cohort of medicare beneficiaries

“…Six initial conformations were prepared for PHREM and PHMD simulations in each pH region. These were obtained by equilibrating the Model 1 structure in the 1OMT PDB file86 for 100 ps at 300 K with different initial velocities. Additional simulation details were as described in “Materials and Methods” section.…”

Reproducing Basic pKa Values for Turkey Ovomucoid Third Domain Using a Polarizable Force Field

“…OMTKY3 is a 56-residue protein solved by both x-ray crystallography and NMR28,29. The protein has five acidic residues (Asp7, Glu10, Glu19, Asp27, and Glu43) and six basic residues (Lys13, Arg21, Lys29, Lys34, His52, and Lys55).…”