FLYA

Fully automated structure determination of proteins in solution

Fully automated structure determination of proteins in solution (FLYA) yields, without human intervention, three-dimensional protein structures starting from a set of multidimensional NMR spectra. The core FLYA automated resonance assignment algorithm determines NMR chemical shift assignments on the basis of peak lists from any combination of multidimensional through-bond or through-space NMR experiments for proteins. Backbone and side-chain assignments can be determined. All experimental data are used simultaneously, thereby exploiting optimally the redundancy present in the input peak lists and circumventing potential pitfalls of assignment strategies in which results obtained in a given step remain fixed input data for subsequent steps. Instead of prescribing a specific assignment strategy, the FLYA resonance assignment algorithm requires only experimental peak lists and the primary structure of the protein, from which the peaks expected in a given spectrum can be generated by applying a set of rules, defined in a straightforward way by specifying through-bond or through-space magnetization transfer pathways. The algorithm determines the resonance assignment by finding an optimal mapping between the set of expected peaks that are assigned by definition but have unknown positions and the set of measured peaks in the input peak lists that are initially unassigned but have a known position in the spectrum. The FLYA resonance assignment algorithm thus has the reliability and flexibility to replace most manual and semi-automatic assignment procedures for NMR studies of proteins. Automated chemical shift assignment can be followed by combined automated NOESY assignment and structure calculation. The purely computational FLYA method is suitable for substituting all manual spectra analysis and thus overcomes a main efficiency limitation of the NMR method for protein structure determination.

Availability

• FLYA calculations are carried out with the program CYANA. FLYA is not available as a separate program.

References

FLYA algorithm:

• Schmidt, E. & Güntert, P. A new algorithm for reliable and general NMR resonance assignment. J. Am. Chem. Soc. 134, 12817–12829 (2012)

FLYA applications:

• Schmidt, E., Gath, J., Habenstein, B., Ravotti, F., Székely, K., Huber, M., Buchner, L., Böckmann, A., Meier, B. H. & Güntert, P. Automated solid-state NMR resonance assignment of protein microcrystals and amyloids. J. Biomol. NMR 56, 243–254 (2013)

• Schmidt, E. & Güntert, P. Reliability of exclusively NOESY-based automated resonance assignment and structure determination of proteins. J. Biomol. NMR 57, 193-204 (2013)

• Aeschbacher, T., Schmidt, E., Blatter, M., Maris, C., Duss, O., Allain, F. H.-T., Güntert, P. & Schubert, M. Automated and assisted RNA resonance assignment using NMR chemical shift statistics. Nucl. Acids Res. 41, e172 (2013)

• Krähenbühl, B., El Bakkali, I., Schmidt, E., Güntert, P. & Wider, G. Automated NMR resonance assignment strategy for RNA via the phosphodiester backbone based on high-dimensional through-bond APSY experiments. J. Biomol. NMR 59, 87-93 (2014)

• Schmidt, E., Ikeya, T., Takeda, M., Löhr, F., Buchner, L., Ito, Y., Kainosho, M. & Güntert, P. Automated resonance assignment of the 21 kDa stereo-array isotope labeled thioldisulfide oxidoreductase DsbA. J. Magn. Reson. 249, 88–93 (2014)

• Schmidt, E. & Güntert, P. Automated structure determination from NMR spectra. Meth. Mol. Biol. 1261, 303–329 (2015)

Combined automated NOESY cross peak assignment and structure calculation:

• Güntert, P. & Buchner, L. Combined automated NOE assignment and structure calculation with CYANA. J. Biomol. NMR 62, 453-471 (2015)

• Herrmann, T., Güntert, P. & Wüthrich, K. Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J. Mol. Biol. 319, 209–227 (2002)

Evaluation of combined automated NOESY cross peak assignment and structure calculation:

• Buchner, L. & Güntert, P. Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA. J. Biomol. NMR 62, 81–95 (2015)