CASD-NMR 2: robust and accurate unsupervised analysis of raw NOESY spectra and protein structure determination with UNIO

Abstract

UNIO is a comprehensive software suite for protein NMR structure determination that enables full automation of all NMR data analysis steps involved--including signal identification in NMR spectra, sequence-specific backbone and side-chain resonance assignment, NOE assignment and structure calculation. Within the framework of the second round of the community-wide stringent blind NMR structure determination challenge (CASD-NMR 2), we participated in two categories of CASD-NMR 2, namely using either raw NMR spectra or unrefined NOE peak lists as input. A total of 15 resulting NMR structure bundles were submitted for 9 out of 10 blind protein targets. All submitted UNIO structures accurately coincided with the corresponding blind targets as documented by an average backbone root mean-square deviation to the reference proteins of only 1.2 Å. Also, the precision of the UNIO structure bundles was virtually identical to the ensemble of reference structures. By assessing the quality of all UNIO structures submitted to the two categories, we find throughout that only the UNIO-ATNOS/CANDID approach using raw NMR spectra consistently yielded structure bundles of high quality for direct deposition in the Protein Data Bank. In conclusion, the results obtained in CASD-NMR 2 are another vital proof for robust, accurate and unsupervised NMR data analysis by UNIO for real-world applications.

Structure of fully protonated proteins by proton-detected magic-angle spinning NMR

“…Not surprisingly, due to the high quality of the input data, an efficient network-anchored assignment of the contacts (66) resulted in a defined fold of the protein already in the first cycle of the iterative protocol. This is a crucial criterion certifying the reliability of a result in an unsupervised data analysis run (35).…”

“…However, a high deuteration level severely limits observation of side-chain signals, which are essential for the determination of a protein structure at high resolution. The redundancy of information intrinsic to spectra of side-chain protonated proteins, which leads to a mutually supportive network of distance restraints, is also crucial to an unbiased and robust spectral analysis by unsupervised algorithms (33)(34)(35)(36).…”

Modern Technologies of Solution Nuclear Magnetic Resonance Spectroscopy for Three-dimensional Structure Determination of Proteins Open Avenues for Life Scientists

“…Furthermore, recently, integrated NMR software platforms offering systematic and semi-automatic biomolecular structure determination, e.g. PONDEROSA-C/S [16], [18], [126] and UNIO [19], [87], [88], [95], [96], [97], have been developed. Moreover, global fold determination of desired proteins has now become easier owing to the development of programs, e.g.…”

“…Programs for automated NOE assignments and molecular modeling, e.g., CYANA [86], [90], [122], Xplor-NIH [123], AUREMOL (http://www.auremol.de/), critical assessment of automated structure determination of proteins by NMR (CASD-NMR) developed by the e-NMR project (http://haddock.chem.uu.nl/enmr/eNMR-portal.html) [19], [124], [125], PONDEROSA-C/S (http://ponderosa.nmrfam.wisc.edu/) developed by the National Magnetic Resonance Facility at Madison (NMRFAM) (http://www.nmrfam.wisc.edu/software.htm) [16], [18], [126] and UNIO (http://perso.ens-lyon.fr/torsten.herrmann/Herrmann/Software.html) [19], [87], [88], [95], [96], [97], are used for solution structure determination of biomolecules such as proteins and nucleic acids. In this mini-review, we will show an example of the program CYANA, which is used widely for NMR structure determination, to explain the general workflow of protein structure calculation.…”

“…Recent development of software and a number of web-based resources, which reduce the burden of complex NMR data analysis, have contributed to the systematic integration of sophisticated semi-automated NMR platforms for structure determination of biomolecules [15], [16], [17], [18], [19]. Such advances, along with improvements in NMR hardware, have lowered the knowledge barrier to facilitate entry into the field of structural biology by NMR for non-specialists.…”