Increased Reliability of Nuclear Magnetic Resonance Protein Structures by Consensus Structure Bundles

SummaryNuclear magnetic resonance (NMR) structures are represented by bundles of conformers calculated from different randomized initial structures using identical experimental input data. The spread among these conformers indicates the precision of the atomic coordinates. However, there is as yet no reliable measure of structural accuracy, i.e., how close NMR conformers are to the “true” structure. Instead, the precision of structure bundles is widely (mis)interpreted as a measure of structural quality. Attempts to increase precision often overestimate accuracy by tight bundles of high precision but much lower accuracy. To overcome this problem, we introduce a protocol for NMR structure determination with the software package CYANA, which produces, like the traditional method, bundles of conformers in agreement with a common set of conformational restraints but with a realistic precision that is, throughout a variety of proteins and NMR data sets, a much better estimate of structural accuracy than the precision of conventional structure bundles

Inclusive Spaces 2.0: Critical spatial thinking und (Medien-)Performanzen

Im Rahmen des partizipatorischen Forschungsprojekts 'Inclusive Spaces 2.0 – Meine Schule, mein Block' wurde durch die Verwendung digitaler Tools sowie einem kreativen Design versucht, eine derart gerahmte Form von 'critical spatial thinking' über ein gemeinsames Forschen zu den Räumen von Schulen und Nachbarschaften zu befördern. Wie im Artikel gezeigt wird, verweisen die im Rahmen des Projekts produzierten Medienperformanzen die Rückgriffe von jungen Personen auf eine solche Denkweise. So werden im empirischen Teil des Beitrags verschiedene Medienperformanzen der in das Projekt involvierten Jugendlichen exemplarisch angeführt, über welche die hierarchische Konstruktion von Räumen thematisiert wurden. Am Ende des Artikels wird das Potenzial von 'critical spatial thinking' sowie die Inklusivität des im Projekt verfolgten medientechnologischen Designs diskutiert

Automated solid-state NMR resonance assignment of protein microcrystals and amyloids

Solid-state NMR is an emerging structure determination technique for crystalline and non-crystalline protein assemblies, e.g., amyloids. Resonance assignment constitutes the first and often very time-consuming step to a structure. We present ssFLYA, a generally applicable algorithm for automatic assignment of protein solid-state NMR spectra. Application to microcrystals of ubiquitin and the Ure2 prion C-terminal domain, as well as amyloids of HET-s(218-289) and α-synuclein yielded 88-97% correctness for the backbone and side-chain assignments that are classified as self-consistent by the algorithm, and 77-90% correctness if also assignments classified as tentative by the algorithm are include

Host-switching by a vertically transmitted rhabdovirus in Drosophila

A diverse range of endosymbionts are found within the cells of animals. As these endosymbionts are normally vertically transmitted, we might expect their evolutionary history to be dominated by host-fidelity and cospeciation with the host. However, studies of bacterial endosymbionts have shown that while this is true for some mutualists, parasites often move horizontally between host lineages over evolutionary timescales. For the first time, to our knowledge, we have investigated whether this is also the case for vertically transmitted viruses. Here, we describe four new sigma viruses, a group of vertically transmitted rhabdoviruses previously known in Drosophila. Using sequence data from these new viruses, and the previously described sigma viruses, we show that they have switched between hosts during their evolutionary history. Our results suggest that sigma virus infections may be short-lived in a given host lineage, so that their long-term persistence relies on rare horizontal transmission events between hosts

The maximum standardized uptake value in patients with recurrent or persistent prostate cancer after radical prostatectomy and PSMA-PET-guided salvage radiotherapy-a multicenter retrospective analysis

Purpose This study aims to evaluate the association of the maximum standardized uptake value (SUVmax) in positron-emission tomography targeting prostate-specific membrane antigen (PSMA-PET) prior to salvage radiotherapy (sRT) on biochemical recurrence free survival (BRFS) in a large multicenter cohort.Methods Patients who underwent (68) Ga-PSMA11-PET prior to sRT were enrolled in four high-volume centers in this retrospective multicenter study. Only patients with PET-positive local recurrence (LR) and/or nodal recurrence (NR) within the pelvis were included. Patients were treated with intensity-modulated-sRT to the prostatic fossa and elective lymphatics in case of nodal disease. Dose escalation was delivered to PET-positive LR and NR. Androgen deprivation therapy was administered at the discretion of the treating physician. LR and NR were manually delineated and SUVmax was extracted for LR and NR. Cox-regression was performed to analyze the impact of clinical parameters and the SUVmax-derived values on BRFS.Results Two hundred thirty-five patients with a median follow-up (FU) of 24 months were included in the final cohort. Two-year and 4-year BRFS for all patients were 68% and 56%. The presence of LR was associated with favorable BRFS (p = 0.016). Presence of NR was associated with unfavorable BRFS (p = 0.007). While there was a trend for SUVmax values >= median (p = 0.071), SUVmax values >= 75% quartile in LR were significantly associated with unfavorable BRFS (p = 0.022, HR: 2.1, 95%CI 1.1-4.6). SUVmax value in NR was not significantly associated with BRFS. SUVmax in LR stayed significant in multivariate analysis (p = 0.030). Sensitivity analysis with patients for who had a FU of > 12 months (n = 197) confirmed these results.Conclusion The non-invasive biomarker SUVmax can prognosticate outcome in patients undergoing sRT and recurrence confined to the prostatic fossa in PSMA-PET. Its addition might contribute to improve risk stratification of patients with recurrent PCa and to guide personalized treatment decisions in terms of treatment intensification or de-intensification. This article is part of the Topical Collection on Oncology-Genitourinary

Methods for automated structure determination by NMR spectroscopy

The knowledge of three-dimensional structures of biomolecules is fundamental for the understanding of their function. Nuclear magnetic resonance (NMR) spectroscopy represents besides X-ray crystallography one of the two most widely used techniques to study macromolecules at atomic resolution. Its application has long been a laborious task that could take months and required the expertise of an experienced scientist, however, owing to the tremendous effort that has been put into the development of respective computer algorithms, structure determination by NMR spectroscopy of small- to medium sized proteins is nowadays routinely performed. CYANA is one widely used software package, which combines the majority of individual steps towards a three-dimensional structure. The most common application of the program, however, restricts to the combined automated NOE assignment and structure calculation based on NOESY peak lists and an existing chemical shift assignment. Completely automated structure determination starting from NMR spectra is to date technically possible with CYANA, however, not yet routinely applied. In order to achieve this long-term goal, the individual steps need to become more robust with regard to data imperfections such as peak overlap, spectral artifacts or a limited amount of NMR data. The work presented in this thesis should be placed within the context of increasing the reliability and improving the accuracy of structures determined by CYANA on the basis of solution- as well as solid-state NMR data. The chapter “Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA” comprises an extensive study on the robustness of the combined automated NOE assignment and structure calculation algorithm based on experimental solution NMR data sets that were modified in multiple ways to mimic different kinds of data imperfections. The results show that the algorithm is remarkably robust with regard to imperfections of the NOESY peak lists and the chemical shift tolerances but susceptible to lacking or erroneous resonance assignments, in particular for nuclei that are involved in many NOESY cross peaks. In the chapter “Peakmatch – A simple and robust tool for peaklist matching” a method to achieve self-consistency of the chemical shift referencing among a set of peak lists is presented. The Peakmatch algorithm matches a set of peak lists to a specified reference peak list, neither of which have to be assigned, by optimizing an assignment-free match-score function. The algorithm has been extensively tested on the basis of experimental NMR data sets of five different proteins. The results show that peak lists from many different types of spectra can be matched reliably as long as they contain at least two corresponding dimensions. NMR structures are represented by bundles of conformers whose spread indicates the precision of the atomic coordinates. However, there is as yet no reliable measure of structural accuracy, i.e. how close NMR conformers are to the “true” structure. Instead, the precision of structure bundles is widely (mis)interpreted as a measure of structural quality. Attempts to increase the precision thus often yield tight structure bundles where the precision overestimates the accuracy. To overcome this problem, the chapter “Increased reliability of NMR protein structures by consensus structure bundles” introduces a new protocol for NMR structure determination with the software package CYANA that produces bundles of conformers with a realistic precision that is throughout a large number of test data sets a much better estimate of the structural accuracy than the precision of conventional structure bundles. Solid-state NMR is a powerful technique to study molecules which are not amenable to either solution NMR or X-ray crystallography. Despite the reporting of individual atomic resolution structures of membrane proteins and amyloid fibrils based on solid-state NMR data, the application is far from routine. One major obstacle that hinders structure determination by solid-state NMR is the overall lower quality of the solid-state NMR spectra. It is therefore necessary to increase the robustness of the computer algorithms in order to improve the results when using lower quality solid-state NMR spectra. The chapter “Structure calculations of the model protein GB1 from solid-state NMR data” presents structure calculations on the basis of a set of two-dimensional solid-state NMR experiments of the model protein GB1. The most important result obtained from these test calculations is that the limitation of structural accuracy can be attributed to inaccurate distance information resulting from the limited correlation between peak intensities and distance, which is especially severe in spin diffusion-based solid-state NMR experiments. The chapter “Full relaxation matrix-based correction of relayed polarization transfer for solid-state NMR structure calculation” therefore introduces a method which corrects experimental peak intensities for spin diffusion in order to improve the distance information from solid-state NMR spectra. The results show that the structural accuracy can be significantly improved when using the corrected distance information, however, strongly dependent on the preliminary structural model that is required as input for the method

Combined automated NOE assignment and structure calculation with CYANA

The automated assignment of NOESY cross peaks has become a fundamental technique for NMR protein structure analysis. A widely used algorithm for this purpose is implemented in the program CYANA. It has been used for a large number of structure determinations of proteins in solution but was so far not described in full detail. In this paper we present a complete description of the CYANA implementation of automated NOESY assignment, which differs extensively from its predecessor CANDID by the use of a consistent probabilistic treatment, and we discuss its performance in the second round of the critical assessment of structure determination by NMR

Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA

The automated assignment of NOESY cross peaks has become a fundamental technique for NMR protein structure analysis. A widely used algorithm for this purpose is implemented in the program CYANA. It has been used for a large number of structure determinations of proteins in solution but a systematic evaluation of its performance has not yet been reported. In this paper we systematically analyze the reliability of combined automated NOESY assignment and structure calculation with CYANA under a variety of conditions on the basis of the experimental NMR data sets of ten proteins. To evaluate the robustness of the algorithm, the original high-quality experimental data sets were modified in different ways to simulate the effect of data imperfections, i.e. incomplete or erroneous chemical shift assignments, missing NOESY cross peaks, inaccurate peak positions, inaccurate peak intensities, lower dimensionality NOESY spectra, and higher tolerances for the matching of chemical shifts and peak positions. The results show that the algorithm is remarkably robust with regard to imperfections of the NOESY peak lists and the chemical shift tolerances but susceptible to lacking or erroneous resonance assignments, in particular for nuclei that are involved in many NOESY cross peaks

Combined automated NOE assignment and structure calculation with CYANA

The automated assignment of NOESY cross peaks has become a fundamental technique for NMR protein structure analysis. A widely used algorithm for this purpose is implemented in the program CYANA. It has been used for a large number of structure determinations of proteins in solution but was so far not described in full detail. In this paper we present a complete description of the CYANA implementation of automated NOESY assignment, which differs extensively from its predecessor CANDID by the use of a consistent probabilistic treatment, and we discuss its performance in the second round of the critical assessment of structure determination by NMR.ISSN:0925-2738ISSN:1573-500

Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA

The automated assignment of NOESY cross peaks has become a fundamental technique for NMR protein structure analysis. A widely used algorithm for this purpose is implemented in the program CYANA. It has been used for a large number of structure determinations of proteins in solution but a systematic evaluation of its performance has not yet been reported. In this paper we systematically analyze the reliability of combined automated NOESY assignment and structure calculation with CYANA under a variety of conditions on the basis of the experimental NMR data sets of ten proteins. To evaluate the robustness of the algorithm, the original high-quality experimental data sets were modified in different ways to simulate the effect of data imperfections, i.e. incomplete or erroneous chemical shift assignments, missing NOESY cross peaks, inaccurate peak positions, inaccurate peak intensities, lower dimensionality NOESY spectra, and higher tolerances for the matching of chemical shifts and peak positions. The results show that the algorithm is remarkably robust with regard to imperfections of the NOESY peak lists and the chemical shift tolerances but susceptible to lacking or erroneous resonance assignments, in particular for nuclei that are involved in many NOESY cross peaks.ISSN:0925-2738ISSN:1573-500