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Abstract Multidimensional NMR spectra are the basis for studying proteins by NMR spectroscopy and crucial for the development and evaluation of methods for biomolecular NMR data analysis. Nevertheless, in contrast to derived data such as chemical shift assignments in the BMRB and protein structures in the PDB databases, this primary data is in general not publicly archived. To change this unsatisfactory situation, we present a standardized set of solution NMR data comprising 1329 2–4-dimensional NMR spectra and associated reference (chemical shift assignments, structures) and derived (peak lists, restraints for structure calculation, etc.) annotations. With the 100-protein NMR spectra dataset that was originally compiled for the development of the ARTINA deep learning-based spectra analysis method, 100 protein structures can be reproduced from their original experimental data. The 100-protein NMR spectra dataset is expected to help the development of computational methods for NMR spectroscopy, in particular machine learning approaches, and enable consistent and objective comparisons of these methods.

Abstract Background The automation of objectively selecting amino acid residue ranges for structure superpositions is important for meaningful and consistent protein structure analyses. So far there is no widely-used standard for choosing these residue ranges for experimentally determined protein structures, where the manual selection of residue ranges or the use of suboptimal criteria remain commonplace. Results We present an automated and objective method for finding amino acid residue ranges for the superposition and analysis of protein structures, in particular for structure bundles resulting from NMR structure calculations. The method is implemented in an algorithm, CYRANGE, that yields, without protein-specific parameter adjustment, appropriate residue ranges in most commonly occurring situations, including low-precision structure bundles, multi-domain proteins, symmetric multimers, and protein complexes. Residue ranges are chosen to comprise as many residues of a protein domain that increasing their number would lead to a steep rise in the RMSD value. Residue ranges are determined by first clustering residues into domains based on the distance variance matrix, and then refining for each domain the initial choice of residues by excluding residues one by one until the relative decrease of the RMSD value becomes insignificant. A penalty for the opening of gaps favours contiguous residue ranges in order to obtain a result that is as simple as possible, but not simpler. Results are given for a set of 37 proteins and compared with those of commonly used protein structure validation packages. We also provide residue ranges for 6351 NMR structures in the Protein Data Bank. Conclusions The CYRANGE method is capable of automatically determining residue ranges for the superposition of protein structure bundles for a large variety of protein structures. The method correctly identifies ordered regions. Global structure superpositions based on the CYRANGE residue ranges allow a clear presentation of the structure, and unnecessary small gaps within the selected ranges are absent. In the majority of cases, the residue ranges from CYRANGE contain fewer gaps and cover considerably larger parts of the sequence than those from other methods without significantly increasing the RMSD values. CYRANGE thus provides an objective and automatic method for standardizing the choice of residue ranges for the superposition of protein structures.

Chemical shift transfer (CST) is a well-established technique in NMR spectroscopy that utilizes the chemical shift assignment of one protein (source) to identify chemical shifts of another (target). Given similarity between source and target systems (e.g., using homologs), CST allows the chemical shifts of the target system to be assigned using a limited amount of experimental data. In this study, we propose a deep-learning based workflow, ARTINA-CST, that automates this procedure, allowing CST to be carried out within minutes or hours of computational time and strictly without any human supervision. We characterize the efficacy of our method using three distinct synthetic and experimental datasets, demonstrating its effectiveness and robustness even when substantial differences exist between the source and target proteins. With its potential applications spanning a wide range of NMR projects, including drug discovery and protein interaction studies, ARTINA-CST is anticipated to be a valuable method that facilitates research in the field.

Peptides and proteins containing non-canonical amino acids (ncAAs) are a large and important class of biopolymers. They include non-ribosomally synthesised peptides, post-translationally modified proteins, expressed or synthesised proteins containing unnatural amino acids, and peptides and proteins that are chemically modified. Here, we describe a general procedure for generating atomic descriptions required to incorporate ncAAs within popular NMR structure determination software such as CYANA, CNS, Xplor-NIH and ARIA. This procedure is made publicly available via the existing Automated Topology Builder (ATB) server (https://atb.uq.edu.au, last access: 17 February 2023) with all submitted ncAAs stored in a dedicated database. The described procedure also includes a general method for linking of side chains of amino acids from CYANA templates. To ensure compatibility with other systems, atom names comply with IUPAC guidelines. In addition to describing the workflow, 3D models of complex natural products generated by CYANA are presented, including vancomycin. In order to demonstrate the manner in which the templates for ncAAs generated by the ATB can be used in practice, we use a combination of CYANA and CNS to solve the structure of a synthetic peptide designed to disrupt Alzheimer-related protein–protein interactions. Automating the generation of structural templates for ncAAs will extend the utility of NMR spectroscopy to studies of more complex biomolecules, with applications in the rapidly growing fields of synthetic biology and chemical biology. The procedures we outline can also be used to standardise the creation of structural templates for any amino acid and thus have the potential to impact structural biology more generally.

An improved method for in-cell NMR is developed using a reporter to evaluate protein delivery and delivery parameters to different cell lines and applied to IDPs and folded proteins including structure determination of GB1 at 1.1 Å resolution.

In this manuscript the authors report accurate multi-state protein structures of the PDZ domain using biological NMR. By looking into protein structural states, the authors report an allosteric pathway at atomic resolution that validates previously reported low resolution findings and uncovered a structural hallmark of the allosteric ligand binding to the PDZ domain.

The analysis of protein NMR spectra is time-consuming and can occupy a human expert for weeks or months. The researchers in this work present a deep learning-based method that delivers signal positions, chemical shift assignments, and structures of proteins within hours after completion of the NMR measurements.

Amyloid-β (Aβ) is present in humans as a 39- to 42-amino acid residue metabolic product of the amyloid precursor protein. Although the two predominant forms, Aβ(1-40) and Aβ(1-42), differ in only two residues, they display different biophysical, biological, and clinical behavior. Aβ(1-42) is the more neurotoxic species, aggregates much faster, and dominates in senile plaque of Alzheimer's disease (AD) patients. Although small Aβ oligomers are believed to be the neurotoxic species, Aβ amyloid fibrils are, because of their presence in plaques, a pathological hallmark of AD and appear to play an important role in disease progression through cell-to-cell transmissibility. Here, we solved the 3D structure of a disease-relevant Aβ(1-42) fibril polymorph, combining data from solid-state NMR spectroscopy and mass-per-length measurements from EM. The 3D structure is composed of two molecules per fibril layer, with residues 15-42 forming a double-horseshoe-like cross-β-sheet entity with maximally buried hydrophobic side chains. Residues 1-14 are partially ordered and in a β-strand conformation, but do not display unambiguous distance restraints to the remainder of the core structure.

The structures and dynamics of large proteins can be studied with methyl-based NMR but peak assignment is still challenging. Here the authors present MethylFLYA that allows automated assignment of methyl groups and apply it to five proteins with molecular weights in the range from 28 to 358 kDa.

NMR structure determination is challenging for proteins with a molecular weight above 30 kDa and atomic-resolution structure determination from cryo-EM data is currently not the rule. Here the authors describe an integrated structure determination approach that simultaneously uses NMR and EM data and allows them to determine the structure of the 468 kDa dodecameric aminopeptidase TET2 complex.

Abstract A key function of reversible protein phosphorylation is to regulate protein–protein interactions, many of which involve short linear motifs (3–12 amino acids). Motif‐based interactions are difficult to capture because of their often low‐to‐moderate affinities. Here, we describe phosphomimetic proteomic peptide‐phage display, a powerful method for simultaneously finding motif‐based interaction and pinpointing phosphorylation switches. We computationally designed an oligonucleotide library encoding human C‐terminal peptides containing known or predicted Ser/Thr phosphosites and phosphomimetic variants thereof. We incorporated these oligonucleotides into a phage library and screened the PDZ (PSD‐95/Dlg/ZO‐1) domains of Scribble and DLG1 for interactions potentially enabled or disabled by ligand phosphorylation. We identified known and novel binders and characterized selected interactions through microscale thermophoresis, isothermal titration calorimetry, and NMR. We uncover site‐specific phospho‐regulation of PDZ domain interactions, provide a structural framework for how PDZ domains accomplish phosphopeptide binding, and discuss ligand phosphorylation as a switching mechanism of PDZ domain interactions. The approach is readily scalable and can be used to explore the potential phospho‐regulation of motif‐based interactions on a large scale.

The Bcr-Abl tyrosine kinases p210 and p190 are linked to different leukemias and differ by the Dbl homology (DH) and Pleckstrin-homology (PH) domains. Here the authors characterize structures of the Bcr-Abl p210 DH and PH domains and find that the PH domain is important for the cellular localization and signaling network of p210.

An automated NMR chemical shift assignment algorithm was developed using multi-objective optimization techniques. The problem is modeled as a combinatorial optimization problem and its objective parameters are defined separately in different score functions. Some of the heuristic approaches of evolutionary optimization are employed in this problem model. Both, a conventional genetic algorithm and multi-objective methods, i.e., the non-dominated sorting genetic algorithms II and III (NSGA2 and NSGA3), are applied to the problem. The multi-objective approaches consider each objective parameter separately, whereas the genetic algorithm followed a conventional way, where all objectives are combined in one score function. Several improvement steps and repetitions on these algorithms are performed and their combinations are also created as a hyper-heuristic approach to the problem. Additionally, a hill-climbing algorithm is also applied after the evolutionary algorithm steps. The algorithms are tested on several different datasets with a set of 11 commonly used spectra. The test results showed that our algorithm could assign both sidechain and backbone atoms fully automatically without any manual interactions. Our approaches could provide around a 65% success rate and could assign some of the atoms that could not be assigned by other methods.

Aunque es cierto que el endecasílabo de Dante y Petrarca fue imitado en la Península ya desde el siglo XV, se debe sin embargo a Garcilaso y Boscán, lectores de Sannazaro, Bembo y Bernardo Tasso, su definitiva aclimatación en el canon poético español. Y es que la novedad de Petrarca, lo que Bernardo Tasso y Herrera llamarán su leggiadria, no había sido entendida antes de 1500. También en el dominio de la sintaxis y el ritmo, los poemas de Garcilaso suponen un paso adelante: los hay, como el soneto XI o la estrofa inicial de la Canción III, sin punto hasta el final, lo que les confiere una estructura unitaria y redonda. Volvemos a encontrar la figura del círculo en la Égloga tercera donde el poeta trata de superar el tiempo a través del mito: inscribir el tiempo de la existencia en el orden cíclico del mito constituye, de hecho, la suprema ambición del poeta toledano. Keywords: Endecasílabo, Petrarca, leggiadria, Garcilaso, estructuras circulares, tiempo cíclico.

El análisis de las opciones a favor o contra el título nos permite enfocar la trayectoria poética de JRJ desde otra perspectiva. Se observan, en efecto, cambios de actitud sorprendentes. Si la renuncia al título individual es constante en la fase melancólico-musical, que va desde Arias tristes hasta Pastorales, ocurre lo contrario en algunas obras de madurez y, sobre todo, en Diario de un poeta recién casado, donde el poema aspira a ser pensamiento-palabra capaz de conferir eternidad al instante. Keywords: modernismo, técnicas impresionistas, simbolismo, poética de la madurez, titulogía

En esta revisión de «El curioso impertinente», que incluye un panorama de la historia de su recepción en los últimos veinte años, se comparan los resultados de cuatro lecturas con la de quien escribe. La relección crítica de estas interpretaciones, que adoptan perspectivas distintas, se desarrolla en tres etapas: en primer lugar, se examinan algunas propuestas relacionadas con las fuentes de la novela, sin abandonar la idea de que la novela del «Curioso» es obra profundamente original; después, se comentan las cuatro lecturas, que tienen en común la tendencia a privilegiar el análisis del contenido; por último, se insiste en la necesidad de superar una exégesis limitada a las cuestiones argumentales y de prestar atención también a los aspectos narrativos y discursivos.

We compiled an NMR data set consisting of exact nuclear Overhauser enhancement (eNOE) distance limits, residual dipolar couplings (RDCs) and scalar (J) couplings for GB3, which forms one of the largest and most diverse data set for structural characterization of a protein to date. All data have small experimental errors, which are carefully estimated. We use the data in the research article Vogeli et al., 2015, Complementarity and congruence between exact NOEs and traditional NMR probes for spatial decoding of protein dynamics, J. Struct. Biol., 191, 3, 306–317, doi:10.1016/j.jsb.2015.07.008 [1] for cross-validation in multiple-state structural ensemble calculation. We advocate this set to be an ideal test case for molecular dynamics simulations and structure calculations.

Bien que la genèse des Fiancés s’étende sur une période de plus de vingt ans, notre étude montre que les modifications essentielles se font entre 1823 et 1827. En comparant la première version, appelée aussi Fermo et Lucia, à la première édition des Fiancés de 1827, on s’avise que les deux romans racontent en principe la même histoire, qui assume toutefois des significations bien différentes. Est révélatrice, dans cette perspective, l’analyse comparée des deux incipit (cap. I) correspondant à des descriptions de paysage. Dès la première phrase, Fermo et Lucia insiste sur le devenir, tandis que Les Fiancés met en scène un changement cyclique entre permanence et mouvement. Une autre différence concerne la fonction des points cardinaux dans ces deux descriptions : l’axe Nord-Sud suggérant la voie vers la civilisation n’est mise en valeur que dans Fermo et Lucia. Au lieu de l’expérience avant tout cognitive du promeneur, interprétable comme une figure du lecteur, le roman des PS donne lieu à une expérience à la fois éthique et esthétique de l’espace.