GSATools: Analysis of allosteric communication and functional local motions using a structural alphabet

Motivation: GSATools is a free software package to analyze conformational ensembles and to detect functional motions in proteins by means of a structural alphabet. The software integrates with the widely used GROMACS simulation package and can generate a range of graphical outputs. Three applications can be supported: (i) investigation of the conformational variability of local structures; (ii) detection of allosteric communication; and (iii) identification of local regions that are critical for global functional motions. These analyses provide insights into the dynamics of proteins and allow for targeted design of functional mutants in theoretical and experimental studies. Availability: The C source code of the GSATools, along with a set of pre-compiled binaries, is freely available under GNU General Public License from http://mathbio.nimr.mrc.ac.uk/wiki/GSATools. Contact: alessandro.pandini@kcl. ac.uk or [email protected] Supplementary information: Supplementary data are available at Bioinformatics online. © 2013 The Author 2013. Published by Oxford University Press

Stress-Free Two-Way Shape Memory Effect of Poly(ethylene glycol)/ Poly(epsilon-caprolactone) Semicrystalline Networks

In this work, poly(ethylene glycol) (PEG)/poly(epsilon- caprolactone) (PCL) semicrystalline networks were prepared by photo-cross-linking of methacrylated macromonomers with different molecular weights and in different proportions to obtain amphiphilic materials capable of displaying properly designed shape memory effects. Networks based on PCL 10 kDa and PEG 3 kDa showed suitable thermal and mechanical properties with well-separated crystallization and melting regions to achieve a self-standing two-way shape memory effect. Particularly, after the application of a specific thermomechanical history, these materials are capable of cyclically changing their shape between two configurations upon cooling-heating cycles in the absence of any external load applied. The effect of the composition of the networks and of the employed thermomechanical parameters, such as the applied strain and the actuation temperature, was investigated to shed light on the shape memory mechanism for this class of materials, which are considered promising for applications in the biomedical field and as reversible actuators for soft robotics

Reversible Stress-Driven and Stress-Free Two-Way Shape Memory Effect in a Sol-Gel Crosslinked Polycaprolactone

The two-way shape memory effect is the ability of a material to change its shape between two configurations upon application and removal of a stimulus, and, among shape memory polymers, it is featured only by few systems, such as semicrystalline networks. When studied under tensile conditions, it consists of elongation-contraction cycles along cooling and heating across the crystallization and melting region, typically under the application of a constant load. However, recent studies on crosslinked semicrystalline co-polymers demonstrate that also a completely stress-free, or self-sustained, two-way effect may be achieved through specific thermomechanical cycles. This effect is currently regarded with interest for the development of intrinsically reversible sensors and actuators, and it may also be displayed by simpler materials, as homopolymer-based semicrystalline networks. Only seldom articles investigate this possibility, therefore in this work the two-way shape memory behavior is studied on a poly(e-caprolactone) system, crosslinked by means of a sol-gel approach. The effect is studied both under stress-driven and stress-free condition, by applying properly set-up thermo-mechanical histories. The results allow to describe the effect as a function of temperature, to reveal the dependence on specific testing parameters and to compare the extent of the reversible strain variation under these two conditions

Retentive device for intravesical drug delivery based on water-induced shape memory response of poly(vinyl alcohol): design concept and 4D printing feasibility

The use of shape memory polymers exhibiting water-induced shape recovery at body temperature and water solubility was proposed for the development of indwelling devices for intravesical drug delivery. These could be administered via catheter in a suitable temporary shape, retained in the bladder for a programmed period of time by recovery of the original shape and eliminated with urine following dissolution/erosion. Hot melt extrusion and fused deposition modeling 3D printing were employed as the manufacturing techniques, the latter resulting in 4D printing because of the shape modifications undergone by the printed item over time. Pharmaceutical-grade poly(vinyl alcohol) was selected based on its hot-processability, availability in different molecular weights and on preliminary data showing water-induced shape memory behavior. Specimens having various original and temporary geometries as well as compositions, successfully obtained, were characterized by differential scanning calorimetry and dynamic-mechanical thermal analysis as well as for fluid uptake, mass loss, shape recovery and release behavior. The samples exhibited the desired ability to recover the original shape, consistent in kinetics with the relevant thermo-mechanical properties, and concomitant prolonged release of a tracer. Although preliminary in scope, this study indicated the viability of the proposed approach to the design of retentive intravesical delivery systems

Machine Learning Prediction of Allosteric Drug Activity from Molecular Dynamics

© 2021 The Authors. Allosteric drugs have been attracting increasing interest over the past few years. In this context, it is common practice to use high-throughput screening for the discovery of non-natural allosteric drugs. While the discovery stage is supported by a growing amount of biological information and increasing computing power, major challenges still remain in selecting allosteric ligands and predicting their effect on the target protein’s function. Indeed, allosteric compounds can act both as inhibitors and activators of biological responses. Computational approaches to the problem have focused on variations on the theme of molecular docking coupled to molecular dynamics with the aim of recovering information on the (long-range) modulation typical of allosteric proteins.AIRC IG 2017 - ID. 20019 project; AIRC Fellowship; EC Research Innovation Action H2020 Programme Project HPC-EUROPA3 (INFRAIA-2016-1-730897)

Coevolved mutations reveal distinct architectures for two core proteins in the bacterial flagellar motor

Switching of bacterial flagellar rotation is caused by large domain movements of the FliG protein triggered by binding of the signal protein CheY to FliM. FliG and FliM form adjacent multi-subunit arrays within the basal body C-ring. The movements alter the interaction of the FliG C-terminal (FliGC) "torque" helix with the stator complexes. Atomic models based on the Salmonella entrovar C-ring electron microscopy reconstruction have implications for switching, but lack consensus on the relative locations of the FliG armadillo (ARM) domains (amino-terminal (FliGN), middle (FliGM) and FliGC) as well as changes during chemotaxis. The generality of the Salmonella model is challenged by the variation in motor morphology and response between species. We studied coevolved residue mutations to determine the unifying elements of switch architecture. Residue interactions, measured by their coevolution, were formalized as a network, guided by structural data. Our measurements reveal a common design with dedicated switch and motor modules. The FliM middle domain (FliMM) has extensive connectivity most simply explained by conserved intra and inter-subunit contacts. In contrast, FliG has patchy, complex architecture. Conserved structural motifs form interacting nodes in the coevolution network that wire FliMM to the FliGC C-terminal, four-helix motor module (C3-6). FliG C3-6 coevolution is organized around the torque helix, differently from other ARM domains. The nodes form separated, surface-proximal patches that are targeted by deleterious mutations as in other allosteric systems. The dominant node is formed by the EHPQ motif at the FliMMFliGM contact interface and adjacent helix residues at a central location within FliGM. The node interacts with nodes in the N-terminal FliGc α-helix triad (ARM-C) and FliGN. ARM-C, separated from C3-6 by the MFVF motif, has poor intra-network connectivity consistent with its variable orientation revealed by structural data. ARM-C could be the convertor element that provides mechanistic and species diversity.JK was supported by Medical Research Council grant U117581331. SK was supported by seed funds from Lahore University of Managment Sciences (LUMS) and the Molecular Biology Consortium

Una procedura per la valutazione dei limiti di utilizzo di O-Ring sottoposti ad intensi fasci di neutroni

Si presenta una procedura per la previsione della durata di utilizzo di O-ring in materiale polimerico impiegati nei bersagli per la produzione di fasci di ioni radioattivi. Si sono dapprima condotte prove di tenuta a vuoto e analisi a elementi finiti di un O-ring di riferimento operante con diversi livelli di interferenza con la cava, identificando la precompressione limite per la tenuta e la corrispondente pressione di contatto con la cava. Si sono poi effettuate prove di trazione e di Compression Set su campioni di O-ring in EPDM, preventivamente sottoposti a diversi livelli di irraggiamento in campi misti di neutroni e gamma, analizzando l’effetto della dose assorbita sul comportamento meccanico del materiale e sulle corrispondenti proprietà resistenziali, e definendo opportune leggi costitutive. Si sono infine simulate le progressive modifiche di comportamento della guarnizione indotte dall’irraggiamento, prevedendone la durata in esercizio in termini di tenuta e di resistenza strutturale

Specialized dynamical properties of promiscuous residues revealed by simulated conformational ensembles

The ability to interact with different partners is one of the most important features in proteins. Proteins that bind a large number of partners (hubs) have been often associated with intrinsic disorder. However, many examples exist of hubs with an ordered structure, and evidence of a general mechanism promoting promiscuity in ordered proteins is still elusive. An intriguing hypothesis is that promiscuous binding sites have specific dynamical properties, distinct from the rest of the interface and pre-existing in the protein isolated state. Here, we present the first comprehensive study of the intrinsic dynamics of promiscuous residues in a large protein data set. Different computational methods, from coarse-grained elastic models to geometry-based sampling methods and to full-atom Molecular Dynamics simulations, were used to generate conformational ensembles for the isolated proteins. The flexibility and dynamic correlations of interface residues with a different degree of binding promiscuity were calculated and compared considering side chain and backbone motions, the latter both on a local and on a global scale. The study revealed that (a) promiscuous residues tend to be more flexible than nonpromiscuous ones, (b) this additional flexibility has a higher degree of organization, and (c) evolutionary conservation and binding promiscuity have opposite effects on intrinsic dynamics. Findings on simulated ensembles were also validated on ensembles of experimental structures extracted from the Protein Data Bank (PDB). Additionally, the low occurrence of single nucleotide polymorphisms observed for promiscuous residues indicated a tendency to preserve binding diversity at these positions. A case study on two ubiquitin-like proteins exemplifies how binding promiscuity in evolutionary related proteins can be modulated by the fine-tuning of the interface dynamics. The interplay between promiscuity and flexibility highlighted here can inspire new directions in protein-protein interaction prediction and design methods. © 2013 American Chemical Society

RNA-seq dataset of subcutaneous adipose tissue: Transcriptional differences between obesity and healthy women

In this data article, we present the dataset from the RNA-Seq analysis of subcutaneous adipose tissue collected from 5 healthy normal weight women (NW, age 37 +/- 6.7 years, BMI 24.3 +/- 0.9 kg/m(2)) and 5 obese women (OBF, age 41 +/- 12.5 years, BMI 38.2 +/- 4.6 kg/m(2)). Raw data obtained from Illumina NextSeq 500 sequencer were processed through BlueBee (R) Genomics Platform while differential expression analysis was performed with the DESeq2 R package and deposited in the GEO public repository with GSE166047 as accession number. Specifically, 20 samples divided between NW (control), OBF (obese women), OBM (obese male) and OBT2D (obese women with diabetes) are deposited in the GSE166047. We hereby describe only 10 samples (5 healthy normal weight women reported as NW and 5 obese women reported as OBF) because we refer to the data published in the article "Transcriptional characterization of Subcutaneous Adipose Tissue in obesity affected women highlights metabolic dysfunction and implications for lncRNAs" (DOI: 10.1016/j.ygeno.2021.09.014). Pathways analyses were performed on g:Profiler, Enrichr, ClueGO and GSEA to gain biological insights on gene expression. Raw data reported in GEO database along with detailed methods description reported in this data article could be reused for comparisons with other datasets on the topic to obtain transcriptional differences in a wider co-hort. Moreover, detailed pathways analysis along with cross-referenced data with other datasets will allow to identify novel dysregulated pathways and genes responsible for this regulation. The biological interpretation of this dataset, along with related in vitro experiments, is reported by Rey et al., in Genomics (DOI: 10.1016/j.ygeno.2021.09.014). (C) 2021 Published by Elsevier Inc

Comparative analysis of homology models of the Ah receptor ligand binding domain: Verification of structure-function predictions by site-directed mutagenesis of a nonfunctional receptor

The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that mediates the biological and toxic effects of a wide variety of structurally diverse chemicals, including the toxic environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). While significant interspecies differences in AHR ligand binding specificity, selectivity, and response have been observed, the structural determinants responsible for those differences have not been determined, and homology models of the AHR ligand-binding domain (LBD) are available for only a few species. Here we describe the development and comparative analysis of homology models of the LBD of 16 AHRs from 12 mammalian and nonmammalian species and identify the specific residues contained within their ligand binding cavities. The ligand-binding cavity of the fish AHR exhibits differences from those of mammalian and avian AHRs, suggesting a slightly different TCDD binding mode. Comparison of the internal cavity in the LBD model of zebrafish (zf) AHR2, which binds TCDD with high affinity, to that of zfAHR1a, which does not bind TCDD, revealed that the latter has a dramatically shortened binding cavity due to the side chains of three residues (Tyr296, Thr386, and His388) that reduce the amount of internal space available to TCDD. Mutagenesis of two of these residues in zfAHR1a to those present in zfAHR2 (Y296H and T386A) restored the ability of zfAHR1a to bind TCDD and to exhibit TCDD-dependent binding to DNA. These results demonstrate the importance of these two amino acids and highlight the predictive potential of comparative analysis of homology models from diverse species. The availability of these AHR LBD homology models will facilitate in-depth comparative studies of AHR ligand binding and ligand-dependent AHR activation and provide a novel avenue for examining species-specific differences in AHR responsiveness. © 2013 American Chemical Society