Conservation and specialization in PAS domain dynamics

The PAS (Per-ARNT-Sim) superfamily is presented as a well-suited study case to demonstrate how comparison of functional motions among distant homologous proteins with conserved fold characteristics may give insight into their functional specialization. Based on the importance of structural flexibility of the receptive structures in anticipating the signal-induced conformational changes of these sensory systems, the dynamics of these structures were analysed. Molecular dynamics was proved to be an effective method to obtain a reliable picture of the dynamics of the crystal structures of HERG, phy3, PYP and FixL, provided that an extensive conformational space sampling is performed. Other reliable sources of dynamic information were the ensembles of NMR structures of hPASK, HIF-2α and PYP. Essential dynamics analysis was successfully employed to extract the relevant information from the sampled conformational spaces. Comparison of motion patterns in the essential subspaces, based on the structural alignment, allowed identification of the specialized region in each domain. This appears to be evolved in the superfamily by following a specific trend, that also suggests the presence of a limited number of general solutions adopted by the PAS domains to sense external signals. These findings may give insight into unknown mechanisms of PAS domains and guide further experimental studies. © The Author 2005. Published by Oxford University Press. All rights reserved

Predicting the accuracy of protein-ligand docking on homology models

Ligand-protein docking is increasingly used in Drug Discovery. The initial limitations imposed by a reduced availability of target protein structures have been overcome by the use of theoretical models, especially those derived by homology modeling techniques. While this greatly extended the use of docking simulations, it also introduced the need for general and robust criteria to estimate the reliability of docking results given the model quality. To this end, a large-scale experiment was performed on a diverse set including experimental structures and homology models for a group of representative ligand-protein complexes. A wide spectrum of model quality was sampled using templates at different evolutionary distances and different strategies for target-template alignment and modeling. The obtained models were scored by a selection of the most used model quality indices. The binding geometries were generated using AutoDock, one of the most common docking programs. An important result of this study is that indeed quantitative and robust correlations exist between the accuracy of docking results and the model quality, especially in the binding site. Moreover, state-of-the-art indices for model quality assessment are already an effective tool for an a priori prediction of the accuracy of docking experiments in the context of groups of proteins with conserved structural characteristics.Contract/grant sponsor: National Institutes of Health; contract/grant numbers: ES00768

Myokardiales Risiko bei Karotisendarteriektomie und Stent

Zusammenfassung: Die Karotisstenose ist eine der wichtigsten Ursachen des ischämischen Schlaganfalls. Die Thrombendarteriektomie (TEA) reduziert das Schlaganfallrisiko bei Patienten mit symptomatischen und symptomfreien Karotisstenosen. Die Stentdilatation stellt eine Alternative zum chirurgischen Eingriff dar, ist jedoch mit einem erhöhten Risiko periprozeduraler Schlaganfälle verbunden. Das Risiko eines periprozeduralen Myokardinfarkts (MI) dagegen wird in den Studien sehr unterschiedlich angegeben. Einige Studien zeigten ein erhöhtes MI-Risiko bei der TEA im Vergleich zur Stentdilatation, während andere Studien keinen solchen Unterschied fanden. Grund dafür sind Unterschiede in den Studienpopulationen sowie in der Definition und Erfassung von MI. Unter Berücksichtigung sämtlicher Daten aus randomisierten Studien ist das periprozedurale MI-Risiko bei der TEA gegenüber der Stentbehandlung erhöht. Periprozedurale MI erhöhen ebenso wie Schlaganfälle die Langzeitmortalität und stellen somit ernst zu nehmende Komplikationen dar. Die Stentdilatation kann deswegen bei Patienten mit erhöhtem koronaren Risiko und klarer Indikation zur Revaskularisation einer Karotisstenose eine Alternative zur TEA darstelle

Structural and functional characterization of the aryl hydrocarbon receptor ligand binding domain by homology modeling and mutational analysis

The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that is activated by a structurally diverse array of synthetic and natural chemicals, including toxic halogenated aromatic hydrocarbons such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Analysis of the occurring in the AhR ligand binding and activation processes requires structural information on the AhR Per-Arnt-Sim (PAS) B-containing ligand binding domain, for which no experimentally determined structure has been reported. With the availability of extensive structural information on homologous PAS-containing proteins, a reliable model of the mouse AhR PAS B domain was developed by comparative modeling techniques. The PAS domain structures of the functionally related hypoxia-inducible factor 2α (HIF-2α) and AhR nuclear translocator (ARNT) proteins, which exhibit the highest degree of sequence identity and similarity with AhR, were chosen to develop a two-template model. To confirm the features of the modeled domain, the effects of point mutations in selected residue positions on both TCDD binding to the AhR and TCDD-dependent transformation and DNA binding were analyzed. Mutagenesis and functional analysis results are consistent with the proposed model and confirm that the cavity modeled in the interior of the domain is indeed involved in ligand binding. Moreover, the physicochemical characteristics of some residues and of their mutants, along with the effects of mutagenesis on TCDD and DNA binding, also suggest some key features that are required for ligand binding and activation of mAhR at a molecular level, thus providing a framework for further studies. © 2007 American Chemical Society

Detection of the TCDD binding-fingerprint within the Ah receptor ligand binding domain by structurally driven mutagenesis and functional analysis

The aryl hydrocarbon receptor (AhR) is a ligand-dependent, basic helix-loop-helix Per-Arnt-Sim (PAS)-containing transcription factor that can bind and be activated by structurally diverse chemicals, including the toxic environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Our previous three-dimensional homology model of the mouse AhR (mAhR) PAS B ligand binding domain allowed identification of the binding site and its experimental validation. We have extended this analysis by conducting comparative structural modeling studies of the ligand binding domains of six additional highaffinity mammalian AhRs. These results, coupled with site-directed mutagenesis and AhR functional analysis, have allowed detection of the "TCDD binding-fingerprint" of conserved residues within the ligand binding cavity necessary for high-affinity TCDD binding and TCDD-dependent AhR transformation DNA binding. The essential role of selected residues was further evaluated using molecular docking simulations of TCDD with both wild-type and mutant mAhRs. Taken together, our results dramatically improve our understanding of the molecular determinants of TCDD binding and provide a basis for future studies directed toward rationalizing the observed species differences in AhR sensitivity to TCDD and understanding the mechanistic basis for the dramatic diversity in AhR ligand structure. © 2009 American Chemical Society

Computational approaches to shed light on molecular mechanisms in biological processes

Computational approaches based on Molecular Dynamics simulations, Quantum Mechanical methods and 3D Quantitative Structure-Activity Relationships were employed by computational chemistry groups at the University of Milano-Bicocca to study biological processes at the molecular level. The paper reports the methodologies adopted and the results obtained on Aryl hydrocarbon Receptor and homologous PAS proteins mechanisms, the properties of prion protein peptides, the reaction pathway of hydrogenase and peroxidase enzymes and the defibrillogenic activity of tetracyclines. © Springer-Verlag 2007

CAUSA INCONSUETA DI COIN LESION

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Diffusion weighted imaging, apparent diffusion coefficient maps and stroke etiology

Objective : In acute ischemic stroke, the number and distribution of lesions on diffusion weighted imaging (DWI) have been shown to give clues to the underlying pathogenetic mechanisms. The objective of this study was to determine whether lesion features on DWI differ between stroke due to large artery atherosclerosis (LAA) and cardioembolism (CE), and to assess the role of apparent diffusion coefficient maps (ADC). Methods : We retrospectively studied 83 consecutive patients with stroke caused by either LAA (n = 40) or cardioembolism (n = 43). DWI lesions were characterized by number, size, distribution (i. e. lesion pattern) and signal intensity on ADC maps. In part A, all hyperintense DWI lesions regardless of their ADC were compared. In part B, only hyperintense DWI lesions with hypointense appearance on ADC maps (i. e. acute lesions) were assessed. Results : Part A: The frequency of multiple hyperintense DWI lesions (LAA: 28/40, CE: 21/43; p 1 circulation (i. e. anterior plus posterior or bilateral anterior circulations) was present in 5 LAA-patients (13 %) and 4 CE-patients (9 %). Lesion size did not differ between LAA-stroke (35.1 ± 33.7 mm) and CE-stroke (35.4 ± 27.8 mm). Part B: Multiple hyperintense DWI lesions with low ADC occurred in 23/40 LAA-patients and in 15/43 CE-patients (p 1 circulation occurred only in CE-stroke (n = 3; 7%) and never in LAA-stroke. Conclusions : (1) Multiple ischemic lesions occur significantly more often in LAA-stroke than in CE-stroke. (2) ADC maps are important in the comparison of DWI lesion patterns; DWI lesions in > 1 circulation can only be assigned to a cardioembolic etiology if they appear hypointense on ADC map

Transfer learning for atomistic simulations using GNNs and kernel mean embeddings

Interatomic potentials learned using machine learning methods have been successfully applied to atomistic simulations. However, accurate models require large training datasets, while generating reference calculations is computationally demanding. To bypass this difficulty, we propose a transfer learning algorithm that leverages the ability of graph neural networks (GNNs) to represent chemical environments together with kernel mean embeddings. We extract a feature map from GNNs pre-trained on the OC20 dataset and use it to learn the potential energy surface from system-specific datasets of catalytic processes. Our method is further enhanced by incorporating into the kernel the chemical species information, resulting in improved performance and interpretability. We test our approach on a series of realistic datasets of increasing complexity, showing excellent generalization and transferability performance, and improving on methods that rely on GNNs or ridge regression alone, as well as similar fine-tuning approaches

Stop, Collaborate, and Listen: A Faculty Learning Community Developed to Address Gaps in Pre-Service Education about Interdisciplinary Collaboration

There is a notable lack of opportunity for students in pre-service professional training programs and faculty in higher education to collaborate and work together, across disciplines within a common area of professional expertise. In this case, a faculty learning community (FLC) was formed to create a set of video-based simulations based on relevant topics for Committee on Special Education (CSE) meetings, used to inform the development of an Individualized Education Program. These materials were made available across departments and universities, establishing a common language and set of CSE practices. Additionally, a structured three-level text reading and discussion provided faculty with an opportunity for professional development, networking, and scholarship. The project was completed following Cox’s 16 Recommendations for a Faculty Learning Community as a guideline for the successful implementation of the project, the creation of course materials, and analysis of faculty learning outcomes. It is important to note that the FLC process applies to a wide range of disciplines as a means of engaging faculty in responsive and reflective teaching practices as well as professional development