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650 results for “Molecular Mechanics”
Molecular Simulation Elaborating the Structural Mechanism of Spiri forming nitrilase from Bacillus safensis
<p><span>Nitrilases are indispensable in the biocatalytic hydrolysis of nitrile compounds, which presents promising applications in industrial biocatalysis and environmental remediation. In this study, we conduct an extensive investigation into the structural and functional properties of <em>Bacillus safensis </em>nitrilase (<em>BsNIT</em>), highlighting its assembly, substrate binding mechanisms, stability, evolutionary relationships, and active site conservation. Using a combination of molecular modeling and extensive molecular dynamics simulations, we unveil the intricate architecture of <em>BsNIT</em>, which exhibits a left-handed spiri-forming structure stabilized by interchain interactions and salt-bridge formations. The substrate-binding pocket, surrounded by aromatic residues, displays multifaceted accessibility through distinct channels. Our simulations reveal substrate-specific catalytic orientations, with glutaronitrile and 4-cyanobutanoic acid displaying stable binding, while benzonitrile exhibits a propensity for rapid product diffusion. Analysis of active site conservation emphasizes the functional significance of preserved catalytic residues, providing insights into <em>BsNIT</em>'s catalytic efficiency. This comprehensive study offers a thorough understanding of <em>BsNIT</em>'s structure-function relationships, paving the way for future advancements in enzyme engineering and bioremediation strategies targeting nitrile pollutants.</span></p>
Datasets and geometries for "MORE-Q, Dataset for molecular olfactorial receptor engineering by quantum mechanics"
<p>We introduce the MORE-Q dataset, a quantum-mechanical (QM) dataset encompassing the structural and electronic data of non-covalent molecular sensors formed by combining 18 mucin-derived olfactorial receptors with 102 body odor volatilome (BOV) molecules. To have a better understanding of their intra- and inter-molecular interactions, we have performed accurate QM calculations in different stages of the sensor design and, accordingly, MORE-Q splits into three subsets: i) MORE-Q-G1: QM data of 18 receptors and 102 BOV molecules, ii) MORE-Q-G2: QM data of 23, 838 BOV-receptor configurations, and iii) MORE-Q-G3: QM data of 1, 836 BOV-receptor-graphene systems. Each subset involves geometries optimized using GFN2-xTB with D4 dispersion correction and up to 39 physicochemical properties, including global and local properties as well as binding features, all computed at the tightly converged PBE+D3 level of theory. By addressing BOV-receptor-graphene systems from a QM perspective, MORE-Q can serve as a benchmark dataset for state-of-the-art machine learning methods developed to predict binding features. This, in turn, can provide valuable insights for developing the next-generation mucin-derived olfactory receptor sensing devices.</p> <p>The dataset is provided in 3 HDF5 based files. One can also find here a README file with technical usage details and examples of how to access the information stored in the dataset (see createDF.py). We also offer a Github repository for user guide, see https://github.com/LiC1117/MORE-Q.</p> <p>For more details, one can refer to the manuscript doi: <a href="https://doi.org/10.1038/s41597-025-04616-6" rel="nofollow">https://doi.org/10.1038/s41597-025-04616-6</a></p>
Quantum mechanical double slit for molecular scattering
<p>Interference observed in a double-slit experiment most conclusively demonstrates the wave properties of particles. We construct a quantum mechanical double-slit interferometer by rovibrationally exciting D2 (v=2, j=2) molecules in a biaxial state using Stark-induced adiabatic Raman passage. In D2(v=2, j=2)→D2(v=2, j'=0) rotational relaxation via a cold collision with ground state He, the entangled bond axis orientations in the biaxial state act as two slits generating two indistinguishable quantum mechanical pathways connecting initial and final states of the colliding system. The interference disappears when we decouple the two orientations of the bond axis by separately constructing the uniaxial states of D2, unequivocally establishing the double-slit action of the biaxial state. This double slit opens new possibilities in the coherent control of molecular collisions.</p>
Spliced isoforms of the cardiac Nav1.5 channel modify channel activation by distinct structural mechanisms: Molecular dynamics coordinate and trajectory files
<p>Molecular dynamics files associated with the publication: Spliced isoforms of the cardiac Nav1.5 channel modify channel activation by distinct structural mechanisms</p>
Machine-guided path sampling to discover mechanisms of molecular self-organization (Training and validation data)
<p>Training and validation data for the Nature Computational Science manuscript "Machine-guided path sampling to discover mechanisms of molecular self-organization"</p>
Comparative Study of Molecular Mechanics Force Fields for β-peptidic Foldamers: Folding and Self-Association
<p>Molecular dynamics simulation input files and Python scripts used for preparing the runs and analyzing the trajectories.</p>
Molecular mechanisms of seasonal brain shrinkage and regrowth in Sorex araneus
<div class="page"> <div class="layoutArea"> <div class="column"> <p>Human brains typically grow through development, then remain the same size in adulthood, and often shrink through age-related degeneration that induces cognitive decline and impaired functionality. In most cases, however, the neural and organismal changes that accompany shrinkage, especially early in the process, remain unknown. Paralleling neurodegenerative phenotypes, the Eurasian common shrew <em>Sorex</em> <em>araneus</em>, shrinks its brain in autumn through winter, but then reverses this process by rapidly regrowing the brain come spring. To identify the molecular underpinnings and parallels to human neurodegeneration of this unique brain size change, we analyzed multi-organ, season-specific transcriptomics and metabolomic data. Simultaneous with brain shrinkage, we discovered system-wide metabolic shifts from lipid to glucose metabolism, as well as neuroprotection of brain metabolic homeostasis through reduced cholesterol efflux. These mechanisms rely on a finely tuned brain-liver crosstalk that results in changes in expression of human markers of aging and neurodegeneration in Parkinson's disease and Huntington's disease. We propose metabolic shifts with signals that cross the brain-blood barrier are central to seasonal brain size changes in <em>S. araneus</em>, with potential implications for therapeutic treatment of human neurodegeneration.</p> </div> </div> </div>
Molecular Mechanisms of Volume Overload-Aim 1(SCCOR in Cardiac Dysfunction and Disease)
ClinicalTrials.gov study NCT01052428. IPD Sharing: Not stated. Countries: 1. Publications: 36.
Molecular Mechanisms of Exercise Benefits to Insulin Resistant People
ClinicalTrials.gov study NCT04158375. IPD Sharing: NO. Countries: 1. Publications: 1.
Data from: Elucidation of molecular mechanisms of sex-based arrhythmias
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Data from: A molecular mechanism for bright color variation in parrots
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Data from: Cellular and molecular mechanisms that shape the development and evolution of tail vertebral proportion in mice and jerboas
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Molecular mechanism underlying SNARE-mediated membrane fusion enlightened by all-atom molecular dynamics simulations
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Transcriptome analysis of Drosophila suzukii reveals molecular mechanisms conferring pyrethroid and spinosad resistance
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Data from: Comparative transcriptomics revealed parallel evolution and innovation of photosymbiosis molecular mechanisms in a marine bivalve
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Quantum mechanical double slit for molecular scattering
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Molecular mechanism of SNHG11 in human osteosarcoma cells
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Parallel molecular mechanisms for enzyme temperature adaptation
<p><span>The mechanisms that underly the adaptation enzyme activities and stabilities to temperature are fundamental to our understanding of molecular evolution and how enzymes work. Herein, we investigate the molecular and evolutionary mechanisms of enzyme temperature adaption, combining deep mechanistic studies with comprehensive sequence analyses of thousands of enzymes. We show that temperature adaptation in ketosteroid isomerase (KSI) arises primarily from one residue change with limited, local epistasis</span><span> and we establish the underlying physical mechanisms</span><span>. </span>This residue change occurs in diverse KSI backgrounds, suggesting parallel adaptation to temperature. We identify residues associated with organismal growth temperature in 1005 diverse bacterial enzyme families, suggesting widespread parallel adaptation. We assess the properties of these residues, molecular interactions and interaction networks that appear to underly temperature adaptation.</p>
TRACE Dataset: Predicting molecular mechanisms of hereditary diseases by using their tissue-selective manifestation
<p>Features dataset, as described in Simonovsky, Eyal, et al. "Predicting molecular mechanisms of hereditary diseases by using their tissue‐selective manifestation." <i>Molecular Systems Biology</i> (2023): e11407.</p><p>Article: https://doi.org/10.15252/msb.202211407</p><p>Code: https://github.com/eyalsim/trace</p>
An Integrated Protocol for Exploring Molecular Mechanisms of Schizophrenia Using DNA Microarray Datasets
<p>The gene expression matrices, annotation information of probes and sample descriptions for GSE87610, GSE92538, GSE93577 and GSE93987. </p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.