Bibliografías temáticas / Continuous conformational variability of biomolecules

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Literatura académica sobre el tema "Continuous conformational variability of biomolecules"

Autor: Grafiati

Publicado: 25 de mayo de 2024

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Artículos de revistas sobre el tema "Continuous conformational variability of biomolecules"

Vuillemot, Rémi, Mohamad Harastani, Ilyes Hamitouche y Slavica Jonic. "MDSPACE and MDTOMO Software for Extracting Continuous Conformational Landscapes from Datasets of Single Particle Images and Subtomograms Based on Molecular Dynamics Simulations: Latest Developments in ContinuousFlex Software Package". International Journal of Molecular Sciences 25, n.º 1 (19 de diciembre de 2023): 20. http://dx.doi.org/10.3390/ijms25010020.

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Cryo electron microscopy (cryo-EM) instrumentation allows obtaining 3D reconstruction of the structure of biomolecular complexes in vitro (purified complexes studied by single particle analysis) and in situ (complexes studied in cells by cryo electron tomography). Standard cryo-EM approaches allow high-resolution reconstruction of only a few conformational states of a molecular complex, as they rely on data classification into a given number of classes to increase the resolution of the reconstruction from the most populated classes while discarding all other classes. Such discrete classification approaches result in a partial picture of the full conformational variability of the complex, due to continuous conformational transitions with many, uncountable intermediate states. In this article, we present the software with a user-friendly graphical interface for running two recently introduced methods, namely, MDSPACE and MDTOMO, to obtain continuous conformational landscapes of biomolecules by analyzing in vitro and in situ cryo-EM data (single particle images and subtomograms) based on molecular dynamics simulations of an available atomic model of one of the conformations. The MDSPACE and MDTOMO software is part of the open-source ContinuousFlex software package (starting from version 3.4.2 of ContinuousFlex), which can be run as a plugin of the Scipion software package (version 3.1 and later), broadly used in the cryo-EM field.

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Luchinat, Claudio. "Exploring the conformational heterogeneity of biomolecules: theory and experiments". Physical Chemistry Chemical Physics 18, n.º 8 (2016): 5684–85. http://dx.doi.org/10.1039/c6cp90029a.

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This themed collection reports on recent progress in the investigation of the conformational variability of biomolecules (proteins and nucleic acids), both from an experimental and theoretical point of view.

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DeVore, Kira y Po-Lin Chiu. "Probing Structural Perturbation of Biomolecules by Extracting Cryo-EM Data Heterogeneity". Biomolecules 12, n.º 5 (24 de abril de 2022): 628. http://dx.doi.org/10.3390/biom12050628.

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Single-particle cryogenic electron microscopy (cryo-EM) has become an indispensable tool to probe high-resolution structural detail of biomolecules. It enables direct visualization of the biomolecules and opens a possibility for averaging molecular images to reconstruct a three-dimensional Coulomb potential density map. Newly developed algorithms for data analysis allow for the extraction of structural heterogeneity from a massive and low signal-to-noise-ratio (SNR) cryo-EM dataset, expanding our understanding of multiple conformational states, or further implications in dynamics, of the target biomolecule. This review provides an overview that briefly describes the workflow of single-particle cryo-EM, including imaging and data processing, and new methods developed for analyzing the data heterogeneity to understand the structural variability of biomolecules.

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Sorzano, C. O. S., A. Jiménez, J. Mota, J. L. Vilas, D. Maluenda, M. Martínez, E. Ramírez-Aportela et al. "Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy". Acta Crystallographica Section F Structural Biology Communications 75, n.º 1 (1 de enero de 2019): 19–32. http://dx.doi.org/10.1107/s2053230x18015108.

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Single-particle analysis by electron microscopy is a well established technique for analyzing the three-dimensional structures of biological macromolecules. Besides its ability to produce high-resolution structures, it also provides insights into the dynamic behavior of the structures by elucidating their conformational variability. Here, the different image-processing methods currently available to study continuous conformational changes are reviewed.

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Ma, Shaoqing, Zhiwei Li, Shixiang Gong, Chengbiao Lu, Xiaoli Li y Yingwei Li. "High Frequency Electromagnetic Radiation Stimulates Neuronal Growth and Hippocampal Synaptic Transmission". Brain Sciences 13, n.º 4 (19 de abril de 2023): 686. http://dx.doi.org/10.3390/brainsci13040686.

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Terahertz waves lie within the rotation and oscillation energy levels of biomolecules, and can directly couple with biomolecules to excite nonlinear resonance effects, thus causing conformational or configuration changes in biomolecules. Based on this mechanism, we investigated the effect pattern of 0.138 THz radiation on the dynamic growth of neurons and synaptic transmission efficiency, while explaining the phenomenon at a more microscopic level. We found that cumulative 0.138 THz radiation not only did not cause neuronal death, but that it promoted the dynamic growth of neuronal cytosol and protrusions. Additionally, there was a cumulative effect of terahertz radiation on the promotion of neuronal growth. Furthermore, in electrophysiological terms, 0.138 THz waves improved synaptic transmission efficiency in the hippocampal CA1 region, and this was a slow and continuous process. This is consistent with the morphological results. This phenomenon can continue for more than 10 min after terahertz radiation ends, and these phenomena were associated with an increase in dendritic spine density. In summary, our study shows that 0.138 THz waves can modulate dynamic neuronal growth and synaptic transmission. Therefore, 0.138 terahertz waves may become a novel neuromodulation technique for modulating neuron structure and function.

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Valimehr, Sepideh, Rémi Vuillemot, Mohsen Kazemi, Slavica Jonic y Isabelle Rouiller. "Analysis of the Conformational Landscape of the N-Domains of the AAA ATPase p97: Disentangling the Continuous Conformational Variability in Partially Symmetrical Complexes". International Journal of Molecular Sciences 25, n.º 6 (16 de marzo de 2024): 3371. http://dx.doi.org/10.3390/ijms25063371.

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Single-particle cryo-electron microscopy (cryo-EM) has been shown to be effective in defining the structure of macromolecules, including protein complexes. Complexes adopt different conformations and compositions to perform their biological functions. In cryo-EM, the protein complexes are observed in solution, enabling the recording of images of the protein in multiple conformations. Various methods exist for capturing the conformational variability through analysis of cryo-EM data. Here, we analyzed the conformational variability in the hexameric AAA + ATPase p97, a complex with a six-fold rotational symmetric core surrounded by six flexible N-domains. We compared the performance of discrete classification methods with our recently developed method, MDSPACE, which uses 3D-to-2D flexible fitting of an atomic structure to images based on molecular dynamics (MD) simulations. Our analysis detected a novel conformation adopted by approximately 2% of the particles in the dataset and determined that the N-domains of p97 sway by up to 60° around a central position. This study demonstrates the application of MDSPACE in analyzing the continuous conformational changes in partially symmetrical protein complexes, systems notoriously difficult to analyze due to the alignment errors caused by their partial symmetry.

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Pancera, S. M., H. Gliemann, D. F. S. Petri y T. Schimmel. "Adsorption Behaviour of Creatine Phosphokinase onto Silicon Wafers: Comparison between Ellipsometric and Atomic Force Microscopy Data". Microscopy and Microanalysis 11, S03 (diciembre de 2005): 56–60. http://dx.doi.org/10.1017/s1431927605050889.

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Protein adsorption plays a major role in a variety of important technological and biological processes [1-2] and the understanding of the fundamental factors that determine protein adsorption are imperative to the development of biocompatible materials and biotechnological devices [3-4] as for example biosensors [5]. The adsorption of proteins on surfaces is a complex process. Due to the large size and different shapes of these adsorbing particles, the interactions between the adsorbed proteins on the surface can be strongly influentiated by the fact that the particles may undergo conformational changes upon adsorption [6-7]. In a previous work the adsorption behaviour of creatine phosphokinase (CPK) onto hydrophilic (silicon wafers and amino-terminated surfaces) and hydrophobic (Polystyrene, PS, coated wafers) substrates was investigated by means of null-ellipsometry and contact angle measurements [8]. This previous ellipsometric study led to a model, where CPK adsorption takes place in four stages: (i) a diffusive one, where all the arriving biomolecules are immediately adsorbed; (ii) the arriving biomolecules might stick on the latter and afterward diffuse to the free sites on the substrate, followed by conformational changes [6-7], (iii) formation of a monolayer and (iv) continuous and irreversible adsorption. A multilayer system might be formed, as well as aggregation processes might play a role at this stage. In this work Atomic Force Microscopy (AFM) measurements under water were done in order to confirm this four steps model and to observe changes in the film topography and homogeneity along the adsorption process. The thickness of the adsorbed CPK biofilm obtained by ellipsometry was also compared with that obtained by the wet AFM method.

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Harastani, Mohamad, Mikhail Eltsov, Amélie Leforestier y Slavica Jonic. "TomoFlow: Analysis of Continuous Conformational Variability of Macromolecules in Cryogenic Subtomograms based on 3D Dense Optical Flow". Journal of Molecular Biology 434, n.º 2 (enero de 2022): 167381. http://dx.doi.org/10.1016/j.jmb.2021.167381.

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Wang, Chenzheng, Yuexia Lin, Devin Bougie y Richard E. Gillilan. "Predicting data quality in biological X-ray solution scattering". Acta Crystallographica Section D Structural Biology 74, n.º 8 (24 de julio de 2018): 727–38. http://dx.doi.org/10.1107/s2059798318005004.

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Biological small-angle X-ray solution scattering (BioSAXS) is now widely used to gain information on biomolecules in the solution state. Often, however, it is not obvious in advance whether a particular sample will scatter strongly enough to give useful data to draw conclusions under practically achievable solution conditions. Conformational changes that appear to be large may not always produce scattering curves that are distinguishable from each other at realistic concentrations and exposure times. Emerging technologies such as time-resolved SAXS (TR-SAXS) pose additional challenges owing to small beams and short sample path lengths. Beamline optics vary in brilliance and degree of background scatter, and major upgrades and improvements to sources promise to expand the reach of these methods. Computations are developed to estimate BioSAXS sample intensity at a more detailed level than previous approaches, taking into account flux, energy, sample thickness, window material, instrumental background, detector efficiency, solution conditions and other parameters. The results are validated with calibrated experiments using standard proteins on four different beamlines with various fluxes, energies and configurations. The ability of BioSAXS to statistically distinguish a variety of conformational movements under continuous-flow time-resolved conditions is then computed on a set of matched structure pairs drawn from the Database of Macromolecular Motions (http://molmovdb.org). The feasibility of experiments is ranked according to sample consumption, a quantity that varies by over two orders of magnitude for the set of structures. In addition to photon flux, the calculations suggest that window scattering and choice of wavelength are also important factors given the short sample path lengths common in such setups.

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Mora-Navarro, Camilo, Mario E. Garcia, Prottasha Sarker, Emily W. Ozpinar, Jeffrey R. Enders, Saad Khan, Ryan C. Branski y Donald O. Freytes. "Monitoring decellularization via absorbance spectroscopy during the derivation of extracellular matrix scaffolds". Biomedical Materials 17, n.º 1 (26 de noviembre de 2021): 015008. http://dx.doi.org/10.1088/1748-605x/ac361f.

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Abstract Extracellular matrix (ECM) is a complex structure composed of bioactive molecules representative of the local tissue microenvironment. Decellularized ECM biomaterials harness these biomolecules for regenerative medicine applications. One potential therapeutic application is the use of vocal fold (VF) specific ECM to restore the VFs after injury. ECM scaffolds are derived through a process of decellularization, which aims to remove unwanted immunogenic biomolecules (e.g. DNA) while preserving the composition of the ECM. The effectiveness of the decellularization is typically assessed at the end by quantifying ECM attributes such as final dsDNA content. However, batch-to-batch variability in ECM manufacturing remains a significant challenge for the standardization, cost-effectiveness, and scale-up process. The limited number of tools available for in-process control heavily restricts the uncovering of the correlations between decellularization process parameters and ECM attributes. In this study, we developed a technique applicable to both the classical batch method and semi-continuous decellularization systems to trace the decellularization of two laryngeal tissues in real-time. We hypothesize that monitoring the bioreactor’s effluent absorbance at 260 nm as a function of time will provide a representative DNA release profile from the tissue and thus allow for process optimization. The DNA release profiles were obtained for laryngeal tissues and were successfully used to optimize the derivation of VF lamina propria-ECM (auVF-ECM) hydrogels. This hydrogel had comparable rheological properties to commonly used biomaterials to treat VF injuries. Also, the auVF-ECM hydrogel promoted the down-regulation of CCR7 by THP-1 macrophages upon lipopolysaccharide stimulation in vitro suggesting some anti-inflammatory properties. The results show that absorbance profiles are a good representation of DNA removal during the decellularization process thus providing an important tool to optimize future protocols.

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Tesis sobre el tema "Continuous conformational variability of biomolecules"

Harastani, Mohamad. "Image analysis methods development for in vitro and in situ cryo-electron tomography studies of conformational variability of biomolecular complexes : Case of nucleosome structural and dynamics studies". Electronic Thesis or Diss., Sorbonne université, 2022. http://www.theses.fr/2022SORUS283.

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La tomographie électronique cryogénique (cryo-TE) permet de visualiser des complexes biomoléculaires in situ. Les données 3D de biomolécules produites à l'aide de cryo-ET sont bruitées, souffrent d'anisotropies spatiales et sont difficiles à analyser individuellement. Les biomolécules sont flexibles et l'analyse de leur variabilité conformationnelle est nécessaire pour comprendre leurs mécanismes fonctionnels. Les méthodes standards de traitement de données de cryo-ET moyennent plusieurs copies de biomolécules individuelles pour obtenir des structures à des résolutions plus élevées et considèrent que la variabilité conformationnelle biomoléculaire est discrète plutôt que continue en utilisant la classification. Cette thèse présente les deux premières méthodes de traitement de données cryo-ET pour l'analyse de la variabilité conformationnelle continue biomoléculaire, HEMNMA-3D et TomoFlow. HEMNMA-3D analyse des données expérimentales avec les directions de mouvement simulées par l'Analyse de Modes Normaux et permet la découverte d'une large gamme de mouvements biomoléculaires. TomoFlow extrait des mouvements à partir des données en utilisant la technique de vision par ordinateur de Flux Optique. Je montre le potentiel de ces deux méthodes sur des données cryo-ET expérimentales de variabilité conformationnelle des nucléosomes dans les cellules. Les deux méthodes montrent des résultats cohérents, faisant la lumière sur la variabilité conformationnelle des nucléosomes dans les cellules
Cryogenic electron tomography (cryo-ET) allows visualizing biomolecular complexes in situ. 3D data of biomolecules produced using cryo-ET are noisy, suffer from spacial anisotropies, and are difficult to analyze individually. Biomolecules are flexible, and analyzing their conformational variability is necessary to understand their functional mechanisms. Standard cryo-ET data processing methods average multiple copies of individual biomolecules to obtain structures at higher resolutions and consider that biomolecular conformational variability is discrete rather than continuous using the classification. This thesis presents the first two cryo-ET data processing methods for analyzing biomolecular continuous conformational variability, HEMNMA-3D and TomoFlow. HEMNMA-3D analyzes experimental data with the motion directions simulated by Normal Mode Analysis and allows the discovery of a large range of biomolecular motions. TomoFlow extracts motions from the data using the computer vision technique of Optical Flow. I show the potential of these two methods on experimental cryo-ET data of nucleosome conformational variability in cells. The two methods show coherent results, shedding light on the conformational variability of nucleosomes in cells

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Hamitouche, Ilyes. "Machine learning for determining continuous conformational transitions of biomolecular complexes from single-particle cryo-electron microscopy images". Electronic Thesis or Diss., Sorbonne université, 2023. http://www.theses.fr/2023SORUS047.

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Au cours de mon travail de thèse, j'ai développé trois méthodes basées sur l'apprentissage profond pour extraire la variabilité conformationnelle continue des complexes biomoléculaires à partir d’images de cryo microscopie électronique de particules isolées. Les trois méthodes suivantes sont décrites dans ce manuscrit de thèse, ainsi que leurs résultats sur des données de test : DeepHEMNMA supervisée, Cryo-VIT supervisée, et Cryo-VIT non supervisée. DeepHEMNMA est une méthode de détermination rapide de l'espace conformationnel qui utilise un réseau de neurones convolutifs pour accélérer une méthode précédemment développée pour l'analyse conformationnelle continue, HEMNMA , qui combine une simulation du mouvement calculée par l'analyse des modes normaux (NMA) avec une approche de traitement d'image. Contrairement à DeepHEMNMA, les approches Cryo-ViT apprennent à faire correspondre chaque image à un grand nombre de coordonnées atomiques à l'aide d'un autoencodeur variationnel
During my thesis, I developed three methods based on deep learning to extract continuous conformational variability of biomolecular complexes from single-particle cryo electron microscopy images. The following three methods are described in this thesis manuscript, along with their results on test data: supervised DeepHEMNMA, supervised Cryo-VIT, and unsupervised Cryo-VIT. DeepHEMNMA is a fast conformational space determination method that uses a convolutional neural network to accelerate a previously developed method for continuous conformational analysis, HEMNMA , which combines a motion simulation computed by normal mode analysis (NMA) with an image processing approach. In contrast to DeepHEMNMA, the Cryo-ViT approaches learn to match each image to a large number of atomic coordinates using a variational autoencoder

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Actas de conferencias sobre el tema "Continuous conformational variability of biomolecules"

Hamitouche, Ilyes y Slavica Jonic. "Deep learning of elastic 3D shapes for cryo electron microscopy analysis of continuous conformational changes of biomolecules". En 2021 29th European Signal Processing Conference (EUSIPCO). IEEE, 2021. http://dx.doi.org/10.23919/eusipco54536.2021.9616013.

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