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, and 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, no. 1 (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, no. 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, and Po-Lin Chiu. "Probing Structural Perturbation of Biomolecules by Extracting Cryo-EM Data Heterogeneity." Biomolecules 12, no. 5 (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, et al. "Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy." Acta Crystallographica Section F Structural Biology Communications 75, no. 1 (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, and Yingwei Li. "High Frequency Electromagnetic Radiation Stimulates Neuronal Growth and Hippocampal Synaptic Transmission." Brain Sciences 13, no. 4 (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, and 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, no. 6 (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, and T. Schimmel. "Adsorption Behaviour of Creatine Phosphokinase onto Silicon Wafers: Comparison between Ellipsometric and Atomic Force Microscopy Data." Microscopy and Microanalysis 11, S03 (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, and Slavica Jonic. "TomoFlow: Analysis of Continuous Conformational Variability of Macromolecules in Cryogenic Subtomograms based on 3D Dense Optical Flow." Journal of Molecular Biology 434, no. 2 (2022): 167381. http://dx.doi.org/10.1016/j.jmb.2021.167381.

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Wang, Chenzheng, Yuexia Lin, Devin Bougie, and Richard E. Gillilan. "Predicting data quality in biological X-ray solution scattering." Acta Crystallographica Section D Structural Biology 74, no. 8 (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, et al. "Monitoring decellularization via absorbance spectroscopy during the derivation of extracellular matrix scaffolds." Biomedical Materials 17, no. 1 (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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