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Relevant bibliographies by topics / Continuous conformational variability of biomolecules

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Journal articles

Academic literature on the topic 'Continuous conformational variability of biomolecules'

Author: Grafiati

Published: 25 May 2024

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Journal articles on the topic "Continuous conformational variability of biomolecules"

1

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 classificati

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2

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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3

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 targe

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4

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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5

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

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6

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 ro

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7

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 conformation

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8

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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9

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

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10

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 a

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