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

Author: Grafiati

Published: 25 May 2024

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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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11

Rakhimov, Adil, Miras Zekebayev, Aray Kuatbek, and Vyacheslav Dyachkov. "Comparison of dosimetry parameters of three-dimensional conformational radiation therapy and volumetric modulated arc therapy on the example of treatment of a patient with salivary gland adenocarcinoma." Oncologia i radiologia Kazakhstana 59, no. 1 (2021): 25–30. http://dx.doi.org/10.52532/2521-6414-2021-1-59-25-30.

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Relevance: An optimal choice of radiation therapy method is the main prerequisite for successful completion of treatment. Continuous analysis of radiation therapy methods’ advantages and comparing their parameters and dose load in typical cases will serve to increase the treatment efficacy and reduce the unavoidable load on critical organs. Purpose: To check the plans of treatment by volumetric modulated arc therapy (VMAT) and three-dimensional conformal radiation therapy (3D-CRT) methods, make their comparison, and identify the advantages using an exa

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12

Tissino, Erika, Tamara Bittolo, Dania Benedetti, et al. "The VLA-4 Integrin Is Constitutively Activated in a Subset of CD49d-Expressing CLL: A Relationship with the Autonomous BCR-Mediated Signaling?" Blood 132, Supplement 1 (2018): 5531. http://dx.doi.org/10.1182/blood-2018-99-111450.

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Abstract Introduction. In chronic lymphocytic leukemia (CLL), CD49d, the alpha chain of the heterodimer CD49d/CD29 (VLA-4), is a strong negative prognosticator, and a key player of tumor cell-microenvironment interactions. The adhesive properties of VLA-4 can be rapidly inside-out activated by signals through the B-cell receptor (BCR), thus favoring the capability of the integrin to interact with its specific ligands. In this context, VLA-4 needs to be maintained in an activated state by a continuous stream of inside-out signals from the BCR, which can be triggered by canonical antigens as wel

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13

Harastani, Mohamad, Mikhail Eltsov, Amélie Leforestier, and Slavica Jonic. "HEMNMA-3D: Cryo Electron Tomography Method Based on Normal Mode Analysis to Study Continuous Conformational Variability of Macromolecular Complexes." Frontiers in Molecular Biosciences 8 (May 19, 2021). http://dx.doi.org/10.3389/fmolb.2021.663121.

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Cryogenic electron tomography (cryo-ET) allows structural determination of biomolecules in their native environment (in situ). Its potential of providing information on the dynamics of macromolecular complexes in cells is still largely unexploited, due to the challenges of the data analysis. The crowded cell environment and continuous conformational changes of complexes make difficult disentangling the data heterogeneity. We present HEMNMA-3D, which is, to the best of our knowledge, the first method for analyzing cryo electron subtomograms in terms of continuous conformational changes of compl

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14

Dsouza, Raison, Ghoncheh Mashayekhi, Roshanak Etemadpour, Peter Schwander, and Abbas Ourmazd. "Energy landscapes from cryo-EM snapshots: a benchmarking study." Scientific Reports 13, no. 1 (2023). http://dx.doi.org/10.1038/s41598-023-28401-w.

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AbstractBiomolecules undergo continuous conformational motions, a subset of which are functionally relevant. Understanding, and ultimately controlling biomolecular function are predicated on the ability to map continuous conformational motions, and identify the functionally relevant conformational trajectories. For equilibrium and near-equilibrium processes, function proceeds along minimum-energy pathways on one or more energy landscapes, because higher-energy conformations are only weakly occupied. With the growing interest in identifying functional trajectories, the need for reliable mapping

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15

Dashti, Ali, Ghoncheh Mashayekhi, Mrinal Shekhar, et al. "Retrieving functional pathways of biomolecules from single-particle snapshots." Nature Communications 11, no. 1 (2020). http://dx.doi.org/10.1038/s41467-020-18403-x.

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Abstract A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Sustained effort has resulted in an impressive arsenal of tools for determining the static structures. But under physiological conditions, macromolecules undergo continuous conformational changes, a subset of which are functionally important. Techniques for capturing the continuous conformational changes underlying function are essential for further progress. Here, we present chemically-detailed conformational movies of bio

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16

Nierzwicki, Łukasz, and Giulia Palermo. "Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules." Frontiers in Molecular Biosciences 8 (April 5, 2021). http://dx.doi.org/10.3389/fmolb.2021.641208.

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Single-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today’s cryo-EM maps can frequently reach the atomic-level resolution, while often containing a range of resolutions, with conformationally variable regions obtained at 6 Å or worse. Low resolution density maps obtained for protein flexible domains, as well as the ensemble of coexisting conformational states arising from cryo-EM, poses new challenges and opportuni

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17

Bogetti, Xiaowei, and Sunil Kumar Saxena. "Integrating Electron Paramagnetic Resonance Spectroscopy and Computational Modeling to Measure Protein Structure and Dynamics." ChemPlusChem, October 6, 2023. http://dx.doi.org/10.1002/cplu.202300506.

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Electron paramagnetic resonance (EPR) has become a powerful probe of conformational heterogeneity and dynamics of biomolecules. In this review, we discuss different computational modeling techniques that enrich the interpretation of EPR measurements of dynamics or distance restraints. A variety of spin labels are surveyed to provide a background for the discussion of modeling tools. Molecular dynamics (MD) simulations of models containing spin labels provide dynamical properties of biomolecules and their labels. These simulations can be used to predict EPR spectra, sample stable conformations

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18

Vuillemot, Rémi, Isabelle Rouiller, and Slavica Jonić. "MDTOMO method for continuous conformational variability analysis in cryo electron subtomograms based on molecular dynamics simulations." Scientific Reports 13, no. 1 (2023). http://dx.doi.org/10.1038/s41598-023-37037-9.

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AbstractCryo electron tomography (cryo-ET) allows observing macromolecular complexes in their native environment. The common routine of subtomogram averaging (STA) allows obtaining the three-dimensional (3D) structure of abundant macromolecular complexes, and can be coupled with discrete classification to reveal conformational heterogeneity of the sample. However, the number of complexes extracted from cryo-ET data is usually small, which restricts the discrete-classification results to a small number of enough populated states and, thus, results in a largely incomplete conformational landscap

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19

Giraldo-Barreto, Julian, Sebastian Ortiz, Erik H. Thiede, et al. "A Bayesian approach to extracting free-energy profiles from cryo-electron microscopy experiments." Scientific Reports 11, no. 1 (2021). http://dx.doi.org/10.1038/s41598-021-92621-1.

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AbstractCryo-electron microscopy (cryo-EM) extracts single-particle density projections of individual biomolecules. Although cryo-EM is widely used for 3D reconstruction, due to its single-particle nature it has the potential to provide information about a biomolecule’s conformational variability and underlying free-energy landscape. However, treating cryo-EM as a single-molecule technique is challenging because of the low signal-to-noise ratio (SNR) in individual particles. In this work, we propose the cryo-BIFE method (cryo-EM Bayesian Inference of Free-Energy profiles), which uses a path co

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20

Zhang, Jingxing, Rundong Wu, Yancong Feng, et al. "Optically Tunable Multistable Liquid Crystal Grating for Anti‐Counterfeiting through Multilayer Continuous Phase Analysis." Advanced Optical Materials, March 27, 2024. http://dx.doi.org/10.1002/adom.202302423.

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AbstractOptically tunable liquid‐crystal (LC) gratings have remarkable applications in the field of image analysis for anti‐counterfeiting. However, existing tunable LC gratings suffer from limited adjustable ranges and weak stability. The spacing variability and accuracy of the grating cannot satisfy the demands of continuous analysis. This study presents a novel approach to anti‐counterfeiting through multilayer continuous phase analysis (MCPA) based on the continuous multistable states of the LC grating. This optically tunable LC grating featuring continuous multistable states is successful

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21

Punjani, Ali, and David J. Fleet. "3DFlex: determining structure and motion of flexible proteins from cryo-EM." Nature Methods, May 11, 2023. http://dx.doi.org/10.1038/s41592-023-01853-8.

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AbstractModeling flexible macromolecules is one of the foremost challenges in single-particle cryogenic-electron microscopy (cryo-EM), with the potential to illuminate fundamental questions in structural biology. We introduce Three-Dimensional Flexible Refinement (3DFlex), a motion-based neural network model for continuous molecular heterogeneity for cryo-EM data. 3DFlex exploits knowledge that conformational variability of a protein is often the result of physical processes that transport density over space and tend to preserve local geometry. From two-dimensional image data, 3DFlex enables t

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22

Harastani, Mohamad, Rémi Vuillemot, Ilyes Hamitouche, Nima Barati Moghadam, and Slavica Jonic. "ContinuousFlex: Software package for analyzing continuous conformational variability of macromolecules in cryo electron microscopy and tomography data." Journal of Structural Biology, October 2022, 107906. http://dx.doi.org/10.1016/j.jsb.2022.107906.

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23

Ribeiro, I., F. Pires, C. R. C. Calado, and M. Gallard. Molina. "P–769 FTIR spectroscopy analysis reveals differences between human embryo culture media composition by type of formulation and by manufacturer." Human Reproduction 36, Supplement_1 (2021). http://dx.doi.org/10.1093/humrep/deab130.768.

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Abstract Study question Can we detect the variation in different commercial human embryo culture media composition by Fourier-transform infrared (FTIR) spectroscopic analysis? Summary answer The spectra reveals distint features that allow distinguishing between continuous and sequential media, as well as between manufacturers of the same media type. What is known already: Manufacturers do not fully disclose commercially available culture media formulations. For this reason, it is important to gain insight into de differences between the available formulations, in order to understand how they m

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24

Reynolds, Matthew J., Carla Hachicho, Ayala G. Carl, Rui Gong, and Gregory M. Alushin. "Bending forces and nucleotide state jointly regulate F-actin structure." Nature, October 26, 2022. http://dx.doi.org/10.1038/s41586-022-05366-w.

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AbstractATP-hydrolysis-coupled actin polymerization is a fundamental mechanism of cellular force generation1–3. In turn, force4,5 and actin filament (F-actin) nucleotide state6 regulate actin dynamics by tuning F-actin’s engagement of actin-binding proteins through mechanisms that are unclear. Here we show that the nucleotide state of actin modulates F-actin structural transitions evoked by bending forces. Cryo-electron microscopy structures of ADP–F-actin and ADP-Pi–F-actin with sufficient resolution to visualize bound solvent reveal intersubunit interfaces bridged by water molecules that cou

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25

Holguin, Bianka A., Zacariah L. Hildenbrand, and Ricardo A. Bernal. "Insights Into the Role of Heat Shock Protein 27 in the Development of Neurodegeneration." Frontiers in Molecular Neuroscience 15 (March 30, 2022). http://dx.doi.org/10.3389/fnmol.2022.868089.

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Small heat shock protein 27 is a critically important chaperone, that plays a key role in several essential and varied physiological processes. These include thermotolerance, apoptosis, cytoskeletal dynamics, cell differentiation, protein folding, among others. Despite its relatively small size and intrinsically disordered termini, it forms large and polydisperse oligomers that are in equilibrium with dimers. This equilibrium is driven by transient interactions between the N-terminal region, the α-crystallin domain, and the C-terminal region. The continuous redistribution of binding partners r

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