Robust spatiotemporal organization of mitotic events in mechanically perturbed C. elegans embryos
Biophys J. 2024 Apr 3:S0006-3495(24)00243-1. doi: 10.1016/j.bpj.2024.03.041. Online ahead of print.ABSTRACTEarly embryogenesis of the nematode Caenorhabditis elegans progresses in an autonomous fashion within a protective chitin eggshell. Cell division timing and the subsequent, mechanically guided positioning of cells is virtually invariant between individuals, especially before gastrulation. Here, we have challenged this stereotypical developmental program in early stages by mechanically perturbing the embryo, without breaking its eggshell. Compressing embryos to about 2/3 of their unperturbed diameter only resulted in m...
Source: Biophysical Journal - April 5, 2024 Category: Physics Authors: Vincent Borne Matthias Weiss Source Type: research
Base Pair Dynamics, Electrostatics, and Thermodynamics at the LTR-III Quadruplex:Duplex Junction
Biophys J. 2024 Apr 3:S0006-3495(24)00244-3. doi: 10.1016/j.bpj.2024.03.042. Online ahead of print.ABSTRACTG-quadruplexes (GQs) play key regulatory roles within the human genome and have also been identified to play similar roles in other eukaryotes, bacteria, archaea, and viruses. Human immunodeficiency virus 1 (HIV-1), the etiological agent of acquired immunodeficiency syndrome (AIDS), can form two GQs in its long terminal repeat (LTR) promoter region, each of which act to regulate viral gene expression in opposing manners. The major LTR GQ, called LTR-III, is a distinct hybrid GQ containing a 12-nucleotide duplex loop a...
Source: Biophysical Journal - April 5, 2024 Category: Physics Authors: Haley M Michel Justin A Lemkul Source Type: research
AI in Cellular Engineering and Reprogramming
Biophys J. 2024 Apr 4:S0006-3495(24)00245-5. doi: 10.1016/j.bpj.2024.04.001. Online ahead of print.ABSTRACTDuring the last decade, Artificial Intelligence (AI) has increasingly been applied in biophysics and related fields, including cellular engineering and reprogramming, offering novel approaches to understand, manipulate, and control cellular function. The potential of AI lies in its ability to analyze complex datasets and generate predictive models. AI algorithms can process large amounts of data from single-cell genomics and multiomic technologies, allowing researchers to gain mechanistic insights into the control of ...
Source: Biophysical Journal - April 5, 2024 Category: Physics Authors: Sara Capponi Shangying Wang Source Type: research
The rotamer of the second sphere histidine in AA9 Lytic polysaccharide monooxygenase is pH-dependent
Biophys J. 2024 Apr 2:S0006-3495(24)00246-7. doi: 10.1016/j.bpj.2024.04.002. Online ahead of print.ABSTRACTLytic polysaccharides monooxygenases (LPMOs) catalyze a reaction that is crucial for the biological decomposition of various biopolymers and for the industrial conversion of plant biomass. Despite the importance of LPMOs, the exact molecular-level nature of the reaction mechanism is still debated today. Here, we investigated the pH dependent conformation of a second sphere histidine (His) that we call the "stacking histidine", which is conserved in fungal AA9 LPMOs, and is speculated to assist catalysis in several of ...
Source: Biophysical Journal - April 4, 2024 Category: Physics Authors: Ingvild Isaksen Suvamay Jana Christina M Payne Bastien Bissaro Åsmund K Røhr Source Type: research
Energy landscapes of homopolymeric RNAs revealed by deep unsupervised learning
Biophys J. 2024 Apr 2:S0006-3495(24)00247-9. doi: 10.1016/j.bpj.2024.04.003. Online ahead of print.ABSTRACTConformational dynamics of RNA plays crucial for variety of cellular functions including acting as regulators of gene expression to being molecular scaffolds and sensors. The liquid-liquid phase separation of RNAs and the formation of stress granules partly relies on RNA's conformational plasticity and its ability to engage in multivalent interactions. Recent experiments with homopolymeric and low-complexity RNAs have revealed significant differences in phase separations due to differences in base chemistry of RNA uni...
Source: Biophysical Journal - April 4, 2024 Category: Physics Authors: Vysakh Ramachandran Davit A Potoyan Source Type: research
The rotamer of the second sphere histidine in AA9 Lytic polysaccharide monooxygenase is pH-dependent
Biophys J. 2024 Apr 2:S0006-3495(24)00246-7. doi: 10.1016/j.bpj.2024.04.002. Online ahead of print.ABSTRACTLytic polysaccharides monooxygenases (LPMOs) catalyze a reaction that is crucial for the biological decomposition of various biopolymers and for the industrial conversion of plant biomass. Despite the importance of LPMOs, the exact molecular-level nature of the reaction mechanism is still debated today. Here, we investigated the pH dependent conformation of a second sphere histidine (His) that we call the "stacking histidine", which is conserved in fungal AA9 LPMOs, and is speculated to assist catalysis in several of ...
Source: Biophysical Journal - April 4, 2024 Category: Physics Authors: Ingvild Isaksen Suvamay Jana Christina M Payne Bastien Bissaro Åsmund K Røhr Source Type: research
Energy landscapes of homopolymeric RNAs revealed by deep unsupervised learning
Biophys J. 2024 Apr 2:S0006-3495(24)00247-9. doi: 10.1016/j.bpj.2024.04.003. Online ahead of print.ABSTRACTConformational dynamics of RNA plays crucial for variety of cellular functions including acting as regulators of gene expression to being molecular scaffolds and sensors. The liquid-liquid phase separation of RNAs and the formation of stress granules partly relies on RNA's conformational plasticity and its ability to engage in multivalent interactions. Recent experiments with homopolymeric and low-complexity RNAs have revealed significant differences in phase separations due to differences in base chemistry of RNA uni...
Source: Biophysical Journal - April 4, 2024 Category: Physics Authors: Vysakh Ramachandran Davit A Potoyan Source Type: research
Contribution of different macromolecules to the diffusion of a 40 nm particle in Escherichia coli
In this study, we sought to quantify the crowding experienced by an exogenous 40 nm fluorescent particle in the cytoplasm of E. coli under different growth conditions. By performing single particle tracking measurements in cells selectively depleted of DNA and/or mRNA, we determined the contribution to crowding of mRNA, DNA and remaining cellular components, i.e., mostly proteins and ribosomes. To estimate this contribution to crowding, we quantified the difference of the particle's diffusion coefficient in conditions with and without those macromolecules. We found that the contributions of the three classes of components ...
Source: Biophysical Journal - March 31, 2024 Category: Physics Authors: Jos é Losa Matthias Heinemann Source Type: research
An atomistic characterisation of high-density lipoprotein subpopulation models and the conserved 'LN' region of ApoA-I
This study reveals that previously characterised ellipsoidal HDL3a and HDL2a models revert to a more spherical geometry in an atomistic representation due to the enhanced conformational flexibility afforded to the apoA-I protein secondary structure, allowing for enhanced surface lipid packing and lower overall surface hydrophobicity. Indeed, the proportional surface hydrophobicity and apoA-I exposure reduced with increasing HDL size, consistent with previous characterisations. Furthermore, solvent exposure of the 'LN' region of apoA-I was exclusively limited to the smallest HDL3c model within the timescale of the simulatio...
Source: Biophysical Journal - March 31, 2024 Category: Physics Authors: Chris J Malajczuk Ricardo L Mancera Source Type: research
Contribution of different macromolecules to the diffusion of a 40 nm particle in Escherichia coli
In this study, we sought to quantify the crowding experienced by an exogenous 40 nm fluorescent particle in the cytoplasm of E. coli under different growth conditions. By performing single particle tracking measurements in cells selectively depleted of DNA and/or mRNA, we determined the contribution to crowding of mRNA, DNA and remaining cellular components, i.e., mostly proteins and ribosomes. To estimate this contribution to crowding, we quantified the difference of the particle's diffusion coefficient in conditions with and without those macromolecules. We found that the contributions of the three classes of components ...
Source: Biophysical Journal - March 31, 2024 Category: Physics Authors: Jos é Losa Matthias Heinemann Source Type: research
An atomistic characterisation of high-density lipoprotein subpopulation models and the conserved 'LN' region of ApoA-I
This study reveals that previously characterised ellipsoidal HDL3a and HDL2a models revert to a more spherical geometry in an atomistic representation due to the enhanced conformational flexibility afforded to the apoA-I protein secondary structure, allowing for enhanced surface lipid packing and lower overall surface hydrophobicity. Indeed, the proportional surface hydrophobicity and apoA-I exposure reduced with increasing HDL size, consistent with previous characterisations. Furthermore, solvent exposure of the 'LN' region of apoA-I was exclusively limited to the smallest HDL3c model within the timescale of the simulatio...
Source: Biophysical Journal - March 31, 2024 Category: Physics Authors: Chris J Malajczuk Ricardo L Mancera Source Type: research
Contribution of different macromolecules to the diffusion of a 40 nm particle in Escherichia coli
In this study, we sought to quantify the crowding experienced by an exogenous 40 nm fluorescent particle in the cytoplasm of E. coli under different growth conditions. By performing single particle tracking measurements in cells selectively depleted of DNA and/or mRNA, we determined the contribution to crowding of mRNA, DNA and remaining cellular components, i.e., mostly proteins and ribosomes. To estimate this contribution to crowding, we quantified the difference of the particle's diffusion coefficient in conditions with and without those macromolecules. We found that the contributions of the three classes of components ...
Source: Biophysical Journal - March 31, 2024 Category: Physics Authors: Jos é Losa Matthias Heinemann Source Type: research
An atomistic characterisation of high-density lipoprotein subpopulation models and the conserved 'LN' region of ApoA-I
This study reveals that previously characterised ellipsoidal HDL3a and HDL2a models revert to a more spherical geometry in an atomistic representation due to the enhanced conformational flexibility afforded to the apoA-I protein secondary structure, allowing for enhanced surface lipid packing and lower overall surface hydrophobicity. Indeed, the proportional surface hydrophobicity and apoA-I exposure reduced with increasing HDL size, consistent with previous characterisations. Furthermore, solvent exposure of the 'LN' region of apoA-I was exclusively limited to the smallest HDL3c model within the timescale of the simulatio...
Source: Biophysical Journal - March 31, 2024 Category: Physics Authors: Chris J Malajczuk Ricardo L Mancera Source Type: research
Contribution of different macromolecules to the diffusion of a 40 nm particle in Escherichia coli
In this study, we sought to quantify the crowding experienced by an exogenous 40 nm fluorescent particle in the cytoplasm of E. coli under different growth conditions. By performing single particle tracking measurements in cells selectively depleted of DNA and/or mRNA, we determined the contribution to crowding of mRNA, DNA and remaining cellular components, i.e., mostly proteins and ribosomes. To estimate this contribution to crowding, we quantified the difference of the particle's diffusion coefficient in conditions with and without those macromolecules. We found that the contributions of the three classes of components ...
Source: Biophysical Journal - March 31, 2024 Category: Physics Authors: Jos é Losa Matthias Heinemann Source Type: research
An atomistic characterisation of high-density lipoprotein subpopulation models and the conserved 'LN' region of ApoA-I
This study reveals that previously characterised ellipsoidal HDL3a and HDL2a models revert to a more spherical geometry in an atomistic representation due to the enhanced conformational flexibility afforded to the apoA-I protein secondary structure, allowing for enhanced surface lipid packing and lower overall surface hydrophobicity. Indeed, the proportional surface hydrophobicity and apoA-I exposure reduced with increasing HDL size, consistent with previous characterisations. Furthermore, solvent exposure of the 'LN' region of apoA-I was exclusively limited to the smallest HDL3c model within the timescale of the simulatio...
Source: Biophysical Journal - March 31, 2024 Category: Physics Authors: Chris J Malajczuk Ricardo L Mancera Source Type: research
