Lipid droplets as substrates for protein phase separation
Biophys J. 2024 Mar 9:S0006-3495(24)00180-2. doi: 10.1016/j.bpj.2024.03.015. Online ahead of print.ABSTRACTMembrane-associated protein phase separation plays critical roles in cell biology, driving essential cellular phenomena from immune signaling to membrane traffic. Importantly, by reducing dimensionality from three to two dimensions, lipid bilayers can nucleate phase separation at far lower concentrations compared to those required for phase separation in solution. How might other intracellular lipid substrates, such as lipid droplets, contribute to nucleation of phase separation? Distinct from bilayer membranes, lipid...
Source: Biophysical Journal - March 11, 2024 Category: Physics Authors: Advika Kamatar Jack P K Bravo Feng Yuan Liping Wang Eileen M Lafer David W Taylor Jeanne C Stachowiak Sapun H Parekh Source Type: research
The open channel state in anion channelrhodopsin GtACR1 is a red-absorbing intermediate
We report evidence for a red-absorbing intermediate being responsible for channel opening.PMID:38462839 | DOI:10.1016/j.bpj.2024.03.006 (Source: Biophysical Journal)
Source: Biophysical Journal - March 11, 2024 Category: Physics Authors: Istvan Szundi David S Kliger Source Type: research
Taking mechanomicrobiology from local to global
Biophys J. 2024 Mar 8:S0006-3495(24)00179-6. doi: 10.1016/j.bpj.2024.03.014. Online ahead of print.NO ABSTRACTPMID:38461369 | DOI:10.1016/j.bpj.2024.03.014 (Source: Biophysical Journal)
Source: Biophysical Journal - March 10, 2024 Category: Physics Authors: W R Harcombe Source Type: research
Coupling of zinc and GTP binding drives G-domain folding in Acinetobacter baumannii ZigA
Biophys J. 2024 Mar 8:S0006-3495(24)00175-9. doi: 10.1016/j.bpj.2024.03.010. Online ahead of print.ABSTRACTCOG0523 proteins, also known as nucleotide-dependent metallochaperones, are a poorly understood class of small P-loop G3E GTPases. Multiple family members play critical roles in bacterial pathogen survival during an infection as part of the adaptive response to host-mediated "nutritional immunity." Our understanding of the structure, dynamics, and molecular-level function of COG0523 proteins, apart from the eukaryotic homologue, Zng1, remains in its infancy. Here, we use X-ray absorption spectroscopy to establish that...
Source: Biophysical Journal - March 9, 2024 Category: Physics Authors: Maximillian K Osterberg Ally Smith Courtney Campbell Daniel Deredge Timothy L Stemmler David P Giedroc Source Type: research
The ATPase Asymmetry: Novel Computational Insight into Coupling Diverse F < sub > O < /sub > Motors with Tripartite F < sub > 1 < /sub >
This study investigates the coupling patterns between 8- and 9-fold FO motors and the constant 3-fold F1 motor using coarse-grained molecular dynamics (MD) simulations. We unveil that in the case of a 9-fold FO motor, a 3-3-3 motion is most likely to occur, while a 3-3-2 motion predominates with an 8-fold FO motor. Furthermore, our findings propose a revised model for the coupling method, elucidating that the pathways' energy usage is primarily influenced by F1 rotation and conformational changes hindered by the b-subunits. Our results present a crucial step towards comprehending the energy landscape and mechanisms governi...
Source: Biophysical Journal - March 9, 2024 Category: Physics Authors: Shintaroh Kubo Yasushi Okada Source Type: research
Mitigating Transcription Noise Via Protein Sharing in Syncytial Cells
Biophys J. 2024 Mar 8:S0006-3495(24)00174-7. doi: 10.1016/j.bpj.2024.03.009. Online ahead of print.ABSTRACTBursty transcription allows nuclei to concentrate the work of transcribing mRNA into short, intermittent intervals, potentially reducing transcriptional interference. However, bursts of mRNA production can increase noise in protein abundances. Here we formulate models for gene expression in syncytia, or multinucleate cells, showing that protein abundance noise may be mitigated locally via spatial averaging of diffuse proteins. Our modeling shows a universal reduction in protein noise, that increases with the average n...
Source: Biophysical Journal - March 9, 2024 Category: Physics Authors: Alex Mayer Jiayu Li Grace McLaughlin Amy Gladfelter Marcus Roper Source Type: research
Coupling of zinc and GTP binding drives G-domain folding in Acinetobacter baumannii ZigA
Biophys J. 2024 Mar 8:S0006-3495(24)00175-9. doi: 10.1016/j.bpj.2024.03.010. Online ahead of print.ABSTRACTCOG0523 proteins, also known as nucleotide-dependent metallochaperones, are a poorly understood class of small P-loop G3E GTPases. Multiple family members play critical roles in bacterial pathogen survival during an infection as part of the adaptive response to host-mediated "nutritional immunity." Our understanding of the structure, dynamics, and molecular-level function of COG0523 proteins, apart from the eukaryotic homologue, Zng1, remains in its infancy. Here, we use X-ray absorption spectroscopy to establish that...
Source: Biophysical Journal - March 9, 2024 Category: Physics Authors: Maximillian K Osterberg Ally Smith Courtney Campbell Daniel Deredge Timothy L Stemmler David P Giedroc Source Type: research
The ATPase Asymmetry: Novel Computational Insight into Coupling Diverse F < sub > O < /sub > Motors with Tripartite F < sub > 1 < /sub >
This study investigates the coupling patterns between 8- and 9-fold FO motors and the constant 3-fold F1 motor using coarse-grained molecular dynamics (MD) simulations. We unveil that in the case of a 9-fold FO motor, a 3-3-3 motion is most likely to occur, while a 3-3-2 motion predominates with an 8-fold FO motor. Furthermore, our findings propose a revised model for the coupling method, elucidating that the pathways' energy usage is primarily influenced by F1 rotation and conformational changes hindered by the b-subunits. Our results present a crucial step towards comprehending the energy landscape and mechanisms governi...
Source: Biophysical Journal - March 9, 2024 Category: Physics Authors: Shintaroh Kubo Yasushi Okada Source Type: research
Mitigating Transcription Noise Via Protein Sharing in Syncytial Cells
Biophys J. 2024 Mar 8:S0006-3495(24)00174-7. doi: 10.1016/j.bpj.2024.03.009. Online ahead of print.ABSTRACTBursty transcription allows nuclei to concentrate the work of transcribing mRNA into short, intermittent intervals, potentially reducing transcriptional interference. However, bursts of mRNA production can increase noise in protein abundances. Here we formulate models for gene expression in syncytia, or multinucleate cells, showing that protein abundance noise may be mitigated locally via spatial averaging of diffuse proteins. Our modeling shows a universal reduction in protein noise, that increases with the average n...
Source: Biophysical Journal - March 9, 2024 Category: Physics Authors: Alex Mayer Jiayu Li Grace McLaughlin Amy Gladfelter Marcus Roper Source Type: research
How and When to Measure Mitochondrial Inner Membrane Potentials
Biophys J. 2024 Mar 6:S0006-3495(24)00176-0. doi: 10.1016/j.bpj.2024.03.011. Online ahead of print.ABSTRACTThe scientific literature on mitochondria has increased significantly over the years, due to findings that these organelles have widespread roles in the onset and progression of pathological conditions such as metabolic disorders, neurodegenerative and cardiovascular diseases, inflammation, and cancer. Researchers have extensively explored how mitochondrial properties and functions are modified in different models, often using fluorescent inner mitochondrial membrane potential (ΔΨm) probes to assess functional mitoc...
Source: Biophysical Journal - March 8, 2024 Category: Physics Authors: Alicia J Kowaltowski Fernando Abdulkader Source Type: research
Hydration Water Drives the Self-assembly of Guanosine Monophosphate
We present the temperature-dependent terahertz (1.5-12 THz, 50-400 cm-1) absorptivity spectra of aqueous Na2GMP solution (GMP) in comparison with the aqueous solutions of other RNA nucleotides. Distinct absorption features were observed in the spectrum of GMP, which we attribute to the intramolecular modes of the self-assemblies (i.e., G-complexes) that, at 1 M, start to form at 313 K and below. Changes in broad band features of the terahertz spectrum were also observed, which we associate with the release of hydration water in the temperature-dependent formation of G-quadruplex (G4). Using a state-of-the-art THz calorimet...
Source: Biophysical Journal - March 8, 2024 Category: Physics Authors: Yu Heng Tao Simon Schulke Gerhard Schwaab Gareth L Nealon Simone Pezzotti Stuart I Hodgetts Alan R Harvey Vincent P Wallace Martina Havenith Source Type: research
Interplay between environmental yielding and dynamic forcing modulates bacterial growth
Biophys J. 2024 Mar 7:S0006-3495(24)00173-5. doi: 10.1016/j.bpj.2024.03.008. Online ahead of print.ABSTRACTMany bacterial habitats-ranging from gels and tissues in the body to cell-secreted exopolysaccharides in biofilms-are rheologically complex, undergo dynamic external forcing, and have unevenly-distributed nutrients. How do these features jointly influence how the resident cells grow and proliferate? Here, we address this question by studying the growth of Escherichia coli dispersed in granular hydrogel matrices with defined and highly-tunable structural and rheological properties, under different amounts of external f...
Source: Biophysical Journal - March 8, 2024 Category: Physics Authors: Anna M Hancock Sujit S Datta Source Type: research
How and When to Measure Mitochondrial Inner Membrane Potentials
Biophys J. 2024 Mar 6:S0006-3495(24)00176-0. doi: 10.1016/j.bpj.2024.03.011. Online ahead of print.ABSTRACTThe scientific literature on mitochondria has increased significantly over the years, due to findings that these organelles have widespread roles in the onset and progression of pathological conditions such as metabolic disorders, neurodegenerative and cardiovascular diseases, inflammation, and cancer. Researchers have extensively explored how mitochondrial properties and functions are modified in different models, often using fluorescent inner mitochondrial membrane potential (ΔΨm) probes to assess functional mitoc...
Source: Biophysical Journal - March 8, 2024 Category: Physics Authors: Alicia J Kowaltowski Fernando Abdulkader Source Type: research
Hydration Water Drives the Self-assembly of Guanosine Monophosphate
We present the temperature-dependent terahertz (1.5-12 THz, 50-400 cm-1) absorptivity spectra of aqueous Na2GMP solution (GMP) in comparison with the aqueous solutions of other RNA nucleotides. Distinct absorption features were observed in the spectrum of GMP, which we attribute to the intramolecular modes of the self-assemblies (i.e., G-complexes) that, at 1 M, start to form at 313 K and below. Changes in broad band features of the terahertz spectrum were also observed, which we associate with the release of hydration water in the temperature-dependent formation of G-quadruplex (G4). Using a state-of-the-art THz calorimet...
Source: Biophysical Journal - March 8, 2024 Category: Physics Authors: Yu Heng Tao Simon Schulke Gerhard Schwaab Gareth L Nealon Simone Pezzotti Stuart I Hodgetts Alan R Harvey Vincent P Wallace Martina Havenith Source Type: research
Interplay between environmental yielding and dynamic forcing modulates bacterial growth
Biophys J. 2024 Mar 7:S0006-3495(24)00173-5. doi: 10.1016/j.bpj.2024.03.008. Online ahead of print.ABSTRACTMany bacterial habitats-ranging from gels and tissues in the body to cell-secreted exopolysaccharides in biofilms-are rheologically complex, undergo dynamic external forcing, and have unevenly-distributed nutrients. How do these features jointly influence how the resident cells grow and proliferate? Here, we address this question by studying the growth of Escherichia coli dispersed in granular hydrogel matrices with defined and highly-tunable structural and rheological properties, under different amounts of external f...
Source: Biophysical Journal - March 8, 2024 Category: Physics Authors: Anna M Hancock Sujit S Datta Source Type: research
