Sarcomere, troponin, and myosin X-ray diffraction signals can be resolved in single cardiomyocytes Tuesday, July 2, 2024 SIGNIFICANCE In the last decades, X-ray diffraction has advanced our understanding of filament activation dynamics in skeletal muscle. However, the structural dynamics of individual cardiac cells were so far elusive in the X-ray diffraction data due to ensemble averaging. We show that fourth generation synchrotron radiation, with an optimized beam preparation and balanced spatial resolution in real and reciprocal space enables the recording of high quality diffraction images for individual cardiac cells, including both equatorial and meridional reflection. Read more
Insight into Molecular Basis and Dynamics of Full-length CRaf Kinase in Cellular Signaling Mechanisms Saturday, June 29, 2024 Raf kinases play key roles in signal transduction in cells for regulating proliferation, differentiation, and survival. Despite decades of research into functions and dynamics of Raf kinases with respect to other cytosolic proteins, understanding Raf kinases is limited by the lack of their full-length structures at the atomic resolution. Here, we present the first model of the full-length CRaf kinase obtained from Artificial Intelligence/Machine Learning (AI/ML) algorithms with a converging ensemble of structures simulated by large-scale temperature replica exchange simulations. Read more
Bioelectricity and molecular signaling Saturday, June 29, 2024 With great pleasure, we share this special issue celebrating the contributions of Richard (Rick) Aldrich, our dear friend, colleague, and past president of the Biophysical Society. Read more
Core-shell model of the clusters of CPEB4 isoforms preceding liquid-liquid phase separation Friday, June 28, 2024 Protein solutions can undergo liquid-liquid phase separation (LLPS), where a dispersed phase with a low protein concentration coexists with coacervates with a high protein concentration. We focus on the low complexity N-terminal domain of cytoplasmic polyadenylation element binding-4 protein, CPEB4NTD, and its isoform depleted of the Exon4, CPEB4Δ4NTD. They both exhibit LLPS, but in contrast to most systems undergoing LLPS, the single-phase regime preceding LLPS consists mainly of soluble protein clusters. Read more
Conformational rigidity of thermophilic cytochrome c'-α is associated with slow binding of nitric oxide Wednesday, June 26, 2024 Cytochromes c′-α are nitric oxide (NO)-binding heme proteins derived from bacteria that can thrive in a wide range of temperature environments. Studies of mesophilic Alcaligenes xylosoxidans cytochrome c′-α (AxCP-α) have revealed an unusual NO-binding mechanism involving both heme faces, in which NO first binds to form a distal hexa-coordinate Fe(II)-NO (6cNO) intermediate and then displaces the proximal His to form a proximal penta-coordinate Fe(II)-NO (5cNO) final product. Here we characterize a thermally stable cytochrome c′-α from thermophilic Hydrogenophilus thermoluteolus (PhCP-α) to understand how protein thermal stability affects NO binding. Read more
Conformations of influenza A M2 protein in DOPC/DOPS and E. coli native lipids and proteins Tuesday, June 25, 2024 We compared the conformations of the transmembrane domain (TMD) of influenza A M2 (IM2) protein reconstituted in DOPC/DOPS bilayers to those in isolated E. coli membranes, having preserved its native proteins and lipids. IM2 is a single-pass transmembrane protein known to assemble into a homo-tetrameric proton channel. To represent this channel, we made a construct containing the IM2’s TMD region flanked by the juxtamembrane residues. The single cysteine substitution, L43C, of leucine located in the bilayer polar region was paramagnetically tagged with a methanethiosulfonate nitroxide label for the ESR (electron spin resonance) study. Read more
Automated Collective Variable Discovery for MFSD2A transporter from molecular dynamics simulations Tuesday, June 25, 2024 Biomolecules often exhibit complex free energy landscapes in which long-lived metastable states are separated by large energy barriers. Overcoming these barriers to robustly sample transitions between the metastable states with classical molecular dynamics (MD) simulations presents a challenge. To circumvent this issue, collective variable (CV)-based enhanced sampling MD approaches are often employed. Traditional CV selection relies on intuition and prior knowledge of the system. This approach introduces bias, which can lead to incomplete mechanistic insights. Read more
Hi-C guided many-polymer model to decipher 3D genome organization Tuesday, June 25, 2024 SIGNIFICANCE Knowledge on 3D genome structure is of paramount importance to gain accurate understanding of the impact of genome organization on cellular function. We propose a minimalist polymer physics approach that leverages Hi-C data as the sole input to reconstruct 3D genome structures. Demonstrating great versatility in modeling 3D genome structures, our method not only holds significant promise for future studies to decipher structure-function relationship at genomic level and the principles of 3D chromosome folding, but can also be extended to explore the effects of genomic plasticity across biological species on their speciation and evolution. Read more
Time-resolved fluorescence of tryptophan characterizes membrane perturbation by cyclic lipopeptides Friday, June 21, 2024 Viscosin is a membrane-permeabilizing, cyclic lipopeptide (CLiP) produced by Pseudomonas species. Here, we have studied four synthetic analogs (L1W, V4W, L5W, L7W), each with one leucine (Leu; L) or valine residue exchanged for tryptophan (Trp; W) by means of time-resolved fluorescence spectroscopy of Trp. To this end, we recorded the average fluorescence lifetime, rotational correlation time and limiting anisotropy, dipolar relaxation time and limiting extent of relaxation, rate constant of acrylamide quenching, effect of H2O-D2O exchange, and time-resolved halfwidth of the spectrum in the absence and presence of POPC liposomes. Read more
Modulating Ca2+ influx into adrenal chromaffin cells with short duration nanosecond electric pulses Friday, June 21, 2024 Isolated bovine adrenal chromaffin cells exposed to single 2, 4 or 5 ns pulses undergo a rapid, transient rise in intracellular Ca2+ mediated by Ca2+ entry via voltage-gated Ca2+ channels (VGCC), mimicking the activation of these cells in vivo by acetylcholine. However, pulse durations 150 ns or longer elicit larger amplitude and longer-lived Ca2+ responses due to Ca2+ influx via both VGCC and a yet to be identified plasma membrane pathway(s). To further our understanding of the differential effects of ultrashort versus longer pulse durations on Ca2+ influx, chromaffin cells were loaded with Calcium Green-1 and exposed to single 3, 5, 11, 25 or 50 ns pulses applied at their respective Ca2+ activation threshold electric fields. Read more
Coupling the role of lipids to the conformational dynamics of the ABC transporter P-glycoprotein Friday, June 21, 2024 The ATP-binding cassette transporter P-glycoprotein (P-gp) is a multidrug efflux pump that is overexpressed in a variety of cancers and associated with the drug-resistance phenomenon. P-gp structures were previously determined in detergent and in nanodiscs, in which different transmembrane helix conformations were found, “straight” and “kinked,” respectively, indicating a possible role of the lipid environment on the P-gp structural ensemble. Here, we investigate the dynamic conformational ensembles and protein-lipid interactions of two human P-gp inward-open conformers, straight and kinked, employing all-atom molecular dynamics (MD) simulations in asymmetric multicomponent lipid bilayers that mimic the highly specialized hepatocyte membrane in which P-gp is expressed. Read more
After the Gold Rush – Getting Far from the Shallow in Studying Asymmetric Membranes Wednesday, June 19, 2024 Read more