- by Gaur, P., Bain, F. E., Meah, R., Spies, M.The human genome contains numerous repetitive nucleotide sequences that display a propensity to fold into non-canonical DNA structures including G-quadruplexes (G4s). G4s have both positive and negative impacts on various aspects of nucleic acid metabolism including DNA replication, DNA repair and RNA transcription. Poly (ADP-ribose) polymerase (PARP1), an important anticancer drug target, has been recently shown to bind a subset of G4s, and to undergo auto-PARylation. The mechanism of this interaction, however, is poorly understood. Utilizing Mass Photometry (MP) and [β¦]
- by Lapsien, M., Bonus, M., Gahan, L., Raguin, A., Gohlke, H.We introduce PyPE_RESP, a tool to facilitate and standardize partial atomic charge derivation using the RESP approach. PyPE_RESP builds upon the open-source Python package RDKit for chemoinformatics and the AMBER suite for molecular simulations. PyPE_RESP provides an easy setup of multi-conformer and multi-molecule Re-strained Electrostatic Potential (RESP) fitting while allowing a comprehensive definition of charge constraint groups through multiple methods. As a command line tool, PyPE_RESP can be integrated into batch processes. The software enables the derivation of partial atomic [β¦]
- by Rufa, D., Fass, J., Chodera, J. D.Alchemical free energy methods using molecular mechanics (MM) force fields are essential tools for predicting thermodynamic properties of small molecules, especially via free energy calculations that can estimate quantities relevant for drug discovery such as affinities, selectivities, the impact of target mutations, and ADMET properties. While traditional MM forcefields rely on hand-crafted, discrete atom types and parameters, modern approaches based on graph neural networks (GNNs) learn continuous embedding vectors that represent chemical environments from which MM parameters can be generated. [β¦]
- by Santoro, G., Rolli, E., Ricci, A., Cademartiri, L.Response mechanisms preserve steady states in complex systems (including living systems). These mechanisms respond with characteristic timescales. Therefore, they can be identified and probed with oscillatory forcing. This approach is rarely used in plant biology. Sub-circadian intermittent illumination (i.e., square waves of light/dark periods of equal duration) of Arabidopsis thaliana plants cause remarkable phenotypical effects. We show these effects are highly dependent on the duration of the light-dark cycle, identifying characteristic timescales in three distinct windows (10.5-42 s, 168-336 s, [β¦]
- by Sheu, S.-S., Beutner, G., Yuh, H.-J., Goldenberg, I., Wallace, D., Porter, G., Moss, A. J.Studies have shown that low magnetic fields (LMFs) of less than 1 x 10-3 Tesla (T) affect numerous biological events, including bacteria and plant growth, bird migration, and human brain activity. On a cellular level, LMFs affect ion channel activities, intracellular Ca2+ concentrations, and mitochondrial reactive oxygen species (mROS) generation. However, the mechanisms that could account for these effects are controversial. Here, we show that applying a static LMF, ranging from ~2.7 x 10-4 to ~1.9 x 10-3 T, to [β¦]
- by Pokorna, P., Mlynsky, V., Sponer, J., Stadlbauer, P.RNA G-quadruplexes (rG4s) are vital structural elements in gene regulation and genome stability. In untranslated regions of mRNAs, rG4s influence translation efficiency and mRNA localization. Additionally, rG4s of long non-coding RNAs and telomeric RNA play roles in RNA processing and cellular aging. Despite their significance, atomic-level folding mechanisms of rG4s remain poorly understood due to their complexity. We used enhanced-sampling all-atom molecular dynamics simulations to model the folding of an r(GGGA)3GGG sequence into a parallel-stranded rG4. The folding pathways suggest [β¦]
- by Bacek, T., Xu, Y., Peng, L., Oetomo, D., Tan, Y.Human walking is remarkably adaptable, allowing individuals to maintain efficiency and stability across diverse conditions. This study investigates how healthy young adults adapt step length and push-off force to varying speeds and cadences under functional asymmetry induced by a unilateral knee constraint, simulating hemiparetic gait. A dataset of 19 participants walking across 30 conditions was used to examine these adaptations in both absolute terms and symmetry metrics. Results reveal that functional asymmetry disproportionately impacts propulsion, with constrained-leg force decreasing significantly [β¦]
- by Satheesh, T., Singh, R. K., Gaur, P., Shahu, S., Ramakrishnan, S., Srivastava, M., Neogi, S., Choubey, S., Ganji, M.The xenogeneic silencer protein Lsr2 from Mycobacterium tuberculosis plays a critical role in its survival and pathogenesis. Lsr2 is a nucleoid-associated protein that interacts with DNA in vivo and regulates many genes. Purified Lsr2 forms nucleoprotein filaments with DNA molecules leading to highly compacted DNA conformations. However, the physical mechanism underlying Lsr2-mediated DNA compaction, resulting in gene regulation, remains elusive. We employed a combination of biochemical assay, single-molecule imaging, and molecular dynamics simulations to investigate the governing principles of Lsr2-mediated [β¦]
- by Tsaturyan, A.The plasma membrane is a liquid lipid bilayer containing both dissolved proteins and proteins anchoring the membrane to the underlying actin cortex. Membrane tension, a 2D analog of pressure in a 3D liquid, is believed to play a crucial role in organizing essential processes within cells and tissues. This, along with recent, conflicting data on the speed of membrane tension propagation, highlights the need for a comprehensive mechanical model to describe tension in the cortex-anchored plasma membrane as a function [β¦]
- by Juarez-Contreras, I., Lopes, L. J. S., Holt, J., Yu-Liao, L., O'Shea, K., Ruiz-Ruiz, J., Sodt, A., Budin, I.Sterols are among the most abundant lipids in eukaryotic cells, yet are synthesized through notoriously long metabolic pathways. It has been proposed that the molecular evolution of such pathways must have required each step to increase the capacity of its product to condense and order phospholipids. Here we carry out a systematic analysis of the ergosterol pathway that leverages the yeast vacuoles capacity to phase-separate as a predictive biophysical readout for each intermediate. In the post-synthetic steps specific to ergosterol [β¦]
- by Ghimire, H. M., Malekzadeh, M., Lim, J. E., Madabushi, S. S., Zampini, M. A., Camacho, A., Hu, W., Storme, G., Malki, M. M. A., Hui, S. K.Background/ObjectivesBone marrow (BM) adipocytes are critical in progressing solid tumor metastases and hematological malignancies across pediatric to aging populations. Single-point biopsies remain the gold standard for monitoring BM diseases, including hematologic malignancies, but are limited in capturing the full complexity of loco-regional and global BM microenvironments. Non-invasive imaging techniques like Magnetic Resonance Imaging (MRI), could offer valuable alternatives for real-time evaluation of BM diseases in both preclinical translational and clinical studies. MethodsWe developed a preclinical proton density fat fraction (PDFF) [β¦]
- by Stewart, W. C., Jayaprakash, C., Das, J.Recent single-cell experiments that measure copy numbers of over 40 proteins in individual cells at different time points [time-stamped snapshot (TSS) data] exhibit cell-to-cell variability. Because the same cells cannot be tracked over time, TSS data provide key information about the time-evolution of protein abundances that could yield mechanisms that underlie signaling kinetics. We recently developed a generalized method of moments (GMM) based approach that estimates parameters of mechanistic models using TSS data. However, when multiple mechanistic models potentially explain [β¦]
- by Tang, Q., Cai, X., Liu, Y., Zhang, Y., Yan, X., Zhou, F., Zhang, J., Li, Q., Li, K., Deng, B., Wang, L., Li, J., Zhu, Y., Fan, C., Hu, J.Whole-brain imaging has revolutionized neuroscience research, providing comprehensive insights into neural networks across the entire brain. This powerful approach has greatly advanced our understanding of brain functions and the mechanisms underlying various diseases. One primary challenge in whole-brain imaging technology is to achieve high-resolution observation of neural networks at large scales. Although Golgi method allows labeling random neurons in their entirety in the brain, visualizing individual dendritic trees, and tracing long-distance axonal projections, the lengthy processing time pose a limit [β¦]
- by Biglione, F. A., Palatnik, J. F., Gonzalez Schain, N. D., Rasia, R. M.Growth-regulating factors (GRFs) belong to a plant-specific family of transcription factors which display important roles in plant growth and development. GRF transcriptional activity is finely tuned by regulatory processes involving post-transcriptional silencing exerted by miRNA396, and protein-protein interactions involving a family of co-transcriptional regulators known as GRF-interacting factors (GIFs). In this way, expression of GRF target genes is modulated by a highly complex interplay between GRF/GIF isoform diversity and expression patterns along with miR396 and GIF gradients throughout plant tissues. [β¦]
- by Tsay, K., Keller, T., Fichou, Y., Freed, J. H., Han, S., Srivastava, M.Pulsed Dipolar ESR Spectroscopy (PDS) is a uniquely powerful technique to characterize the structural property of intrinsically disordered proteins (IDPs) and polymers and the conformational evolution of IDPs and polymers, e.g. during assembly, by offering the probability distribution of segment end-to-end distances. However, it is challenging to determine distance distribution P(r) of IDPs by PDS because of the uncertain and broad shape information that is intrinsic to the distance distribution of IDPs. We demonstrate here that the Srivastava-Freed Singular Value [β¦]
- by Benavides, O. R., White, B. P., Kaunas, R., Gregory, C. A., Walsh, A. R.Light-sheet microscopy is an increasingly popular imaging tool for studying biological processes, however, it generally requires the use of exogenous fluorescent contrast agents which can be toxic to live cells. Light-sheet tomography is the label-free analog of light-sheet microscopy, utilizing elastic scattering contrast to visualize the structure of the biological sample. Here, we present a multi-modal polarization light-sheet microscopy and tomography (PL{micro}To) system for on-line, non-destructive, and non-invasive volumetric imaging of human mesenchymal stem cells, also referred to as mesenchymal [β¦]
- by Happel, L., Griseldis, O., Grudtsyna, V., Jain, H. P., Sknepnek, R., Doostmohammadi, A., Voigt, A.P-atic liquid crystal theories offer new perspectives on how cells self-organize and respond to mechanical cues. Understanding and quantifying the underlying orientational orders is therefore essential for unraveling the physical mechanisms that govern tissue dynamics. Due to the deformability of cells this requires quantifying their shape. We introduce rigorous mathematical tools and a reliable framework for such shape analysis. Applying this to segmented cells in MDCK monolayers and computational approaches for active vertex models and multiphase field models challenges previous [β¦]
- by Zhang, X., Taniguchi, R., Ye, S., Shibata, Y.The photosynthetic reaction is driven by the cooperation of two light-excited pigment-protein supercomplexes: photosystem II (PSII) and photosystem I (PSI). The efficiency of the excitation of the two PSs relies on the exquisite organization of their light-harvesting antenna under environmental fluctuations. However, since the antenna-protein composition within cells remains elusive, the in vivo events arising from antenna variations cannot be accurately explored. Here, we implemented the single-pixel excitation-emission spectroscopy of Chlamydomonas cells under 80 K using a cryogenic optical microscope. [β¦]
- by Woodbury, L. S., Angsutararux, P., Marras, M., Wagner, E. S., Abella, C., Li, A., Silva, J. R.Opening of the cardiac voltage-gated Na+ channel (Nav1.5) is responsible for robust depolarization of the cardiac action potential, while inactivation, which rapidly follows, allows for repolarization. Regulation of both the voltage- and time-dependent kinetics of Nav1.5 inactivation can alter the ability of the heart to initiate and sustain a re-entrant arrhythmia. The C-terminal domain (CTD) of Nav1.5 has been shown to modulate fast inactivation of the channel, and multiple auxiliary proteins bind to the CTD, including calmodulin (CaM) and intracellular [β¦]
- by Liu, S., Pani, S., Khan, S. A., Becerra, F. E., Lidke, K. A.According to Rayleighs criterion, two incoherent emitters with a separation below the diffraction limit are not resolvable with a conventional fluorescence microscope. One method of Super-Resolution Microscopy (SRM) breaks the diffraction-limited resolution by precisely estimating the centroid position of spatiotemporally independent emitters. However, conventional detection methods of SRM techniques are not optimal for estimating the separation of two simultaneously excited emitters. Recently, a number of detection methods based on modal imaging were developed to achieve the quantum Cramer-Rao lower bound [β¦]