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Membrane proteins play crucial roles in biological signaling and represent key targets in drug discovery, garnering significant experimental and computational attention. Recent advances in computational screening techniques have enabled the development of more accurate and efficient binding affinity calculation methods. Among these, the Molecular Mechanics Poisson Boltzmann Surface Area (MMPBSA) method has gained widespread adoption in large-scale simulations due to its computational efficiency.

Non-palmitoylated Stx1A (colored red in left) disfavor binding to SNAP25 to form a t-SNARE complex by lying flat on the plasma membrane. Palmitoyl chains in Stx1A (middle) stabilize the Stx1A conformation, which facilitates the t-SNARE complex (right) formation and the upstream steps of fusion like docking and priming and spontaneous release.

For swimming bacteria near surfaces, pairwise encounters inevitably occur and impact their social behavior. However, we know little about how the encounter events influence bacterial dynamics due to the limitations in tracking interplaying bacteria in 3D. Herein, we elucidated the motions of encountering E. coli using a combination of 3D holographic tracking experiments and hydrodynamic simulations. We find encounters with other cells induce transient yet remarkable fluctuations in the swimming speed and angle of E.

Eukaryotic interphase chromosomes maintain a three-dimensional conformation within the nucleus and undergo fluctuations. However, the analysis of chromosome conformational fluctuations has been mainly limited to chromosome conformation capture data that record the contact frequencies between chromosomal regions. Herein, we investigated chromosome fluctuations as polymers based on experimental data from sequential fluorescence in situ hybridization (seqFISH)+ using a multiomics methodology. To describe the principal modes of chromosome fluctuations, we applied principal component analysis to the three-dimensional conformation information of single chromosomes in 446 mouse embryonic stem cells (mESCs) obtained from seqFISH+ data analysis for spatial genomics and signals of nuclear factors (histone marks, repeat DNAs, and proteins in interchromosomal nuclear compartments).

Ongoing improvements of genetically encoded fluorescent proteins have enhanced cellular localization studies and performance of bio-sensors, such as environmentally or mechanically sensitive FRET pairs, in cell biological and biophysical research. The brightest yellow fluorescent protein, widely used in these studies is YPet, derived from the jellyfish Aequorea victoria via the GFP derivative Venus. YPet dimerizes at concentrations used in cellular studies (KD1-2 = 3.4 μM) which impacts quantitative interpretation of emission intensity, rotational freedom, energy transfer and lifetime.

This special issue explores how cells regulate the movement of materials into and out of the cytosol, especially during fusion and budding, which involve significant changes in membrane shape. These processes are central to normal functions such as exocytosis, endocytosis, synaptic transmission, and intracellular trafficking, but also play a role when cells respond to damage or infection—like when pathogens manipulate host membranes (1,2,3). The articles featured here examine the membrane’s role as a signaling platform, the proteins that drive fusion and budding, and the physical principles underlying these events.

The thermodynamics of arginine-phosphate binding is key to cellular signaling, protein-nucleic acid interactions, and membrane protein dynamics. In biomolecules, monoester phosphates are typically employed as strong electrostatic anchors strategically placed in switch domains to mediate specific interactions. In the diester configuration, phosphate groups act as ubiquitous connectors in all nucleic acids and polar lipids, while also engaging in less specific but multiple electrostatic interactions.

ATP synthase, the enzyme responsible for regenerating adenosine triphosphate (ATP) in the cell, comprises a proton-translocating motor in the cell membrane (labelled FO in bacteria, mitochondria and chloroplasts), coupled by a common stalk to a catalytic motor F1 that synthesises or hydrolyses ATP, depending on the direction of rotation. The detailed mechanisms of FO, F1 and their coupling in ATP synthase have been elucidated through structural studies, single molecule experiments and molecular modelling.

The emergence of resistance mutations in the SARS-CoV-2 spike (S) protein presents a challenge for monoclonal antibody treatments like sotrovimab. Understanding the structural, dynamics, and molecular features of these mutations is essential for therapeutic advancements. However, the intricate landscape of potential mutations and critical residues conferring resistance to mAbs like sotrovimab remains elusive. This study introduces an integrated framework that combines interface protein design, machine learning, hybrid quantum mechanics/molecular mechanics (QM/MM) methodologies, all-atom and coarse-grained molecular dynamics (MD) simulations, and correlation analysis.

Statement of Significance: The N-degron pathway is a critical protein quality control system that regulates cellular homeostasis by targeting specific proteins for degradation. GID4, a key component of this pathway, recognizes substrates primarily through their N-terminal proline or hydrophobic residues, but the molecular mechanisms underlying this recognition remain poorly understood. This study combines molecular dynamics simulations and binding energy calculations to reveal how GID4 dynamically adapts its structure to bind both proline and non-proline N-terminal residues. We uncover a hybrid recognition mechanism involving conformational selection and induced fit, providing new insights into GID4’s substrate specificity. These findings enhance our understanding of protein degradation pathways and may inform strategies to modulate these processes for therapeutic purposes.

Segmented Fluorescence Correlation Spectroscopy (FCS) improves the accuracy of FCS measurements in cells by analyzing data in short temporal segments. We have recently demonstrated the possibility of performing segmented FCS using a commercial confocal laser scanning microscope, enabling the measurement of molecular diffusion in different subcellular regions. In this study, we apply segmented FCS to investigate the dynamics of poly(ADP-ribose) polymerase 1 (PARP1), a protein playing a central role in DNA damage response.