Biophysical reviews最新文献

Reactive oxygen and nitrogen species, such as superoxide and peroxynitrite anions, are produced in our body as a result of normal metabolic functions or under pathologic conditions (oxidative and nitro-oxidative stress). A well-documented battery of antioxidant enzymes and cofactors are in place to fight this stress and restore the redox balance of the cell. However, comprehensive information on the generation of these reactive species by exposing cell components to ultraviolet (UV) light, specifically UVA and UVB sunlight, is scarce or missing. In this short review, we attempt to cover several enzymes and cofactors that are targets of UV radiation as it relates to the production (or consumption) of these oxidants, and, when known, discuss the underlying mechanisms. Because of their key importance, UV light effects on DNA are briefly discussed.

Poly(ADP‒ribose) polymerases (PARPs) consume NAD⁺ to synthesize poly(ADP‒ribose) (PAR) primarily via post-translational modification. PAR is degraded mainly by poly (ADP-ribose) glycohydrolase (PARG). PAR can be linear or branched and can have up to 200 monomers. With two phosphates per monomer, PAR is highly negatively charged. PAR can be recognized by specific protein domains and has been described as a "glue" or scaffold for the assembly of multiprotein complexes. PAR is involved in several diverse cellular structures and functions, including DNA replication, transcription, DNA repair, chromatin structure and imprinting regulation, mitotic spindle assembly, cell‒cell junctions, cytoplasmic granule formation, biomineralization and the formation of pathological aggregates. Here, we review the effects of ultraviolet radiation (UVR) on mammalian cells, emphasizing the participation of PAR metabolism in the novel paradigm of liquid‒liquid phase separation (LLPS). Further studies demand interdisciplinary approaches, undoubtedly requiring contributions from biophysicists.

Supplementary information: The online version contains supplementary material available at 10.1007/s12551-025-01294-x.

The spike protein encoded by the SARS-CoV-2 has become one of the most studied macromolecules in recent years due to its central role in COVID-19 pathogenesis. The spike protein's receptor-binding domain (RBD) directly interacts with the host-encoded receptor protein, ACE2. This review critically examines computational insights into RBD's interaction with ACE2 and with therapeutic antibodies designed to interfere with this interaction. We begin by summarizing insights from early computational studies on pre-pandemic SARS-CoV-1 RBD interactions and how these early studies shaped the understanding of SARS-CoV-2. Next, we highlight key theoretical contributions that revealed the molecular mechanisms behind the binding affinity of SARS-CoV-2 RBD against ACE2, and the structural changes that have enhanced the infectivity of emerging variants. Special attention is given to the "RBD charge rule", a predictive framework for determining variant infectivity based on the electrostatic properties of the RBD. Towards applying the computational insights to therapy, we discuss a multiscale computational protocol for optimizing monoclonal antibodies to improve binding affinity across multiple spike protein variants, including representatives from the Omicron family. Finally, we explore how these insights can inform the development of future vaccines and therapeutic interventions for combating future coronavirus diseases.

Malaria is a life-threatening parasitic disease and remains a significant global health problem, associated with high morbidity and mortality. Malaria cases are widely spread, but the highest incidence occurs in tropical and subtropical areas, especially in developing countries. Despite all efforts to control the disease, the number of cases increased by 5 million from 2021 to 2022. The mechanisms of malaria pathogenesis are still not fully understood. This, combined with the parasite's recurrent ability to develop resistance to standard treatments, hinders effective disease management and control. Therefore, a deep understanding of parasite biology, along with the various aspects of host-parasite interactions, is essential for malaria elimination. Extracellular vesicles (EVs) are membrane-enclosed vesicles which are secreted by a variety of cells. These tiny structures have emerged as a key component in the mechanisms of pathogenesis of different parasitic diseases, promoting cell-to-cell communication, even in distance. In this review, we explore the latest advancements in EV research in the malaria field, focusing on their role in pathophysiology, as well as their potential as diagnostic tools, alternative therapeutic strategies, and vaccine development. We conclude by highlighting key elements in EV research that could provide insights into the translational application of EVs.

Fluorescence is one of the most widely used techniques in biological sciences. Its exceptional sensitivity and versatility make it a tool of first choice for quantitative studies in biophysics. The concept of phasors, originally introduced by Charles Steinmetz in the late nineteenth century for analyzing alternating current circuits, has since found applications across diverse disciplines, including fluorescence spectroscopy. The main idea behind fluorescence phasors was posited by Gregorio Weber in 1981. By analyzing the complementary nature of pulse and phase fluorometry data, he shows that two magnitudes-denoted as G and S-derived from the frequency-domain fluorescence measurements correspond to the real and imaginary parts of the Fourier transform of the fluorescence intensity in the time domain. This review provides a historical perspective on how the concept of phasors originates and how it integrates into fluorescence spectroscopy. We discuss their fundamental algebraic properties, which enable intuitive model-free analysis of fluorescence data despite the complexity of the underlying phenomena. Some applications in molecular biophysics illustrate the power of this approach in studying diverse phenomena, including protein folding, protein interactions, phase transitions in lipid mixtures, and formation of high-order structures in nucleic acids.

The hydrophobe/amphiphile efflux-1 (HAE-1) family, part of the Resistance-Nodulation-Division (RND) superfamily, plays a critical role in the development of multidrug resistance (MDR) in bacteria. Known for its broad substrate transport capacity, this family of efflux pumps can actively expel a wide range of molecules, including antibiotics, salts, and dyes, thereby reducing the intracellular concentration of toxic substances. These transporters, which form efflux systems, are primarily found in bacteria within the phylum Pseudomonadota (Proteobacteria), where they are strongly associated with increased resistance and enhanced virulence, thus contributing to bacterial survival in hostile environments. In addition, efflux systems are composed of two other protein components: Membrane Fusion Proteins (MFPs) and Outer Membrane Factors (OMFs). Notably, several bacterial species identified by the World Health Organization (WHO) as urgent priorities for new antibiotic development, such as Escherichia coli and Pseudomonas aeruginosa, have well-studied HAE-1 efflux systems, such as AcrAB-TolC and MexAB-OprM. These systems efficiently transport molecules from the periplasm to the extracellular space, facilitating bacterial persistence. In this review, we examined the current knowledge of HAE-1 efflux transporters and their roles in the physiology and survival of bacteria in the Pseudomonadota phylum.

Since the early advent of nanotechnology, proteins, peptides, and amino acids have frequently been used to synthesize and stabilize metallic and ceramic nanoparticles. Also, several signaling peptides and enzymes have the activity modulated by the association with nanostructured particles and films. Lately, with the discovery of giant magnetoresistance and chiral-induced spin selectivity, an innovative nanotechnological use of amino acids and proteins emerged. Enantiomeric pairs of amino acids, peptides, and other biomolecules have been used as templates for growing chiral distorted nanocrystals and for chiral functionalization of achiral nanoparticles. More recently, circularly polarized light has been raised as an alternative for synthesizing enantiomeric pairs of plasmonic nanocrystals on anisotropic seeds. These chiral nanostructured materials exhibit unique properties with applications in biological and technological fields harnessed in various applications, including biosensing, asymmetric catalysis, and optical devices. This review presents the experimental strategies and mechanisms of chirality transfer to plasmonic and ceramic nanoparticles using peptide templates and circularly polarized light.

Bacterial communication is essential for survival, adaptation, and collective behavior. While chemical signaling, such as quorum sensing, has been extensively studied, physical cues play a significant role in bacterial interactions. This review explores the diverse range of physical stimuli, including mechanical forces, electromagnetic fields, temperature, acoustic vibrations, and light that bacteria may experience with their environment and within a community. By integrating these diverse communication pathways, bacteria can coordinate their activities and adapt to changing environmental conditions. Furthermore, we discuss how these physical stimuli modulate bacterial growth, lifestyle, motility, and biofilm formation. By understanding the underlying mechanisms, we can develop innovative strategies to combat bacterial infections and optimize industrial processes.

Recurrent neural networks are frequently studied in terms of their information-processing capabilities. The structural properties of these networks are seldom considered, beyond those emerging from the connectivity tuning necessary for network training. However, real biological networks have non-contingent architectures that have been shaped by evolution over eons, constrained partly by information-processing criteria, but more generally by fitness maximization requirements. Here, we examine the topological properties of existing biological networks, focusing in particular on gene regulatory networks in bacteria. We identify structural features, both local and global, that dictate the ability of recurrent networks to store information on the fly and process complex time-dependent inputs.

Magnesium sulfate (MgSO₄) is a therapeutically versatile agent used across various medical conditions. This review integrates experimental and computational findings to elucidate the clinical, cellular, molecular, and electronic mechanisms underlying MgSO₄'s therapeutic effects, focusing on its antioxidant properties. MgSO₄ remains the gold standard treatment for preeclampsia and eclampsia, preventing seizures and mitigating oxidative damage. In preterm birth, it offers fetal neuroprotection, although its efficacy as a tocolytic agent is limited. MgSO₄ also shows promise in treating respiratory conditions, notably severe asthma, where it acts as a bronchodilator. Its applications extend to anesthesia, pain management, and cardiac arrhythmias, reflecting its diverse pharmacological actions. Advanced computational methods, including molecular dynamics simulations and quantum chemistry calculations, have revealed how MgSO₄ interacts with cell membranes and neutralizes hydroxyl radicals. These studies suggest that MgSO₄'s antioxidant effects stem from its ability to stabilize membrane structures and modulate electron transfer processes. The therapeutic effects are mediated through multiple pathways, including calcium channel modulation, NMDA receptor antagonism, and anti-inflammatory mechanisms. Although generally safe, MgSO₄ requires careful monitoring due to its narrow therapeutic window. Future research should focus on precision dosing strategies, innovative delivery systems, and expanded therapeutic applications. A comprehensive understanding of MgSO₄'s molecular mechanisms and clinical applications will further optimize its therapeutic use.

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