BIOPHYSICAL CHEMISTRY生物物理化学
BIOPHYSICAL CHEMISTRY(英文缩写 BIOPHYS CHEM),ISSN 0301-4622,eISSN 1873-4200,中文译名:生物物理化学 是一本学术期刊。本页汇总该期刊的最新影响因子、分区信息以及最新收录于 PubMed 的文献,帮助您快速了解期刊全貌。
发文量统计区间：2025-09-27 至 2026-09-27，按本站收录文献的发表日期统计。
期刊介绍
历年影响因子趋势
| JCR 数据年份 | 影响因子 | JCR 分区 |
|---|---|---|
| 2021 | 3.628 | Q2 |
| 2022 | 3.800 | Q2 |
| 2023 | 3.300 | Q1 |
| 2024 | 2.200 | Q3 |
| 2025 | 2.300 | Q3 |
BIOPHYSICAL CHEMISTRY 最新收录文献
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1. Structure-guided delineation of umbelliferyl phosphate-based disruptors of the c-Myb-CBP/p300 KIX protein-protein interaction.
PMID:日期:2026-12-01The interaction between c-Myb and the CBP/p300 KIX domain is a critical transcriptional regulatory event and an attractive target for the development of candidate disruptors of the recombinant c-Myb-KIX interaction. In this study, we used an integrated computational and experimental strategy to identify new small molecules capable of disrupting this protein-protein interaction. A focused Umbelliferyl phosphate scaffold library was subjected to stepwise virtual screening via drug-likeness assessment and docking to the c-Myb-binding region of the KIX domain and short molecular dynamics refinement. Selected compounds were then evaluated by 500 ns molecular dynamics simulations, MM/PBSA analysis, free energy landscape (FEL) mapping, and finally by microscale thermophoresis (MST) assay. Computational analyses showed that stable ligand binding did not necessarily translate into disruption of the c-Myb-KIX interface, allowing separation of compounds that stabilized the complex from those predicted to weaken it. Consistent with this distinction, ΔΔGanalysis identified only MUP and Naphthol AS-BI phosphate as protein-protein interaction-weakening ligands, with Naphthol AS-BI phosphate showing the strongest predicted disruptive effect (ΔΔG=+3.25 kcal/mol), whereas DiFMUP and Naphthol AS-D phosphate were predicted to stabilize the complex. Among the tested molecules, Naphthol AS-BI phosphate showed the clearest disruption-like behavior in silico and was the most potent inhibitor in vitro, with an IC₅₀ of 18.9 ± 0.6 μM. Importantly, MUP emerged as the most promising umbelliferyl phosphate-derived hit, displaying measurable inhibitory activity (IC₅₀ = 33.5 ± 0.3 μM) comparable to the reference Naphthol AS-E phosphate (IC₅₀ = 31.2 ± 1.3 μM) and a more favorable predicted ADMET profile. Overall, this work identifies new chemical starting points for targeting the c-Myb-CBP/p300 KIX interaction and supports MUP as an attractive scaffold for further optimization.
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2. How glycosaminoglycans mediate procathepsin K maturation: New insights from computational studies.
PMID:日期:2026-12-01Cathepsins are predominantly cysteine proteases that function in lysosomes and the extracellular matrix, where they regulate essential proteolytic processes. They are synthesised as inactive zymogens (procathepsins), in which an N-terminal propeptide blocks access to the active site and is removed during maturation. Glycosaminoglycans (GAGs), a class of linear, sulfated polysaccharides composed of repeating disaccharide units, are known to modulate both cathepsin activity and proenzyme processing. Here, we use molecular modelling to elucidate the role of GAGs in the maturation of procathepsin K. Molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations identify putative allosteric sites on the procathepsin surface that mediate GAG recognition. Microsecond-scale MD simulations of the most stable complexes, analysed via principal component analysis (PCA), reveal GAG-dependent shifts in the conformational landscape of the proenzyme. To probe environmental effects, we further simulate apo and GAG-bound procathepsin K under lysosomal conditions (pH 4). These simulations demonstrate a synergistic interplay between acidification and GAG binding in promoting activation. While low pH destabilises propeptide secondary structure, GAG binding at a distinct allosteric hotspot amplifies this effect, promoting helix unwinding and facilitating propeptide dissociation. Overall, our results provide a molecular-level framework for GAG-assisted maturation of procathepsin K, highlighting cooperative environmental and allosteric regulation of zymogen activation.
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3. Optimizing separation conditions for melittin purification from bee venom using molecular dynamics simulations.
PMID:日期:2026-12-01Melittin, an anticancer peptide, is the main component of bee venom. However, bee venom also contains phospholipase A2 and hyaluronidase-toxic enzymes that induce inflammatory responses. To facilitate therapeutic applications of melittin, these toxic components must be isolated and removed. This study explored optimal conditions for separating phospholipase A2 and hyaluronidase from bee venom using molecular dynamics simulations. pH = 10 was identified as the optimal condition for melittin separation, as significant conformational changes in melittin were observed at pH = 12. Additionally, a temperature of 30 °C was found to be ideal for melittin separation, whereas a temperature of 40 °C altered its secondary structure and reduced its hydrophilicity. These findings provide a foundational framework for protein separation processes, ensuring that melittin maintains its therapeutic integrity during purification.
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4. Carvacrol potentiates gentamicin against Staphylococcus aureus via disrupting bacterial respiratory bioenergetics.
4. 卡瓦罗通过破坏细菌呼吸生物能量学增强庆大霉素对金黄色葡萄球菌的作用PMID:日期:2026-12-01The emergence of methicillin-resistant Staphylococcus aureus (MRSA) calls for novel antibiotic adjuvants. Carvacrol (Car), a natural monoterpene phenol derived from the essential oils of aromatic plants, exhibits membrane-active properties and has potential as an antibacterial adjuvant. Here, we found that Car markedly enhanced the bactericidal activities of Gentamicin (Gen) against MRSA. Mechanistically, Car dissipated membrane potential, inhibited respiratory chain dehydrogenase activity, and depleted intracellular ATP. Moreover, Car promoted membrane lipid peroxidation, ultimately leading to structural and functional membrane damage and bacterial death. Notably, pharmacological perturbation of respiratory and metabolic pathways further supported that this synergistic effect depends on bacterial respiratory bioenergetics. In addition, the combination showed favorable in vivo antibacterial efficacy in both Galleria mellonella and murine infection models, without apparent toxicity under the tested conditions. Collectively, these findings indicate that Car may serve as a natural antibacterial adjuvant for combination therapy against drug-resistant infections.
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5. Modulation of the phospholipid dynamics and bilayer water accessibility with the membrane-associated nucleation of β-amyloid (Aβ) peptides.
PMID:日期:2026-11-01Membrane disruption along the amyloidogenic aggregation of β-amyloid (Aβ) peptides is considered a molecular mechanism for the Aβ-induced cell toxicity and death. Yet, the underlying structural basis for the harmful Aβ-membrane interactions that lead to disruption remains poorly understood. We have been utilizing solid-state nuclear magnetic resonance (ssNMR) spectroscopy to explore the intermediate states of membrane-associated Aβ aggregation, as well as their roles in membrane disruption process. Aligning with this general objective, complementary quantitative ssNMR spectroscopy focusing on the modulation of phospholipid dynamics in membrane bilayers will provide useful insight about how these intermediate states influence the physicochemical properties and architecture of membranes. In the current work, we systematically investigate how specific molecular motions of phospholipids change in the presence of membrane-associated 40- and 42-residue Aβ isoforms, within the time frame of nucleation processes. Physicochemical parameters, including the lipid headgroup and lateral diffusive motion correlation time, the lipid alkyl chain to headgroup HH cross relaxation rate, and the HO-assisted HC cross polarization rate to lipid alkyl Cs, were monitored by various ssNMR spectroscopic approaches. The outcomes suggest a general rigidification of bilayers upon instant Aβ-bilayer interactions across different bilayer phospholipid compositions and Aβ isoforms, accompanied by increase of water accessibility to bilayer interiors. These observations, together with the knowledge of molecular structural evolution of Aβ within the same time frame, help to establish a molecular-level, schematic explanation of the membrane-associated Aβ nucleation process.
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6. Solid-state NMR methods to investigate biomolecular condensates, protein phase transition, phase separation and coacervates.
PMID:日期:2026-11-01The formation of biomolecular condensates has been linked to a broad range of essential cellular processes, including immune signaling cascades, mRNA transport, and autophagy. Conversely, phase-separated condensates have also been associated with aberrant protein misfolding and subsequent aggregation in neurodegenerative disease-related processes. Protein phase separation and phase transitions involve the formation of heterogeneous and dynamic assemblies that can evolve into gel-like or semi-crystalline states, which are challenging to characterize using high-resolution structural biology techniques. Solid-state nuclear magnetic resonance (NMR) spectroscopy now offers a broad arsenal of methods to probe the structural and dynamic features of viscous condensates, elastic solids, coacervates and rigid protein assemblies. This review provides an overview of solid-state NMR approaches that are readily applicable and discusses potential methodological developments to investigate protein condensates and coacervates as well as to study protein phase separation and phase transitions.
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7. Advances in ratiometric fluorescent probes for quantitative imaging of endogenous hydrogen sulfide.
PMID:日期:2026-11-01Hydrogen sulfide (H₂S) has emerged as a crucial endogenous gaseous signaling molecule involved in diverse physiological and pathological processes, including vascular regulation, neuronal transmission, inflammation, and cellular redox homeostasis. The transient and highly reactive nature of endogenous H₂S necessitates the development of highly sensitive and selective analytical techniques capable of real-time detection in living systems. Among various sensing strategies, ratiometric fluorescent probes have attracted considerable attention due to their inherent ability to provide self-calibrated signals, thereby minimizing environmental interference and enabling quantitative imaging of H₂S in complex biological environments. Recent advances in probe design have introduced novel molecular scaffolds, organelle-targeted fluorophores, near-infrared emitters, and reaction-based sensing mechanisms that significantly enhance sensitivity, selectivity, and spatiotemporal resolution. These probes exploit diverse photophysical mechanisms including intramolecular charge transfer (ICT), fluorescence resonance energy transfer (FRET), excited-state intramolecular proton transfer (ESIPT), and photoinduced electron transfer (PET). In addition, nanomaterial-integrated probes and reversible sensing platforms have further improved quantitative detection and long-term monitoring of endogenous H₂S dynamics. Recent studies have demonstrated successful application of these probes in cellular systems, zebrafish, and mammalian disease models such as oxidative stress and acute liver injury. This review comprehensively summarizes the recent progress in ratiometric fluorescent probes for quantitative imaging of endogenous H₂S, focusing on molecular design strategies, sensing mechanisms, biological applications, and emerging technological trends. Furthermore, current challenges and future research directions are discussed to guide the development of next-generation H₂S imaging tools for biomedical and translational research.
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8. Enhanced solid-state NMR sensitivity of α-synuclein fibrils using a MAS cryoprobe.
PMID:日期:2026-11-01Solid-state NMR spectroscopy is increasingly used to investigate the structure and dynamics of a wide range of chemical, material, and biological systems. Although limited sensitivity has long posed a major challenge, the recently developed MAS cryoprobe substantially alleviates this limitation. By enhancing the signal-to-noise (S/N) ratio without requiring sample freezing, the MAS cryoprobe is particularly well suited for studies of non-isotropic systems, including rigid solids (e.g., amyloid fibrils), semi-solids (e.g., membrane mimetics), and soft materials (e.g., nanodiscs and hydrogels). In this study, we demonstrate the enhanced sensitivity of solid-state NMR experiments on α-synuclein fibrils using a MAS cryoprobe. Compared with a conventional MAS probe, substantial improvements in S/N were observed in CPMAS, refocused INEPT, and 2D CC chemical-shift correlation spectra. The increased sensitivity enables the detection of slowly decaying signals in the indirect dimension, thereby accelerating the acquisition of high-resolution multidimensional solid-state NMR data. These results highlight the potential of MAS cryoprobes for structural studies of samples that are scarce, unstable, or transient, such as amyloid intermediaries.
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9. {"_":"Exploring the effect of carbon support dimensionality on FeN-based acetone sensors.","sub":["4"]}
PMID:日期:2026-11-01This inclusive innovation study presents a computational investigation into the design of biosensors capable of detecting volatile organic compound (VOC) biomarkers. Density functional theory (DFT) calculations were employed to examine the adsorption behavior of acetone, a clinically relevant biomarker, compared to common interfering atmospheric molecules (N, CO, and HO) on FeN-doped nanostructures. Three distinct FeN-doped nanostructures were considered, including a 0-dimensional fullerene (F-FeN), a 1-dimensional carbon nanotube (C-FeN), and a 2-dimensional graphene (G-FeN). Ab initio molecular dynamics (AIMD) simulations confirmed the thermodynamic stability of all three systems under ambient conditions. Adsorption energy analysis revealed that G-FeN exhibits the strongest interaction with acetone, with a calculated adsorption energy of -0.82 eV. While F-FeN and C-FeN demonstrated slightly superior recovery times and broader detection ranges, G-FeN displayed a pronounced current suppression within the voltage window of 0-2 V, highlighting its superior suitability as an acetone sensor relative to its 0D and 1D counterparts. Moreover, the presence of interfering air molecules N, CO, and HO) further enhances the adsorption energy of acetone, suggesting cooperative effects that may improve sensor selectivity under realistic operating conditions.
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10. Phase separation and protein aggregation in neurodegenerative diseases.
PMID:日期:2026-11-01Neurodegenerative diseases such as Alzheimer's, Parkinson's, frontotemporal dementia, and ALS are characterized by amyloid protein aggregation involving intrinsically disordered proteins that are also capable of liquid-liquid phase separation (LLPS). LLPS, known to drive the formation of dynamic membraneless organelles essential for cellular functions, can play a role in limiting fibrillation process or aberrantly transition into solid aggregates under pathological conditions. Here we review how mutations, post-translational modifications, and environmental factors can modulate LLPS of proteins like Tau, TDP-43, FUS, and α-synuclein, potentially regulating amyloid aggregation. We also examine the interplay of these proteins exploring how LLPS and condensate maturation could impinge on the emergence of co-pathologies contributing to disease progression. Finally we discuss emerging therapeutic strategies, aimed at modulating phase separation dynamics.