Faraday Discussions最新文献

{"title":"Investigating temperature influences on shell growth and microstructural variations in bay scallops: insights from multiscale microscopy","authors":"Benazir Khurshid, Arnaud Benchetrite, Lise Guichaoua, Nicolas Brodusch, Bryce D. Stewart, Roland Kröger, Raynald Gauvin, Martin Mallet, Réjean Tremblay and Natalie Reznikov","doi":"10.1039/D5FD00023H","DOIUrl":"10.1039/D5FD00023H","url":null,"abstract":"<p >Scallops (order Pectinida) are well-known for their robust and beautiful calcitic shells that protect them from external impacts and predators. Scallops respond to environmental conditions, including water temperature, salinity, and food supply, which are reflected in the shell growth rates and patterning. The bay scallop (<em>Argopecten irradians</em>) is a species of high ecological and aquacultural value in North America, and its habitat may expand towards higher latitudes with inevitable global warming. To investigate the effect of water temperature on the accretion rate and the polycrystalline microstructure of the Bay scallop shell, we conducted a controlled growth experiment on juveniles, 4 weeks following their larval metamorphosis. Approximately 400 individuals, collected from a hatchery 4 weeks after metamorphosis, were then reared in reconstituted seawater for 9 weeks at 23 °C and 26 °C. At 7-, 9-, 11-, and 13-weeks post-metamorphosis, calcein was added to the water for 7 hours for fluorescent staining, and then equal batches of scallops were collected and fixed. Morphologic characterization of bay scallop shells included micro-computed X-ray tomography for 3D measurements to measure shell thickness, and fluorescence light microscopy for accretion rate assessment. We used mechanical testing of complete shells in compression to assess their stiffness, strength and toughness. Microstructural analysis of the shells included scanning electron microscopy and crystallographic analysis by electron backscattered diffraction. The scallops reared in warmer water exhibited a faster growth rate with shells showing higher calcite grain misorientation, no difference in relative shell thickness, and inconclusive difference in the shell mechanical properties. This study may help us to understand the multifarious implications of climate change.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"261 ","pages":" 501-519"},"PeriodicalIF":3.1,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/fd/d5fd00023h?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144148705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Silylated peptides as building blocks for material synthesis using sol–gel polymerization†","authors":"Mehmet B. Karakaplan, Vinay S. Tiwari, Omer Agazani, Cécile Echalier, Gilles Subra and Meital Reches","doi":"10.1039/D5FD00014A","DOIUrl":"10.1039/D5FD00014A","url":null,"abstract":"<p >The bottom-up approach exploits simple building blocks to generate new materials with desired physical and chemical characteristics. Here, we combine two bottom-up routes that occur under mild conditions, self-assembly and sol–gel synthesis, to program the shape and structure of materials. While self-assembly occurs through non-covalent interactions, sol–gel synthesis involves forming covalent bonds. As a proof of concept, we chose the self-assembled peptide Phe-Phe and its fluorinated analogue Phe(4-F)-Phe(4-F) to template the sol–gel process. These peptides were silylated to allow their self-mineralization. Scanning electron microscopy and atomic force microscope analysis revealed the formation of rod-shaped structures for the silylated Phe-Phe while spherical particles were formed by its fluorinated analogue. The size of the particles ranges from nano to micron scale. Fourier transform infrared spectrometry suggested the presence of parallel β-sheet secondary structure and siloxane bond formation that can stabilize these structures. Overall this approach can be adopted for other self-assembled peptides for generating new materials using a bottom-up approach.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"260 ","pages":" 204-214"},"PeriodicalIF":3.1,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/fd/d5fd00014a?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109143","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"List of participants","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"257 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143430618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phosphatidylserine affinity for and flip-flop dependence on Ca2+ and Mg2+ ions","authors":"Preston P. Hymas and John C. Conboy","doi":"10.1039/D4FD00206G","DOIUrl":"10.1039/D4FD00206G","url":null,"abstract":"<p >Ca<small>²⁺</small> ions are believed to play a crucial role in regulating lipid membrane asymmetry by modulating the activity of flippases, floppases, and scramblases. Dysregulation of Ca<small>²⁺</small> homeostasis, and subsequent loss of phosphatidylserine (PS) lipid asymmetry, is associated with physiological conditions such as blood clotting, neurodegeneration, and apoptosis. Yet, despite the prominence of Ca<small>²⁺</small> with regards to PS flip-flop, the specific actions of Ca<small>²⁺</small> are not fully understood and detailed mechanisms remain elusive. Much focus has been placed on enzymatic interactions, while the endogenous interactions of Ca<small>²⁺</small> ions with PS and the direct role Ca<small>²⁺</small> ions play on maintaining PS asymmetry have not been characterized in detail, a potentially crucial gap in understanding. In the current study the binding affinities of Ca<small>²⁺</small> ions to planar supported lipid membranes containing PS were measured <em>via</em> sum-frequency vibrational spectroscopy (SFVS). Evaluation of binding affinity obtained from SFVS peak area analysis yielded an affinity of 1.3 × 10<small>⁵</small> M<small>⁻¹</small>. The rate of PS flip-flop was also measured in the presence and absence of Ca<small>²⁺</small><em>via</em> SFVS, with a nearly five-fold decrease in the rate of translocation when Ca<small>²⁺</small> ions are present. Controls which tested Mg<small>²⁺</small> with PS or phosphatidylcholine (PC) with Ca<small>²⁺</small> did not show similar slowing effects, highlighting the specificity of the PS–Ca<small>²⁺</small> interaction. For the binary lipid mixture tested, the disparity in the PS flip-flop rate would be sufficient to produce an 82% PS asymmetry if Ca<small>²⁺</small> ions are localized to one side of the membrane. These studies have important implications for the non-enzymatic role Ca<small>²⁺</small> ions may play in the maintenance of PS asymmetry.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"259 ","pages":" 384-415"},"PeriodicalIF":3.1,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/fd/d4fd00206g?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Silica biomineralization in plants alters the structure of lignin†","authors":"Srinath Palakurthy, Michael Elbaum and Rivka Elbaum","doi":"10.1039/D5FD00011D","DOIUrl":"10.1039/D5FD00011D","url":null,"abstract":"<p >Biomineralization of silica is a major process in plants, which may contribute 3–10% of tissue dry weight. For reasons that remain unclear, plants containing silica are less sensitive to abiotic and biotic stress. In particular, the mechanisms of silica deposition and stress amelioration are still not fully understood. Silica resides mostly in the extracellular volume (the apoplast) which is made of the lignocellulosic cell wall. In a previous work we showed that synthetic lignin catalyses the formation of silica nanoparticles at RC-OSi(OH)<small>₃</small> positions. Since the phenolic O-4 position is the most reactive during lignin polymerization, the binding sites form at the expense of β-O-4 lignin backbone bonds. Therefore, synthetic lignin becomes more branched when polymerized in the presence of silicic acid, as compared to lignin polymerized without silicic acid. To study lignin–silica relationships in the plant, we extracted lignin from stems of wild type sorghum and compared it to lignin extracted from mutants exhibiting high and low silica contents. The thermal stability of both non-extracted biomass and extracted lignin was measured using thermogravimetric analysis (TGA). High-silica biomass was thermally less stable than low-silica biomass, suggesting lower content of ether (β-O-4) linkages. This interpretation was supported by gas chromatography-mass spectroscopy (GC-MS). Fourier transform infrared (FTIR) and X-ray photoelectron spectra (XPS) indicated lignin with C–O–Si modifications in all genotypes and further showed silicic acid binding to lignin phenolics and carbonyl moieties. Our results show that lignin extracted from genotypes with native-silicon levels have higher affinity to silicic acid, catalysing silica deposition through Si–O-4 (Si–phenoxyl) bonds, and suggest that the presence of silicic acid during <em>in vivo</em> lignin polymerization reduces β-O-4 ether linkages.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"261 ","pages":" 359-379"},"PeriodicalIF":3.1,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/fd/d5fd00011d?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144172067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Detection limits of calcium by EELS, TEM-EDX and X-ray absorption spectroscopy for biomineralization studies","authors":"Peter Rez, Lothar Houben, Yu-Feng Meng, Assaf Gal, Zdravko Kochovski and Benedikt Haas","doi":"10.1039/D5FD00001G","DOIUrl":"10.1039/D5FD00001G","url":null,"abstract":"<p >To investigate the mechanisms of biomineral formation it is necessary to determine Ca concentrations in the vicinity of growing minerals at the highest spatial resolution. All techniques that use ionizing radiation will be limited by the onset of radiation damage. Limits to the minimum concentrations of Ca and minimum number of Ca atoms that can be detected are determined for EELS in TEM using the Ca L<small>₂₃</small> signal, and EDX in TEM using the Ca Kα line. A similar approach is used to set limits on what can be achieved <em>via</em> soft X-ray absorption spectroscopy detecting the Ca L<small>₂₃</small> features. Due to the large background, the lowest concentrations that can be detected <em>via</em> EELS are about 1 mM. Although the collection efficiency for EDX is inferior to that of EELS, the much lower background signal means that concentrations of about 0.05 mM could be detected, 20 times better than EELS. The spatial resolution of soft X-ray absorption spectroscopy is much lower, about 20 nm, but since the Ca L<small>₂₃</small> lines are at lower energies than the oxygen K edge that dominates the spectrum, the detection limits for Ca in an aqueous environment can be as low as 35 nM.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"261 ","pages":" 68-80"},"PeriodicalIF":3.1,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144179558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Surfactant-like peptide gels are based on cross-β amyloid fibrils†","authors":"Abhinaba Das, Ordy Gnewou, Xiaobing Zuo, Fengbin Wang and Vincent P. Conticello","doi":"10.1039/D4FD00190G","DOIUrl":"10.1039/D4FD00190G","url":null,"abstract":"<p >Surfactant-like peptides, in which hydrophilic and hydrophobic residues are encoded within different domains in the peptide sequence, undergo facile self-assembly in aqueous solution to form supramolecular hydrogels. These peptides have been explored extensively as substrates for the creation of functional materials since a wide variety of amphipathic sequences can be prepared from commonly available amino acid precursors. The self-assembly behavior of surfactant-like peptides has been compared to that observed for small molecule amphiphiles in which nanoscale phase separation of the hydrophobic domains drives the self-assembly of supramolecular structures. Here, we investigate the relationship between sequence and supramolecular structure for a pair of bola-amphiphilic peptides, Ac-KLIIIK-NH<small>₂</small> (<strong>L2</strong>) and Ac-KIIILK-NH<small>₂</small> (<strong>L5</strong>). Despite similar length, composition, and polar sequence pattern, <strong>L2</strong> and <strong>L5</strong> form morphologically distinct assemblies, nanosheets and nanotubes, respectively. Cryo-EM helical reconstruction was employed to determine the structure of the <strong>L5</strong> nanotube at near-atomic resolution. Rather than displaying self-assembly behavior analogous to conventional amphiphiles, the packing arrangement of peptides in the <strong>L5</strong> nanotube displayed steric zipper interfaces that resembled those observed in the structures of β-amyloid fibrils. Like amyloids, the supramolecular structures of the <strong>L2</strong> and <strong>L5</strong> assemblies were sensitive to conservative amino acid substitutions within an otherwise identical amphipathic sequence pattern. This study highlights the need to better understand the relationship between sequence and supramolecular structure to facilitate the development of functional peptide-based materials for biomaterials applications.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"260 ","pages":" 35-54"},"PeriodicalIF":3.1,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12082393/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Influence of peptide chirality on their protein-triggered supramolecular hydrogelation†","authors":"Shahaji H. More, Tetiana Dorosh, Jean-Yves Runser, Alexis Bigo-Simon, Rachel Schurhammer, Vincent Ball, Leandro Jacomine, Marc Schmutz, Alain Chaumont, Pierre Schaaf and Loïc Jierry","doi":"10.1039/D5FD00007F","DOIUrl":"10.1039/D5FD00007F","url":null,"abstract":"<p >Many articles describe the use of enzymes to induce the formation of a supramolecular hydrogel. These enzymes catalyze the transformation of water-soluble precursors, often short peptides, into hydrogelators. The use of non-enzymatic proteins to induce or stabilize peptide self-assembly is a rarely reported phenomenon, which raises fundamental questions: how can a protein induce peptide self-assembly? How is the peptide recognized and how does it, or the peptide assembly, interact with the protein? The heptapeptide Fmoc-GFFYE–NH–(CH<small>₂</small>)<small>₂</small>–<em>s-s</em>–(CH<small>₂</small>)<small>₂</small>–NH–CO–(CH<small>₂</small>)<small>₂</small>–CO–EE–OH, called <small>L</small>-<strong>1</strong> (<small>L</small> = natural chiral amino acids), is a water-soluble compound leading to an increasingly viscous solution over time due to the formation of nanofibers, but does not result in hydrogel (at least not within 3 months). When bovine serum albumin (BSA) is added to a freshly prepared solution of <small>L</small>-<strong>1</strong>, a hydrogel is obtained in less than 10 min. The variation in the <small>L</small>-<strong>1</strong>/BSA ratio has an impact on the gelation rate and the mechanical properties of the resulting hydrogel. Thus, the protein appears to act as (i) a catalyst and (ii) a cross-linking point. Strikingly, if the enantiomer <small>D</small>-<strong>1</strong> (<small>D</small> = unnatural chiral amino acids) is used instead of <small>L</small>-<strong>1</strong>, the mixture with BSA remains liquid and non-viscous. Similar behavior is also observed for other proteins. Spectroscopic analyses (CD, fluorescence) and electronic microscopy images confirm that the <small>L</small>-<strong>1</strong> peptide self-assembles in nanofibers of 10 nm diameter through β-sheet organization, which is not the case for the peptide <small>D</small>-<strong>1</strong>. A molecular dynamics study shows that BSA is capable of interacting with both enantiomer peptides <small>L</small>-<strong>1</strong> and <small>D</small>-<strong>1</strong>. However, interaction with <small>L</small>-<strong>1</strong> tends to unfold the peptide backbone, making the interaction with the protein more stable and promoting the assembly of <small>L</small>-<strong>1</strong> peptides. Conversely, the interaction between BSA and <small>D</small>-<strong>1</strong> is more dynamic and appears to be less spatially localized on the BSA. Furthermore, in this interaction, the <small>D</small>-<strong>1</strong> peptide keeps its globular conformation. These results highlight the impact of a short peptide’s chirality on protein-triggered supramolecular hydrogelation.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"260 ","pages":" 310-327"},"PeriodicalIF":3.1,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/fd/d5fd00007f?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075000","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the temperature dependence of β-hairpin peptide self-assembly†","authors":"Tuan D. Samdin, Xiaoyi Wang, Galit Fichman and Joel P. Schneider","doi":"10.1039/D5FD00018A","DOIUrl":"10.1039/D5FD00018A","url":null,"abstract":"<p >Herein, we study the role that hydrophobicity plays in the temperature-dependent self-assembly of a family of β-hairpin peptide amphiphiles through the lens of thermally folding a protein from its cold-denatured state. This was facilitated by the development of new computational tools to measure solvent-accessible charge (SAC) and solvent-accessible hydrophobicity (SAH) at the resolution of atomic groups. Peptides in their disordered states are characterized by large SAH values that shift their thermal assembly transitions to observable temperatures, which is not possible for most native proteins, allowing comparisons amongst peptides to be made. We find that peptides with large SAH values assemble into β-sheet-rich fibers at lower temperatures and at faster rates than peptides having smaller SAH values. This is consistent with peptide assembly being driven by the hydrophobic effect, which involves the release of ordered water from hydrophobic moieties during assembly. We also find that peptide SAH values correlate linearly with <em>T</em><small>_g</small>, the midpoint of the transition defining monomeric peptide transitioning to fibrils, for peptides of similar charge. Interestingly, the data also suggest that although entropy drives assembly, the exact temperature at which the assembly transition takes place is likely influenced by additional thermodynamic considerations.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"260 ","pages":" 113-131"},"PeriodicalIF":3.1,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951687","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Immune cell activation produces locally scrambled foci of plasma membrane lipids","authors":"Daryna Sputay, Milka Doktorova, Sze Ham Chan, Emma Han Guo, Hong-Yin Wang, Joseph H. Lorent, Ilya Levental and Kandice R. Levental","doi":"10.1039/D4FD00205A","DOIUrl":"10.1039/D4FD00205A","url":null,"abstract":"<p >Most eukaryotic cells maintain a large disparity in lipid compositions between the cytosolic and external leaflets of the plasma membrane (PM) bilayer. This lipid asymmetry is maintained by energy-consuming flippase enzymes that selectively drive phospholipids into the cytosolic leaflet, often against large concentration gradients. Scramblases, activated by intracellular Ca<small>²⁺</small> or apoptotic signaling, shuttle phospholipids down their concentration gradient to release lipid asymmetry. Such scrambling is typically evidenced by exposure of phosphatidylserine (PS) to the external leaflet and is associated with many physiological processes, most notably blood clotting and cell death, but also activation of immune cells. Here, we show that both PS and phosphatidylethanolamine (PE) appear on the PM external leaflet following immune receptor-mediated activation of mast cells. We also observe similar effects in T cells. Importantly, in contrast to wholesale release of PM asymmetry induced by calcium ionophores or apoptosis, we show that scrambling in activated immune cells is focal, with small, stable regions of surface exposed PS. These scrambled foci are calcium dependent, have lower lipid packing than their surrounding outer leaflet, and are reversible. These observations of local, transient scrambling during physiological activation of healthy immune cells suggest important roles for the lateral and transbilayer organization of membrane lipids.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"259 ","pages":" 45-59"},"PeriodicalIF":3.1,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12067185/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143956543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}