PH-induced morphological changes of proteinaceous viral shells.
Ontology highlight
ABSTRACT:
SUBMITTER: Roshal D
PROVIDER: S-EPMC6440952 | biostudies-literature | 2019 Mar
REPOSITORIES: biostudies-literature
Publications
pH-induced morphological changes of proteinaceous viral shells.
Roshal D D Konevtsova O O Lošdorfer Božič A A Podgornik R R Rochal S S
Scientific reports 20190329 1
Changes in environmental pH can induce morphological changes in empty proteinaceous shells of bacteriophages in vitro that are very similar to changes occurring in viral capsids in vivo after encapsidation of DNA. These changes in capsid shape and size cannot be explained with a simple elastic model alone. We propose a new theoretical framework that combines the elasticity of thin icosahedral shells with the pH dependence of capsid charge distribution. Minimization of the sum of elastic and elec ...[more]
Similar Datasets
Project description:The function-optimized properties of biominerals arise from the hierarchical organization of primary building blocks. Alteration of properties in response to environmental stresses generally involves time-intensive processes of resorption and reprecipitation of mineral in the underlying organic scaffold. Here, we report that the load-bearing shells of the brachiopod Discinisca tenuis are an exception to this process. These shells can dynamically modulate their mechanical properties in response to a change in environment, switching from hard and stiff when dry to malleable when hydrated within minutes. Using ptychographic X-ray tomography, electron microscopy and spectroscopy, we describe their hierarchical structure and composition as a function of hydration to understand the structural motifs that generate this adaptability. Key is a complementary set of structural modifications, starting with the swelling of an organic matrix on the micron level via nanocrystal reorganization and ending in an intercalation process on the molecular level in response to hydration.
| S-EPMC8433230 | biostudies-literature
Project description:Bivalve shells are increasingly used as archives for high-resolution paleoclimate analyses. However, there is still an urgent need for quantitative temperature proxies that work without knowledge of the water chemistry-as is required for δ18O-based paleothermometry-and can better withstand diagenetic overprint. Recently, microstructural properties have been identified as a potential candidate fulfilling these requirements. So far, only few different microstructure categories (nacreous, prismatic and crossed-lamellar) of some short-lived species have been studied in detail, and in all such studies, the size and/or shape of individual biomineral units was found to increase with water temperature. Here, we explore whether the same applies to properties of the crossed-acicular microstructure in the hinge plate of Arctica islandica, the microstructurally most uniform shell portion in this species. In order to focus solely on the effect of temperature on microstructural properties, this study uses bivalves that grew their shells under controlled temperature conditions (1, 3, 6, 9, 12 and 15°C) in the laboratory. With increasing temperature, the size of the largest individual biomineral units and the relative proportion of shell occupied by the crystalline phase increased. The size of the largest pores, a specific microstructural feature of A. islandica, whose potential role in biomineralization is discussed here, increased exponentially with culturing temperature. This study employs scanning electron microscopy in combination with automated image processing software, including an innovative machine learning-based image segmentation method. The new method greatly facilitates the recognition of microstructural entities and enables a faster and more reliable microstructural analysis than previously used techniques. Results of this study establish the new microstructural temperature proxy in the crossed-acicular microstructures of A. islandica and point to an overarching control mechanism of temperature on the micrometer-scale architecture of bivalve shells across species boundaries.
| S-EPMC7909638 | biostudies-literature
Project description:Human bocavirus 1 (HBoV1) and HBoV2-4 infect children and immunocompromised individuals, resulting in respiratory and gastrointestinal infections, respectively. Using cryo-electron microscopy and image reconstruction, the HBoV2 capsid structure was determined to 2.7 Å resolution at pH 7.4 and compared to the previously determined HBoV1, HBoV3, and HBoV4 structures. Consistent with previous findings, surface variable region (VR) III of the capsid protein VP3, proposed as a host tissue-tropism determinant, was structurally similar among the gastrointestinal strains HBoV2-4, but differed from HBoV1 with its tropism for the respiratory tract. Towards understanding the entry and trafficking properties of these viruses, HBoV1 and HBoV2 were further analyzed as species representatives of the two HBoV tropisms. Their cell surface glycan-binding characteristics were analyzed, and capsid structures determined to 2.5-2.7 Å resolution at pH 5.5 and 2.6, conditions normally encountered during infection. The data showed that glycans with terminal sialic acid, galactose, GlcNAc or heparan sulfate moieties do not facilitate HBoV1 or HBoV2 cellular attachment. With respect to trafficking, conformational changes common to both viruses were observed at low pH conditions localized to the VP N-terminus under the 5-fold channel, in the surface loops VR-I and VR-V and specific side-chain residues such as cysteines and histidines. The 5-fold conformational movements provide insight into the potential mechanism of VP N-terminal dynamics during HBoV infection and side-chain modifications highlight pH-sensitive regions of the capsid.IMPORTANCE Human bocaviruses (HBoVs) are associated with disease in humans. However, the lack of an animal model and a versatile cell culture system to study their life cycle limits the ability to develop specific treatments or vaccines. This study presents the structure of HBoV2, at 2.7 Å resolution, determined for comparison to the existing HBoV1, HBoV3, and HBoV4 structures, to enable the molecular characterization of strain and genus-specific capsid features contributing to tissue tropism and antigenicity. Furthermore, HBoV1 and HBoV2 structures determined under acidic conditions provide insight into capsid changes associated with endosomal and gastrointestinal acidification. Structural rearrangements of the capsid VP N-terminus, at the base of the 5-fold channel, demonstrate a disordering of a "basket" motif as pH decreases. These observations begin to unravel the molecular mechanism of HBoV infection and provide information for control strategies.
| S-EPMC8103701 | biostudies-literature
Project description:In the presence of 10-50 mM-fructose, enterocytes of organ-cultured pig intestinal-mucosal explants fail to glycosylate correctly their newly synthesized microvillar enzymes, and instead degrade them [Danielsen (1989) J. Biol. Chem. 264, 13726-13729]. In the present work, this degradation was shown to occur extremely rapidly as the microvillar enzyme aminopeptidase N (EC 3.4.11.2) was hardly detectable after a 10 min pulse with [35S]methionine. The abnormal biosynthesis of membrane glycoproteins affected both the morphology and the function of the Golgi complex as well as the microvillar membrane. Thus the stack of Golgi cisternae was condensed and devoid of dilated rims, and the secretion of a non-glycosylated protein, apolipoprotein A-1, was almost completely blocked in the presence of fructose, showing that transport through the secretory pathway is disturbed even for proteins unaffected by the defective glycosylation. The microvilli of the brush-border membrane were markedly shortened (by about 40%) in the presence of fructose, and incorporation of newly made actin into the microvillar cytoskeleton was similarly decreased. By affecting membrane glycoprotein synthesis, the common dietary sugar fructose thus profoundly perturbs the exocytic membrane traffic in the enterocyte.
| S-EPMC1130574 | biostudies-other
Project description:We examined substrate-induced conformational changes in MjNhaP1, an archaeal electroneutral Na(+)/H(+)-antiporter resembling the human antiporter NHE1, by electron crystallography of 2D crystals in a range of physiological pH and Na(+) conditions. In the absence of sodium, changes in pH had no major effect. By contrast, changes in Na(+) concentration caused a marked conformational change that was largely pH-independent. Crystallographically determined, apparent dissociation constants indicated ∼10-fold stronger Na(+) binding at pH 8 than at pH 4, consistent with substrate competition for a common ion-binding site. Projection difference maps indicated helix movements by about 2 Å in the 6-helix bundle region of MjNhaP1 that is thought to contain the ion translocation site. We propose that these movements convert the antiporter from the proton-bound, outward-open state to the Na(+)-bound, inward-open state. Oscillation between the two states would result in rapid Na(+)/H(+) antiport. DOI: http://dx.doi.org/10.7554/eLife.01412.001.
| S-EPMC3900740 | biostudies-literature
Project description:Histamine is one of the most basic biogenic amino-compounds, which is composed of imidazole and a flexible ethylamine side chain moiety. Histamine is known to take the form of various types of cations, free base, monocation and dication form, where its conformational change is highly sensitively to the pH conditions. The details of these changes are still controversial due to a lack of detailed information on its crystal structures. Thus, in this study, the molecular packing structures of histidine at various pH were analyzed via X-ray diffraction in combination with vibrational spectroscopy and energy calculations. A variety of molecular conformations including the tautomeric phenomenon was found to be intimately related with intra- and intermolecular hydrogen bonds. The role of the hydrogen bonds was studied also to check the possibility of high proton conductivity of histamine, as predicted by computer simulation. Consequently, the thus-predicted proton conductivity was confirmed for the first time experimentally. During the heating process, the conductivity showed the relatively high maximum value of 10-4 S cm-1 at around 60 °C, which is related to the effective proton transfer between the amino NH group of one histamine unit and the imidazole ring of another.
| S-EPMC9065317 | biostudies-literature
Project description:Viral fusion proteins undergo dramatic conformational transitions during membrane fusion. For viruses that enter through the endosome, these conformational rearrangements are typically pH sensitive. Here, we provide a comprehensive review of the molecular interactions that govern pH-dependent rearrangements and introduce a paradigm for electrostatic residue pairings that regulate progress through the viral fusion coordinate. Analysis of structural data demonstrates a significant role for side-chain protonation in triggering conformational change. To characterize this behavior, we identify two distinct residue pairings, which we define as Histidine-Cation (HisCat) and Anion-Anion (AniAni) interactions. These side-chain pairings destabilize a particular conformation via electrostatic repulsion through side-chain protonation. Furthermore, two energetic control mechanisms, thermodynamic and kinetic, regulate these structural transitions. This review expands on the current literature by identification of these residue clusters, discussion of data demonstrating their function, and speculation of how these residue pairings contribute to the energetic controls.
| S-EPMC3701885 | biostudies-literature
Project description:Introduction Charring process affects the preservation potential of seeds, resulting in limited perceptions of crop assemblages recovered from archaeological layers. Therefore, the specifics of the charring process deserve further investigation. Colloquially referred to as the “Five Grains” (五谷), bread wheat (Triticum aestivum), foxtail millet (Setaria italica), broomcorn millet (Panicum miliaceum), rice (Oryza sativa), and soybean (Glycine max) represent a set of four major cultivated cereals and a pulse constituting crucial staple food in Chinese history and the most frequently discovered crops at archaeological sites in China Methods This paper aims to understand the changes in size, volume, and weight loss of grains under variable aerobic charring conditions. The size and weight were measured for the untreated specimens and the specimens heated at different temperatures and over different time-periods. Results We found that temperature and exposure time directly affected the grain size. Specifically, the grains of most species shrank at lower temperatures and expanded rapidly at higher temperatures. Discussion Among the “Five Grains”, soybean was the type least affected by charring, followed by wheat, rice, and millet. Volume and weight can be used as conversion factors to minimize the bias in quantitative representation due to varied charring preservation potential. For rice, wheat and soybean, the variation in volume is smaller. For millet, both volume and weight can be used as the control to understand the consequences of charring for the assemblage. Further experiments and comparisons of ancient samples are needed in future studies to investigate other factors that affect the preservation of charred plant remains.
| S-EPMC9935936 | biostudies-literature
Project description:Nanoparticles (NPs) show various properties depending on their composition, size, and surface coating, which shape their interactions with biological systems. In particular, NPs have been shown to interact with immune cells, that represent a sensitive surveillance system of external and internal stimuli. In this light, in vitro models represent useful tools for investigating nano-bio-interactions in immune cells of different organisms, including invertebrates. In this work, the effects of selected types of NPs with different core composition, size and functionalization (custom-made PVP-AuNP and commercial nanopolystyrenes PS-NH2 and PS-COOH) were investigated in the hemocytes of the marine bivalve Mytilus galloprovincialis. The role of exposure medium was evaluated using either artificial seawater (ASW) or hemolymph serum (HS). Hemocyte morphology was investigated by scanning electron microscopy (SEM) and different functional parameters (lysosomal membrane stability, phagocytosis, and lysozyme release) were evaluated. The results show distinct morphological and functional changes induced in mussel hemocytes depending on the NP type and exposure medium. Mussel hemocytes may represent a powerful alternative in vitro model for a rapid pre-screening strategy for NPs, whose utilization will contribute to the understanding of the possible impact of environmental exposure to NPs in marine invertebrates.
| S-EPMC7918069 | biostudies-literature
Project description:Metal halide perovskite nanocrystals, an emerging class of materials for advanced photonic and optoelectronic applications, are mainly fabricated with colloidal chemistry routes. On the quest for new properties according to application needs, new perovskite systems of various morphologies and levels of doping and alloying have been developed, often also involving post-synthesis reactions. Recently, laser irradiation in liquids has been utilized as a fast method to synthesize or transform materials and interesting laser-induced transformations on nanocrystals were induced. These studies in general have been limited to small nanocrystals (~15 nm). In the case of halide perovskites, fragmentation or anion exchange have been observed in such laser-based processes, but no crystal structure transformations were actually observed or deliberately studied. Nanocrystals are more sensitive to light exposure compared to the corresponding bulk crystals. Additional factors, such as size, morphology, the presence of impurities, and others, can intricately affect the photon absorption and heat dissipation in nanocrystal suspensions during laser irradiation. All these factors can play an important role in the final morphologies and in the time required for these transformations to unfold. In the present work, we have employed a 513 nm femtosecond (fs) laser to induce different transformations in large nanocrystals, in which two phases coexist in the same particle (Cs4PbBr6/CsPbBr3 nanohexagons of ~100 nm), dispersed in dichlorobenzene. These transformations include: (i) the exfoliation of the primary nanohexagons and partial anion exchange; (ii) fragmentation in smaller nanocubes and partial anion exchange; (iii) side-by-side-oriented attachment, fusion, and formation of nanoplatelets and complete anion exchange; (iv) side-by-side attachment, fusion, and formation of nanosheets. Partial or complete Br-Cl anion exchange in the above transformations was triggered by the partial degradation of dichlorobenzene. In addition to the detailed analysis of the various nanocrystal morphologies observed in the various transformations, the structure-photoluminescence relationships for the different samples were analyzed and discussed.
| S-EPMC8879588 | biostudies-literature