Tuning the Photocycle Kinetics of Bacteriorhodopsin in Lipid Nanodiscs

AbstractMonodisperse lipid nanodiscs are particularly suitable for characterizing membrane protein in near-native environment. To study the lipid-composition dependence of photocycle kinetics of bacteriorhodopsin (bR), transient absorption spectroscopy was utilized to monitor the evolution of the photocycle intermediates of bR reconstituted in nanodiscs composed of different ratios of the zwitterionic lipid (DMPC, dimyristoyl phosphatidylcholine; DOPC, dioleoyl phosphatidylcholine) to the negatively charged lipid (DOPG, dioleoyl phosphatidylglycerol; DMPG, dimyristoyl phosphatidylglycerol). The characterization of ion-exchange chromatography showed that the negative surface charge of nanodiscs increased as the content of DOPG or DMPG was increased. The steady-state absorption contours of the light-adapted monomeric bR in nanodiscs composed of different lipid ratios exhibited highly similar absorption features of the retinal moiety at 560 nm, referring to the conservation of the tertiary structure of bR in nanodiscs of different lipid compositions. In addition, transient absorption contours showed that the photocycle kinetics of bR was significantly retarded and the transient populations of intermediates N and O were decreased as the content of DMPG or DOPG was reduced. This observation could be attributed to the negatively charged lipid heads of DMPG and DOPG, exhibiting similar proton relay capability as the native phosphatidylglycerol (PG) analog lipids in the purple membrane. In this work, we not only demonstrated the usefulness of nanodiscs as a membrane-mimicking system, but also showed that the surrounding lipids play a crucial role in altering the biological functions, e.g., the ion translocation kinetics of the transmembrane proteins

Uncovering the Role of Bicarbonate in Calcium Carbonate Formation at Near-Neutral pH

Mechanistic pathways relevant to mineralization are not well-understood fundamentally, let alone in the context of their biological and geological environments. Through quantitative analysis of ion association at near-neutral pH, we identify the involvement of HCO3− ions in CaCO3 nucleation. Incorporation of HCO3− ions into the structure of amorphous intermediates is corroborated by solid-state nuclear magnetic resonance spectroscopy, complemented by quantum mechanical calculations and molecular dynamics simulations. We identify the roles of HCO3− ions as being through (i) competition for ion association during the formation of ion pairs and ion clusters prior to nucleation and (ii) incorporation as a significant structural component of amorphous mineral particles. The roles of HCO3− ions as active soluble species and structural constituents in CaCO3 formation are of fundamental importance and provide a basis for a better understanding of physiological and geological mineralization. © 2021 The Authors. Angewandte Chemie International Edition published by Wiley-VCH Gmb

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Characterization of Phosphorus Species in Human Dentin by Solid-State NMR

The rat has been considered as an appropriate animal model for the study of the mineralization process in humans. In this work, we found that the phosphorus species in human dentin characterized by solid-state NMR spectroscopy consist mainly of orthophosphate and hydrogen phosphate. Some orthophosphates are found in a disordered phase, where the phosphate ions are hydrogen-bonded to structural water, some present a stoichiometric apatite structure, and some a hydroxyl-depleted apatite structure. The results of this study are largely the same as those previously obtained for rat dentin. However, the relative amounts of the various phosphorus species in human and rat dentin are dramatically different. In particular, stoichiometric apatite is more abundant in human dentin than in rat dentin, whereas the converse is true for disordered-phase orthophosphates. Furthermore, spatial proximity among all phosphorus species in human dentin is identical within experimental error, in contrast to what observed for rat dentin. Although it is not clear how these spectroscopic data could relate to the hierarchical structure or the mechanical properties of teeth, our data reveal that the molecular structures of human and rat dentin at different growth stages are not exactly the same

Preparation and Structural Characterization of Free-Standing Octacalcium-Phosphate-Rich Thin Films

Free-standing films of calcium phosphates exhibit many favorable properties for tissue engineering. In this work, a thin film of calcium phosphate is prepared in a liposome suspension using the method of ammonia gas diffusion. The thickness of the film is about 10 μm, and the lateral dimensions are on the length scale of millimeter. The results of powder X-ray diffraction and transmission electron microscopy show that the thin films contain the mineral phases of hydroxyapatite and octacalcium phosphate (OCP). Using solid-state NMR spectroscopy, in particular the technique of heteronuclear correlation spectroscopy with variable contact time, the major crystalline phase of the thin film has been confirmed to be OCP

Formation and near-infrared emission of CsPbI3 nanoparticles embedded in Cs4PbI6 crystals

This work was financially supported by the Advanced Research Center of Green Materials Science and Technology from The Featured Area Research Center Program within the framework of the Higher Education Sprout Project by the Ministry of Education (107L9006), the Ministry of Science and Technology in Taiwan (Contracts MOST 109-2113-M-002-020-MY3, MOST 107-2113-M-002-008-MY3, MOST 110-2923-M-002-017-MY3, MOST 107-2923-M-002-004-MY3, and MOST 107-3017-F-002-001), the National Science Center Poland Grant Opus (nos. 2016/23/B/ST3/03911 and 2019/33/B/ST3/00406), and the National Center for Research and Development Poland Grant (no. PL-TW/VIII/1/2021).Cs4PbI6, as a rarely investigated member of the Cs4PbI6(X is a halogen element) family, has been successfully synthesized at low temperatures, and the synthetic conditions have been optimized. Metal iodides such as LiI, KI, NiI2, CoI2, and ZnI2, as additives, play an important role in enhancing the formation of the Cs4PbI6 microcrystals. ZnI2 with the lowest dissociation energy is the most efficient additive to supply iodide ions, and its amount of addition has also been optimized. Strong red to near-infrared (NIR) emission properties have been detected, and its optical emission centers have been identified to be numerous embedded perovskite-type α-CsPbI3 nanocrystallites (∼5 nm in diameter) based on investigations of temperature- and pressure-dependent photoluminescent properties. High-resolution transmission electron microscopy was used to detect these hidden nanoparticles, although the material was highly beam-sensitive and confirmed a “raisin bread”-like structure of the Cs4PbI6 crystals. A NIR mini-LED for the biological application has been successfully fabricated using as-synthesized Cs4PbI6 crystals. This work provides information for the future development of infrared fluorescent nanoscale perovskite materials.PostprintPeer reviewe

Site Specific NMR Characterization of Abeta-40 Oligomers Cross Seeded by Abeta-42 Oligomers

Extracellular accumulation of β amyloid peptides of 40 (Aβ40) and 42 residues (Aβ42) has been considered as one of the hallmarks in the pathology of Alzheimer’s disease. In this work, we are able to prepare oligomeric aggregates of Aβ with uniform size and high structural homogeneity. Our experimental design is to incubate Aβ peptides in reverse micelles (RMs) so that the peptides could aggregate only through a single nucleation process and the size of the oligomers is confined by the physical dimension of the reverse micelles. The hence obtained Aβ oligomers (AβOs) are 23 nm in diameter and they belong to the category of high molecular-weight (MW) oligomers. The solid-state NMR data revealed that Aβ40Os adopt the structural motif of β-loop-β but the chemical shifts manifested that they are structurally different from low-MW AβOs and mature fibrils. From the thioflavin-T results, we found that high-MW Aβ42Os can seed the fibrillization of Aβ40 monomers. Our protocol allows performing cross-seeding experiments among oligomeric species. By comparing the chemical shifts of Aβ40Os cross seeded by Aβ42Os and those of Aβ40Os prepared in the absence of Aβ42Os, we observed that the structures of E11, K16, and E22 were altered, whereas the backbone conformation of the β-sheet region near the C-terminus is structurally invariant. The use of reverse micelles allows hitherto the most detailed characterization of the structural variability of Aβ40Os