Thermodynamics of oligomerization and Helix-to-sheet structural transition of amyloid ß-protein on anionic phospholipid vesicles.

Understanding oligomerization and aggregation of the amyloid-ß protein is important to elucidate the pathological mechanisms of Alzheimer's disease, and lipid membranes play critical roles in this process. In addition to studies reported by other groups, our group has also reported that the negatively-charged lipid bilayers with a high positive curvature induced α-helix-to-ß-sheet conformational transitions of amyloid-ß-(1-40) upon increase in protein density on the membrane surface and promoted amyloid fibril formation of the protein. Herein, we investigated detailed mechanisms of the conformational transition and oligomer formation of the amyloid-ß protein on the membrane surface. Changes in the fractions of the three protein conformers (free monomer, membrane-bound α-helix-rich conformation, and ß-sheet-rich conformation) were determined from the fluorescent spectral changes of the tryptophan probe in the protein. The helix-to-sheet structural transition on the surface was described by a thermodynamic model of octamer formation driven by entropic forces including hydrophobic interactions. These findings provide useful information for understanding the self-assembly of amyloidogenic proteins on lipid membrane surfaces.

Impact of transmembrane peptides on individual lipid motions and collective dynamics of lipid bilayers.

The fluid nature of lipid bilayers is indispensable for the dynamic regulation of protein function and membrane morphology in biological membranes. Membrane-spanning domains of proteins interact with surrounding lipids and alter the physical properties of lipid bilayers. However, there is no comprehensive view of the effects of transmembrane proteins on the membrane's physical properties. Here, we investigated the effects of transmembrane peptides with different flip-flop-promoting abilities on the dynamics of a lipid bilayer employing complemental fluorescence and neutron scattering techniques. The quasi-elastic neutron scattering and fluorescence experiments revealed that lateral diffusion of the lipid molecules and the acyl chain motions were inhibited by the inclusion of transmembrane peptides. The neutron spin-echo spectroscopy measurements indicated that the lipid bilayer became more rigid but more compressible and the membrane viscosity increased when the transmembrane peptides were incorporated into the membrane. These results suggest that the inclusion of rigid transmembrane structures hinders individual and collective lipid motions by slowing down lipid diffusion and increasing interleaflet coupling. The present study provides a clue for understanding how the local interactions between lipids and proteins change the collective dynamics of the lipid bilayers, and therefore, the function of biological membranes.

Fine-Tuning and Enhancement of pH-Dependent Membrane Permeation of Cyclic Peptides by Utilizing Noncanonical Amino Acids with Extended Side Chains.

The development of cyclic peptides that exhibit pH-sensitive membrane permeation is a promising strategy for tissue-selective drug delivery. We investigated the pH-dependent interactions of designed cyclic peptides bearing noncanonical amino acids of long acidic side chains with lipid membranes, including surface binding, insertion, and translocation across the membrane. As the length of the side chain of acidic amino acid increased, the binding affinity of the peptides to phosphatidylcholine bilayer surfaces decreased, while the pH for the 50% insertion of the peptides into the bilayers increased. The pH for membrane permeation of the peptides increased with the side chain length, resulting in specific membrane permeation at pH ∼6.5. The longer side chain of acidic amino acids improved the maximum rate of membrane permeation at low pH, where both entropic and enthalpic contributions affected the permeation. Our peptide also showed intracellular delivery of cargo molecules into living cells in a pH-dependent manner.

The Nanometer-Scale Proximity of Bilayers Facilitates Intermembrane Lipid Transfer.

Biological membranes approach one another in various biological phenomena, such as lipid transport at membrane contact sites and membrane fusion. The proximity of two bilayers may cause environmental changes in the interbilayer space and alter the dynamics of lipid molecules. Here, we investigate the structure and dynamics of vesicles aggregated due to the depletion attraction caused by polyethylene glycol (PEG) through static and dynamic small-angle neutron scattering. Manipulation of the interbilayer distance using PEG-conjugated lipids reveals that lipid molecules rapidly transfer between vesicles when the opposing bilayers are within ∼2 nm of each other. This distance corresponds to a region in which water molecules are more structured than in bulk water. Kinetic analysis suggests that the decrease in water entropy is responsible for the progression of lipid transfer. These results provide a basis for understanding the dynamic function of biomembranes in confined regions.

Amphipathic peptide-phospholipid nanofibers: Kinetics of fiber formation and molecular transfer between assemblies.

Understanding the kinetics of nano-assembly formation is important to elucidate the biological processes involved and develop novel nanomaterials with biological functions. In the present study, we report the kinetic mechanisms of nanofiber formation from a mixture of phospholipids and the amphipathic peptide 18A[A11C], carrying cysteine substitution of the apolipoprotein A-I-derived peptide 18A at residue 11. 18A[A11C] with acetylated N-terminus and amidated C-terminus can associate with phosphatidylcholine to form fibrous aggregates at neutral pH and lipid-to-peptide molar ratio of ∼1, although the reaction pathways of self-assembly remain unclear. Here, the peptide was added to giant 1-palmitoyl-2-oleoyl phosphatidylcholine vesicles to monitor nanofiber formation under fluorescence microscopy. The peptide initially solubilized the lipid vesicles into particles smaller than the resolution of optical microscope, and fibrous aggregates appeared subsequently. Transmission electron microscopy and dynamic light scattering analyses revealed that the vesicle-solubilized particles were spherical or circular, measuring ∼10-20 nm in diameter. The rate of nanofiber formation of 18A with 1,2-dipalmitoyl phosphatidylcholine from the particles was proportional to the square of lipid-peptide concentration in the system, suggesting that the association of particles, accompanied by conformational changes, was the rate-limiting step. Moreover, molecules in the nanofibers could be transferred between aggregates faster than those in the lipid vesicles. These findings provide useful information for the development and control of nano-assembling structures using peptides and phospholipids.

Career satisfaction among acute care resident physicians in Japan.

Aim: With the introduction of the new national board certification system, sustainable education of acute care physicians has become an important topic. Prior surveys have addressed the job satisfaction of young acute care physicians. However, there have been limited nationwide surveys. The purpose of this study was to investigate the career satisfaction of senior acute care resident physicians, and to identify factors affecting their career satisfaction. Methods: An anonymous multiple-choice questionnaire was administered to candidates at the national board examination in 2018 regarding their career satisfaction. Data were analyzed with factor analysis and multivariable analysis with a logistic regression model to identify factors affecting career satisfaction. Results: There were 427 respondents and the response rate was 98.2%. There were 332 male respondents (80.8%). Factors that correlated with career satisfaction were training systems, working conditions, personal learning, and stress-related factors. High job satisfaction was found in 137 (36.6%) of the respondents. Logistic regression analysis showed that the factors significantly associated with high job satisfaction were: training systems (odds ratio [OR] 2.18; 95% confidence interval [CI], 1.43-3.33), working conditions (OR 1.78; 95% CI, 1.25-2.53), and personal learning (OR 1.55; 95% CI, 1.02-2.36). There was no significant correlation between high career satisfaction and intention to switch to another specialty. Conclusion: High job satisfaction in senior acute care residents requires the development of a teaching environment, an optimized work environment, and encouragement of personal learning.

Thermodynamics for the Self-Assembly of Alkylated Peptides.

Self-assembling peptides form aggregates with various nanostructures such as spheres, sheets, and fibers and have potential applications in nanomedicine and drug delivery. The alkylation of peptides is a promising strategy for controlling the self-assembly of peptides. In this study, we investigated the thermodynamic properties associated with the aggregation of alkyl-chain-modified self-assembling peptides. The tripeptide sequence, KYF, which has been reported to form fibrous aggregates via self-assembly, was modified with various fatty acids at the N-terminus. The fibrous morphology of the aggregates was observed by transmission electron microscopy and atomic force microscopy. Thioflavin T fluorescence and circular dichroism spectroscopy revealed the formation of ß-sheet structures. The critical micelle concentration and its temperature dependence were determined to obtain the thermodynamic parameters for aggregation. The results showed that the aggregation was an entropy-driven process at low temperatures, whereas it was enthalpy-driven at high temperatures. The negative heat capacity changes for aggregation suggested that hydrophobic interactions were the major driving force for self-assembly. Other entropic and enthalpic interactions were also contributed in part to the self-assembly. We individually identified the contributions of the peptide and alkyl chain moiety to the self-assembly. These contributions can be explained by the theoretical values for the self-assembly of each component. The results of this study provide fundamental insights into the design of self-associating peptides.

Flip-Flop Promotion Mechanisms by Model Transmembrane Peptides.

Lipid transbilayer movement (flip-flop) is regulated by membrane proteins that are involved in homeostasis and signaling in eukaryotic cells. In the plasma membrane, an asymmetric lipid composition is maintained by energy-dependent unidirectional transport. Energy-independent flip-flop promotion by phospholipid scramblases disrupts the asymmetry in several physiological processes, such as apoptosis and blood coagulation. In the endoplasmic reticulum, rapid flip-flop is essential for bilayer integrity because phospholipids are synthesized only in the cytoplasmic leaflet. Phospholipid scramblases are also involved in lipoprotein biogenesis, autophagosome formation, and viral infection. Although several scramblases have been identified and investigated, the precise flip-flop promotion mechanisms are not fully understood. Model transmembrane peptides are valuable tools for investigating the general effects of lipid-peptide interactions. We focus on the development of model transmembrane peptides with flip-flop promotion abilities and their mechanisms.

Energetic and Structural Insights into Phospholipid Transfer from Membranes with Different Curvatures by Time-Resolved Neutron Scattering.

Understanding how lipid dynamics change with membrane curvature is important given that biological membranes constantly change their curvature and morphology through membrane fusion and endo-/exocytosis. Here, we used time-resolved small-angle neutron scattering and time-resolved fluorescence to characterize the properties and dynamics of phospholipids in vesicles with different curvatures. Dissociation of phospholipids from vesicles required traversing an energy barrier comprising positive enthalpy and negative entropy. However, lipids in membranes with high positive curvature have dense acyl chain packing and loose headgroup packing, leading to hydrophobic hydration due to water penetration into the membrane. These properties were found to lower the hydrophobic hydration enhancement associated with phospholipid dissociation and mitigate the acyl chain packing of lipids adjacent to the space created by the lipid dissociation, resulting in an increase in activation entropy. The results of this study provide important insights into the functions of biomembranes in relation to their dynamic structural changes.

Kinetic Mechanism of Amyloid-ß-(16-22) Peptide Fibrillation.

The kinetic mechanism of amyloid fibril formation by a peptide fragment containing seven residues of the amyloid-ß protein Aß-(16-22) was investigated. We found that the N- and C-terminal unprotected Aß-(16-22), containing no aggregation nuclei, showed rapid fibrillation within seconds to minutes in a neutral aqueous buffer solution. The fibrillation kinetics were well described by the nucleation-elongation model, suggesting that primary nucleation was the rate-limiting step. On the basis of both experimental and theoretical analyses, the aggregated nucleus was estimated to be composed of 6-7 peptide molecules, wherein the two ß-sheets were associated with their hydrophobic surfaces. Thin fibers with widths of 10-20 nm were formed, which increased their length and thickness, attaining a width of >20 nm over several tens of minutes, probably owing to the lateral association of the fibers. Electrostatic and hydrophobic interactions play important roles in aggregation. These results provide a basis for understanding the fibrillation of short peptides.

Improvement of Thermal Stability of Amphipathic Peptide-Phospholipid Nanodiscs via Lateral Association of α-Helices by Disulfide Cross-Linking.

Amphipathic α-helical peptides have been reported to form discoidal particles or nanodiscs with phospholipids, in which a lipid bilayer patch is encircled by peptides. Peptide-based nanodiscs have broad applicability because of their ease of preparation, size flexibility, and structural plasticity. We previously revealed that the nanodiscs formed by apolipoprotein-A-I-derived peptide 18A showed temperature-dependent structural destabilization above the gel-to-liquid-crystalline phase transition temperature of the lipid bilayer. It has been suggested that this destabilization is due to the migration of peptides bound to the edge of the discs to the bilayer surface. In this study, we designed a peptide that could stabilize nanodisc structures against the phase transition of lipid bilayers by disulfide cross-linking of peptides. An 18A-dimer cross-linked by a proline residue, 37pA (Ac-18A-P-18A-CONH2), also showed thermal destabilization of nanodiscs like 18A. However, cross-linking the sides of the two α-helices of the cysteine-substituted analogue 37pA-C2 with disulfide bonds led to the formation of nanodiscs that were more stable to temperature changes. This stabilizing effect was mainly due to the formation of a cyclic 37pA-C2 monomer by intramolecular disulfide cross-linking. These results suggest that the lateral association of two α-helices, which is the basis of the double-belt structure, is an important factor for the implementation of stable nanodiscs. The results of this study will help in development of more stable nanoparticles with membrane proteins in the future.

Risk factors for bleeding complications during venovenous extracorporeal membrane oxygenation as a bridge to recovery.

BACKGROUND: Bleeding complications during venovenous extracorporeal membrane oxygenation (V-V ECMO) can be critical. However, there is limited information on the associated risk factors. This study investigated the risk factors for bleeding complications during V-V ECMO as a bridge to recovery. METHODS: This single-center retrospective study enrolled 59 patients (bleeding and non-bleeding groups) who received V-V ECMO from 2012 to 2020, to evaluate whether peak activated partial thromboplastin time (APTT) value, lowest platelet count, and mobilization to sitting on the edge of the bed during V-V ECMO were risk factors for bleeding complications, defined according to the Extracorporeal Life Support Organization guidelines. Age, sex, body mass index, Sequential Organ Failure Assessment score, and ECMO duration before bleeding complications were covariates in the multivariate logistic regression analysis. RESULTS: Thirty-one (53%) participants experienced 36 bleeding complications; the ECMO cannulation site, gastrointestinal tract, and nasopharyngeal region were the most common bleeding sites. The use of transfusion products and length of ECMO and intensive care unit stay were significantly and medical costs were non-significantly increased in the bleeding group. Peak APTT (odds ratio [OR] 1.03, 95% confidence interval [CI] 1.01-1.05, p < 0.01) was significantly associated whereas the lowest platelet count (OR 0.96, 95% CI 0.82-1.13, p = 0.66) was unassociated with bleeding complications during ECMO. Achieving mobilization (OR 0.14, 95% CI 0.02-1.17, p = 0.07) decreased the trend of risk for bleeding complications. CONCLUSIONS: Peak APTT might be an independent modifiable factor for bleeding complications during V-V ECMO. The protective effect of mobilization during V-V ECMO requires further investigation.

PharmacoDB 2.0: improving scalability and transparency of in vitro pharmacogenomics analysis.

Cancer pharmacogenomics studies provide valuable insights into disease progression and associations between genomic features and drug response. PharmacoDB integrates multiple cancer pharmacogenomics datasets profiling approved and investigational drugs across cell lines from diverse tissue types. The web-application enables users to efficiently navigate across datasets, view and compare drug dose-response data for a specific drug-cell line pair. In the new version of PharmacoDB (version 2.0, https://pharmacodb.ca/), we present (i) new datasets such as NCI-60, the Profiling Relative Inhibition Simultaneously in Mixtures (PRISM) dataset, as well as updated data from the Genomics of Drug Sensitivity in Cancer (GDSC) and the Genentech Cell Line Screening Initiative (gCSI); (ii) implementation of FAIR data pipelines using ORCESTRA and PharmacoDI; (iii) enhancements to drug-response analysis such as tissue distribution of dose-response metrics and biomarker analysis; and (iv) improved connectivity to drug and cell line databases in the community. The web interface has been rewritten using a modern technology stack to ensure scalability and standardization to accommodate growing pharmacogenomics datasets. PharmacoDB 2.0 is a valuable tool for mining pharmacogenomics datasets, comparing and assessing drug-response phenotypes of cancer models.

Orchestrating and sharing large multimodal data for transparent and reproducible research.

Reproducibility is essential to open science, as there is limited relevance for findings that can not be reproduced by independent research groups, regardless of its validity. It is therefore crucial for scientists to describe their experiments in sufficient detail so they can be reproduced, scrutinized, challenged, and built upon. However, the intrinsic complexity and continuous growth of biomedical data makes it increasingly difficult to process, analyze, and share with the community in a FAIR (findable, accessible, interoperable, and reusable) manner. To overcome these issues, we created a cloud-based platform called ORCESTRA ( orcestra.ca ), which provides a flexible framework for the reproducible processing of multimodal biomedical data. It enables processing of clinical, genomic and perturbation profiles of cancer samples through automated processing pipelines that are user-customizable. ORCESTRA creates integrated and fully documented data objects with persistent identifiers (DOI) and manages multiple dataset versions, which can be shared for future studies.

Development of membrane-insertable lipid scrambling peptides: A time-resolved small-angle neutron scattering study.

Phospholipid transbilayer movement (flip-flop) in the plasma membrane is regulated by membrane proteins to maintain cell homeostasis and interact with other cells. The promotion of flip-flop by phospholipid scramblases causes the loss of membrane lipid asymmetry, which is involved in apoptosis, blood coagulation, and viral infection. Therefore, compounds that can artificially control flip-flop in the plasma membrane are of biological and medical interest. Here, we have developed lipid scrambling transmembrane peptides that can be inserted into the membrane. Time-resolved small-angle neutron scattering measurements revealed that the addition of peptides containing a glutamine residue at the center of the hydrophobic sequence to lipid vesicles induces the flip-flop of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine. Peptides without the glutamine residue had no effect on the flip-flop. Because the glutamine-containing peptides exhibited scramblase activity in monomeric form, the polar glutamine residue would be exposed to the hydrocarbon region of the membrane, perturbing the membrane and promoting the lipid flip-flop. These scrambling peptides would be valuable tools to regulate lipid flip-flop in the plasma membrane.

Amphipathic Peptide-Phospholipid Nanofibers: Phospholipid Specificity and Dependence on Concentration and Temperature.

The design of nanoassemblies is an important part of the development of new materials for applications in nanomedicine and biosensors. In our previous study, cysteine substitution of the apolipoprotein A-I-derived peptide 18A at residue 11, 18A[A11C], bound to 1-palmitoyl-2-oleoylphosphatidylcholine to form fibrous aggregates at a lipid-to-peptide molar ratio of ≤2 and a fiber diameter of 10-20 nm. However, the mechanisms underlying the lipid-peptide interactions that enable nanofiber formation remain unclear. Here, we evaluated the phospholipid specificity, concentration dependence, and temperature dependence of the formation of 18A[A11C]-lipid nanofibers. Nanofibers were found to form in the presence of specific phospholipids and have a constant lipid/peptide stoichiometry of 1.2 ± 0.2. Moreover, an increase in the length of the acyl chain in phosphatidylcholines was found to increase the structural stability of the nanofibers. These results indicate that specific molecular interactions between peptides and both the headgroups and acyl chains of phospholipids are involved in nanofiber formation. Furthermore, the formation and disassembly of the nanofibers were reversibly controlled by changes in temperature and concentration. The results of the present study provide an insight into the creation of nanoassembling structures.

Temperature- and composition-dependent conformational transitions of amphipathic peptide-phospholipid nanodiscs.

Nanodiscs are discoidal particles in which a lipid bilayer is encircled by amphipathic molecules such as proteins, peptides, or synthetic polymers. The apolipoprotein-A-I-derived peptide 18A is known to form nanodiscs in the presence of phospholipids, but the detailed mechanism of the formation and deformation of these nanodiscs in response to changes in the surrounding environment is not well understood. Here, we investigated the temperature- and composition-dependent structural changes of 18A-phosphatidylcholine complexes using fluorescence spectroscopy, dynamic light scattering, circular dichroism, static 31P NMR, and electron microscopy. We found that the nanodiscs in fast isotropic rotational motion increased in size above the gel-to-liquid-crystalline phase transition temperature of the lipid bilayers, resulting in the formation of enlarged nanodiscs and a lamellar phase. The lamellar phase was found to be oriented along the magnetic field. Further increase in temperature induced the formation of lipid vesicles. These transformations were explained using a transition model based on the migration of the peptide from the rim of the nanodiscs to the liquid-crystalline bilayer phase. The study outcomes provide a basis for understanding the design principles of discoidal nanostructures for structural biology and nanomedicine applications.

Biophysical parameters of the Sec14 phospholipid exchange cycle - Effect of lipid packing in membranes.

Sec14, a yeast phosphatidylinositol/phosphatidylcholine transfer protein, functions at the trans-Golgi membranes. It lacks domains involved in protein-protein or protein-lipid interactions and consists solely of the Sec14 domain; hence, the mechanism underlying Sec14 function at proper sites remains unclear. In this study, we focused on the lipid packing of membranes and evaluated its association with in vitro Sec14 lipid transfer activity. Phospholipid transfer assays using pyrene-labelled phosphatidylcholine suggested that increased membrane curvature as well as the incorporation of phosphatidylethanolamine accelerated the lipid transfer. The quantity of membrane-bound Sec14 significantly increased in these membranes, indicating that "packing defects" of the membranes promote the membrane binding and phospholipid transfer of Sec14. Increased levels of phospholipid unsaturation promoted Sec14-mediated PC transfer, but had little effect on the membrane binding of the protein. Our results demonstrate the possibility that the location and function of Sec14 are regulated by the lipid packing states produced by a translocase activity at the trans-Golgi network.

Urea-Assisted Reconstitution of Discoidal High-Density Lipoprotein.

High-density lipoprotein (HDL) is a naturally occurring composite of lipids and lipid-binding proteins. The cholate dialysis method, first reported by Jonas in 1969, is the most widely used approach for reconstituting discoidal HDL (dHDL) in test tubes with phospholipids and the most dominant protein, apolipoprotein A-1 (apoA-I). Here, we show that a dHDL-relevant complex can also be prepared by gently mixing 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and apoA-I or its mutants in ethanol/H2O solutions containing urea at a concentration of a few molar and then incubating the mixture at the gel-liquid crystalline phase transition temperature in test tubes. Subsequent purification steps involve quick dialysis following size exclusion chromatography. The yields (73 ± 3% and 70 ± 1% protein and DMPC, respectively) of the resulting HDL-like nanoparticles, designated as uHDL, were comparable to the values of 68 ± 9% and 71 ± 12% obtained in the cholate dialysis method. Using apoA-I and two mutants, the key factor in this method was found to be urea at the folded and unfolded transition midpoint concentration. By using this urea-assisted method in the presence of a hydrophobic drug, all-trans-retinoic acid (ATRA), one-step preparation of ATRA-loaded uHDL was also possible. The loading efficiency was comparable to that in the mixing of ATRA and uHDL or dHDL reconstituted by the cholate dialysis method. Atomic force microscopy analysis revealed that uHDL and ATRA-loaded uHDL were discoidal. Our urea-assisted method is an easy and efficient method for reconstituting dHDL and can be utilized to prepare various drug-dHDL complexes.