Real-Time Observation for Dynamic Oscillation during Self-Assembly and Clearance of Aß42.

The dynamic oscillation implicated in structural heterogeneity during the self-assembly of amyloid peptide 1-42 (Aß42) may play a crucial role in eliciting cellular responses. We developed a real-time monitoring platform to observe an oscillatory non-equilibrium interaction that dominated the Aß42 clearance by neuronal cells during interplay with an oscillator (lipopolysaccharide, LPS). Molecular dynamics studies indicated that the electrostatic and hydrophobic segments of LPS involved in the temporary heteromolecular association and slightly decelerated the intrinsic thermally-induced protein dynamics of Aß42. A bait-specific intervention strategy could temporarily slow down the self-propagation of Aß42 to extend the lifetime of autonomous oscillation and augment Aß42 clearance of neuronal cells. The lifetime increment of oscillation shows a bait concentration-dependent manner to reflect the non-equilibrium binding strength. This relationship may serve as a predictor for Alzheimer's disease drug discovery.

Not out of the woods yet: Signatures of the prolonged negative genetic consequences of a population bottleneck in a rapidly re-expanding wader, the black-faced spoonbill Platalea minor.

The long-term persistence of a population which has suffered a bottleneck partly depends on how historical demographic dynamics impacted its genetic diversity and the accumulation of deleterious mutations. Here we provide genomic evidence for the genetic effect of a recent population bottleneck in the endangered black-faced spoonbill (Platalea minor) after its rapid population recovery. Our data suggest that the bird's effective population size, Ne , had been relatively stable (7500-9000) since 22,000 years ago; however, a recent brief yet severe bottleneck (Ne  = 20) which we here estimated to occur around the 1940s wiped out >99% of its historical Ne in roughly three generations. Despite a >15-fold population recovery since 1988, we found that black-faced spoonbill population has higher levels of inbreeding (7.4 times more runs of homozygosity) than its sister species, the royal spoonbill (P. regia), which is not thought to have undergone a marked population contraction. Although the two spoonbills have similar levels of genome-wide genetic diversity, our results suggest that selection on more genes was relaxed in the black-faced spoonbill; moreover individual black-faced spoonbills carry more putatively deleterious mutations (Grantham's score > 50), and may therefore express more deleterious phenotypic effects than royal spoonbills. Here we demonstrate the value of using genomic indices to monitor levels of genetic erosion, inbreeding and mutation load in species with conservation concerns. To mitigate the prolonged negative genetic effect of a population bottleneck, we recommend that all possible measures should be employed to maintain population growth of a threatened species.

Strict allopatric speciation of sky island Pyrrhula erythaca species complex.

Increasing evidence of post-divergence gene flow between taxa is shifting our understanding on the mode of speciation. A fundamental question arises concerning the circumstances under which strict allopatric speciation still holds true. Sky island populations might undergo reduced gene flow by niche conservatism to highland habitats and follow divergence in an allopatric manner. In this study, we tested this hypothesis in the sky island Grey-headed Bullfinch (Pyrrhula erythaca) species complex via statistical analyses of both genetic and ecological data. Results of coalescent-based analysis of multiple nuclear loci suggested that P. e. owstoni likely colonized Taiwan island during the severe mid-Pleistocene glacial climate followed by strictly allopatric divergence from P. e. erythaca distributed in Himalayas-Hengduan mountains and central North China. Results of ecological niche modeling suggested that their speciation may be attributed to the niche conservatism of these birds and the lack of a suitable ecological corridor during subsequent milder glacial episodes. In addition, we delimited the traditionally defined P. erythaca into two full species, P. erythaca in the Asian mainland and P. owstoni on the island of Taiwan, based on both genetic and behavioural evidences. These results suggest that ecology can have a dynamic role in allowing highland populations to expand their ranges and isolated by habitat barriers to diversify in a strictly allopatric manner.

Effects of Cholesterol on Water Permittivity of Biomimetic Ion Pair Amphiphile Bilayers: Interplay between Membrane Bending and Molecular Packing.

Ion pair amphiphile (IPA), a molecular complex composed of a pair of cationic and anionic amphiphiles, is an inexpensive phospholipid substitute to fabricate vesicles with various pharmaceutical applications. Modulating the physicochemical and permeation properties of IPA vesicles are important for carrier designs. Here, we applied molecular dynamics simulations to examine the cholesterol effects on the structures, mechanics, and water permittivity of hexadecyltrimethylammonium-dodecylsulfate (HTMA-DS) and dodecyltrimethylammonium- hexadecylsulfate (DTMA-HS) IPA bilayers. Structural and mechanical analyses indicate that both IPA systems are in gel phase at 298 K. Adding cholesterol induces alkyl chain ordering around the rigid sterol ring and increases the cavity density within the hydrophilic region of both IPA bilayers. Furthermore, the enhanced alkyl chain ordering and the membrane deformation energy induced by cholesterol increase the permeation free energy penalty. In contrast, cholesterol has minor effects on the water local diffusivities within IPA membranes. Overall, the cholesterol reduces the water permittivity of rigid IPA membranes due to the synergistic effects of increased alkyl chain ordering and enhanced membrane mechanical modulus. The results provide molecular insights into the effects of molecular packing and mechanical deformations on the water permittivity of biomimetic IPA membranes, which is critical for designing IPA vesicular carriers.

Importance of Hydrophilic Groups on Modulating the Structural, Mechanical, and Interfacial Properties of Bilayers: A Comparative Molecular Dynamics Study of Phosphatidylcholine and Ion Pair Amphiphile Membranes.

An ion pair amphiphile (IPA), a molecular complex composed of two oppositely charged amphiphiles, is a phospholipid mimic which differs from a phospholipid only in the hydrophilic compositions. Here, we utilized molecular dynamics (MD) simulations to compare the bilayer systems composed of phosphatidylcholines (PC) and alkyltrimethylammonium-alkylsulfate IPAs with various alkyl chain lengths. The membrane properties for both liquid-disordered (Ld) and gel (S) phase bilayers were examined via running simulations above and below the main transition temperatures. The electrostatic attraction between the IPA hydrophilic groups leads to a more ordered molecular packing within both S and Ld phase IPA membranes, as revealed by the molecular area, deuterium order parameter, and gauche conformation analyses. Furthermore, IPA bilayers possess a higher area compressibility modulus, molecular tilt modulus, and effective bending rigidity than PC systems. The variation of hydrophilic groups of IPA also leads to fewer hydrogen bonds on the membrane surface and smaller electrostatic potentials for the biomimetic bilayer. The non-covalently linked head groups of IPA further decouple alkyl tilting and surface water retention. The combined results reveal the importance of hydrophilic groups of amphiphiles on modulating the membrane properties, which also provides insights for designs of biomimetic membranes.

Interplay between alkyl chain asymmetry and cholesterol addition in the rigid ion pair amphiphile bilayer systems.

Ion pair amphiphile (IPA), a molecular complex composed of a pair of cationic and anionic surfactants, has been proposed as a novel phospholipid substitute. Controlling the physical stability of IPA vesicles is important for its application developments such as cosmetic and drug deliveries. To investigate the effects of IPA alkyl chain combinations and the cholesterol additive on the structural and mechanical properties of IPA vesicular bilayers, we conducted a series of molecular dynamics studies on the hexadecyltrimethylammonium-dodecylsulfate (HTMA-DS) and dodecyltrimethylammonium-hexadecylsulfate (DTMA-HS) IPA bilayers with cholesterol. We found that both IPA bilayers are in the gel phase at 298 K, consistent with experimental observations. Compared with the HTMA-DS system, the DTMA-HS bilayer has more disordered alkyl chains in the hydrophobic region. When adding cholesterol, it induces alkyl chain ordering around its rigid sterol ring. Yet, cholesterol increases the molecular areas for all species and disturbs the molecular packing near the hydrophilic region and the bilayer core. Cholesterol also promotes the alkyl chain mismatch between the IPA moieties, especially for the DTMA-HS bilayer. The combined effects lead to non-monotonically enhancement of the membrane mechanical moduli for both IPA-cholesterol systems. Furthermore, cholesterol can form H-bonds with the alkylsulfate and thus enhance the contribution of alkylsulfate to the overall mechanical moduli. Combined results provide valuable molecular insights into the roles of each IPA component and the cholesterol on modulating the IPA bilayer properties.

Mechanism of IAPP amyloid fibril formation involves an intermediate with a transient ß-sheet.

Amyloid formation is implicated in more than 20 human diseases, yet the mechanism by which fibrils form is not well understood. We use 2D infrared spectroscopy and isotope labeling to monitor the kinetics of fibril formation by human islet amyloid polypeptide (hIAPP or amylin) that is associated with type 2 diabetes. We find that an oligomeric intermediate forms during the lag phase with parallel ß-sheet structure in a region that is ultimately a partially disordered loop in the fibril. We confirm the presence of this intermediate, using a set of homologous macrocyclic peptides designed to recognize ß-sheets. Mutations and molecular dynamics simulations indicate that the intermediate is on pathway. Disrupting the oligomeric ß-sheet to form the partially disordered loop of the fibrils creates a free energy barrier that is the origin of the lag phase during aggregation. These results help rationalize a wide range of previous fragment and mutation studies including mutations in other species that prevent the formation of amyloid plaques.

Basis function sampling: a new paradigm for material property computation.

Wang-Landau sampling, and the associated class of flat histogram simulation methods have been remarkably helpful for calculations of the free energy in a wide variety of physical systems. Practically, convergence of these calculations to a target free energy surface is hampered by reliance on parameters which are unknown a priori. Here, we derive and implement a method built upon orthogonal functions which is fast, parameter-free, and (importantly) geometrically robust. The method is shown to be highly effective in achieving convergence. An important feature of this method is its ability to attain arbitrary levels of description for the free energy. It is thus ideally suited to in silico measurement of elastic moduli and other material properties related to free energy perturbations. We demonstrate the utility of such applications by applying our method to calculate the Frank elastic constants of the Lebwohl-Lasher model of liquid crystals.

Molecular Effects of Li+-Coordinating Binders and Negatively Charged Binders on the Li+ Local Mobility near the Electrolyte/LiFePO4 Cathode Interface within Lithium-Ion Batteries.

The development of lithium-ion batteries (LIBs) is important in the realm of energy storage. Understanding the intricate effects of binders on the Li+ transport at the cathode/electrolyte interface in LIBs remains a challenge. This study utilized molecular dynamics simulations to compare the molecular effects of conventional polyvinylidene difluoride (PVDF), Li+-coordinating polyethylene oxide (PEO), and negatively charged polystyrene sulfonate (PSS) binders on local Li+ mobility at the electrolyte/LiFePO4 (LFP) cathode interface. By examining concentration profiles of Li+, three different polymer binders, and anions near Li+-rich LFP and Li+-depleted FePO4 (FP) surfaces, we found a superior performance of the negatively charged PSS on enhancing Li+ distribution near the Li+-depleted FP surface. The radial distribution function and coordination number analyses revealed the potent interactions of PEO and PSS with Li+ disrupting Li+ coordination with electrolyte solvents. Our simulations also revealed the effects of non-uniform binder dispersions on the Li+ local mobility near the cathode surface. The combined results provide a comparative insight into Li+ transport at the electrolyte/cathode interface influenced by distinct binder chemistries, offering a profound understanding of the binder designs for high-performance LIBs.

Convergent evolution of kidney sizes and supraorbital salt glands for birds living in saline habitats.

Only a small number of avian species inhabit salty environments. To understand how they adapted, we examined the evolution of kidney sizes, supraorbital salt glands (SSGs), and the utilization of salty habitats across 230 species spanning 25 avian orders. Phylogenetic analysis indicates that SSGs, large kidneys, and thriving in salty habitats emerged convergently in birds. Transition rate analysis reveals that species possessing SSGs and large kidneys tended to move from low-to high-salinity environments, while others moved in the opposite direction. However, habitat salinity also influenced kidney evolution; lineages residing in high-salinity environments tended to develop larger kidneys than those in low-salinity environments. Our findings suggest that SSGs and large kidneys may have evolved through adaptation to high salinity. Overall, habitat conditions and physiological traits influenced avian adaptation to salty environments in a reciprocal manner. These results shed the new light on the evolutionary mechanisms underlying functional diversity in birds.

High-Performance Semiconducting Carbon Nanotube Transistors Using Naphthalene Diimide-Based Polymers with Biaxially Extended Conjugated Side Chains.

Polymer-wrapped single-walled carbon nanotubes (SWNTs) are a potential method for obtaining high-purity semiconducting (sc) SWNT solutions. Conjugated polymers (CPs) can selectively sort sc-SWNTs with different chiralities, and the structure of the polymer side chains influences this sorting capability. While extensive research has been conducted on modifying the physical, optical, and electrical properties of CPs through side-chain modifications, the impact of these modifications on the sorting efficiency of sc-SWNTs remains underexplored. This study investigates the introduction of various conjugated side chains into naphthalene diimide-based CPs to create a biaxially extended conjugation pattern. The CP with a branched conjugated side chain (P3) exhibits reduced aggregation, resulting in improved wrapping ability and the formation of larger bundles of high-purity sc-SWNTs. Grazing incidence X-ray diffraction analysis confirms that the potential interaction between sc-SWNTs and CPs occurs through π-π stacking. The field-effect transistor device fabricated with P3/sc-SWNTs demonstrates exceptional performance, with a significantly enhanced hole mobility of 4.72 cm2 V-1 s-1 and high endurance/bias stability. These findings suggest that biaxially extended side-chain modification is a promising strategy for improving the sorting efficiency and performance of sc-SWNTs by using CPs. This achievement can facilitate the development of more efficient and stable electronic devices.

Low but highly geographically structured genomic diversity of East Asian Eurasian otters and its conservation implications.

Populations of Eurasian otters Lutra lutra, one of the most widely distributed apex predators in Eurasia, have been depleted mainly since the 1950s. However, a lack of information about their genomic diversity and how they are organized geographically in East Asia severely impedes our ability to monitor and conserve them in particular management units. Here, we re-sequenced and analyzed 20 otter genomes spanning continental East Asia, including a population at Kinmen, a small island off the Fujian coast, China. The otters form three genetic clusters (one of L. l. lutra in the north and two of L. l. chinensis in the south), which have diverged in the Holocene. These three clusters should be recognized as three conservation management units to monitor and manage independently. The heterozygosity of the East Asian otters is as low as that of the threatened carnivores sequenced. Historical effective population size trajectories inferred from genomic variations suggest that their low genomic diversity could be partially attributed to changes in the climate since the mid-Pleistocene and anthropogenic intervention since the Holocene. However, no evidence of genetic erosion, mutation load, or high level of inbreeding was detected in the presumably isolated Kinmen Island population. Any future in situ conservation efforts should consider this information for the conservation management units.

Effect of proline mutations on the monomer conformations of amylin.

The formation of human islet amyloid polypeptide (hIAPP) is implicated in the loss of pancreatic ß-cells in type II diabetes. Rat amylin, which differs from human amylin at six residues, does not lead to formation of amyloid fibrils. Pramlintide is a synthetic analog of human amylin that shares three proline substitutions with rat amylin. Pramlintide has a much smaller propensity to form amyloid aggregates and has been widely prescribed in amylin replacement treatment. It is known that the three prolines attenuate ß-sheet formation. However, the detailed effects of these proline substitutions on full-length hIAPP remain poorly understood. In this work, we use molecular simulations and bias-exchange metadynamics to investigate the effect of proline substitutions on the conformation of the hIAPP monomer. Our results demonstrate that hIAPP can adopt various ß-sheet conformations, some of which have been reported in experiments. The proline substitutions perturb the formation of long ß-sheets and reduce their stability. More importantly, we find that all three proline substitutions of pramlintide are required to inhibit ß conformations and stabilize the α-helical conformation. Fewer substitutions do not have a significant inhibiting effect.

α-helix to ß-hairpin transition of human amylin monomer.

The human islet amylin polypeptide is produced along with insulin by pancreatic islets. Under some circumstances, amylin can aggregate to form amyloid fibrils, whose presence in pancreatic cells is a common pathological feature of Type II diabetes. A growing body of evidence indicates that small, early stage aggregates of amylin are cytotoxic. A better understanding of the early stages of the amylin aggregation process and, in particular, of the nucleation events leading to fibril growth could help identify therapeutic strategies. Recent studies have shown that, in dilute solution, human amylin can adopt an α-helical conformation, a ß-hairpin conformation, or an unstructured coil conformation. While such states have comparable free energies, the ß-hairpin state exhibits a large propensity towards aggregation. In this work, we present a detailed computational analysis of the folding pathways that arise between the various conformational states of human amylin in water. A free energy surface for amylin in explicit water is first constructed by resorting to advanced sampling techniques. Extensive transition path sampling simulations are then employed to identify the preferred folding mechanisms between distinct minima on that surface. Our results reveal that the α-helical conformer of amylin undergoes a transformation into the ß-hairpin monomer through one of two mechanisms. In the first, misfolding begins through formation of specific contacts near the turn region, and proceeds via a zipping mechanism. In the second, misfolding occurs through an unstructured coil intermediate. The transition states for these processes are identified. Taken together, the findings presented in this work suggest that the inter-conversion of amylin between an α-helix and a ß-hairpin is an activated process and could constitute the nucleation event for fibril growth.

Molecular effects of site-specific phosphate-methylated primer on the structure and motions of Taq DNA polymerase.

Polymerase chain reaction (PCR) is a powerful molecular biology assay for gene detection and quantification. Conventional DNA primers for PCR often suffer from poor sensitivity in specific gene detection. Recently, oligonucleotides containing methyl phosphotriester (MPTE-DNA) have been developed with enhanced DNA hybridization and improved gene detection sensitivity. Yet, site-specific MPTE-modifications on DNA primers have been reported to affect PCR amplification efficiencies while the detailed mechanism remains elusive. Here, we utilized molecular dynamics (MD) simulation to examine the effects of site-specific MPTE-modified primers on the structure and motions of DNA/Taq polymerase complexes. All tested MPTE-DNA/Taq complexes exhibited RMSD values below 2 Å, indicating insignificant effects of all methylation sites on the complex stability. The energetic and hydrogen-bonding analyses suggest minor effects of methylation at t-3, t-4, t-6, and t-7 positions on the DNA-Taq interaction. Principal component analyses further reveal that only t-3, and t-7 methylations preserve the motions of the Taq thumb domain. The site-specific methylation affects the interaction between DNA and the surrounding protein residues, resulting in allosteric-like effects on the DNA/Taq complex. The MD data complement the best experimentally observed PCR efficacies for the t-3 and t-7 positions among all tested MPTE-primers. The unveiled molecular insights can benefit the design of novel PCR primers for improving genetic testing platforms.

Parallel ß-sheet vibrational couplings revealed by 2D IR spectroscopy of an isotopically labeled macrocycle: quantitative benchmark for the interpretation of amyloid and protein infrared spectra.

Infrared spectroscopy is playing an important role in the elucidation of amyloid fiber formation, but the coupling models that link spectra to structure are not well tested for parallel ß-sheets. Using a synthetic macrocycle that enforces a two stranded parallel ß-sheet conformation, we measured the lifetimes and frequency for six combinations of doubly (13)C═(18)O labeled amide I modes using 2D IR spectroscopy. The average vibrational lifetime of the isotope labeled residues was 550 fs. The frequencies of the labels ranged from 1585 to 1595 cm(-1), with the largest frequency shift occurring for in-register amino acids. The 2D IR spectra of the coupled isotope labels were calculated from molecular dynamics simulations of a series of macrocycle structures generated from replica exchange dynamics to fully sample the conformational distribution. The models used to simulate the spectra include through-space coupling, through-bond coupling, and local frequency shifts caused by environment electrostatics and hydrogen bonding. The calculated spectra predict the line widths and frequencies nearly quantitatively. Historically, the characteristic features of ß-sheet infrared spectra have been attributed to through-space couplings such as transition dipole coupling. We find that frequency shifts of the local carbonyl groups due to nearest neighbor couplings and environmental factors are more important, while the through-space couplings dictate the spectral intensities. As a result, the characteristic absorption spectra empirically used for decades to assign parallel ß-sheet secondary structure arises because of a redistribution of oscillator strength, but the through-space couplings do not themselves dramatically alter the frequency distribution of eigenstates much more than already exists in random coil structures. Moreover, solvent exposed residues have amide I bands with >20 cm(-1) line width. Narrower line widths indicate that the amide I backbone is solvent protected inside the macrocycle. This work provides calculated and experimentally verified couplings for parallel ß-sheets that can be used in structure-based models to simulate and interpret the infrared spectra of ß-sheet containing proteins and protein assemblies, such as amyloid fibers.

Excimer laser micromachining of aspheric microlens arrays based on optimal contour mask design and laser dragging method.

This paper presents an improved excimer laser micromachining method for fabricating arrayed microstructures with a predesigned surface profile. The proposed method is developed from a conventional biaxial laser dragging method, but numerical analysis and optimal pattern design on the contour mask are introduced so that the machined surface profiles can be well controlled and matched to the designed profiles. To demonstrate the capability of this new approach, an array of aspheric microlenses that have analog surfaces for minimizing the focal spot sizes of the lenses is designed and fabricated. An array of 10×10 microlenses with an aperture size of 100 µm and a designed aspheric profile are obtained experimentally. The machined surface profiles are closely matched to their designed ones, with a profile deviation of less than 1 µm. Furthermore, the machined surfaces are smooth, with an average surface roughness of around 2 nm. Optical measurements on these machined aspheric microlenses show minimized focal spot sizes approaching their optical diffraction limits.

Solute Diffusivity and Local Free Volume in Cross-Linked Polymer Network: Implication of Optimizing the Conductivity of Polymer Electrolyte.

The diffusion of small molecules or ions within polymeric materials is critical for their applications, such as polymer electrolytes. Cross-linking has been one of the common strategies to modulate solute diffusivity and a polymer's mechanical properties. However, various studies have shown different effects of cross-linking on altering the solute transports. Here, we utilized coarse-grained molecular dynamics simulation to systematically analyze the effects of cross-linking and polymer rigidity of solute diffusive behaviors. Above the glass transition temperature Tg, the solute diffusion followed the Vogel-Tammann-Fulcher (VTF) equation, D = D0 e-Ea/R(T-T0). Other than the conventional compensation relation between the activation energy Ea and the pre-exponential factor D0, we also identified a correlation between Ea and Vogel temperature T0. We further characterized an empirical relation between T0 and cross-linking density. Integrating the newly identified correlations among the VTF parameters, we formulated a relation between solute diffusion and the cross-linking density. The combined results proposed the criteria for the optimal solute diffusivity in cross-linked polymers, providing generic guidance for novel polymer electrolyte design.

Divergent effects of cholesterol on the structure and fluidity of liposome and catanionic vesicle membranes.

Lipid-like ion-pair amphiphile vesicles, or catanionic vesicles, have emerged as potential drug carriers. The effects of cholesterol on the properties of catanionic vesicles have yet been systematically studied. Here, we compared the effects of cholesterol on the structures and fluidities of dipalmitoylphosphatidylcholine liposomes and catanionic vesicles with similar main transition temperatures (Tm ). For liposomes, fluorescence anisotropy (FA) thermograms reveal typical condensing and disordering effects of cholesterol above and below Tm respectively. In contrast, FA and molecular simulation data reveal that catanionic bilayers below Tm are more fluidic due to shorter alkyl chains. This leads to only condensing effects of cholesterol for catanionic vesicles at all temperatures. Our results provide important insights into the fabrication of catanionic vesicles as novel drug carriers.

Revised Atomic Charges for OPLS Force Field Model of Poly(Ethylene Oxide): Benchmarks and Applications in Polymer Electrolyte.

Poly(ethylene oxide) (PEO)-based polymers are common hosts in solid polymer electrolytes (SPEs) for high-power energy devices. Molecular simulations have provided valuable molecular insights into structures and ion transport mechanisms of PEO-based SPEs. The calculation of thermodynamic and kinetic properties rely crucially on the dependability of the molecular force fields describing inter- and intra-molecular interactions with the target system. In this work, we reparametrized atomic partial charges for the widely applied optimized potentials for liquid simulations (OPLS) force field of PEO. The revised OPLS force field, OPLSR, improves the calculations of density, thermal expansion coefficient, and the phase transition of the PEO system. In particular, OPLSR greatly enhances the accuracy of the calculated dielectric constant of PEO, which is critical for simulating polymer electrolytes. The reparameterization method was further applied to SPE system of PEO/LiTFSI with O:Li ratio of 16:1. Based on the reparametrized partial charges, we applied separate charge-scaling factors for PEO and Li salts. The charge-rescaled OPLSR model significantly improves the resulting kinetics of Li+ transport while maintaining the accurate description of coordination structures within PEO-based SPE. The proposed OPLSR force field can benefit the future simulation studies of SPE systems.