Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries.

Most membrane proteins are modified by covalent addition of complex sugars through N- and O-glycosylation. Unlike proteins, glycans do not typically adopt specific secondary structures and remain very mobile, shielding potentially large fractions of protein surface. High glycan conformational freedom hinders complete structural elucidation of glycoproteins. Computer simulations may be used to model glycosylated proteins but require hundreds of thousands of computing hours on supercomputers, thus limiting routine use. Here, we describe GlycoSHIELD, a reductionist method that can be implemented on personal computers to graft realistic ensembles of glycan conformers onto static protein structures in minutes. Using molecular dynamics simulation, small-angle X-ray scattering, cryoelectron microscopy, and mass spectrometry, we show that this open-access toolkit provides enhanced models of glycoprotein structures. Focusing on N-cadherin, human coronavirus spike proteins, and gamma-aminobutyric acid receptors, we show that GlycoSHIELD can shed light on the impact of glycans on the conformation and activity of complex glycoproteins.

Tidying up the conformational ensemble of a disordered peptide by computational prediction of spectroscopic fingerprints.

The most advanced structure prediction methods are powerless in exploring the conformational ensemble of disordered peptides and proteins and for this reason the "protein folding problem" remains unsolved. We present a novel methodology that enables the accurate prediction of spectroscopic fingerprints (circular dichroism, infrared, Raman, and Raman optical activity), and by this allows for "tidying up" the conformational ensembles of disordered peptides and disordered regions in proteins. This concept is elaborated for and applied to a dodecapeptide, whose spectroscopic fingerprint is measured and theoretically predicted by means of enhanced-sampling molecular dynamics coupled with quantum mechanical calculations. Following this approach, we demonstrate that peptides lacking a clear propensity for ordered secondary-structure motifs are not randomly, but only conditionally disordered. This means that their conformational landscape, or phase-space, can be well represented by a basis-set of conformers including about 10 to 100 structures. The implications of this finding have profound consequences both for the interpretation of experimental electronic and vibrational spectral features of peptides in solution and for the theoretical prediction of these features using accurate and computationally expensive techniques. The here-derived methods and conclusions are expected to fundamentally impact the rationalization of so-far elusive structure-spectra relationships for disordered peptides and proteins, towards improved and versatile structure prediction methods.

Biomolecule-mimetic nanomaterials for photothermal and photodynamic therapy of cancers: Bridging nanobiotechnology and biomedicine.

Nanomaterial-based phototherapy has become an important research direction for cancer therapy, but it still to face some obstacles, such as the toxic side effects and low target specificity. The biomimetic synthesis of nanomaterials using biomolecules is a potential strategy to improve photothermal therapy (PTT) and photodynamic therapy (PDT) techniques due to their endowed biocompatibility, degradability, low toxicity, and specific targeting. This review presents recent advances in the biomolecule-mimetic synthesis of functional nanomaterials for PTT and PDT of cancers. First, we introduce four biomimetic synthesis methods via some case studies and discuss the advantages of each method. Then, we introduce the synthesis of nanomaterials using some biomolecules such as DNA, RNA, protein, peptide, polydopamine, and others, and discuss in detail how to regulate the structure and functions of the obtained biomimetic nanomaterials. Finally, potential applications of biomimetic nanomaterials for both PTT and PDT of cancers are demonstrated and discussed. We believe that this work is valuable for readers to understand the mechanisms of biomimetic synthesis and nanomaterial-based phototherapy techniques, and will contribute to bridging nanotechnology and biomedicine to realize novel highly effective cancer therapies.

Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans.

Despite their fundamental biological relevance, structure-property relationships in N-glycans are fundamentally lacking, and their highly multidimensional compositional and conformational phase spaces remain largely unexplored. The torsional flexibility of the glycosidic linkages and the ring dynamics result in wide, rugged free-energy landscapes that are difficult to sample in molecular dynamics simulations. We show that a novel enhanced-sampling scheme combining replica exchange with solute and collective-variable tempering, enabling transitions over all relevant energy barriers, delivers converged distributions of solvated N-glycan conformers. Several dimensionality-reduction algorithms are compared and employed to generate conformational free-energy maps in two dimensions. Together with an originally developed conformation-based nomenclature scheme that uniquely identifies glycan conformers, our modeling procedure is applied to reveal the effect of chemical substitutions on the conformational ensemble of selected high-mannose-type and complex glycans. Moreover, the structure-prediction capabilities of two commonly used glycan force fields are assessed via the theoretical prediction of experimentally available nuclear magnetic resonance J-coupling constants. The results especially confirm the key role of ω and ψ torsion angles in discriminating between different conformational states and suggest an intriguing correlation between the torsional and ring-puckering degrees of freedom that may be biologically relevant.

Lessons from a Challenging System: Accurate Adsorption Free Energies at the Amino Acid/ZnO Interface.

We undertake steps to overcome four challenges that have hindered the understanding of ZnO/biomolecule interfaces at the atomic scale: parametrization of a classical force field, ZnO surface termination and amino acid protonation state in methanol, and convergence of enhanced sampling molecular dynamics simulations. We predict adsorption free energies for histidine, serine, cysteine, and tryptophan in remarkable agreement with experimental measurements obtained via a novel indicator-displacement assay. Adsorption is driven by direct surface/amino-acid interactions mediated by terminal hydroxyl groups and stabilized by strongly structured methanol solvation shells.

Bio-interfactants as double-sided tapes for graphene oxide.

We present a versatile and highly substrate-independent approach for preparing multisandwich layers based on thermally reduced Graphene Oxide (rGO) which gets strongly attached by bio-interfactants using a layer-by-layer (LBL) aqueous dipping and rinsing process. The process allows for the deposition of homogeneous ultra-thin films (∼5.5 nm) in distinct surface topographies, thicknesses and compositions by varying the bio-interfactant layer(s). The layers formed on quartz or other semi conductive material are electrically conductive, flexible, and transparent. The here-developed approach could be applied for the fabrication of wearables, sensors, and antistatic transparent films.

Structural and Computational Assessment of the Influence of Wet-Chemical Post-Processing of the Al-Substituted Cubic Li7La3Zr2O12.

Li7La3Zr2O12 (LLZO) and related compounds are considered as promising candidates for future all-solid-state Li-ion battery applications. Still, the processing of those materials into thin membranes with the right stoichiometry and crystal structure is difficult and laborious. The sensitivity of the Li-ion conductive garnets against moisture and the associated Li+/H+ cation exchange makes their processing even more difficult. Formulation of suitable polymer/ceramic hybrid solid state electrolytes could be a prosperous way to reach the future large scale production of solid state Li-ion batteries. In fact, solvent mediated and/or slurry based wet-processing of the LLZO, e.g., tape-casting, could result in irreversible Li-ion loss of the pristine material due to Li+/H+ cation exchange. The concomitant structural changes and loss in functionality in terms of Li-ion conductivity are the results of the above process. Therefore, in the present work a systematic study on the chemical stability and structural retention of Al-substituted LLZO in different solvents is reported. It was found that Li+/H+ exchange in LLZO occurs upon solvent immersion, and its magnitude is dependent on the availability of -OH functional groups of the solvent molecules. As a result, a larger degree of Li+/H+ exchange causes higher increase of the lattice parameter of the LLZO, determined by synchrotron diffraction analyses. The expansion of the cubic unit cell was ascertained, when Li+ was replaced by H+ in the host lattice, by ab initio computational studies. The application of the most common solvent as dispersion medium, i.e., high purity water, causes the most significant Li+/H+ exchange and, therefore, structural change, while acetonitrile was proven to be the best suitable solvent for wet postprocessing of LLZO. Finally, computational calculations suggested that the Li+/H+ exchange could result in diminished ionic, i.e., mixed Li+-H+, conductivity due to the insertion of protons with lower mobility than that of Li-ions.

Graphene-based nanoplatforms for surface-enhanced Raman scattering sensing.

Surface-enhanced Raman scattering (SERS) is one of the important techniques for sensing applications in biological analysis, disease diagnosis, environmental science, and food safety. Graphene provides an excellent nanoplatform for SERS sensing due to its two-dimensional flat structure, uniform electronic and photonic properties, excellent mechanical stability, atomic uniformity, and high biocompatibility. In this review, we summarize recent advances in the fabrication of various graphene-based nanoplatforms for SERS sensing. We present the strategies, such as self-assembly, in situ synthesis, one-pot synthesis, liquid phase reduction, and biomimetic synthesis, for the fabrication of graphene-based hybrid metallic and alloy nanoplatforms, and then demonstrate the potential applications of graphene-based nanoplatforms for the SERS sensing of ions, organic dyes, pesticides, bacteria, DNA, proteins, cells, and other chemicals in great detail. In addition, we also discuss the future development of this interesting research field and provide several perspectives. This work will be helpful for readers to understand the fabrication and sensing mechanisms of graphene-based SERS sensing nanoplatforms; meanwhile, it will promote the development of new materials and novel methods for high performance sensing and biosensing applications.

Simulated and experimental force spectroscopy of lysozyme on silica.

The force spectra of proteins detaching from oxide surfaces measured by atomic force microscopy (AFM) often present complex patterns of peaks, which are difficult to correlate with individual bond-breaking events at the atomic scale. In this work we rationalize experimental AFM force spectra of hen-egg-white lysozyme detaching from silica by means of all-atom steered molecular dynamics (SMD) simulations. In particular, we demonstrate that the native tertiary structure of lysozyme is preserved if, and only if, its four intramolecular disulfide bridges are intact. Otherwise, the protein pulled off the surface undergoes severe unfolding, which is well captured by SMD simulations in explicit solvent. Implicit solvent simulations, on the contrary, wrongly predict protein unfolding even in the presence of S-S bridges, due to the lack of additional structural stabilization provided by the water's hydrogen-bond network within and surrounding the protein. On the basis of our combined experimental and theoretical findings, we infer that the rugged force spectra characteristic of lysozyme/silica interfaces are not due to the successive breaking of internal disulfide bonds leading to partial unfolding events. Rather, they reflect the detachment of several molecules bound to the same AFM tip, each anchored to the surface via multiple hydrogen and ionic bonds.

Interactions at the Silica-Peptide Interface: Influence of the Extent of Functionalization on the Conformational Ensemble.

In this contribution, the effect of silica particle size (28 and 210 nm) and surface chemistry (i.e., hydroxyl, methyl, or amino groups) on peptide binding response is studied with a specific emphasis on the effect of the extent of functionalization on binding. Exhaustive characterization of the silica surfaces was crucial for knowledge of the chemistry and topography of the solid surface under study and, thus, to understand their impact on adsorption and the conformational ensemble of the peptides. The extent of surface functionalization was shown to be particle-size dependent, a higher level of 3-aminopropyl functionality being obtained for smaller particles, whereas a higher degree of methyl group functionality was found for the larger particles. We demonstrated that peptide interactions at the aqueous interface were not only influenced by the surface chemistry but also by the extent of functionalization where a "switch" of peptide adsorption behavior was observed, whereas the changes in the conformational ensemble revealed by circular dichroism were independent of the extent of functionalization. In addition to electrostatic interactions and hydrogen bonding driving interaction at the silica-peptide interface, the data obtained suggested that stronger interactions such as hydrophobic and/or covalent interactions may moderate the interaction. The insights gained from this peptide-mineral study give a more comprehensive view of mechanisms concerning mineral-peptide interactions which may allow for the design and synthesis of novel (nano)materials with properties tailored for specific applications.

Recent Advances in Nanoporous Membranes for Water Purification.

Nanoporous materials exhibit wide applications in the fields of electrocatalysis, nanodevice fabrication, energy, and environmental science, as well as analytical science. In this review, we present a summary of recent studies on nanoporous membranes for water purification application. The types and fabrication strategies of various nanoporous membranes are first introduced, and then the fabricated nanoporous membranes for removing various water pollutants, such as salt, metallic ions, anions, nanoparticles, organic chemicals, and biological substrates, are demonstrated and discussed. This work will be valuable for readers to understand the design and fabrication of various nanoporous membranes, and their potential purification mechanisms towards different water pollutants. In addition, it will be helpful for developing new nanoporous materials for quick, economic, and high-performance water purification.

Anti-Staphylococcal Calopins from Fruiting Bodies of Caloboletus radicans.

Three new and seven known calopins were isolated from Caloboletus radicans. The structures of the new cyclocalopins, 8-deacetylcyclocalopin B (1), cyclocalopin A-15-ol (2), and 12,15-dimethoxycyclocalopin A (3), were mainly elucidated by NMR and MS data analysis. The stereochemistry of 1-3 was assigned based on NOE correlations and coupling constants and by comparison of their CD spectra with those of similar known calopins. While 1-10 were inactive against two cancer cell lines, they displayed anti-staphylococcal activity against methicillin-resistant Staphylococcus aureus strains (MRSA) with MIC values of 16-256 µg/mL. Moreover, some calopins were active against the fish pathogen Enterococcus faecalis F1B1.

Anchoring of Iron Oxyhydroxide Clusters at H and L Ferritin Subunits.

Ferritin (Fn) proteins or their isolated subunits can be used as biomolecular templates for the selectively heterogeneous nucleation and growth of nanoparticles, in particular of iron oxyhydroxides. To shed light on the atomistic mechanisms of ferritin-promoted mineralization, in this study we perform molecular dynamics simulations to investigate the anchoring sites for Fe(III) clusters on Fn subunit assemblies using models of goethite and ferrihydrite nanoparticles. For this aim, we develop and parametrize a classical force field for Fe(III) oxyhydroxides based on reference density functional theory calculations. We then reveal that stable Fn-nanoparticle contacts are formed not only via negatively charged amino acid residues (glutamic and aspartic acid) but also, in a similar amount, via positively charged (lysine and arginine) and neutral (histidine) residues. A large majority of the anchoring sites are situated at the inner side of protein cages, consistent with the natural iron storage function of ferritin in many organisms. A slightly different distribution of anchoring sites is observed on heavy (H) and light (L) Fn subunits, with the former offering a larger amount of negative and neutral sites than the latter. This finding is exploited to develop a Fn mineralization protocol in which immobilized Fn subunits are first loaded with Fe2+ ions in a long "activation" step before starting their oxidation to Fe3+. This leads to the formation of very dense and uniform iron oxide films, especially when H subunits are employed.

Adsorption of DNA Fragments at Aqueous Graphite and Au(111) via Integration of Experiment and Simulation.

We combine single molecule force spectroscopy measurements with all-atom metadynamics simulations to investigate the cross-materials binding strength trends of DNA fragments adsorbed at the aqueous graphite C(0001) and Au(111) interfaces. Our simulations predict this adsorption at the level of the nucleobase, nucleoside, and nucleotide. We find that despite challenges in making clear, careful connections between the experimental and simulation data, reasonable consistency between the binding trends between the two approaches and two substrates was evident. On C(0001), our simulations predict a binding trend of dG > dA ≈ dT > dC, which broadly aligns with the experimental trend. On Au(111), the simulation-based binding strength trends reveal stronger adsorption for the purines relative to the pyrimadines, with dG ≈ dA > dT ≈ dC. Moreover, our simulations provide structural insights into the origins of the similarities and differences in adsorption of the nucleic acid fragments at the two interfaces. In particular, our simulation data offer an explanation for the differences observed in the relative binding trend between adenosine and guanine on the two substrates.

Variability of Zinc Oxide Dissolution Rates.

Zinc oxide (ZnO) is of widespread use for numerous applications, including many in the cosmetic industry. Thus, ZnO particles are quite likely to enter the environment. ZnO may be harmful because of the release of cytotoxic Zn2+ ions during dissolution reactions. Here, we analyze the dissolution kinetics of the polar zinc-terminated (000-1) and nonpolar (10-10) crystal surfaces in ultrapure water to examine the impact of the crystal defects on dissolution. By using a complementary approach of atomic force microscopy and vertical scanning interferometry, we quantify the difference in reaction rate between the crystal faces, the overall range of rate variability, and the rate components that combine to an overall rate. The mean dissolution rate of the (000-1) crystal surface is more than 4 times that of the (10-10) surface. By using the rate spectrum analysis, we observed an overall dissolution rate variability of more than 1 order of magnitude. The rate components and the range of dissolution rate are important input parameters in reactive transport models for the prediction of potential release of Zn2+ into the environment.

Growth and structure of ultrathin praseodymium oxide layers on ruthenium(0001).

The growth, morphology, structure, and stoichiometry of ultrathin praseodymium oxide layers on Ru(0001) were studied using low-energy electron microscopy and diffraction, photoemission electron microscopy, atomic force microscopy, and X-ray photoelectron spectroscopy. At a growth temperature of 760 °C, the oxide is shown to form hexagonally close-packed (A-type) Pr2O3(0001) islands that are up to 3 nm high. Depending on the local substrate step density, the islands either adopt a triangular shape on sufficiently large terraces or acquire a trapezoidal shape with the long base aligned along the substrate steps.

Irreversible Damage of Polymer Membranes During Attenuated Total Reflection Infrared Analysis.

Analyzing polymer membranes by attenuated total reflection infrared spectroscopy (ATR-IR) can lead to irreversible damage to the material and induces systematic errors in the data. Attenuated total reflection infrared spectroscopy is a common tool for analyzing the surface of polymer membranes. In order to provide sufficient contact between the membrane and the internal reflection element (i.e., the ATR crystal), pressure is applied via a metal stamp. This procedure, however, can lead to mechanical damage. In this work, we study this damage using the example of a polyethersulfone (PES) membrane for water filtration and we show how the damage can be avoided. Attenuated total reflection infrared spectroscopy, laser-scanning microscopy (LSM), and atomic force microscopy (AFM) are employed to understand the mechanically-induced phenomena at the molecular and macroscopic scales. The data reveal that the mechanical impact does not only result in a compressed membrane structure with smaller pores, but it also leads to deformations at the molecular level. Moreover, in light of the mechanical damage, a detailed analysis of the PES IR spectrum indicates that several previous vibrational assignments of peaks may be incorrect and that many published results may be biased and should be revisited.

Physisorption of α-chymotrypsin on SiO2 and TiO2: A comparative study via experiments and molecular dynamics simulations.

In order to understand fundamental interactions at the interface between immobilized enzymes and ceramic supports, the authors compare the adsorption features of chymotrypsin on SiO2 and TiO2 colloidal particles by means of a combination of adsorption experiments and molecular dynamics simulations. While the dependency of the adsorption amount on pH is consistent with the trend predicted the Derjaguin-Landau-Verwey-Overbeek theory, other effects can only be rationalized if the atomic-scale details of the water-mediated protein-surface interactions are considered. On both surfaces, a clear driving force for the formation of a double monolayer at the saturation coverage is found. Although nearly equal free energies of adsorption are estimated on the two materials via a Langmuir adsorption analysis, about 50% more proteins per unit of surface can be accommodated on TiO2 than on SiO2. This is probably due to the lower surface diffusion mobility of the adsorbed protein in the latter case. Surface anchoring is realized by a combination of direct ionic interactions between charged proteins and surface sites (more pronounced for SiO2) and distinct structuring of the surface hydration layers in which the contact residues are embedded (more pronounced for TiO2). Finally, normalization of the data with respect to particle surface areas accessible to the proteins, rather than determined by means of the Brunauer-Emmett-Teller nitrogen adsorption isotherm, is crucial for a correct interpretation of the results.

Contact Forces between TiO2 Nanoparticles Governed by an Interplay of Adsorbed Water Layers and Roughness.

Interparticle forces govern the mechanical behavior of granular matter and direct the hierarchical assembling of nanoparticles into supramolecular structures. Understanding how these forces change under different ambient conditions would directly benefit industrial-scale nanoparticle processing units such as filtering and fluidization. Here we rationalize and quantify the contributions of dispersion, capillary, and solvation forces between hydrophilic TiO2 nanoparticles with sub-10 nm diameter and show that the humidity dependence of the interparticle forces is governed by a delicate interplay between the structure of adsorbed water layers and the surface roughness. All-atom molecular dynamics modeling supported by force-spectroscopy experiments reveals an unexpected decrease in the contact forces at increasing humidity for nearly spherical particles, while the forces between rough particles are insensitive to strong humidity changes. Our results also frame the limits of applicability of discrete solvation and continuum capillary theories in a regime where interparticle forces are dominated by the molecular nature of surface adsorbates.

A novel aptasensor based on single-molecule force spectroscopy for highly sensitive detection of mercury ions.

We have developed a novel aptasensor based on single-molecule force spectroscopy (SMFS) capable of detecting mercury ions (Hg(2+)) with sub-nM sensitivity. The single-strand (ss) DNA aptamer used in this work is rich in thymine (T) and readily forms T-Hg(2+)-T complexes in the presence of Hg(2+). The aptamer was conjugated to an atomic force microscope (AFM) probe, and the adhesion force between the probe and a flat graphite surface was measured by single-molecule force spectroscopy (SMFS). The presence of Hg(2+) ions above a concentration threshold corresponding to the affinity constant of the ions for the aptamer (about 5 × 10(9) M(-1)) could be easily detected by a change of the measured adhesion force. With our chosen aptamer, we could reach an Hg(2+) detection limit of 100 pM, which is well below the maximum allowable level of Hg(2+) in drinking water. In addition, this aptasensor presents a very high selectivity for Hg(2+) over other metal cations, such as K(+), Ca(2+), Zn(2+), Fe(2+), and Cd(2+). Furthermore, the effects of the ionic strength and loading rate on the Hg(2+) detection were evaluated. Its simplicity, reproducibility, high selectivity and sensitivity make our SMFS-based aptasensor advantageous with respect to other current Hg(2+) sensing methods. It is expected that our strategy can be exploited for monitoring the pollution of water environments and the safety of potentially contaminated food.