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.

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.

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.

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.

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.

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.

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.

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.

Accuracy of buffered-force QM/MM simulations of silica.

We report comparisons between energy-based quantum mechanics/molecular mechanics (QM/MM) and buffered force-based QM/MM simulations in silica. Local quantities-such as density of states, charges, forces, and geometries-calculated with both QM/MM approaches are compared to the results of full QM simulations. We find the length scale over which forces computed using a finite QM region converge to reference values obtained in full quantum-mechanical calculations is ∼10 Šrather than the ∼5 Špreviously reported for covalent materials such as silicon. Electrostatic embedding of the QM region in the surrounding classical point charges gives only a minor contribution to the force convergence. While the energy-based approach provides accurate results in geometry optimizations of point defects, we find that the removal of large force errors at the QM/MM boundary provided by the buffered force-based scheme is necessary for accurate constrained geometry optimizations where Si-O bonds are elongated and for finite-temperature molecular dynamics simulations of crack propagation. Moreover, the buffered approach allows for more flexibility, since special-purpose QM/MM coupling terms that link QM and MM atoms are not required and the region that is treated at the QM level can be adaptively redefined during the course of a dynamical simulation.

Computational prediction of circular dichroism spectra and quantification of helicity loss upon peptide adsorption on silica.

Circular dichroism (CD) spectroscopy is one of the few experimental techniques sensitive to the structural changes that peptides undergo when they adsorb on inorganic material surfaces, a problem of deep significance in medicine, biotechnology, and materials science. Although the theoretical calculation of the CD spectrum of a molecule in a given conformation can be routinely performed, the inverse problem of extracting atomistic structural details from a measured spectrum is not uniquely determined. Especially complicated is the case of oligopeptides, whose folding/unfolding energy landscapes are often very broad and shallow. This means that the CD spectra measured for either dissolved or adsorbed peptides arise from a multitude of different structures, each present with a probability dictated by their relative free-energy variations, according to Boltzmann statistics. Here we present a modeling method based on replica exchange with solute tempering in combination with metadynamics, which allows us to predict both the helicity loss of a small peptide upon interaction with silica colloids in water and to compute the full CD spectra of the adsorbed and dissolved states, in quantitative agreement with experimental measurements. In our method, the CD ellipticity Θ for any given wavelength λ is calculated as an external collective variable by means of reweighting the biased trajectory obtained using the peptide-SiO2 surface distance and the structural helicity as two independent, internal collective variables. Our results also provide support for the often-employed hypothesis that the Θ intensity at λ = 222 nm is linearly correlated with the peptides' fractional helicity.

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.

Adsorption and reduction of glutathione disulfide on α-Al2O3 nanoparticles: experiments and modeling.

Glutathione disulfide (GSSG; γ-GluCysGly disulfide) was used as a physiologically relevant model molecule to investigate the fundamental adsorption mechanisms of polypeptides onto α-alumina nanoparticles. Its adsorption/desorption behavior was studied by enzymatic quantification of the bound GSSG combined with zeta potential measurements of the particles. The adsorption of GSSG to alumina nanoparticles was rapid, was prevented by alkaline pH, was reversed by increasing ionic strength, and followed a nearly ideal Langmuir isotherm with a standard Gibbs adsorption energy of -34.7 kJ/mol. Molecular dynamics simulations suggest that only one of the two glutathionyl moieties contained in GSSG binds stably to the nanoparticle surface. This was confirmed experimentally by the release of GSH from the bound GSSG upon reducing its disulfide bond with dithiothreitol. Our data indicate that electrostatic interactions via the carboxylate groups of one of the two glutathionyl moieties of GSSG are predominantly responsible for the binding of GSSG to the alumina surface. The results and conclusions presented here can provide a base for further experimental and modeling studies on the interactions of biomolecules with ceramic materials.

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.

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.

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.