Molecular modeling and phylogenetic analyses highlight the role of amino acid 347 of the N1 subtype neuraminidase in influenza virus host range and interspecies adaptation

The N1 neuraminidases (NAs) of avian and pandemic human influenza viruses contain tyrosine and asparagine, respectively, at position 347 on the rim of the catalytic site; the biological significance of this difference is not clear. Here, we used molecular dynamics simulation to model the effects of amino acid 347 on N1 NA interactions with sialyllacto-N-tetraoses 6'SLN-LC and 3'SLN-LC, which represent NA substrates in humans and birds, respectively. Our analysis predicted that Y347 plays an important role in the NA preference for the avian-type substrates. The Y347N substitution facilitates hydrolysis of human-type substrates by resolving steric conflicts of the Neu5Ac2-6Gal moiety with the bulky side chain of Y347, decreasing the free energy of substrate binding, and increasing the solvation of the Neu5Ac2-6Gal bond. Y347 was conserved in all N1 NA sequences of avian influenza viruses in the GISAID EpiFlu database with two exceptions. First, the Y347F substitution was present in the NA of a specific H6N1 poultry virus lineage and was associated with the substitutions G228S and/or E190V/L in the receptor-binding site (RBS) of the hemagglutinin (HA). Second, the highly pathogenic avian H5N1 viruses of the Gs/Gd lineage contained sporadic variants with the NA substitutions Y347H/D, which were frequently associated with substitutions in the HA RBS. The Y347N substitution occurred following the introductions of avian precursors into humans and pigs with N/D347 conserved during virus circulation in these hosts. Comparative evolutionary analysis of site 347 revealed episodic positive selection across the entire tree and negative selection within most host-specific groups of viruses, suggesting that substitutions at NA position 347 occurred during host switches and remained under pervasive purifying selection thereafter. Our results elucidate the role of amino acid 347 in NA recognition of sialoglycan substrates and emphasize the significance of substitutions at position 347 as a marker of host range and adaptive evolution of influenza viruses.

Adsorption Affinities of Small Volatile Organic Molecules on Graphene Surfaces for Novel Nanofiller Design: A DFT Study

The adsorption of organic molecules on graphene surfaces is a crucial process in many different research areas. Nano-sized carbon allotropes, such as graphene and carbon nanotubes, have shown promise as fillers due to their exceptional properties, including their large surface area, thermal and electrical conductivity, and potential for weight reduction. Surface modification methods, such as the "pyrrole methodology", have been explored to tailor the properties of carbon allotropes. In this theoretical work, an ab initio study based on Density Functional Theory is performed to investigate the adsorption process of small volatile organic molecules (such as pyrrole derivatives) on graphene surface. The effects of substituents, and different molecular species are examined to determine the influence of the aromatic ring or the substituent of pyrrole's aromatic ring on the adsorption energy. The number of atoms and presence of π electrons significantly influence the corresponding adsorption energy. Interestingly, pyrroles and cyclopentadienes are 10 kJ mol-1 more stable than the corresponding unsaturated ones. Pyrrole oxidized derivatives display more favorable supramolecular interactions with graphene surface. Intermolecular interactions affect the first step of the adsorption process and are important to better understand possible surface modifications for carbon allotropes and to design novel nanofillers in polymer composites.

Adsorption and Self-Aggregation of Chiral [5]-Aza[6]helicenes on DNA Architecture: A Molecular Dynamics Study

Helicenes are an extremely interesting class of conjugated molecules without asymmetric carbon atoms but with intrinsic chirality. These molecules can interact with double-stranded chiral B-DNA architecture, modifying after their adsorption the hydrophilicity exposed by DNA to the biological environment. They also form ordered structures due to self-aggregation processes with possible different light emissions. Following initial studies based on molecular mechanics (MM) and molecular dynamics (MD) simulations regarding the adsorption and self-aggregation process of 5-aza[5]helicenes on double-stranded B-DNA, this theoretical work investigates the interaction between (M)- and (P)-5-aza[6]helicenes with double-helix DNA. Initially, the interaction of the pure single enantiomer with DNA is studied. Possible preferential absorption in minor or major grooves can occur. Afterward, the interaction of enantiopure compounds (M)- and (P)-5-aza[6]helicenes, potentially occurring in a racemic mixture at different concentrations, was investigated, taking into consideration both competitive adsorption on DNA and the possible helicenes' self-aggregation process. The structural selectivity of DNA binding and the role of helicene concentration in adsorption and the self-aggregation process are interesting. In addition, the ability to form ordered structures on DNA that follow its chiral architecture, thanks to favorable van der Waals intermolecular interactions, is curious.

Surface Interactions between Ketoprofen and Silica-Based Biomaterials as Drug Delivery System Synthesized via Sol–Gel: A Molecular Dynamics Study

Biomaterial-based drug delivery systems for a controlled drug release are drawing increasing attention thanks to their possible pharmaceutical and biomedical applications. It is important to control the local administration of drugs, especially when the drug exhibits problems diffusing across biological barriers. Thus, in an appropriate concentration, it would be released in situ, reducing side effects due to interactions with the biological environment after implantation. A theoretical study based on Molecular Mechanics and Molecular Dynamics methods is performed to investigate possible surface interactions between the amorphous SiO₂ surface and the ketoprofen molecules, an anti-inflammatory drug, considering the role of drug concentration. These theoretical results are compared with experimental data obtained by analyzing, through Fourier transform infrared spectroscopy (FT-IR), the interaction between the SiO₂ amorphous surface and two percentages of the ketoprofen drug entrapped in a silica matrix obtained via the sol–gel method and dried materials. The loaded drug in these amorphous bioactive material forms hydrogen bonds with the silica surface, as found in this theoretical study. The surface interactions are essential to have a new generation of biomaterials not only important for biocompatibility, with specific structural and functional properties, but also able to incorporate anti-inflammatory agents for release into the human body.

Adsorption of Chiral [5]-Aza[5]helicenes on DNA Can Modify Its Hydrophilicity and Affect Its Chiral Architecture: A Molecular Dynamics Study

Helicenes are interesting chiral molecules without asymmetric carbon atoms but with intrinsic chirality. Functionalized 5-Aza[5]helicenes can form non-covalent complexes with anticancer drugs and therefore be potential carriers. The paper highlights the different structural selectivity for DNA binding for two enantiopure compounds and the influence of concentration on their adsorption and self-aggregation process. In this theoretical study based on atomistic molecular dynamics simulations the interaction between (M)- and (P)-5-Aza[5]helicenes with double helix B-DNA is investigated. At first the interaction of single pure enantiomer with DNA is studied, in order to find the preferred site of interaction at the major or minor groove. Afterwards, the interaction of the enantiomers at different concentrations was investigated considering both competitive adsorption on DNA and possible helicenes self-aggregation. Therefore, racemic mixtures were studied. The helicenes studied are able to bind DNA modulating or locally modifying its hydrophilic surface into hydrophobic after adsorption of the first helicene layer partially covering the negative charge of DNA at high concentration. The (P)-enantiomer shows a preferential binding affinity of DNA helical structure even during competitive adsorption in the racemic mixtures. These DNA/helicenes non-covalent complexes exhibit a more hydrophobic exposed surface and after self-aggregation a partially hidden DNA chiral architecture to the biological environment.

Dendrimer Dynamics: A Review of Analytical Theories and Molecular Simulation Methods

The theoretical study of dendrimers is reviewed, considering both analytical approaches and molecular simulation methods. We discuss the effect of molecular symmetry on the degeneracy of the relaxation times, and then the calculation of observable quantities, in particular the intrinsic viscosity, and then the viscoelastic complex modulus and the dynamic structure factor, in comparison with the available experimental data. In particular, the maximum intrinsic viscosity with increasing molar mass is analyzed in some detail. The approximations and/or assumptions of the adopted methods are also described in connection with analogous results for polymer of a different topology, in particular linear and star polymers.

Understanding Surface Interaction and Inclusion Complexes between Piroxicam and Native or Crosslinked β-Cyclodextrins: The Role of Drug Concentration

Drug concentration plays an important role in the interaction with drug carriers affecting the kinetics of release process and toxicology effects. Cyclodextrins (CDs) can solubilize hydrophobic drugs in water enhancing their bioavailability. In this theoretical study based on molecular mechanics and molecular dynamics methods, the interactions between β-cyclodextrin and piroxicam, an important nonsteroidal anti-inflammatory drug, were investigated. At first, both host–guest complexes with native β-CD in the 1:1 and in 2:1 stoichiometry were considered without assuming any initial a priori inclusion: the resulting inclusion complexes were in good agreement with literature NMR data. The interaction between piroxicam and a β-CD nanosponge (NS) was then modeled at different concentrations. Two inclusion mechanisms were found. Moreover, piroxicam can interact with the external NS surface or with its crosslinkers, also forming one nanopore. At larger concentration, a nucleation process of drug aggregation induced by the first layer of adsorbed piroxicam molecules is observed. The flexibility of crosslinked β-CDs, which may be swollen or quite compact, changing the surface area accessible to drug molecules, and the dimension of the aggregate nucleated on the NS surface are important factors possibly affecting the kinetics of release, which shall be theoretically studied in more detail at specific concentrations.

Hydrogen Bonding in a l-Glutamine-Based Polyamidoamino Acid and its pH-Dependent Self-Ordered Coil Conformation

This paper reports on synthesis, acid-base properties, and self-structuring in water of a chiral polyamidoamino acid, M-l-Gln, obtained from the polyaddition of N,N'-methylenebisacrylamide with l-glutamine, with the potential of establishing hydrogen bonds through its prim-amide pendants. The M-l-Gln showed pH-responsive circular dichroism spectra, revealing ordered conformations. Structuring was nearly insensitive to ionic strength but sensitive to denaturing agents. The NMR diffusion studies were consistent with a population of unimolecular nanoparticles thus excluding aggregation. The M-l-Gln had the highest molecular weight and hydrodynamic radius among all polyamidoamino acids described. Possibly, transient hydrogen bonds between l-glutamine molecules and M-l-Gln growing chains facilitated the polyaddition reaction. Theoretical modeling showed that M-l-Gln assumed pH-dependent self-ordered coil conformations with main chain transoid arrangements reminiscent of the protein hairpin motif owing to intramolecular dipole moments and hydrogen bonds. The latter were most numerous at the isoelectric point (pH 4.5), where they mainly involved even topologically distant main chain amide N-H and side chain amide C=O brought to proximity by structuring. Hydrogen bonds at pH 4.5 were also suggested by variable temperature NMR. The 2D NOESY experiments at pH 4.5 confirmed the formation of compact structures through the analysis of the main chain/side chain hydrogen contacts, in line with MD simulations.

A Molecular Dynamics Study of a Photodynamic Sensitizer for Cancer Cells: Inclusion Complexes of γ-Cyclodextrins with C70

Photodynamic therapy is an emerging treatment of tumor diseases. The complexes with γ-cyclodextrins (γ-CD) and fullerenes or their derivatives can be used as photosensitizers by direct injection into cancer cells. Using molecular mechanics and molecular dynamics methods, the stability and the geometry of the 2:1 complexes [(γ-CD)₂/C₇₀] are investigated analyzing the differences with the analogous C₆₀ complexes, studied in a previous theoretical work and experimentally found to be much less efficient in cancer therapy. The inclusion complex of γ-CD and C₇₀ has a 2:1 stoichiometry, the same as C₆₀, but is significantly less stable and displays an unlike arrangement. In vacuo, mimicking an apolar solvent, the complex is compact, whereas in water the two γ-CDs encapsulate C₇₀ forming a relatively stable complex by interacting through their primary rims, however exposing part of C₇₀ to the solvent. Other higher-energy complexes with the γ-CDs facing different rims can form in water, but in all cases part of the hydrophobic C₇₀ surface remains exposed to water. The stability and arrangement of these peculiar amphiphilic inclusion complexes having non-covalent interactions in water can be an important key for cancer therapy to enhance both the solubilization and the fullerene insertion into liposomes or cell membranes.

Self-Structuring in Water of Polyamidoamino Acids with Hydrophobic Side Chains Deriving from Natural α-Amino Acids

This paper reports on synthesis, acid-base properties and self-structuring in water of chiral polyamidoamino acids (PAACs) obtained by polyaddition of N,N'-methylenebisacrylamide with l-alanine, l-valine and l-leucine (M-l-Ala, M-l-Val, M-l-Leu) with potential for selective interactions with biomolecules. The polymers maintained the acid-base properties of amino acids. In water, the circular dichroism spectra of PAACs revealed pH-dependent structuring in the range 3⁻11 and in the wavelength interval 200⁻280 nm. Taking as reference the values at pH 3, the differential molar ellipticities were plotted in the pH interval 3⁻11. Sigmoidal curves were obtained presenting inflection points at pH 8.1, 6.8 and 7.3 for M-l-Ala, M-l-Val and M-l-Leu, respectively, corresponding to the amine half-ionization. Theoretical modeling showed that PAACs assumed stable folded conformations. Intramolecular interactions led to transoid arrangements of the main chain reminiscent of protein hairpin motif. Oligomers with ten repeat units had simulated gyration radii consistent with the hydrodynamic radii obtained by dynamic light scattering.

Self-Ordering Secondary Structure of d- and l-Arginine-Derived Polyamidoamino Acids

This paper reports on synthesis, acid-base properties and pH-dependent structuring in water of d-, l- and d,l-ARGO7, bioinspired polymers obtained by polyaddition of the corresponding arginine stereoisomers with N,N'-methylenebis(acrylamide). The circular dichroism spectra of d- and l-ARGO7 showed a peak at 228 nm and quickly and reversibly responded to pH changes, but were nearly unaffected by temperature, ionic strength, and denaturating agents. Theoretical modeling studies of L-ARGO7 showed that it assumed a folded structure. Intramolecular interactions led to transoid arrangements of the main chain reminiscent of the protein hairpin motif. Torsion angles showed a quite similar distribution at pH 6 and 14 consistent with the similarity of the CD spectra from pH 6 upward.

Superfluorinated and NIR-luminescent gold nanoclusters

A novel class of superfluorinated and NIR-luminescent gold nanoclusters were obtained starting from a branched thiol, bearing 27 equivalent ¹⁹F atoms per molecule. These unprecedented clusters combine in a unique nanosystem both NIR photoluminescence and ¹⁹F NMR properties, thus representing a promising multimodal platform for bioimaging applications.

Inclusion complexes of β-cyclodextrin with tricyclic drugs: an X-ray diffraction, NMR and molecular dynamics study

Tricyclic fused-ring cyclobenzaprine (1) and amitriptyline (2) form 1:1 inclusion complexes with β-cyclodextrin (β-CD) in the solid state and in water solution. Rotating frame NOE experiments (ROESY) showed the same geometry of inclusion for both 1/β-CD and 2/β-CD complexes, with the aromatic ring system entering the cavity from the large rim of the cyclodextrin and the alkylammonium chain protruding out of the cavity and facing the secondary OH rim. These features matched those found in the molecular dynamics (MD) simulations in solution and in the solid state from single-crystal X-ray diffraction of 1/β-CD and 2/β-CD complexes. The latter complex was found in a single conformation in the solid state, whilst the MD simulations in explicit water reproduced the conformational transitions observed experimentally for the free molecule.

Aggregation behavior of amphiphilic cyclodextrins in a nonpolar solvent: evidence of large-scale structures by atomistic molecular dynamics simulations and solution studies

Chemically modified cyclodextrins carrying both hydrophobic and hydrophilic substituents may form supramolecular aggregates or nanostructures of great interest. These systems have been usually investigated and characterized in water for their potential use as nanocarriers for drug delivery, but they can also aggregate in apolar solvents, as shown in the present paper through atomistic molecular dynamics simulations and dynamic light scattering measurements. The simulations, carried out with a large number of molecules in vacuo adopting an unbiased bottom-up approach, suggest the formation of bidimensional structures with characteristic length scales of the order of 10 nm, although some of these sizes are possibly affected by the assumed periodicity of the simulation cell, in particular at longer lengths. In any case, these nanostructures are stable at least from the kinetic viewpoint for relatively long times thanks to the large number of intermolecular interactions of dipolar and dispersive nature. The dynamic light scattering experiments indicate the presence of aggregates with a hydrodynamic radius of the order of 80 nm and a relatively modest polydispersity, even though smaller nanometer-sized aggregates cannot be fully ruled out. Taken together, these simulation and experimental results indicate that amphiphilically modified cyclodextrins do also form large-scale nanoaggregates even in apolar solvents.

Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations

Amphiphilically modified cyclodextrins may form various supramolecular aggregates. Here we report a theoretical study of the aggregation of a few amphiphilic cyclodextrins carrying hydrophobic thioalkyl groups and hydrophilic ethylene glycol moieties at opposite rims, focusing on the initial nucleation stage in an apolar solvent and in water. The study is based on atomistic molecular dynamics methods with a "bottom up" approach that can provide important information about the initial aggregates of few molecules. The focus is on the interaction pattern of amphiphilic cyclodextrin (aCD), which may interact by mutual inclusion of the substituent groups in the hydrophobic cavity of neighbouring molecules or by dispersion interactions at their lateral surface. We suggest that these aggregates can also form the nucleation stage of larger systems as well as the building blocks of micelles, vesicle, membranes, or generally nanoparticles thus opening new perspectives in the design of aggregates correlating their structures with the pharmaceutical properties.

Separation of chiral nanotubes with an opposite handedness by chiral oligopeptide adsorption: A molecular dynamics study

The separation of enantiomeric chiral nanotubes that can form non-covalent complexes with an unlike stability upon adsorption of chiral molecules is a process of potential interest in different fields and applications. Using fully atomistic molecular dynamics simulations, we report in this paper a theoretical study of the adsorption and denaturation of an oligopeptide formed by 16 chiral amino acids having a helical structure in the native state on both the inner and the outer surface of the chiral (10, 20) and (20, 10) single-walled carbon nanotubes having an opposite handedness, and of the armchair (16, 16) nanotube with a similar diameter for comparison. In the final adsorbed state, the oligopeptide loses in all cases its native helical conformation, assuming elongated geometries that maximize its contact with the surface through all the 16 amino acids. We find that the complexes formed by the two chiral nanotubes and the chosen oligopeptide have a strongly unlike stability both when adsorption takes place on the outer convex surface of the nanotube, and when it occurs on the inner concave surface. Thus, our molecular simulations indicate that separation of chiral, enantiomeric carbon nanotubes for instance by chromatographic methods can indeed be carried out using oligopeptides of a sufficient length.

Surface topography effects in protein adsorption on nanostructured carbon allotropes

We report a molecular dynamics (MD) simulation study of protein adsorption on the surface of nanosized carbon allotropes, namely single-walled carbon nanotubes (SWNT) considering both the convex outer surface and the concave inner surface, together with a graphene sheet for comparison. These systems are chosen to investigate the effect of the surface curvature on protein adsorption at the same surface chemistry, given by sp(2) carbon atoms in all cases. The simulations show that proteins do favorably interact with these hydrophobic surfaces, as previously found on graphite which has the same chemical nature. However, the main finding of the present study is that the adsorption strength does depend on the surface topography: in particular, it is slightly weaker on the outer convex surfaces of SWNT and is conversely enhanced on the inner concave SWNT surface, being therefore intermediate for flat graphene. We additionally find that oligopeptides may enter the cavity of common SWNT, provided their size is small enough and the tube diameter is large enough for both entropic and energetic reasons. Therefore, we suggest that proteins can effectively be used to solubilize in water single-walled (and by analogy also multiwalled) carbon nanotubes through adsorption on the outer surface, as indeed experimentally found, and to functionalize them after insertion of oligopeptides within the cavity of nanotubes of appropriate size.

Molecular modelling of protein adsorption on the surface of titanium dioxide polymorphs

This paper reports a molecular modelling study of the adsorption of protein subdomains with unlike secondary structures on different surfaces of ceramic titanium dioxide (TiO(2)), forming a passivating film on titanium biomaterials that provides the interface between the bulk metal and the physiological environment, affecting its biocompatibility and performance. Using molecular dynamics methods, we study the effect of the nanoscale structure of the common TiO(2) polymorphs (rutile, anatase and brookite) on the adsorption of an albumin subdomain and on two connected fibronectin modules, respectively containing α-helices and β-sheets. We find that the larger protein subdomain shows a stronger adsorption, as expected because of its size, but also that the three surfaces behave differently. In particular, brookite shows the weakest adsorption, whereas anatase leads to the strongest intrinsic adsorption, in particular for the fibronectin modules. Moreover, the simulations indicate a significant conformational change of the adsorbed protein subdomains with extensive surface nanopatterning. These results show that classical molecular dynamics methods can provide useful information about the influence of nanostructure and topology on protein physisorption at a fixed surface chemistry.

A molecular dynamics study of the inclusion complexes of C60 with some cyclodextrins

The strongly hydrophobic C(60) fullerene is a carbon allotrope of huge interest in materials science and in pharmaceutical chemistry that can be solubilized in water either by extensive chemical functionalization or by inclusion in appropriate carriers such as the cyclodextrins with formation of host-guest complexes. Here we report a molecular dynamics study of the complexes formed in solution by C(60) with gamma- and delta-cyclodextrins. The most stable host-guest complex stoichiometry is determined to be 2:1 through simulations in vacuo and in explicit water by the stepwise addition of the cyclodextrins to C(60). No a priori assumption about the inclusion stoichiometry and geometry is made. The equilibrium fluctuations of the complexes that can affect the system stability are also investigated within the molecular dynamics runs.

Protein adsorption on biomaterial and nanomaterial surfaces: a molecular modeling approach to study non-covalent interactions

Atomistic computer simulations of protein adsorption on the heterogeneous surface of biomaterials and nanomaterials are reviewed. First, we present a very brief introduction to some relevant issues concerning force fields and the computational methodologies currently used, in particular molecular dynamics simulations for studying non-covalent interactions in general. The main results are then discussed, considering the adsorption of different protein subdomains and of whole proteins on different surfaces of an unlike nature. In particular, we review our results for lysozyme and some protein subdomains with a different secondary structure on a strongly hydrophobic graphite surface and on a highly hydrophilic polymeric surface, and preliminary results of protein adsorption on single-walled carbon nanotubes, focusing on the effect of the surface topography and curvature. We also discuss the results obtained in other groups for other proteins or protein subdomains being adsorbed on ceramic materials, either purely ionic (MgO, hydroxyapatite) or covalent (SiO₂, taken as a model for mica), and on self-assembled monolayers terminated with various chemical functionalities. The insights gained from these simulations are commented on critically, in particular the use of an implicit solvent or the use of explicit water and the lack of final equilibrium usually achieved in the latter case. Finally, we present some open issues for computer simulations of protein adsorption at an interface, and provide an outlook about possible future work in this area.

Protein adsorption on a hydrophobic surface: a molecular dynamics study of lysozyme on graphite

Adsorption of human lysozyme on hydrophobic graphite is investigated through atomistic computer simulations with molecular mechanics (MM) and molecular dynamics (MD) techniques. The chosen strategy follows a simulation protocol proposed by the authors to model the initial and the final adsorption stage on a bare surface. Adopting an implicit solvent and considering 10 starting molecular orientations so that all the main sides of the protein can face the surface, we first carry out an energy minimization to investigate the initial adsorption stage, and then long MD runs of selected arrangements to follow the surface spreading of the protein maximizing its adsorption strength. The results are discussed in terms of the kinetics of surface spreading, the interaction energy, and the molecular size, considering both the footprint and the final thickness of the adsorbed protein. The structural implications of the final adsorption geometry for surface aggregation and nanoscale structural organization are also pointed out. Further MD runs are carried out in explicit water for the native structure and the most stable adsorption state to assess the local stability of the geometry obtained in implicit solvent, and to calculate the statistical distribution of the water molecules around the whole lysozyme and its backbone.

Surface hydration of polymeric (bio)materials: a molecular dynamics simulation study

The surface hydration of some crystalline polymeric (bio)materials is investigated at room temperature using molecular mechanics and molecular dynamics techniques through the statistical distribution of the water molecules as a function of their distance from the surface atoms. Considering different crystalline polymers such as polyethylene, poly(vinylidene fluoride), and poly(m-phenylene isophthalamide), and in particular their different crystal faces, we can take into account unlike surface chemistries and their subnanoscale topologies. Such features are ultimately related to the intermolecular forces between the exposed groups of the specific crystal face and the water molecules, and those among the polymer chains, which also affects the thermal motion of the surface repeat units. We find that the parallel grooves and depressions that can be formed at the surface by the ordered hydrophobic chains may trap the nearest water molecules at short times, unless the (sub) nanoscale pattern is effectively blurred by the thermal motion of the surface units.

Validating a strategy for molecular dynamics simulations of cyclodextrin inclusion complexes through single-crystal X-ray and NMR experimental data: a case study

A theoretical and experimental study about the formation and structure of the inclusion complex (-)-menthyl-O-beta-D-glucopyranoside 1 with beta-cyclodextrin (beta-CD) 2 is presented as paradigmatic case study to test the results of molecular dynamics (MD) simulations. The customary methodological approach-the use of experimental geometrical parameters as restraints for MD runs-is logically reversed and the calculated structures are a posteriori compared with those obtained from NMR spectroscopy in D(2)O solution and single crystal X-ray diffraction so as to validate the simulation procedure. The guest molecule 1 allows for a broad repertoire of intermolecular interactions (dipolar, hydrophobic, hydrogen bonds) concurring to stabilize the host-guest complex, thus providing the general applicability of the simulation procedure to cyclodextrin physical chemistry. Many starting geometries of the host-guest association were chosen, not assuming any a priori inclusion. The simulation protocol, involving energy minimization and MD runs in explicit water, yielded four possible inclusion geometries, ruling out higher-energy outer adducts. By analysis of the average energy at room temperature, the most stable geometry in solution was eventually obtained, while the kinetics of formation showed that it is also kinetically favored. The reliability of such geometry was thoroughly checked against the NOE distances via the pair distribution functions, that is, the statistical distribution of intermolecular distances among selected diagnostic atoms calculated from the MD trajectories at room temperature. An analogous procedure was adopted both with implicit solvent and in vacuo. The most stable geometry matched that found with explicit solvent but major differences were observed in the relative stability of the metastable complexes as a consequence of the lack of hydration on the polar moiety of the guest. Finally, a control set of geometrical parameters of the thermodynamically favored complex matched the corresponding one obtained from the X-ray structure, while local conformational differences were indicative of packing effects.

Computer simulation of bulk mechanical properties and surface hydration of biomaterials

Some intrinsic properties of biomaterials are calculated with atomistic computer simulations through energy minimizations and molecular dynamics methods. The mechanical properties of bulk polymers such as poly(vinyl alcohol) and poly(ethylene terephthalate) are obtained in terms of the Young's modulus, the bulk and shear moduli, and the Poisson ratio below the glass transition temperature. The calculated values apply to an ideal, defect-free sample, and therefore, they correspond to the theoretical upper limit for the mechanical behavior of these materials. The surface hydration of the same polymers and of graphite is analyzed in terms of the statistical distribution of the water molecules near the surfaces of these materials that range from hydrophilic to strongly hydrophobic. Consistent with recent spectroscopic evidence, it is found that water forms relatively ordered hydration shells driven by hydrogen bonds above the hydrophilic surface, but is highly disordered over the hydrophobic one. Therefore, it is suggested that computer simulations provide a new useful tool to investigate various aspects of biomaterials.

Understanding the Performance of Biomaterials through Molecular Modeling: Crossing the Bridge between their Intrinsic Properties and the Surface Adsorption of Proteins

Molecular modeling and computer simulations can yield significant new insight at the atomistic level about the performance of biomaterials in a biological environment. In this paper, we review our approach to a consistent theoretical picture of the bulk and surface properties of biomaterials. The predicted properties do encompass in particular the mechanical behavior and the surface hydration of these materials, and the surface physisorption of proteins, or polypeptides in general. The behavior of nanomaterials such as the carbon allotropes, nanotubes and fullerenes, in a biological environment is also briefly considered.

Sequential adsorption of proteins and the surface modification of biomaterials: a molecular dynamics study

The sequential adsorption of two proteins of the same or of an unlike nature on a heterogeneous hydrophobic surface is investigated through atomistic molecular dynamics simulations. By modeling two real protein fragments having a different secondary structure (alpha-helices or beta-sheets) on a graphite surface, the pre-adsorbed polypeptides are shown to modify the hydropathy of this substrate. Therefore, the graphite surface modified by the first adsorbed protein becomes more similar to a hydrophilic one in terms of both the interaction energy and the size of the second protein after the possible surface spreading.

Adsorption of charged albumin subdomains on a graphite surface

We report some new molecular dynamics simulation results about the adsorption on a hydrophobic graphite surface of two albumin subdomains, each formed by three different alpha-helices, considering the correctly charged side groups at pH = 7 instead of the neutral ones as done in our previous exploratory paper (Raffaini and Ganazzoli, Langmuir 2003;19:3403-3412). We find that the presence of charges affects somewhat the initial adsorption stage on the electrostatically neutral surface, but not the final one. Thus, we recover the result that a monolayer of aminoacids is eventually formed, with a rough parallelism of distant strands to optimize both the intramolecular and the surface interactions. This feature is consistent with the adsorption on the hydrophobic surface being driven by dispersion forces only, and with the "soft" nature of albumin. Additional optimizations of the final monolayer carried out at pH = 3 and 11 do not modify appreciably this picture, suggesting that adsorption on graphite is basically independent of pH. The enhanced hydration of the final adsorption state due to the (delocalized) charges of the side groups is also discussed in comparison with similar results of the neutralized subdomains.

Protein adsorption on the hydrophilic surface of a glassy polymer: a computer simulation study

Using atomistic computer simulations, we study the adsorption of different globular protein fragments with different secondary structures on the surface of a hydrophilic glassy polymer, poly(vinyl alcohol), or PVA, and compare the results with our earlier calculations on hydrophobic graphite. The simulations were mainly carried out with implicit solvent in an effective dielectric medium by energy minimizations and molecular dynamics at room temperature. We find that on the hydrophilic PVA surface the fragments basically retain their globular shape with an incomplete denaturation, at variance with our earlier results for the same fragments on graphite. Correspondingly, the interaction energy between the fragments and the surface is significantly smaller than on graphite, both because less residues are in contact with the surface, and because they interact more weakly. Moreover, very few hydrogen bonds are formed between the adsorbate and the PVA surface, since both the protein fragments and the polymer chains separately optimize these interactions. Additional molecular dynamics simulations in explicit solvent were also performed to study the hydration of the adsorbed fragments and to estimate the possible solvation effects.

Phthalazine PDE IV inhibitors: Conformational study of some 6-methoxy-1,4-disubstituted derivatives

This report describes the detailed conformational analysis and synthesis of a series of phthalazine phosphodiesterase-type (IV) (PDE IV) inhibitors bearing either mono- or dichloro 4-methylenepyridine at the 'down' position of the phthalazine nucleus or different heterocycles at the 'top' position 4 of the phthalazine moiety. Both the mono- and dichloro 4-methylenepyridine units linked at carbon C1 of the phthalazine nucleus show identical conformational behaviour with the substituent preferentially oriented towards the external part of the molecule and the pyridine plane almost orthogonal to that of phthalazine ring. The heterocyclic five-membered rings linked at carbon C4 of phthalazine show quite different conformational behaviour. The 1,3-thiazole ring exists in a well-defined conformation almost coplanar with respect to the phthalazine nucleus while the 1,2,4-triazole and the 1,3-diazole heterocycles show a great conformational freedom with large torsion angles. Compound 3 bearing the thiazole ring at C4 displays the major biological activity, thus suggesting that a planar and rather rigid conformation of the pentacycle should favour the PDE IV inhibition capacity of this class of compounds.

Computer simulation of polypeptide adsorption on model biomaterials

When biomaterials are inserted in a biological environment, for instance in a body implant, proteins do quickly adsorb on the exposed surface. Such process is of fundamental importance, since it directs the subsequent cell adhesion. Here we review recent advances in this field obtained with molecular simulations. While coarse-grained models can provide important general results, as it has long been recognized in polymer science, the hierarchical structure of a very complex copolymer such as a protein, together with the nature of the biomaterial surface suggest that atomistic models are better suited to investigate these phenomena. Thus, after briefly mentioning some common features of coarse-grained and atomistic force fields, we first discuss early theoretical and coarse-grained simulation results about protein adsorption, and then we highlight the main results recently obtained by us with atomistic models. In particular, we discuss some conformational and energetic aspects of the adsorption of protein fragments with different secondary structure on surfaces of different wettability, including hydrophobic graphite and hydrophilic poly(vinylalcohol). We also consider other features, such as the simulation of the materials wettability, the hydration of the adsorbed fragments, their kinetics of spreading, and the sequential adsorption of two protein fragments on top of each other, highlighting the results of general interest.

Molecular dynamics simulation of the adsorption of a fibronectin module on a graphite surface

We report atomistic simulations of the adsorption of a fibronectin type I module on a hydrophobic graphite surface. This module comprises only beta-sheets, unlike the albumin fragments previously investigated by us which contained only alpha-helices (Raffaini, G.; Ganazzoli, F. Langmuir 2003, 19, 3403-3412). As done in the latter case, most simulations are carried out in an effective dielectric medium by energy minimizations and molecular dynamics (MD). Further optimizations and MD runs in the explicit presence of water are also performed to assess the stability of the geometries found and to describe the solvation of the adsorbed fibronectin module. The initial adsorption is accompanied by local rearrangements of the strands in contact with the surface, but the overall molecular structure is largely preserved. Much larger rearrangements take place at longer times as found through the MD runs, with the molecule spreading as much as possible so as to maximize the surface coverage, hence the interaction energy, despite a significant strain energy. Energetic aspects of adsorption together with the concomitant size change are discussed in comparison with our previous results for two albumin fragments.

Macrocycle conformation and self-inclusion phenomena in octakis(3-O-butanoyl-2,6-di-O-pentyl)-gamma-cyclodextrin (Lipodex E) by NMR spectroscopy and molecular dynamics

Octakis(3-O-butanoyl-2,6-di-O-pentyl)-gamma-cyclodextrin (Lipodex E) is a lipophilic chiral selector successfully used for the enantioselective gas chromatographic separation of a multitude of racemic analytes. NMR data (13C chemical shifts, 3J(HH), rotating frame NOEs (ROEs)) and molecular dynamics (MD) simulations point out that the macrocycle is distorted with respect to the canonical truncated-cone shape of native cyclodextrins, although C(8) symmetry is retained on the NMR timescale. ROE data and MD trajectories provide evidence for self-inclusion of one 6-O-pentyl pendant chain within the cavity of Lipodex E. The interpretation of long-range and low-intensity ROEs is supported by the calculation of average internuclear distances by using the radial distribution function (RDF) calculated from MD trajectories. MD simulations are eventually used to compare the flexibility of the macrocycle of Lipodex E with that of native gammaCD.

Albumin adsorption onto pyrolytic carbon: a molecular mechanics approach

A number of implants of cardiac valve prosthesis, vascular prosthesis, and coronary stents present a pyrolytic carbon interface to blood. Plasma protein adsorption is essential for the hemocompatibility of the implanted devices. This work quantitatively evaluates the molecular interaction force between a biomaterial surface (pyrolytic carbon) and plasma protein (albumin) binding sites through a simplified molecular model of the interface consisting of (i) multioriented graphite microcrystallites; (ii) selected fragments of albumin; and (iii) a water environment. A number of simplifying assumptions were made in the calculation: the albumin molecule was divided into hydrophobic and hydrophilic subunits (helices); an idealized clean, nonoxidized polycrystalline graphite surface was assumed to approximate the surface of pyrolytic carbon. The interaction forces between albumin helices and pyrolytic carbon surfaces are evaluated from potential energy data. These forces are decomposed into a normal and a tangential component. The first one is calculated using a docking procedure (F( perpendicular tot MAX) = 4.16 x 10(-20) N). The second one (F( parallel)), calculated by mean of geometric models estimating the energy variation associated with the protein sliding on the material surface, varies within the range +/-9.62 x 10(-21) N. The molecular simulations were performed using the commercial software package Hyperchem 5.0 (Hyperchem, Hypercube, Canada).