Molecular dynamics investigation of an oriented cyclic peptide nanotube in DMPC bilayers

Exploring Cyclic Peptide Nanotube Stability Across Diverse Lipid Bilayers and Unveiling Water Transport Dynamics

Cyclic Peptide Nanotubes (CPNTs) have emerged as compelling candidates for various applications, particularly as nanochannels within lipid bilayers. In this study, the stability of two CPNTs, namely 8 × [(Cys-Gly-Met-Gly)2] and 8 × [(Gly-Leu)4], are comprehensively investigated across different lipid bilayers, including 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), a mixed model membrane (POPE/POPG), and a realistic yeast model membrane. The results demonstrate that both CPNTs maintain their tubular structures in all lipid bilayers, with [(Cys-Gly-Met-Gly)2] showing increased stability over an extended period in these lipid membranes. The insertion of CPNTs shows negligible impact on lipid bilayer properties, including area per lipid, volume per lipid, and bilayer thickness. The study demonstrates that the CPNT preserves its two-line water movement pattern within all the lipid membranes, reaffirming their potential as water channels. The MSD curves further reveal that the dynamics of water molecules inside the nanotube are similar for all the bilayer systems with minor differences that arise due to different lipid environments.

From bonds to interactions: comprehensive molecular characterization via polarizable bond-dipole approach

Accurately characterizing molecular interactions stands as a pivotal requirement for ensuring the reliability of molecular dynamics simulations. In line with our bond-dipole-based interaction model proposed by Gao et al. [X.-C. Gao, Q. Hao and C.-S. Wang, J. Chem. Theory Comput., 2017, 13, 2730-2741.], we have implemented an efficient and concise approach to compute electrostatic potential. This methodology capitalizes on the polarizable nature of chemical bond dipoles, resulting in a model of remarkable simplicity. In this study, we have revised the polarizable bond-dipole-based force field (PBFF) through the meticulous curation of quantum chemical data sets. These data sets encompass a comprehensive collection of 40 000 conformations, including those of water, methylamine, methanol, and N-methylacetamide. Additionally, we incorporate 520 hydrogen-bonded dimers into our data sets. In pursuit of enhanced accuracy in molecular dynamics simulations and a more faithful representation of potential energy landscapes, we undertook the re-optimization of the nonbonded parameters within the PBFF framework. Concurrently, we intricately fine-tuned the bonded parameters. The results of our comprehensive evaluation denote that this newly optimized force field method adeptly and efficiently computes structural characteristics, harmonic frequencies, and interaction energies. Overall, this study provides further validation for the applicability of PBFF in molecular dynamics simulations.

Uncovering the mechanisms of cyclic peptide self-assembly in membranes with the chirality-aware MA(R/S)TINI forcefield

Cyclic peptides (CPs) formed by alternation of D- and L-amino acids (D,L-CPs) can self-assemble into nanotubes (SCPNs) by parallel or/and antiparallel stacking. Different applications have been attributed to these nanotubes, including the disruption of lipid bilayers of specific compositions and the selective transport of ions throughout membranes. Molecular dynamics (MD) simulations have significantly contributed to understand the interaction between CPs, including the structural, dynamic and transport properties of their supramolecular aggregates. The high computational cost of atomic resolution forcefields makes them impractical for simulating the self-assembly of macromolecules, so coarse-grained (CG) models might represent a more feasible solution for this purpose. However, general CG models used for the simulation of biomolecules such as the MARTINI forcefield do not explicitly consider the non-covalent interactions leading to the formation of secondary structure patterns in proteins. This becomes particularly important in the case of CPs due to the D- and L-chirality alternation in their sequence, leading to opposite orientations of the backbone polar groups on both sides of the cyclic ring plane. In order to overcome this limitation, we have extended the MARTINI forcefield to introduce chirality in each residue of the CPs. The new parametrization, which we have called MA(R/S)TINI, reproduces the expected self-assembly patterns for several CP sequences in the presence of different membrane models, explicitly considering the chirality of the CPs and with no significant extra computational cost. Our simulations provide new mechanistic information of how these systems self-assemble in presence of different lipid scenarios, showing that the CP-CP and CP-membrane interactions are sensitive to the peptide sequence chirality. This opens the door to design new bioactive CPs based on CG-MD simulations. A web-based tool for the automatic parameterization of new CP sequences using MA(R/S)TINI, among other functionalities, is under construction (see http://cyclopep.com).

Influence of salt and temperature on the self-assembly of cyclic peptides in water: a molecular dynamics study

It is found in the literature that cyclic peptides (CPs) are able to self-assemble in water to form cyclic peptide nanotubes (CPNTs) and are used extensively in the field of nanotechnology. Several factors influence the formation and stability of these nanotubes in water. However, an extensive study of the contribution of several important factors is still lacking. The purpose of this study is to explore the effect of temperature and salt (NaCl) on the association tendency of CPs. Furthermore, the self-association behavior of CPs in aqueous solutions at various temperatures is also thoroughly discussed. Cyclo-[(Asp-D-Leu-Lys-D-Leu)₂] is considered for this study and a series of classical molecular dynamics (MD) simulations at three different temperatures, viz. 280 K, 300 K, and 320 K, both in pure water and in NaCl solutions of different concentrations are carried out. The calculations of radial distribution functions, preferential interaction parameters, cluster formation and hydrogen bonding properties suggest a strong influence of NaCl concentration on the association propensity of CPs. Low NaCl concentration hinders CP association while high NaCl concentration facilitates the association of CPs. Besides this, the association of CPs is found to be enhanced at low temperature. Furthermore, the thermodynamics of CP association is predominantly found to be enthalpy driven in both the presence and absence of salt. No crossover between enthalpy and entropy in CP association is observed. In addition, the MM-GBSA method is used to investigate the binding free energies of the CP rings that self-assembled to form nanotube like structures at all three temperatures.

Antimicrobial nano-assemblies of tryptocidine C, a tryptophan-rich cyclic decapeptide, from ethanolic solutions

Tryptocidine C (TpcC), a Trp-rich cyclodecapeptide is a minor constituent in the antibiotic tyrothricin complex from Brevibacillus parabrevis. TpcC possesses a high tendency to oligomerise in aqueous solutions and dried TpcC forms distinct self-assembled nanoparticles. High-resolution scanning electron microscopy revealed the influence of different ethanol:water solvent systems on TpcC self-assembly, with the TpcC, dried from a high concentration in 15% ethanol, primarily assembling into small nanospheres with 24.3 nm diameter and 0.05 polydispersity. TpcC at 16 μM, near its CMC, formed a variety of structures such as small nanospheres, large dense nanospheroids and facetted 3-D-crystals, as well as sheets and coarse carpet-like structures which depended on ethanol concentration. Drying 16 μM TpcC from 75% ethanol resulted in highly facetted 3-D crystals, as well as small nanospheres, while those in 10% ethanol preparation had less defined facets. Drying from 20 to 50% ethanol led to polymorphic architectures with a few defined nanospheroids and various small nanoparticles, imbedded in carpet- and sheet-like structures. These polymorphic surface morphologies correlated with maintenance of fluorescence properties and the surface-derived antibacterial activity against Staphylococcus aureus over time, while there was a significant change in fluorescence and loss in activity in the 10% and 75% preparations where 3-D crystals were observed. This indicated that TpcC oligomerisation in solutions with 20-50% ethanol leads to metastable structures with a high propensity for release of antimicrobial moieties, while those leading to crystallisation limit active moieties release. TpcC nano-assemblies can find application in antimicrobial coatings, surface disinfectants, food packaging and wound healing materials.

Molecular Dynamics Simulations of Transmembrane Cyclic Peptide Nanotubes Using Classical Force Fields, Hydrogen Mass Repartitioning, and Hydrogen Isotope Exchange Methods: A Critical Comparison

Self-assembled cyclic peptide nanotubes with alternating D- and L-amino acid residues in the sequence of each subunit have attracted a great deal of attention due to their potential for new nanotechnology and biomedical applications, mainly in the field of antimicrobial peptides. Molecular dynamics simulations can be used to characterize these systems with atomic resolution at different time scales, providing information that is difficult to obtain via wet lab experiments. However, the performance of classical force fields typically employed in the simulation of biomolecules has not yet been extensively tested with this kind of highly constrained peptide. Four different classical force fields (AMBER, CHARMM, OPLS, and GROMOS), using a nanotube formed by eight D,L-α-cyclic peptides inserted into a lipid bilayer as a model system, were employed here to fill this gap. Significant differences in the pseudo-cylindrical cavities formed by the nanotubes were observed, the most important being the diameter of the nanopores, the number and location of confined water molecules, and the density distribution of the solvent molecules. Furthermore, several modifications were performed on GROMOS54a7, aiming to explore acceleration strategies of the MD simulations. The hydrogen mass repartitioning (HMR) and hydrogen isotope exchange (HIE) methods were tested to slow down the fastest degrees of freedom. These approaches allowed a significant increase in the time step employed in the equation of the motion integration algorithm, from 2 fs up to 5-7 fs, with no serious changes in the structural and dynamical properties of the nanopores. Subtle differences with respect to the simulations with the unmodified force fields were observed in the concerted movements of the cyclic peptides, as well as in the lifetime of several H-bonds. All together, these results are expected to contribute to better understanding of the behavior of self-assembled cyclic peptide nanotubes, as well as to support the methods tested to speed up general MD simulations; additionally, they do provide a number of quantitative descriptors that are expected to be used as a reference to design new experiments intended to validate and complement computational studies of antimicrobial cyclic peptides.

Blockade of GRTH/DDX25 Phosphorylation by Cyclic Peptides Provides an Avenue for Developing a Nonhormonal Male Contraceptive

Gonadotropin-regulated testicular RNA helicase (GRTH)/DDX25 is a DEAD-box RNA helicase essential for the completion of spermatogenesis. Our previous studies indicated that blocking the GRTH phospho-site or perturbing the GRTH/protein kinase A (PKA) interface could provide an avenue for developing a nonhormonal male contraceptive. In this study, cyclic peptides were rationally designed and synthesized as promising therapeutic agents. The peptides showed effective delivery into COS-1 and germ cells and a dose-dependent inhibitory effect on GRTH phosphorylation. The peptides inhibit GRTH phosphorylation in the presence of PKA, and binding to the helicase resulted in thermal stabilization of non-phospho GRTH. Increased efficiency in fluorescence resonance energy transfer (FRET) assay revealed their interaction with GRTH. Cyclic peptide exposure of cultures from mice seminiferous tubules resulted in significant inhibition of phospho GRTH. These peptides did not exhibit toxicity. Effective delivery and targeted decrease of in vitro expression of phospho GRTH by cyclic peptides provide a promising angle to develop effective compounds as a nonhormonal male contraceptive.

Effect of Water Models on Transmembrane Self-Assembled Cyclic Peptide Nanotubes

Self-assembling cyclic peptide nanotubes can form nanopores when they are inserted in lipid bilayers, acting as ion and/or water permeable channels. In order to improve the versatility of these systems, it is possible to specifically design cyclic peptides with a combination of natural and non-natural amino acids, enabling the control of the nature of the inner cavity of the channels. Here, the behavior of two types of self-assembling peptide motifs, alternating α-amino acids with γ- or δ-aminocycloalkanecarboxylic acids, is studied via molecular dynamics (MD) simulations. The behavior of water molecules in nanopores is expected to affect the properties of these channels and therefore merits detailed examination. A number of water models commonly used in MD simulations have been validated by how well they reproduce bulk water properties. However, it is less clear how these water models behave in the nanoconfined condition inside a channel. The behavior of four different water models-TIP3P, TIP4P, TIP4P/2005, and OPC-are evaluated in MD simulations of self-assembled cyclic peptide nanotubes of distinct composition and diameter. The dynamic behavior of the water molecules and ions in these designed artificial channels depends subtly on the water model used. TIP3P water molecules move faster than those of TIP4P, TIP4P/2005, and OPC. This demeanor is clearly observed in the filling of the nanotube, in water diffusion within the pore, and in the number and stability of hydrogen bonds of the peptides with water. It was also shown that the water model influences the simulated ion flux through the nanotubes, with TIP3P producing the greatest ion flux. Additionally, the two more recent models, TIP4P/2005 and OPC, which are known to reproduce the experimental self-diffusion coefficient of bulk water quite well, exhibit very similar results under the nanoconfined conditions studied here. Because none of these models have been parametrized specifically for waters confined in peptide nanotubes, this study provides a point of reference for further validation.

Biomimetic Hybrid Systems for Tissue Engineering

Tissue engineering approaches appear nowadays highly promising for the regeneration of injured/diseased tissues. Biomimetic scaffolds are continuously been developed to act as structural support for cell growth and proliferation as well as for the delivery of cells able to be differentiated, and also of bioactive molecules like growth factors and even signaling cues. The current research concerns materials employed to develop biological scaffolds with improved features as well as complex preparation techniques. In this work, hybrid systems based on natural polymers are discussed and the efforts focused to provide new polymers able to mimic proteins and DNA are extensively explained. Progress on the scaffold fabrication technique is mentioned, those processes based on solution and melt electrospinning or even on their combination being mainly discussed. Selection of the appropriate hybrid technology becomes vital to get optimal architecture to reasonably accomplish the final applications. Representative examples of the recent possibilities on tissue regeneration are finally given.

A molecular dynamics investigation on transporting mechanism of glucose through a cyclic peptide nanotube

Cyclic peptide nanotubes (CPNTs) are open-ended, hollow, and tubular structures that are made of several cyclic peptide rings. These structures can act as a transmembrane channel and transport ions or small molecules. In this work, we studied the stability of a cyclic peptide nanotube 8 × [(Trp-D-Leu)4-Gln-D-Leu] into a fully hydrated membrane composed of DPPC/POPC/POPS/cholesterol and also the transport mechanism of β-D-glucose through this nanotube was investigated. Our findings revealed that the CPNT was stable in the lipid bilayer during the simulation time and non-bonded interactions, especially hydrogen bonding have an important role to form a stable CPNT in the membrane. The glucose jumps from a Cα-region into the mid-Cα region and spends more time in this region because of its more desirable interactions with water molecules and the CPNT. In the transport pathway, non-bonded interactions between glucose, water molecules and the CPNT facilitate the transport of the glucose through the CPNT. The collaboration of hydrogen bonds, electrostatic and van der Waals interactions change the pulling force and lead to transport glucose through the CPNT. Potential of mean force (PMF) calculations revealed that the glucose has a minimum value of binding free energy and maximum configurational entropy in MPR regions. These findings can be used to design more CPNTs with different goals such as drug delivery.Communicated by Ramaswamy H. Sarma.

Competitive double-switched self-assembled cyclic peptide nanotubes: a dual internal and external control

"Intelligent" materials based on synthetic small molecules that become functional only under specific conditions provide new opportunities for developing regulated systems aimed at a large number of applications. For instance, biologically active supramolecular entities that are sensitive to environmental conditions, such as the presence of bacterial membranes, are extremely interesting in biomedicine. In this work, we have designed and investigated, using molecular dynamics simulations, a doubly modulable nanotube formed by the self-assembly of cyclic peptides sensitive to both the presence of a lipid membrane and the pH of the aqueous media. The cyclic peptides were designed to self-assemble into peptide nanotubes in the presence of a lipid bilayer and at low pH values. Under these conditions, the residual side chains point outside the cyclic peptides, being exposed to the lipid bilayer, and the inner groups (carboxylic acids) are protonated, thus allowing the permeation of water and preventing that of ions. Higher pH values are expected to create carboxylate groups at the lumen of the peptides, leading to the disassembly of the nanotube, the attraction and translocation of ions towards the hydrophobic core of the bilayer, and eventually killing the target malignant cells. Our results suggest that by introducing a second switch in a membrane sensitive system, it is possible to modulate its interaction with the lipid bilayer. This opens the door to new strategies for the preparation of antimicrobial peptides that interact at the membrane level.

Molecular Dynamics Simulations on the Behaviors of Hydrophilic/Hydrophobic Cyclic Peptide Nanotubes at the Water/Hexane Interface

In this work, nine kinds of amino acid residues, i.e., alanine (A), leucine (L), valine (V), isoleucine (I), tryptophan (W), glutamine (Q), threonine (T), serine (S), and cysteine (C), were selected to construct seven cyclic peptide nanotubes (CPNTs) with diverse hydrophilic/hydrophobic external surfaces, which were further separately inserted at the water/hexane interface to investigate their microstructures and interfacial properties. Molecular dynamics (MD) simulations reveal that all the CPNTs except the QT- and VL-CPNTs have different degrees of tilt, fracture, and shedding at the interface. The end-CPs are more susceptible to the effect of the surroundings than the mid-CPs. The interactions of individual CP subunits with the neighborings disclose the firmness of the mid-CPs and the dissociation of the end-CPs. The results indicate that a hydrophobic CPNT is prone to stay at the interface, while a hydrophilic CPNT easily enters the water phase, resulting in many H-bonds with water. Results in this work enrich the dynamic properties of a hydrophilic/hydrophobic CPNT at the biphase interface at the atomic level.

Hydrogels for Biomedical Applications: Cellulose, Chitosan, and Protein/Peptide Derivatives

Hydrogels based on polysaccharide and protein natural polymers are of great interest in biomedical applications and more specifically for tissue regeneration and drug delivery. Cellulose, chitosan (a chitin derivative), and collagen are probably the most important components since they are the most abundant natural polymers on earth (cellulose and chitin) and in the human body (collagen). Peptides also merit attention because their self-assembling properties mimic the proteins that are present in the extracellular matrix. The present review is mainly focused on explaining the recent advances on hydrogels derived from the indicated polymers or their combinations. Attention has also been paid to the development of hydrogels for innovative biomedical uses. Therefore, smart materials displaying stimuli responsiveness and having shape memory properties are considered. The use of micro- and nanogels for drug delivery applications is also discussed, as well as the high potential of protein-based hydrogels in the production of bioactive matrices with recognition ability (molecular imprinting). Finally, mention is also given to the development of 3D bioprinting technologies.

Conformational changes during permeation of Na+ through a modified cyclic peptide nanotube promote energy landscape roughness

Using a metadynamics approach, we investigate the potential of mean force for Na⁺ permeation inside a cyclic peptide nanotube (CPN) with modified interior as a function of ion position, coordination number, and lumen chemistry. We show that functionalizing the lumen of a CPN with a methyl-benzoic acid group introduces non-periodic variations in the internal energy of the nanotube, which dictate the overall free energy roughness during the permeation of Na⁺. These non-periodic variations arise from the structural dynamics of the functional group, where changes in the dihedral angles induced by the proximity of the ion give rise to conformational changes that increase landscape roughness and thereby decrease transport rate. Our computational framework emphasizes the advantages of using the coordination number as a collective variable to investigate the available conformations during ion permeation through CPNs, and reveals new structure-function relations for chemically tunable CPNs, paving the way for rational design of nano-porous systems with tunable selectivity and flux.

Peptidic Biomaterials: From Self-Assembling to Regenerative Medicine

Peptidic biomaterials represent a particularly exciting topic in regenerative medicine. Peptidic scaffolds can be specifically designed for biomimetic customization for targeted therapy. The field is at a pivotal point where preclinical research is being translated into clinics, so it is crucial to understand the theory and describe the status of this rapidly developing technology. In this review, we highlight major advantages and current limitations of self-assembling peptide-based biomaterials, and we discuss the most widely used classes of assembling peptides, describing recent and promising approaches in tissue engineering, drug delivery, and clinics. We also suggest design strategies and hurdles that still need to be overcome to fully exploit their therapeutic potential.

Molecular dynamics simulations for designing biomimetic pores based on internally functionalized self-assembling α,γ-peptide nanotubes

A molecular dynamics study on internally functionalized peptide nanotubes composed of α- and γ-amino acids self-assembled in lipid bilayers is presented. One of the main advantages of peptide nanotubes composed of γ-amino acids is that the properties of their inner cavities can be tuned by introducing different functions on β-carbon of the γ-amino acid. In the work described here we studied the effect of the presence of different numbers of hydroxyl groups in different positions in the lumen of these channels when they are inserted into a lipid bilayer and assessed how they affect the structural and dynamic behavior of the modified peptide nanotubes as well as the transmembrane transport of different ions. The results provided atomic information about the effect of polar groups on the dynamic, structural and transport properties of this type of peptidic channel upon insertion into lipid bilayers, projecting a promising future for their use as biomimetic channels when properly inner-derivatized. Furthermore, the chemical versatility of the hydroxyl groups in the lumen of the peptide nanotubes would enable appealing applications for these channels, such as a controlled method for the activation/inactivation of the transmembrane transport along the nanopore.

Tailoring the water structure and transport in nanotubes with tunable interiors

Self-assembly of cyclic peptide nanotubes (CPNs) in polymer thin films has opened up the possibility of creating separation membranes with tunable nanopores that can differentiate molecules at the sub-nanometer level. While it has been demonstrated that the interior chemistry of the CPNs can be tailored by inserting functional groups in the nanopore lumen (mCPNs), a design strategy for picking the chemical modifications that lead to particular transport properties has not been established. Drawing from the knowledgebase of functional groups in natural amino acids, here we use molecular dynamics simulations to elucidate how bioinspired mutations influence the transport of water through mCPNs. We show that, at the nanoscale, factors besides the pore size, such as electrostatic interactions and steric effects, can dramatically change the transport properties. We recognize a novel asymmetric structure of water under nanoconfinement inside the chemically functionalized nanotubes and identify that the small non-polar glycine-mimic groups that minimize the steric constraints and confer a hydrophobic character to the nanotube interior are the fastest transporters of water. Our computationally developed experiments on a realistic material system circumvent synthetic challenges, and lay the foundation for bioinspired principles to tailor artificial nanochannels for separation applications such as desalination, ion-exchange and carbon capture.

Modelling peptide nanotubes for artificial ion channels

We investigate the van der Waals interaction of D,L-Ala cyclopeptide nanotubes and various ions, ion-water clusters and C(60) fullerenes, using the Lennard-Jones potential and a continuum approach which assumes that the atoms are smeared over the peptide nanotube providing an average atomic density. Our results predict that Li(+), Na(+), Rb(+) and Cl(-) ions and ion-water clusters are accepted into peptide nanotubes of 8.5 Å internal diameter whereas the C(60) molecule is rejected. The model indicates that the C(60) molecule is accepted into peptide nanotubes of 13 Å internal diameter, suggesting that the interaction energy depends on the size of the molecule and the internal diameter of the peptide nanotube. This result may be useful for the design of peptide nanotubes for drug delivery applications. Further, we also find that the ions prefer a position inside the peptide ring where the energy is minimum. In contrast, Li(+)-water clusters prefer to be in the space between each peptide ring.

Molecular insights on the cyclic peptide nanotube-mediated transportation of antitumor drug 5-fluorouracil

Self-assembled cyclic peptide nanotubes (CPNs) show a potential use in drug delivery. In this study, the CPN composed of (Trp-D-Leu)(4)-Gln-D-Leu was synthesized and tested for the transport of the antitumor drug 5-fluorouracil (5-FU). CPN-mediated release of 5-FU from liposomes experimentally tested the transportation function of the synthetic CPNs. To explore the transportation mechanism of CPNs, computational studies have been performed on the CPN models stacked by 8 subunits, including conventional molecular dynamics (CMD) simulations, and steered molecular dynamics (SMD) simulations in the environment of hydrated dimyristoylphosphatidylcholine (DMPC) lipid bilayer. Our CMD simulations demonstrated that the ortho-CPN is the most stable nanotube, in which the Gln residue is in the ortho-position relative to other residues. The calculated diffusion coefficient value for inner water molecules was 1.068 × 10(-5) cm(2)·s(-1), almost half that of the bulky water and 24 times faster than that of the typical gramicidin A channel. The CPN conserved its hollow structure along the 10 ns CMD simulations, with a tile angle of 50° relative to the normal of DMPC membrane. Results from SMD simulations showed that the 5-FU molecule was transported by hopping through different potential energy minima distributed along subunits, and finally exited the nanotube by escaping from the kink region at the last two subunits. The hopping of 5-FU was driven by switching from hydrophobic interactions between 5-FU and the interior wall of the nanotube to hydrogen bonding interactions of 5-FU with the backbone carbonyl group and amide group of ortho-CPN. The calculated binding free energy profile of 5-FU interacting with the CPN indicated that there was an energy well near the outer end of the nanotube.

Comparative study of predictive computational models for nanoparticle-induced cytotoxicity

With the increasing use of nanomaterials incorporated into consumer products, there is a need for developing approaches to establish "quantitative structure-activity relationships" (QSARs). These relationships could be used to predict various biological responses after exposure to nanomaterials for the purposes of risk analysis. This risk analysis is applicable to manufacturers of nanomaterials in an effort to determine potential hazards. Because metal oxide materials are some of the most widely applicable and studied nanoparticle types for incorporation into cosmetics, food packaging, and paints and coatings, we focused on comparing different approaches for establishing QSARs for this class of materials. Metal oxide nanoparticles are believed, by some, to cause alterations in cellular function due to their size and/or surface area. Others have said that these nanomaterials, because of the oxidized state of the metal, do not induce stress in biological tests systems. This controversy highlights the need to systematically develop structure-activity relationships (i.e., the relationship between physicochemical features to the cellular responses) and tools for predicting potential biological effects after a metal oxide nanomaterial exposure. Here, we attempt to identify a set of properties of two specific metal oxide nanomaterials-TiO(2) and ZnO-that could be used to characterize and predict the induced cellular membrane damage of immortalized human lung epithelial cells. We adopt a mathematical modeling approach that uses the engineered nanomaterial size characterized as a dry nanopowder and the nanomaterial behavior in ultrapure water, phosphate buffer, and cell culture media to predict nanomaterial-induced cellular membrane damage (via lactate dehydrogenase release). Results of these studies provide insights on how engineered nanomaterial features influence cellular responses and thereby outline possible approaches for developing and applying predictive computational models for biological responses caused by exposure to nanomaterials.

Isolation, characterization, and stability of discretely-sized nanolipoprotein particles assembled with apolipophorin-III

BACKGROUND

Nanolipoprotein particles (NLPs) are discoidal, nanometer-sized particles comprised of self-assembled phospholipid membranes and apolipoproteins. NLPs assembled with human apolipoproteins have been used for myriad biotechnology applications, including membrane protein solubilization, drug delivery, and diagnostic imaging. To expand the repertoire of lipoproteins for these applications, insect apolipophorin-III (apoLp-III) was evaluated for the ability to form discretely-sized, homogeneous, and stable NLPs.

METHODOLOGY

Four NLP populations distinct with regards to particle diameters (ranging in size from 10 nm to >25 nm) and lipid-to-apoLp-III ratios were readily isolated to high purity by size exclusion chromatography. Remodeling of the purified NLP species over time at 4 degrees C was monitored by native gel electrophoresis, size exclusion chromatography, and atomic force microscopy. Purified 20 nm NLPs displayed no remodeling and remained stable for over 1 year. Purified NLPs with 10 nm and 15 nm diameters ultimately remodeled into 20 nm NLPs over a period of months. Intra-particle chemical cross-linking of apoLp-III stabilized NLPs of all sizes.

CONCLUSIONS

ApoLp-III-based NLPs can be readily prepared, purified, characterized, and stabilized, suggesting their utility for biotechnological applications.

On the antibacterial action of cyclic peptides: insights from coarse-grained MD simulations

[RRKWLWLW] cyclic peptides have been shown to exhibit remarkable in vitro and in vivo antibacterial activity. Peptides alike seem to be promising for the development of new compounds to combat microbial pathogens, yet the molecular level understanding of their mechanism of action remains unclear. Here, we use coarse-grained (CG) molecular dynamics (MD) simulations of these cyclic peptides interacting with antibacterial cytoplasmic membrane models composed of a mixture of palmitoyl-oleoyl-phosphatidyl-ethanolamine (POPE) and palmitoyl-oleoyl-phosphatidylglycerol (POPG) lipid bilayers to provide a better understanding of their mode of action. In particular, the MD simulations performed at various concentrations of membrane-bound cyclic peptides reveal a novel type of mechanism in which the peptides first self-assemble at the membrane interface into amphipathic nanotubes. At high enough concentrations, coating of the membrane causes extrusion of lipids from the exposed bilayer leaflet, leading ultimately to a release of phospholipid micellar aggregates. Furthermore, the cyclic peptides also induce a drastic change in the lateral pressure profiles of the exposed leaflet, indicating a direct effect on the mechanical properties of the bilayer.

Theoretical characterization of the dynamical behavior and transport properties of alpha,gamma-peptide nanotubes in solution

We present here a molecular dynamics study on a promising class of peptide nanotubes with a partially hydrophobic inner cavity and an easy chemical functionalization of the lumen of the cylindrical structure. The structural and dynamical behavior of the nanotube in water, methanol, and chloroform has been analyzed using state of the art theoretical methods. The nanotube structure is always well preserved, but solvent-dependent dynamic alterations are evident. Such dynamic effects are surprisingly more severe in the most viscous solvent (water), as a consequence of the competition in polar solvents between intra- and intermolecular hydrogen bonds. Stiffness analysis from the collected trajectories helped us to characterize the equilibrium deformability of the nanotube, while steered dynamics simulations were used to determine the magnitude of free energy associated with nanotube growth. Analysis of the carrier and permeation properties of the compounds reveals surprising properties: (i) permeability for the most polar solvent (water), (ii) carrier properties for the most apolar solvent (chloroform), and (iii) neither good permeation nor carrier properties for the intermediate solvent in polarity (methanol). Results reported here constitute the most extensive characterization of these nanotubes presented to date and open many intriguing questions on their stability, dynamics, and transport/carrier properties.

Self-assembly of gibberellic amide assemblies and their applications in the growth and fabrication of ordered gold nanoparticles

Gibberellins are a group of naturally occurring diterpenoid based phytohormones that play a vital role in plant growth and development. In this work, we have studied the self-assembly of gibberellic acid, a phytohormone, which belongs to the family of gibberellins, and designed amide derivatives of gibberellic acid (GA(3)) for the facile, green synthesis of gold nanoparticles. It was found that the derivatives self-assembled into nanofibers and nanoribbons in aqueous solutions at varying pH. Further, upon incubation with tetrachloroaurate, the self-assembled GA(3)-amide derivatives efficiently nucleated and formed gold nanoparticles when heated to 60 degrees C. Energy dispersive x-ray spectroscopy, transmission electron microscopy and scanning electron microscopy analyses revealed that uniform coatings of gold nanoparticles in the 10-20 nm range were obtained at low pH on the nanowire surfaces without the assistance of additional reducing agents. This simple method for the development of morphology controlled gold nanoparticles using a plant hormone derivative opens doors for a new class of plant biomaterials which can efficiently yield gold nanoparticles in an environmentally friendly manner. The gold encrusted nanowires formed using biomimetic methods may lead on to the formation of conductive nanowires, which may be useful for a wide range of applications such as in optoelectronics and sensors. Further, the spontaneous formation of highly organized nanostructures obtained from plant phytohormone derivatives such as gibberellic acid is of particular interest as it might help in further understanding the supramolecular assembly mechanism of more highly organized biological structures.

Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables

A new implementation of the adaptive biasing force (ABF) method is described. This implementation supports a wide range of collective variables and can be applied to the computation of multidimensional energy profiles. It is provided to the community as part of a code that implements several analogous methods, including metadynamics. ABF and metadynamics have not previously been tested side by side on identical systems. Here, numerical tests are carried out on processes including conformational changes in model peptides and translocation of a halide ion across a lipid membrane through a peptide nanotube. On the basis of these examples, we discuss similarities and differences between the ABF and metadynamics schemes. Both approaches provide enhanced sampling and free energy profiles in quantitative agreement with each other in different applications. The method of choice depends on the dimension of the reaction coordinate space, the height of the barriers, and the relaxation times of degrees of freedom in the orthogonal space, which are not explicitly described by the chosen collective variables.

Theory of single-file multiparticle diffusion in narrow pores

Single-file diffusion of multiple strongly interacting particles in a one-dimensional pore is described within a general analytical framework. The theory accounts for nonequilibrium conditions, explicit particle-particle interactions, external potential acting on the particles and the fluctuations of the number of particles due to their exchange with external equilibrium reservoirs. It is shown that the problem can be reduced to a closed hierarchical set of partial differential equations of increasing dimensionality, which can be solved numerically. Our framework allows computing any macroscopic characteristic of multiparticle diffusion in the pore. It is shown that the pore occupancy probabilities and the current are rational functions of external concentrations in the steady state. The theory is tested on a simplified model of the narrow rigid pore inspired by the selectivity filter of biological ion channel. Perspectives and limitations of the theory are discussed.

Determinants of water permeability through nanoscopic hydrophilic channels

Naturally occurring pores show a variety of polarities and sizes that are presumably directly linked to their biological function. Many biological channels are selective toward permeants similar or smaller in size than water molecules, and therefore their pores operate in the regime of single-file water pores. Intrinsic factors affecting water permeability through such pores include the channel-membrane match, the structural stability of the channel, the channel geometry and channel-water affinity. We present an extensive molecular dynamics study on the role of the channel geometry and polarity on the water osmotic and diffusive permeability coefficients. We show that the polarity of the naturally occurring peptidic channels is close to optimal for water permeation, and that the water mobility for a wide range of channel polarities is essentially length independent. By systematically varying the geometry and polarity of model hydrophilic pores, based on the fold of gramicidin A, the water density, occupancy, and permeability are studied. Our focus is on the characterization of the transition between different permeation regimes in terms of the structure of water in the pores, the average pore occupancy and the dynamics of the permeating water molecules. We show that a general relationship between osmotic and diffusive water permeability coefficients in the single-file regime accounts for the time averaged pore occupancy, and that the dynamics of the permeating water molecules through narrow non single file channels effectively behaves like independent single-file columns.