Spontaneous fibril formation by polyalanines; discontinuous molecular dynamics simulations

Fibrillary protein aggregates rich in beta-sheet structure have been implicated in the pathology of several neurodegenerative diseases. In this work, we investigate the formation of fibrils by performing discontinuous molecular dynamics simulations on systems containing 12 to 96 model Ac-KA(14)K-NH(2) peptides using our newly developed off-lattice, implicit-solvent, intermediate-resolution model, PRIME. We find that, at a low concentration, random-coil peptides assemble into alpha-helices at low temperatures. At intermediate concentrations, random-coil peptides assemble into alpha-helices at low temperatures and large beta-sheet structures at high temperatures. At high concentrations, the system forms beta-sheets over a wide range of temperatures. These assemble into fibrils above a critical temperature which decreases with concentration and exceeds the isolated peptide's folding temperature. At very high temperatures and all concentrations, the system is in a random-coil state. All of these results are in good qualitative agreement with those by Blondelle and co-workers on Ac-KA(14)K-NH(2) peptides. The fibrils observed in our simulations mimic the structural characteristics observed in experiments in terms of the number of sheets formed, the values of the intra- and intersheet separations, and the parallel peptide arrangement within each beta-sheet. Finally, we find that when the strength of the hydrophobic interaction between nonpolar side chains is high compared to the strength of hydrogen bonding, amorphous aggregates, rather than fibrillar aggregates, are formed.     

Diphenylalanine Motif Drives Self-Assembling in Hybrid PNA-Peptide Conjugates

Peptides and nucleic acids can self-assemble to give supramolecular structures that find application in different fields, ranging from the delivery of drugs to the obtainment of materials endowed with optical properties. Forces that stabilize the “suprastructures” typically are hydrogen bonds or aromatic interactions; in case of nucleic acids, Watson-Crick pairing drives self-assembly while, in case of peptides, backbone hydrogen bonds and interactions between aromatic side chains trigger the formation of structures, such as nanotubes or ribbons. Molecules containing both aromatic peptides and nucleic acids could in principle exploit different forces to self-assemble. In this work we meant to investigate the self-assembly of mixed systems, with the aim to understand which forces play a major role and determine formation/structure of aggregates. We therefore synthesized conjugates of the peptide FF to the peptide nucleic acid dimer “gc” and characterized their aggregates by different spectroscopic techniques, including NMR, CD and fluorescence.     

Self-assembly of peptide scaffolds in biosilica formation: computer simulations of a coarse-grained model

The self-assembly of model peptides is studied using Brownian dynamics computer simulations. A coarse-grained, bead-spring model is designed to mimic silaffins, small peptides implicated in the biomineralization of certain silica diatom skeletons and observed to promote the formation of amorphous silica nanospheres in vitro. The primary characteristics of the silaffin are a 15 amino acid hydrophilic backbone and two modified lysine residues near the ends of the backbone carrying long polyamine chains. In the simulations, the model peptides self-assemble to form spherical clusters, networks of strands, or bicontinuous structures, depending on the peptide concentration and effective temperature. The results indicate that over a broad range of volume fractions (0.05-25%) the characteristic structural lengthscales fall in the range 12-45 nm. On this basis, we suggest that self-assembled structures act as either nucleation points or scaffolds for the deposition of 10-100 nm silica-peptide building blocks from which diatom skeletons and synthetic nanospheres are constructed.     

Effects of surface interactions on peptide aggregate morphology

The formation of peptide aggregates mediated by an attractive surface is investigated using replica exchange molecular dynamics simulations with a coarse-grained peptide representation. In the absence of a surface, the peptides exhibit a range of aggregate morphologies, including amorphous aggregates, β-barrels and multi-layered fibrils, depending on the chiral stiffness of the chain (a measure of its β-sheet propensity). In contrast, aggregate morphology in the presence of an attractive surface depends more on surface attraction than on peptide chain stiffness, with the surface favoring fibrillar structures. Peptide-peptide interactions couple to peptide-surface interactions cooperatively to affect the assembly process both qualitatively (in terms of aggregate morphology) and quantitatively (in terms of transition temperature and transition sharpness). The frequency of ordered fibrillar aggregates, the surface binding transition temperature, and the sharpness of the binding transition all increase with both surface attraction and chain stiffness.     

Molecular modeling of Ca2+-oligo(α-l-guluronate) complexes: toward the understanding of the junction zone structure in calcium alginate gels

Gelling of alginates in the presence of divalent metal ions is accompanied by the formation of the junction zone, i.e., the region of the alginate chains aggregation. The structure of the junction zone results primarily from the nature of interaction between the ??dimers,?? created by two alginate chains connected via Ca²⁺ ions. We have applied the molecular dynamics technique, in combination with the GROMOS96 biomolecular force field to elucidate the structural features and the stability of such dimer?Cdimer complexes, where the alginate chains were represented by oligomers of ??-l-guluronate. The results indicate that only associations mediated by calcium ions and carboxylic groups are stable during simulations. Hydrogen bonding-type interactions are too weak to support the stability of complexes. The parallel arrangement of two dimers is the favorable one, due to their helical twists, which interfere with the formation of the fully ordered structure of the junction zone.     

Multiparticle sintering dynamics: from fractal-like aggregates to compact structures

Multiparticle sintering is encountered in almost all high temperature processes for material synthesis (titania, silica, and nickel) and energy generation (e.g., fly ash formation) resulting in aggregates of primary particles (hard- or sinter-bonded agglomerates). This mechanism of particle growth is investigated quantitatively by mass and energy balances during viscous sintering of amorphous aerosol materials (e.g., SiO(2) and polymers) that typically have a distribution of sizes and complex morphology. This model is validated at limited cases of sintering between two (equally or unequally sized) particles, and chains of particles. The evolution of morphology, surface area and radii of gyration of multiparticle aggregates are elucidated for various sizes and initial fractal dimension. For each of these structures that had been generated by diffusion limited (DLA), cluster-cluster (DLCA), and ballistic particle-cluster agglomeration (BPCA) the surface area evolution is monitored and found to scale differently than that of the radius of gyration (moment of inertia). Expressions are proposed for the evolution of fractal dimension and the surface area of aggregates undergoing viscous sintering. These expressions are important in design of aerosol processes with population balance equations (PBE) and/or fluid dynamic simulations for material synthesis or minimization and even suppression of particle formation.     

Aggregation modes of the spin mono-labeled tylopeptin B and heptaibin peptaibiotics in frozen solutions of weak polarity as studied by PELDOR spectroscopy

The X band PELDOR spectroscopy was used to investigate the magnetic dipole-dipole interactions in glassy solutions of nitroxide mono-labeled tylopeptin B and heptaibin peptaibiotics at 77 K. Specifically, a study was performed of the tylopeptin B peptides labeled at either position 3, 8, or 13, denoted as T3, T8, and T13, respectively. The heptaibin analogs labeled at either position 2 or 14, denoted as H2 and H14, respectively, were also investigated. It was shown that in frozen glassy peptide solutions in methanol, the spin labels are randomly distributed over the solvent volume. This result points to the absence of specific dipolar interactions between the peptides under these conditions. However, peptide aggregation was detected in weakly polar methanol/toluene environments. To study the properties of the resulting aggregates, we examined the depth of modulation for the PELDOR traces as a function of the concentration of the peptides in solution and the distances between the spin labels in the aggregates. Based on the concentration dependencies, the number of peptide molecules in the aggregates was estimated. We find that this value ranges from 2 to 3, depending on the position of the spin label in the peptide sequence. The combined analysis of the distance spectra and the number of peptide molecules in the aggregates allows us to suggest that dimer formation is the prevailing mode of self-association. In the case of spin-labeled tylopeptin B, the molecules in the dimer are head-to-head oriented. In addition, the distance spectra of the aggregates show that the C-termini of the molecules in the tylopeptin B dimer are more mobile than the Ntermini. This phenomenon leads to an increase in the spread of the distances between the nitroxides as the label position is approaching the peptide C-terminus. For heptaibin, we show that two forms of dimerization (head-to-head and head-to-tail) occur. Finally, in addition to dimers, aggregates containing 3 or 4 peptide molecules, which give broad lines in the distance spectra, are seen in solution.     

Thermodynamics of peptide dimer formation

The Replica Exchange Statistical Temperature Molecular Dynamics algorithm is used to study the equilibrium properties of a peptide monomer and dimer and the thermodynamics of peptide dimer formation. The simulation data are analyzed by the Statistical Temperature Weighted Histogram Analysis Method. Each 10-residue peptide is represented by a coarse-grained model with hydrophobic side chains and has an α-helix as its minimum energy configuration. It is shown that the configurational behavior of the dimer can be divided into four regions as the temperature increases: two folded peptides; one folded and one unfolded peptide; two unfolded peptides; and two spatially separated peptides. Two important phenomena are discussed: in the dimer, one peptide unfolds at a lower temperature than the isolated monomer and the other peptide unfolds at a higher temperature than the isolated monomer. In addition, in the temperature region where one peptide is folded and the other unfolded, the unfolded peptide adopts an extended structure that minimizes the overall surface area of the aggregate. It is suggested that combination of destabilization due to aggregation and the resulting extended configuration of the destabilized peptide could have implications for nucleating β-sheet structures and the ultimate formation of fibrils.     

Molecular modelling of amphipathic basic model peptides: Interactions in aqueous solutions and in the presence of lipids

Molecular modelling calculations based on experimental data obtained in solution and in small unilamellar vesicles are used to study interactions between amphiphilic basic peptides and membranes. The behaviour of such peptides during the initial and final stages of the adsorption process is our primary interest. Primary sequences of 20 amino acid residues were designed with equal numbers of basic lysines and hydrophobic leucines in order to get an amphipathic α helix. First, in solution, aggregates with an increasing number (up to nine) of helical monomers were built up and the hydrophobic solvent accessible surface per monomer was analysed on energy minimised structures. This showed that aggregates with 5–8 of monomers should be equally probable, in reasonable accordance with experimental data. In addition, models of membranes with 21 dimyristoyl-phosphatidylcholine lipids were constructed; amphiphilic peptides were merged into these assemblies with their axes parallel to the monolayer surface and the whole lipid/peptide complex was submitted to a few steps of simulated annealing and further energy minimisation techniques in order to equilibrate alkyl chains in the vicinity of the peptide. These simulations yield an estimation of the penetration depth for the peptide in the monolayer of ∼3.2 ?, whereas experimental approaches to this question were not productive. The modification in the peptide net electrical charge by interchanging Leu in Lys residues in such systems is also examined: for low-charged peptides the penetration depth increases. Received: 20 May 1998 / Accepted : 3 September 1998 / Published online: 7 December 1998     

Structural, thermodynamical, and dynamical properties of oligomers formed by the amyloid NNQQ peptide: insights from coarse-grained simulations

Characterizing the early formed oligomeric intermediates of amyloid peptides is of particular interest due to their links with neurodegenerative diseases. Here we study the NNQQ peptide, known to display parallel β-strands in amyloid fibrils by x-ray microcrystallography, and investigate the structural, thermodynamical, and dynamical properties of 20 NNQQ peptides using molecular dynamics and replica exchange molecular dynamics simulations coupled to a coarse-grained force field. All simulations are initiated from randomized and fully dispersed monomeric conformations. Our simulations reveal that the phase transition is characterized by a change in the oligomer and β-sheet size distributions and the percentage of mixed parallel/antiparallel β-strands when the sheets are formed. At all temperatures, however, the fraction of parallel β-strands remains low, though there are many association/fragmentation events. This work and a growing body of computational studies provide strong evidence that the critical nucleus goes beyond 20 chains and reordering of the β-strands occurs in larger oligomers.     

Control over calcium carbonate phase formation by dendrimer/surfactant templates

Poly(propylene imine) dendrimers that are modified with long alkyl chains self-assemble to form well-defined aggregates. The geometry and surface chemistry of the dendrimer assemblies can be varied through the addition of surfactants. These dendrimer/surfactant aggregates can be tuned to template the formation of the different phases of calcium carbonate. The use of octadecylamine results in the formation of polyhedral aggregates that become embedded within an amorphous calcium carbonate phase that persists in competition with the thermodynamic product, calcite. In combination with hexadecyltrimethylammonium bromide, small spherical aggregates are formed that induce the formation of vaterite. The use of the negatively charged surfactant SDS results in growth retardation by the Ca(2+)-induced agglomeration of dendrimer/surfactant aggregates into giant spherical particles. Eventually these particles become overgrown by rhombohedral calcite.     

Does amino acid sequence determine the properties of Aβ dimer?

The effect of random reshuffling of amino acids on the properties of dimers formed by Aβ peptides is studied using replica exchange molecular dynamics and united atom implicit solvent model. We show that thermodynamics of dimer assembly and the dimer globule-like state are not affected by sequence permutation. Furthermore, sequence reshuffling does not change the distributions of non-local interactions and, to a large extent, amino acids in the dimer volume. To rationalize these results, we demonstrate that Gaussian statistics applies surprisingly well to the end-to-end distances of the peptides in the dimer implying that non-bonded interactions between distant along the chain amino acids are effectively screened. This observation suggests that peptides in the dimer behave as ideal chains in polymer melt, in which amino acids lose their "identity" and therefore the memory of sequence position. As a result large-scale properties of the dimer become universal or sequence independent. Comparison of our simulations with the prior theoretical studies and their implications for experiments are discussed.     

Chemistry of aqueous silica nanoparticle surfaces and the mechanism of selective peptide adsorption

Control over selective recognition of biomolecules on inorganic nanoparticles is a major challenge for the synthesis of new catalysts, functional carriers for therapeutics, and assembly of renewable biobased materials. We found low sequence similarity among sequences of peptides strongly attracted to amorphous silica nanoparticles of various size (15-450 nm) using combinatorial phage display methods. Characterization of the surface by acid base titrations and zeta potential measurements revealed that the acidity of the silica particles increased with larger particle size, corresponding to between 5% and 20% ionization of silanol groups at pH 7. The wide range of surface ionization results in the attraction of increasingly basic peptides to increasingly acidic nanoparticles, along with major changes in the aqueous interfacial layer as seen in molecular dynamics simulation. We identified the mechanism of peptide adsorption using binding assays, zeta potential measurements, IR spectra, and molecular simulations of the purified peptides (without phage) in contact with uniformly sized silica particles. Positively charged peptides are strongly attracted to anionic silica surfaces by ion pairing of protonated N-termini, Lys side chains, and Arg side chains with negatively charged siloxide groups. Further, attraction of the peptides to the surface involves hydrogen bonds between polar groups in the peptide with silanol and siloxide groups on the silica surface, as well as ion-dipole, dipole-dipole, and van-der-Waals interactions. Electrostatic attraction between peptides and particle surfaces is supported by neutralization of zeta potentials, an inverse correlation between the required peptide concentration for measurable adsorption and the peptide pI, and proximity of cationic groups to the surface in the computation. The importance of hydrogen bonds and polar interactions is supported by adsorption of noncationic peptides containing Ser, His, and Asp residues, including the formation of multilayers. We also demonstrate tuning of interfacial interactions using mutant peptides with an excellent correlation between adsorption measurements, zeta potentials, computed adsorption energies, and the proposed binding mechanism. Follow-on questions about the relation between peptide adsorption on silica nanoparticles and mineralization of silica from peptide-stabilized precursors are raised.     

Computational tool to model the packing of polycyclic chains: structural analysis of amorphous polythiophene

A very efficient computational procedure, which was previously developed to generate and relax atomistic models of linear and comb-like amorphous polymers, has been adapted to model the amorphous phase of polycyclic systems. The strategy, which is a based in a generation algorithm that eliminates the torsion strain and a simple Monte Carlo Metropolis method to relax the generated structures, has been used to predict the density of amorphous polythiophene by combining NVT and NPT simulations. The theoretical value is in the excellent agreement with the experimental one, the former being overestimated by only 3-5%. Next, the molecular conformation and the packing of the rings were studied in detail. Interestingly, the amorphous phase of polythiophene can be described as a packing of elongated molecular chains more or less aligned in the same direction, in which the thiophene rings close in the space but belonging to different chains tend to adopt approximate parallel or antiparallel displaced pi-stacked arrangements.     

Self-recognition and aggregation between diblock (charged/neutral) polyelectrolytes by Monte Carlo simulations

The self-recognition between oppositely charged polyelectrolyte-neutral diblock copolymers and aggregate formation is investigated by Monte Carlo simulations. Both matched lengths and charge numbers are critical conditions for self-recognition. The optimum self-recognition occurs between oppositely charged chains with matched charged block lengths and charge numbers. The size of aggregates increases, as the total length and the ratio of charged to neutral beads become larger. Polyelectrolyte networks were observed in some cases containing unmatched chains. The molecular configurations of the entire chains and of the charged and neutral blocks as well as the radial distribution functions of the charged beads are also investigated.     

Self-assembly of beta-sheet forming peptides into chiral fibrillar aggregates

The authors introduce a novel mid-resolution off-lattice coarse-grained model to investigate the self-assembly of beta-sheet forming peptides. The model retains most of the peptide backbone degrees of freedom as well as one interaction center describing the side chains. The peptide consists of a core of alternating hydrophobic and hydrophilic residues, capped by two oppositely charged residues. Nonbonded interactions are described by Lennard-Jones and Coulombic terms. The influence of different levels of "hydrophobic" and "steric" forces between the side chains of the peptides on the thermodynamics and kinetics of aggregation was investigated using Langevin dynamics. The model is simple enough to allow the simulation of systems consisting of hundreds of peptides, while remaining realistic enough to successfully lead to the formation of chiral, ordered beta tapes, ribbons, as well as higher order fibrillar aggregates.     

Self-assembly of amylin(20-29) amide-bond derivatives into helical ribbons and peptide nanotubes rather than fibrils

Uncontrolled aggregation of proteins or polypeptides can be detrimental for normal cellular processes in healthy organisms. Proteins or polypeptides that form these amyloid deposits differ in their primary sequence but share a common structural motif: the (anti)parallel beta sheet. A well-accepted approach for interfering with beta-sheet formation is the design of soluble beta-sheet peptides to disrupt the hydrogen-bonding network; this ultimately leads to the disassembly of the aggregates or fibrils. Here, we describe the synthesis, spectroscopic analysis, and aggregation behavior, imaged by electron microscopy, of several backbone-modified amylin(20-29) derivatives. It was found that these amylin derivatives were not able to form fibrils and to some extent were able to inhibit fibril growth of native amylin(20-29). However, two of the amylin peptides were able to form large supramolecular assemblies, like helical ribbons and peptide nanotubes, in which beta-sheet formation was clearly absent. This was quite unexpected since these peptides have been designed as soluble beta-sheet breakers for disrupting the characteristic hydrogen-bonding network of (anti)parallel beta sheets. The increased hydrophobicity and the presence of essential amino acid side chains in the newly designed amylin(20-29) derivatives were found to be the driving force for self-assembly into helical ribbons and peptide nanotubes. This example of controlled and desired peptide aggregation may be a strong impetus for research on bionanomaterials in which special shapes and assemblies are the focus of interest.     

Modeling of molecular packing and conformation in oligofluorenes

We describe the application of molecular modeling to study problems related to the packing and conformation of oligofluorene molecules in the solid state. First of all, we describe an improved force field for oligofluorenes. The model is based on the MM3 force field for the intramolecular degrees of freedom, but it relies on ab initio calculations for the torsion potential between two monomers and the electrostatic interactions. We also report ab initio calculations of the interaction potentials between fluorene and fluorenone units. The force field has been tested on the crystal structures of a fluorene monomer, a dimer, and a pentamer containing a fluorenone at the center. It has then been employed to study conformational defects of the chains, both in vacuo and in the bulk. We find that certain modes of inversion from right-handed to left-handed helices are also possible within the constraining environment of the crystals. The effect of the presence of two different types of side chains has been also addressed. Finally, the possibility of having two fluorene units parallel and close to each other has been investigated as a model of a ground-state precursor of an excimer. Our simulations show that this configuration is sterically and energetically unfavorable so that formation of an excimer following optical excitation appears to be unlikely.     

Following the aggregation of amyloid-forming peptides by computer simulations

There is experimental evidence suggesting that the toxicity of neurodegenerative diseases such as Alzheimer's disease may result from the soluble intermediate oligomers. It is therefore important to characterize extensively the early steps of oligomer formation at atomic level. As these structures are metastable and short lived, experimental data are difficult to obtain and they must be complemented with numerical simulations. In this work, we use the activation-relaxation technique coupled with a coarse-grained energy model to study in detail the mechanisms of aggregation of four lys-phe-phe-glu (KFFE) peptides. This is the shortest peptide known to form amyloid fibrils in vitro. Our simulations indicate that four KFFE peptides adopt a variety of oligomeric states (tetramers, trimers, and dimers) with various orientations of the chains in rapid equilibrium. This conformational distribution is consistent with all-atom molecular-dynamics simulations in explicit solvent and is sequence dependent; as seen experimentally, the lys-pro-gly-glu (KPGE) peptides adopt disordered structures in solution. Our unbiased simulations also indicate that the assembly process is much more complex than previously thought and point to intermediate structures which likely are kinetic traps for longer chains.     

Effect of Surface Roughness on Structure and Dynamics in Thin Films

We performed Monte Carlo simulations of free‐standing, amorphous polyethylene (PE) thin films at 509 K. The three films are constructed from 9, 36, or 144 independent parent PE chains, with 100 carbon atoms per chain. The two‐dimensional periodic cross‐sectional area of the simulation box is proportional to the number of independent parent chains, with the 144‐chain film having an area four times larger than the 36‐chain film. All three films have a similar bulk density and a comparable thickness between the two free surfaces. The 144‐chain film with the largest periodic surface area has a broader density profile due to the increased roughness of its surfaces. Snapshots of its surfaces along the trajectory indicate dynamic changes in the high and low regions of the rough surfaces. Diffusion of the chains parallel to the free surfaces is suppressed in the 144‐chain film, due to increased surface roughness. The tendency of bonds to orient parallel to the free surface is less pronounced in films with higher surface roughness.