Disassembly of amyloid fibrils by premicellar and micellar aggregates of a tetrameric cationic surfactant in aqueous solution

We report a finding that not only the micelles but also the premicellar aggregates of a star-like tetrameric quaternary ammonium surfactant PATC can disassemble and clear mature β-amyloid Aβ(1-40) fibrils in aqueous solution. Different from other surfactants, PATC self-assembles into network-like aggregates below its critical micelle concentration (CMC). The strong self-assembly ability of PATC even below its CMC enables PATC to disaggregate the Aβ(1-40) fibrils far below the charge neutralization point of the Aβ(1-40) with PATC. There may be two key features of the fibril disassembly induced by the surfactant. First, the positively charged surfactant molecules bind with the negatively charged Aβ(1-40) fibrils through electrostatic interaction. Second, the self-assembly of the surfactant molecules bound onto the Aβ(1-40) fibrils disaggregate the fibrils, and the surfactant molecules form mixed aggregates with the Aβ(1-40) molecules. The result reveals a structural approach of constructing efficient disassembly agents to mature β-amyloid fibrils.     

Exploring the binding mechanism of thioflavin-T to the β-amyloid peptide by blind docking method

Using blind dock method,we find that thioflavin-T(ThT) can bind to both monomers and fibrils of the full-length β-amyloid peptide(Aβ1-42) and has a higher binding affinity to the fibrils.It is shown that the hydrophobic interaction between the ligand(ThT) and substrate(Aβ1-42) are stronger than hydrogen bonds.Furthermore,ThT tends to be located near the C-terminus of Aβ monomer through hydrophobic and electrostatic interactions,while it tends to contact the residues Met35 and Gly27 of the fibril surface mainly through hydrophobic interaction.Finally,according to the docking results and ThT fluorescence assay,a kinetic equation is proposed to deduce the aggregation rate coefficient of Aβ1-42.     

Exploring the inter-molecular interactions in amyloid-β protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations

Aggregation of amyloid-β (Aβ) peptides correlates with the pathology of Alzheimer's disease. However, the inter-molecular interactions between Aβ protofibril remain elusive. Herein, molecular mechanics Poisson-Boltzmann surface area analysis based on all-atom molecular dynamics simulations was performed to study the inter-molecular interactions in Aβ(17-42) protofibril. It is found that the nonpolar interactions are the important forces to stabilize the Aβ(17-42) protofibril, while electrostatic interactions play a minor role. Through free energy decomposition, 18 residues of the Aβ(17-42) are identified to provide interaction energy lower than -2.5 kcal/mol. The nonpolar interactions are mainly provided by the main chain of the peptide and the side chains of nine hydrophobic residues (Leu17, Phe19, Phe20, Leu32, Leu34, Met35, Val36, Val40, and Ile41). However, the electrostatic interactions are mainly supplied by the main chains of six hydrophobic residues (Phe19, Phe20, Val24, Met35, Val36, and Val40) and the side chains of the charged residues (Glu22, Asp23, and Lys28). In the electrostatic interactions, the overwhelming majority of hydrogen bonds involve the main chains of Aβ as well as the guanidinium group of the charged side chain of Lys28. The work has thus elucidated the molecular mechanism of the inter-molecular interactions between Aβ monomers in Aβ(17-42) protofibril, and the findings are considered critical for exploring effective agents for the inhibition of Aβ aggregation.     

Abnormal Beckmann rearrangement in 23-hydroxyiminodiosgenin acetate

A new transformation of the spiroketal side chain of diosgenin is reported: treatment of 23-hydroxyiminodiosgenin acetate with phosphorous oxychloride in pyridine produced an abnormal Beckmann rearrangement directing to the cleavage of the spiroketal side chain and generating 23,24-bisnorchol-5-enic skeletons: (2′R)-3′-cyano-2′-methylpropyl 3β-acetoxy-16α-chloro-23,24-bisnorchol-5-en-22-oate as the main product, and small amounts of (2′R)-3′-cyano-2′-methylpropyl 3β-acetoxy-16β-hydroxy-23,24-bisnorchol-5-en-22-oate and vespertilin acetate.     

Role of water in mediating the assembly of Alzheimer amyloid-beta Abeta16-22 protofilaments

The role of water in promoting the formation of protofilaments (the basic building blocks of amyloid fibrils) is investigated using fully atomic molecular dynamics simulations. Our model protofilament consists of two parallel beta-sheets of Alzheimer Amyloid-beta 16-22 peptides (Ac-K(16)-L(17)-V(18)-F(19)-F(20)-A(21)-E(22)-NH2). Each sheet presents a distinct hydrophobic and hydrophilic face and together self-assemble to a stable protofilament with a core consisting of purely hydrophobic residues (L(17), F(19), A(21)), with the two charged residues (K(16), E(22)) pointing to the solvent. Our simulations reveal a subtle interplay between a water mediated assembly and one driven by favorable energetic interactions between specific residues forming the interior of the protofilament. A dewetting transition, in which water expulsion precedes hydrophobic collapse, is observed for some, but not all molecular dynamics trajectories. In the trajectories in which no dewetting is observed, water expulsion and hydrophobic collapse occur simultaneously, with protofilament assembly driven by direct interactions between the hydrophobic side chains of the peptides (particularly between F-F residues). For those same trajectories, a small increase in the temperature of the simulation (on the order of 20 K) or a modest reduction in the peptide-water van der Waals attraction (on the order of 10%) is sufficient to induce a dewetting transition, suggesting that the existence of a dewetting transition in simulation might be sensitive to the details of the force field parametrization.     

The unique Alzheimer's β-amyloid triangular fibril has a cavity along the fibril axis under physiological conditions

Elucidating the structure of Aβ(1-40) fibrils is of interest in Alzheimer's disease research because it is required for designing therapeutics that target Aβ(1-40) fibril formation at an early stage of the disease. M35 is a crucial residue because of its potential oxidation and its strong interactions across β-strands and across β-sheets in Aβ fibrils. Experimentally, data for the three-fold symmetry structure of the Aβ(9-40) fibril suggest formation of tight hydrophobic core through M35 interactions across the fibril axis and strong I31-V39 interactions between different cross-β units. Herein, on the basis of experimental data, we probe conformers with three-fold symmetry of the full-length Aβ(1-40). Our all-atom molecular dynamics simulations in explicit solvent of conformers based on the ssNMR data reproduced experimental observations of M35-M35 and I31-V39 distances. Our interpretation of the experimental data suggests that the observed ～5-7 ? M35-M35 distance in the fibril three-fold symmetry structure is likely to relate to M35 interactions along the fibril axis, rather than across the fibril axis, since our measured M35-M35 distances across the fibril axis are consistently above 15 ?. Consequently, we revealed that the unique Aβ(1-40) triangular structure has a large cavity along the fibril axis and that the N-termini can assist in the stabilization of the fibril by interacting with the U-turn domains or with the C-termini domains. Our findings, together with the recent cyroEM characterization of the hollow core in Aβ(1-42) fibrils, point to the relevance of a cavity in Aβ(1-40/1-42) oligomers which should be considered when targeting oligomer toxicity.     

Experimental evidence for the reorganization of beta-strands within aggregates of the Abeta(16-22) peptide

Amyloidogenic deposits that accumulate in brain tissue with the progression of Alzheimer's disease contain large amounts of the amyloid beta-peptide. A small fragment of this peptide, comprising residues 16-22 (Abeta(16-22)), forms beta-sheets in isolation, which then aggregate into amyloid fibrils. Here, using isotope edited infrared spectroscopy to probe the secondary structure of the peptide with residue level specificity, we are able to show conclusively that the beta-sheets formed are antiparallel and, following an anneal cycle or prolonged incubation, are in register with the central residue (Phe19) in alignment across all strands. The alignment of strands proceeds via a rapid interchange from one sheet to another. This realignment of the peptide strands into a more favorable registry may have important implications for therapeutics since previous work has shown that well aligned beta-sheets form more stable amyloid fibrils.     

Controlling the morphology of cross beta-sheet assemblies by rational design

Low molecular weight peptidomimetics with simple amphiphilic sequences can help to elucidate the structures of cross beta-sheet assemblies, such as amyloid fibrils. The peptidomimetics described herein comprise a dibenzofuran template, two peptide strands made up of alternating hydrophilic and hydrophobic residues, and carboxyl termini, each of which can be varied to probe the structural requirements for beta-sheet self-assembly processes. The dibenzofuran template positions the strands approximately 10 A apart, allowing corresponding hydrophobic side chains in the strands to pack into a collapsed U-shaped structure. This conformation is stabilized by hydrophobic interactions, not intramolecular hydrogen bonds. Intermolecular stacking of the collapsed peptidomimetics, enabled by intermolecular hydrogen bonding and hydrophobic interactions, affords 25-27 A wide protofilaments having a cross beta-sheet structure. Association of protofilaments, mediated by the dibenzofuran substructures and driven by the hydrophobic effect, affords 50-60 A wide filaments. These widths can be controlled by changing the length of the peptide strands. Further assembly of the filaments into fibrils or ribbons can be controlled by modification of the template, C-terminus, and buffer ion composition.     

Unraveling the mechanism of nanotube formation by chiral self-assembly of amphiphiles

The self-assembly of nanotubes from chiral amphiphiles and peptide mimics is still poorly understood. Here, we present the first complete path to nanotubes by chiral self-assembly studied with C(12)-β(12) (N-α-lauryl-lysyl-aminolauryl-lysyl-amide), a molecule designed to have unique hybrid architecture. Using the technique of direct-imaging cryo-transmission electron microscopy (cryo-TEM), we show the time-evolution from micelles of C(12)-β(12) to closed nanotubes, passing through several types of one-dimensional (1-D) intermediates such as elongated fibrils, twisted ribbons, and coiled helical ribbons. Scattering and diffraction techniques confirm that the fundamental unit is a monolayer lamella of C(12)-β(12), with the hydrophobic tails in the gel state and β-sheet arrangement. The lamellae are held together by a combination of hydrophobic interactions, and two sets of hydrogen-bonding networks, supporting C(12)-β(12) monomers assembly into fibrils and associating fibrils into ribbons. We further show that neither the "growing width" model nor the "closing pitch" model accurately describe the process of nanotube formation, and both ribbon width and pitch grow with maturation. Additionally, our data exclusively indicate that twisted ribbons are the precursors for coiled ribbons, and the latter structures give rise to nanotubes, and we show chirality is a key requirement for nanotube formation.     

Cold Denaturation of α‐Synuclein Amyloid Fibrils

Although amyloid fibrils are associated with numerous pathologies, their conformational stability remains largely unclear. Herein, we probe the thermal stability of various amyloid fibrils. α‐Synuclein fibrils cold‐denatured to monomers at 0–20 °C and heat‐denatured at 60–110 °C. Meanwhile, the fibrils of β2‐microglobulin, Alzheimer’s Aβ1‐40/Aβ1‐42 peptides, and insulin exhibited only heat denaturation, although they showed a decrease in stability at low temperature. A comparison of structural parameters with positive enthalpy and heat capacity changes which showed opposite signs to protein folding suggested that the burial of charged residues in fibril cores contributed to the cold denaturation of α‐synuclein fibrils. We propose that although cold‐denaturation is common to both native proteins and misfolded fibrillar states, the main‐chain dominated amyloid structures may explain amyloid‐specific cold denaturation arising from the unfavorable burial of charged side‐chains in fibril cores.     

Direct evidence for deprotonation of a lysine side chain buried in the hydrophobic core of a protein

We report direct evidence for deprotonation of a lysine side chain buried in the hydrophobic core of a protein, demonstrating heteronuclear 1H-15N NMR data on the Lys-66 side chain amine (Nzeta) group in the delta-PHS/V66K variant of staphylococcal nuclease. Previous crystallographic study has shown that the Lys-66 Nzeta group is completely buried in the hydrophobic core. On the basis of double and triple resonance experiments, we found that the 1Hzeta and 15Nzeta chemical shifts at pH 8.0 and 6 degrees C for the buried lysine are 0.81 and 23.3 ppm, respectively, which are too abnormal to correspond to the protonated (NH3+) state. Further investigations using a model system suggested that the abnormal 1H and 15N chemical shifts represent the deprotonated (NH2) state of the Lys-66 Nzeta group. More straightforward evidence for the deprotonation was obtained with 2D F1-1H-coupled 1H-15N heteronuclear correlation experiments. Observed 15N multiplets clearly indicated that the spin system for the Lys-66 Nzeta group is AX2 (NH2) rather than AX3 (NH3+). Interestingly, although the amine group is buried in the hydrophobic core, the hydrogen exchange between water and the Lys-66 Nzeta group was found to be relatively rapid (93 s(-1) at -1 degrees C), which suggests the presence of a dynamic process such as local unfolding or water penetration. The partial self-decoupling effect on 15Nzeta multiplets due to the rapid hydrogen exchange is also discussed.     

Microstructure of N,N′-bis(cetyldimethyl)-α,ω-propanediammonium dibromide micelle and its dynamics in solution studied by 1H NMR

The characteristics of N,N′-bis(cetyldimethyl)-α,ω-alkane (propane and butane) diammonium dibromide (16-3-16 and 16-4-16) aqueous solutions were studied by one- and two-dimensional ¹H nuclear magnetic resonance (NMR). The measurements of self-diffusion coefficient and inter-proton distance at 318 K suggest that 16-3-16 spherical micelles are formed in the dilute solution at a concentration of 0.26 mmol/l and the polar head groups of the surfactant are in a saw-toothed form staying at the surface of the micelle to overcome the strong electrostatic repulsion force. Relaxation measurements obviously show that the spacer chain is rigid in the surface layer of the hydrophobic micellar core, and the side alkyl chains of 16-3-16 are packed more tightly than those of 16-4-16 in the micellar core. The line-shape analysis of the methyl protons at the end of the side alkyl chain of 16-3-16 and 16-4-16 suggests that two possible momentary morphologies of their side alkyl chains are situated in the micelle, respectively.     

Amyloid–β peptides time-dependent structural modifications: AFM and voltammetric characterization

The human amyloid beta (Aβ) peptides, Aβ_1-40 and Aβ_1-42, structural modifications, from soluble monomers to fully formed fibrils through intermediate structures, were investigated, and the results were compared with those obtained for the inverse Aβ_40-1 and Aβ_42-1, mutant Aβ_1-40Phe¹⁰ and Aβ_1-40Nle³⁵, and rat Aβ_1-40Rat peptide sequences. The aggregation was followed at a slow rate, in chloride free media and room temperature, and revealed to be a sequence-structure process, dependent on the physicochemical properties of each Aβ peptide isoforms, and occurring at different rates and by different pathways. The fibrilization process was investigated by atomic force microscopy (AFM), via changes in the adsorption morphology from: (i) initially random coiled structures of ∼0.6 nm height, corresponding to the Aβ peptide monomers in random coil or in α-helix conformations, to (ii) aggregates and protofibrils of 1.5–6.0 nm height and (iii) two types of fibrils, corresponding to the Aβ peptide in a β-sheet configuration. The reactivity of the carbon electrode surface was considered. The hydrophobic surface induced rapid changes of the Aβ peptide conformations, and differences between the adsorbed fibrils, formed at the carbon surface (beaded, thin, <2.0 nm height) or in solution (long, smooth, thick, >2.0 nm height), were detected. Differential pulse voltammetry showed that, according to their primary structure, the Aβ peptides undergo oxidation in one or two steps, the first step corresponding to the tyrosine amino acids oxidation, and the second one to the histidine and methionine amino acids oxidation. The fibrilization process was electrochemically detected via the decrease of the Aβ peptide oxidation peak currents that occurred in a time dependent manner.     

Constraints on supramolecular structure in amyloid fibrils from two-dimensional solid-state NMR spectroscopy with uniform isotopic labeling

We show that strong constraints on supramolecular structure in amyloid fibrils can be obtained from solid-state nuclear magnetic resonance measurements on samples with uniformly 13C-labeled segments. The measurements exploit two-dimensional (2D) 13C-13C exchange spectroscopy in conjunction with high-speed magic angle spinning, with proton-mediated exchange of 13C nuclear spin magnetization as recently demonstrated by Baldus and co-workers (J. Am. Chem. Soc. 2002, 124, 9704-9705). Proton-mediated 2D exchange spectra of fibrils formed by residues 16-22 of the 40-residue Alzheimer's beta-amyloid peptide show strong nonsequential, intermolecular cross-peaks between alpha-carbons that dictate an antiparallel beta-sheet structure in which residue 16+k aligns with residue 22-k. The strong alpha/alpha cross-peaks are absent from conventional, direct 2D exchange spectra. Proton-mediated 2D exchange spectra of fibrils formed by residues 11-25 indicate an antiparallel beta-sheet structure with a pH-dependent intermolecular alignment. In contrast, proton-mediated 2D exchange spectra of fibrils formed by the full-length beta-amyloid peptide are consistent with a parallel beta-sheet structure. These data show that the supramolecular structure of amyloid fibrils is not determined by the amino acid sequence at the level of 7-residue or 15-residue segments. The proton-mediated 2D exchange spectra additionally demonstrate that the intermolecular alignment in the beta-sheets of these amyloid fibrils is highly ordered, with no detectable evidence for "misalignment" defects.     

Tunable phase‐separation behavior of thermoresponsive polyampholytes through molecular design

Here, we report that carboxylated poly‐l ‐lysine, a polyampholyte, shows lower critical solution temperature (LCST)‐type temperature‐responsive liquid–liquid phase separation and coacervate formation in aqueous solutions. The phase‐separation temperature of polyampholytes is strongly affected by the polymer concentration, balance between the carboxyl and amino groups, hydrophobicity of the side chain, and NaCl concentration in the solution. We concluded that the phase separation was caused by both electrostatic interactions between the carboxyl and amino groups and intermolecular hydrophobic interactions. The addition of NaCl weakened the electrostatic interactions, causing the two phases to remix. The introduction of the hydrophobic moiety decreased the phase‐separation temperature by making the molecular interactions stronger. Finally, temperature‐responsive hydrogels were prepared from the polyampholytes to explore their applicability as biomaterials and in drug delivery systems. The fine‐tuning of the phase‐separation temperature of poly‐l ‐lysine‐based polyampholytes through molecular design should open new avenues for their use in precisely controlled biomedical applications. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55, 876–884     

Self-assembly of multidomain peptides: balancing molecular frustration controls conformation and nanostructure

A series of nine, frustrated, multidomain peptides is described in which forces favoring self-assembly into a nanofiber versus those favoring disassembly could be easily modified. The peptides are organized into an ABA block motif in which the central B block is composed of alternating hydrophilic and hydrophobic amino acids (glutamine and leucine, respectively). This alternation allows the amino acid side chains to segregate on opposite sides of the peptide backbone when it is in a fully extended beta-sheet conformation. In water, packing between two such peptides stabilizes the extended conformation by satisfying the desire of the leucine side chains to exclude themselves from the aqueous environment. Once in this conformation intermolecular backbone hydrogen bonding can readily take place between additional peptides eventually growing into high aspect ratio fibers. B block assembly may continue infinitely or until monomeric peptides are depleted from solution which results in an insoluble precipitate. Block A consists of a variable number of positively charged lysine residues whose electrostatic repulsion at pH 7 works against the desire of the B block to assemble. Here we show that balancing the forces of block A against B allows the formation of controlled length, individually dispersed, and fully soluble nanofibers with a width of 6 +/- 1 nm and length of 120 +/- 30 nm. Analysis by infrared, circular dichroism, and vitreous ice cryo-transmission electron microscopy reveals that the relative sizes of blocks A and B dictate the peptide secondary structure which in turn controls the resulting nanostructure. The system described epitomizes the use of molecular frustration in the design of finite self-assembled structures. These materials, and ones based on their architecture, may find applications where nanostructured control over fiber architecture and chemical functionality is required.     

Formation of colloidal suspension of hydrophobic compounds with an amphiphilic self-assembling peptide

The amphiphilic self-assembling peptide EAK16-II was found to be able to stabilize hydrophobic compounds in aqueous solution. Micro/nanocrystals of a hydrophobic compound, pyrene, and a hydrophobic anticancer agent, ellipticine, were stabilized by EAK16-II to form colloidal suspensions in water. Initial evidence of the association between EAK16-II and hydrophobic compounds was the observation of a clouding phenomenon and a difference in fluorescence spectra of the solution. A further investigation on the interaction between EAK16-II and pyrene was carried out using fluorescence spectroscopy and scanning electron microscopy (SEM). It was found that the pyrene–peptide complex formation required mechanical stirring, and the freshly prepared peptide solution (containing peptide monomers and/or peptide protofibrils) was more effective at stabilizing pyrene than the mature fibrils in aged peptide solutions. The time duration over which the complex formed was about 22 h. The data on the complexation of pyrene and EAK16-II at various concentrations suggested that the maximum amount of stabilized pyrene was concentration dependent. SEM images showed that peptide concentration did not significantly affect the size of the complexes/suspensions but altered the structures of the peptide coating on the surface of the complex. Atomic force microscopy (AFM) was conducted to study the interaction of EAK16-II with a model hydrophobic surface, which provided some detailed information of how peptide adsorbed onto the hydrophobic compounds and stabilize them. This study shows the potential of self-assembling peptides for encapsulation of hydrophobic compounds.     

Molecular-level examination of Cu2+ binding structure for amyloid fibrils of 40-residue Alzheimer's β by solid-state NMR spectroscopy

Cu(2+) binding to Alzheimer's β (Aβ) peptides in amyloid fibrils has attracted broad attention, as it was shown that Cu ion concentration elevates in Alzheimer's senile plaque and such association of Aβ with Cu(2+) triggers the production of neurotoxic reactive oxygen species (ROS) such as H(2)O(2). However, detailed binding sites and binding structures of Cu(2+) to Aβ are still largely unknown for Aβ fibrils or other aggregates of Aβ. In this work, we examined molecular details of Cu(2+) binding to amyloid fibrils by detecting paramagnetic signal quenching in 1D and 2D high-resolution (13)C solid-state NMR (SSNMR) for full-length 40-residue Aβ(1-40). Selective quenching observed in (13)C SSNMR of Cu(2+)-bound Aβ(1-40) suggested that primary Cu(2+) binding sites in Aβ(1-40) fibrils include N(ε) in His-13 and His-14 and carboxyl groups in Val-40 as well as in Glu sidechains (Glu-3, Glu-11, and/or Glu-22). (13)C chemical shift analysis demonstrated no major structural changes upon Cu(2+) binding in the hydrophobic core regions (residues 18-25 and 30-36). Although the ROS production via oxidization of Met-35 in the presence of Cu(2+) has been long suspected, our SSNMR analysis of (13)C(ε)H(3)-S- in M35 showed little changes after Cu(2+) binding, excluding the possibility of Met-35 oxidization by Cu(2+) alone. Preliminary molecular dynamics (MD) simulations on Cu(2+)-Aβ complex in amyloid fibrils confirmed binding sites suggested by the SSNMR results and the stabilities of such bindings. The MD simulations also indicate the coexistence of a variety of Cu(2+)-binding modes unique in Aβ fibril, which are realized by both intra- and intermolecular contacts and highly concentrated coordination sites due to the in-register parallel β-sheet arrangements.     

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.     

Role of alkylated residues in the tetrapeptide self-assembly—A molecular dynamics study

Designing peptide sequences that self-assemble into well-defined nanostructures can open a new venue for the development of novel drug carriers and molecular contrast agents. Current approaches are often based on a linear block-design of amphiphilic peptides where a hydrophilic peptide chain is terminated by a hydrophobic tail. Here, a new template for a self-assembling tetrapeptide (YXKX, Y = tyrosine, X = alkylated tyrosine, K = lysine) is proposed with two distinct sides relative to the peptide's backbone: alkylated hydrophobic residues on one side and hydrophilic residues on the other side. Using all-atom molecular dynamics simulations, the self-assembly pathway of the tetrapeptide is analyzed for two different concentrations. At both concentrations, tetrapeptides self-assembled into a nanosphere structure. The alkylated tyrosines initialize the self-assembly process via a strong hydrophobic effect and to reduce exposure to the aqueous solvent, they formed a hydrophobic core. The hydrophilic residues occupied the surface of the self-assembled nanosphere. Ordered arrangement of tetrapeptides within the nanosphere with the backbone hydrogen bonding led to a beta sheet formation. Alkyl chain length constrained the size and shape of the nanosphere. This study provides foundation for further exploration of self-assembling structures that are based on peptides with hydrophobic and hydrophilic moieties located on the opposite sides of a peptide backbone.