Laminated morphology of nontwisting beta-sheet fibrils constructed via peptide self-assembly

A synthetic peptide has been de novo designed that self-assembles into beta-sheet fibrils exhibiting a nontwisted, stacked morphology. The stacked morphology is constituted by 2.5 nm wide filaments that laterally associate to form flat fibril laminates exceeding 50 nm in width and micrometers in length. The height of each fibril is limited to the length of exactly one peptide monomer in an extended beta-strand conformation, approximately 7 nm. Once assembled, these highly ordered, 2-D structures are stable over a wide range of pH and temperature and exhibit characteristics similar to those of amyloid fibrils. Furthermore, the rate of assembly and degree of fibril lamination can be controlled with kinetic parameters of pH and temperature. Finally, the presence of a diproline peptide between two beta-sheet-forming strands in the peptide sequence is demonstrated to be an important factor in promoting the nontwisting, laminated fibril morphology.     

An artificial beta-sheet that dimerizes through parallel beta-sheet interactions

This Article introduces a simple chemical model of a beta-sheet (artificial beta-sheet) that dimerizes by parallel beta-sheet formation in chloroform solution. The artificial beta-sheet consists of two N-terminally linked peptide strands that are linked with succinic or fumaric acid and blocked along one edge with a hydrogen-bonding template composed of 5-aminoanisic acid hydrazide. The template is connected to one of the peptide strands by a turn unit composed of (S)-2-aminoadipic acid (Aaa). 1H NMR spectroscopic studies show that these artificial beta-sheets fold in CDCl3 solution to form well-defined beta-sheet structures that dimerize through parallel beta-sheet interactions. Most notably, all of these compounds show a rich network of NOEs associated with folding and dimerization. The compounds also exhibit chemical shifts and coupling constants consistent with the formation of folded dimeric beta-sheet structures. The aminoadipic acid unit shows patterns of NOEs and coupling constants consistent with a well-defined turn conformation. The present system represents a significant step toward modeling the type of parallel beta-sheet interactions that occur in protein aggregation.     

A triply templated artificial beta-sheet.

This paper describes the design, synthesis, and structural evaluation of a compound (4) comprising three molecular templates and a peptide strand that mimics a three-stranded protein beta-sheet. Two of the templates mimic the hydrogen-bonding functionality of peptide beta-strands and serve as the top and bottom strands by embracing the peptide strand, which is located in the middle of the sheet. The remaining template holds the three strands next to each other. The synthesis of artificial beta-sheet 4 begins with the bottom template and involves the sequential addition of the middle and top strands. (1)H NMR chemical shift and NOE studies establish that this compound folds to adopt a hydrogen-bonded beta-sheetlike structure in CDCl(3) solution. Chemical shift studies indicate that triply stranded artificial beta-sheet 4 is more tightly folded than its smaller doubly stranded homologue, artificial beta-sheet 1.     

A noncovalent approach to antiparallel beta-sheet formation

Four tripeptide chains, when attached to the same end of a hydrogen-bonded duplex (1.2) with the unsymmetrical, complementary sequences of ADAA/DADD, have been brought into proximity, leading to the formation of four hybrid duplexes, 1a.2a, 1a.2b, 1b.2a, and 1b.2b, each of which contains a two-stranded beta-sheet segment. The extended conformations of the peptide chains were confirmed by 1D and 2D NMR. The peptide strands stay registered through hydrogen bonding and the beta-sheets are stabilized by side chain interactions. Two-dimensional NMR data also indicate that the duplex template prevents further aggregation in the peptide segment. When the peptide chains are attached to the two different termini of the duplex template, NMR studies show the presence of a mixture with no clearly defined conformations. In the absence of the duplex template, the tripeptides are found to associate randomly. Finally, isothermal titration calorimetry studies revealed that the hybrid duplex 1a.2a was more stable than either the duplex template or the peptides alone.     

Templated growth of hybrid structures at the peptide-peptide interface

This study describes the use of peptide vesicular platforms for the templated growth of fibrillar structures to craft hybrids that retain the gross morphological features of two discreet self-assembled peptides. A synthetic triskelion peptide, which results in the rapid emergence of self-assembled spherical structures, was employed as a template. Addition of either one of two different peptides, both of which form long filamentous structures when co-incubated with the triskelion solution, affords hybrids that retain the gross morphology of both the spherical and filamentous structures. It is surmised that this process is aided by hydrogen bonding and the interdigitation of aromatic residues, which leads to the growth of hybrid structures. We believe that observations concerning the surface-assisted growth of peptide fibrils and tubular structures from vesicular platforms may have ramifications for the design and development of peptide-based hybrid materials with controlled hierarchical structures.     

Structural insights into the polymorphism of amyloid-like fibrils formed by region 20-29 of amylin revealed by solid-state NMR and X-ray fiber diffraction

Many unrelated proteins and peptides can assemble into amyloid or amyloid-like nanostructures, all of which share the cross-beta motif of repeat arrays of beta-strands hydrogen-bonded along the fibril axis. Yet, paradoxically, structurally polymorphic fibrils may derive from the same initial polypeptide sequence. Here, solid-state nuclear magnetic resonance (SSNMR) analysis of amyloid-like fibrils of the peptide hIAPP 20-29, corresponding to the region S (20)NNFGAILSS (29) of the human islet amyloid polypeptide amylin, reveals that the peptide assembles into two amyloid-like forms, (1) and (2), which have distinct structures at the molecular level. Rotational resonance SSNMR measurements of (13)C dipolar couplings between backbone F23 and I26 of hIAPP 20-29 fibrils are consistent with form (1) having parallel beta-strands and form (2) having antiparallel strands within the beta-sheet layers of the protofilament units. Seeding hIAPP 20-29 with structurally homogeneous fibrils from a 30-residue amylin fragment (hIAPP 8-37) produces morphologically homogeneous fibrils with similar NMR properties to form (1). A model for the architecture of the seeded fibrils is presented, based on the analysis of X-ray fiber diffraction data, combined with an extensive range of SSNMR constraints including chemical shifts, torsional angles, and interatomic distances. The model features a cross-beta spine comprising two beta-sheets with an interface defined by residues F23, A25, and L27, which form a hydrophobic zipper. We suggest that the energies of formation for fibril form containing antiparallel and parallel beta-strands are similar when both configurations can be stabilized by a core of hydrophobic contacts, which has implications for the relationship between amino acid sequence and amyloid polymorphism in general.     

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.     

The organization and assembly of a beta-sheet formed by a prion peptide in solution: an isotope-edited FTIR study

Insight into the details of protein misfolding diseases requires a detailed understanding of the conformation and dynamics of multistrand beta-sheet aggregates. Here, we report an isotope-edited FTIR study of a model peptide directed at the elucidation of residue-level details of the structure and mechanism of a beta-sheet aggregate. A series of specifically isotope-labeled derivatives of a short peptide (H1) derived from residues 109 through 122 of the prion protein PrPC have been synthesized and characterized by FTIR. On the basis of the analysis of variable temperature FTIR spectra of these peptides in solution, the organization of strands within the beta-sheets has been determined; at equilibrium, the strands form a beta-sheet in which the hydrophobic core (112-122) participates in the sheet structure, resulting in the alignment of residue 117 in all of the strands. The peptides initially form a kinetically trapped intermediate beta-sheet, with a distribution of strand alignments, which can be rearranged into the stable equilibrium conformation by an annealing cycle. These observations are discussed in terms of the biological significance of residue 117 of the prion protein and the mechanism of beta-aggregate nucleation in prion proteins.     

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.     

Stabilization of peptide fibrils by hydrophobic interaction

Hydrophobic interactions play an important role in assembly processes in aqueous environments. In case of peptide amphiphiles, hydrophobicity is combined with hydrogen bonding to yield well-defined peptide-based aggregates. Here, we report a systematic study after the role of hydrophobic interactions on both stabilization and morphology of a peptide fibrillar assembly. For this purpose, alkyl tails were connected to a known beta-sheet forming peptide with the sequence KTVIIE. The introduction of n-alkyl groups induced thermal stability to the assemblies without affecting the morphology of the peptide aggregates.     

Micellization of surfactin and its effect on the aggregate conformation of amyloid beta(1-40)

The aggregation of amyloid beta-peptide (Abeta(1-40)) into fibrils is a key pathological process associated with Alzheimer's disease. This work has investigated the micellization process of biosurfactant surfactin and its effect on the aggregation behavior of Abeta(1-40). The results show that surfactin has strong self-assembly ability to form micelles and the micelles tend to form larger aggregates. Surfactin adopts a beta-turn conformation at low micelle concentration but a beta-sheet conformation at high micelle concentration. The effect of surfactin on the Abeta(1-40) aggregation behavior exhibits a strong concentration-dependent fashion. Below the critical micelle concentration of surfactin, the electrostatic binding of surfactin monomers on Abeta(1-40) causes Abeta(1-40) molecules to unfold. Assisted by the hydrophobic interaction among surfactin monomers on the Abeta(1-40) chain, the conformation of Abeta(1-40) transfers to the beta-sheet structure, which promotes the formation of fibrils. At low surfactin micelle concentration, besides the electrostatic force and hydrophobic interaction, hydrogen bonds formed between surfactin micelles and adjacent Abeta(1-40) peptide chains may promote the ordered organization of these Abeta(1-40) peptide chains, thus leading to the formation of beta-sheets and fibrils to a great extent. At high surfactin micelle concentration, the separating of Abeta(1-40) chains by the excessive surfactin micelles and the aggregation of the complexes of Abeta(1-40) with surfactin micelles inhibit the formation of beta-sheets and fibrils.     

Molecular Structure of Amyloid Fibrils Formed by Residues 127 to 147 of the Human Prion Protein

Amyloid fibrils are filamentous and insoluble forms of peptides or proteins. Proline has long been considered to be incompatible with the cross‐β structural motif of amyloid fibrils. On the basis of solid‐state NMR spectroscopy data, we present a structural model of an in‐register parallel β sheet for the amyloid fibrils formed from a human prion protein fragment, huPrP_127–47. We have developed a simple solid‐state NMR spectroscopy technique to identify solvent‐protected backbone amide protons in a H/D exchange experiment without disaggregating the amyloid fibrils, from which we find that proline residue P₁₃₇ does not disrupt the β‐sheet structure from G₁₂₇ to G₁₄₂. We suggest that the resultant kink at P₁₃₇ generates a twist between adjacent peptide strands to maintain hydrogen bonding in the β‐sheet regions flanking the P₁₃₇ residue. Although proline can be well integrated into the cross‐β structure of amyloid fibrils, the kink formed at the position of the proline residue will considerably weaken the hydrogen bonding between the neighboring strands, especially when the mutation site is near the central region of a β sheet.     

Tuning secondary structure and self-assembly of amphiphilic peptides

Self-assembly is one of nature's mechanisms by which higher order structures are obtained. Two of the main driving forces for self-assembly, hydrophobic interactions and hydrogen bonding, are both present within amphiphilic peptides. Here, it is demonstrated how the intricately interconnected folding and assembly behavior of an N-terminally acylated peptide, with the sequence GANPNAAG, has been tuned by varying its hydrophobic tail and thermal history. The change in interplay between hydrophobic forces and peptide folding allowed the occurrence of different types of aggregation, from soluble peptides with a random coil conformation to aggregated peptides arranged in a beta-sheet assembly, which form helically twisted bilayer ribbons.     

Studies on novel peptidomimetics having bi-directional dispositions of hydroxylated D-Pro-Gly motifs anchored on a C(2)-symmetric iminosugar-based foundation

A rigid pyrrolidine based scaffold comprising of 2,5-dideoxy-2,5-imino-D-idaric acid (1) is developed. Attachment of peptide strands to the carboxylic groups at both ends of this novel template led to the peptidomimetics 2 and 3. Conformational analysis by NMR studies revealed that compounds 2b, 3b and 2c, 3c take interesting turn structures (C(2) symmetric for 2c and 3c) in DMSO-d(6) consisting of identical intramolecular hydrogen bonds at two ends between LeuNH --> sugar-OH as depicted in structure A, whereas 2a and 3a display structures with regular beta-turns with hydrogen bonds between LeuNH --> Boc-C=O in one-half of their molecular frameworks (structure B), characteristic of the turn structures commonly observed in "D-Pro-Gly"-containing peptides. These results suggest that a cis hydroxyl group at the 3-position of the proline residue favors a pseudo beta-turn-like nine-membered ring structure in hydroxyproline-containing peptides involving an intramolecular hydrogen bond between the hydroxyl and the i + 2 backbone amide.     

Design and construction of an open multistranded beta-sheet polypeptide stabilized by a disulfide bridge

The design and characterization of an open eight-stranded beta-sheet in a synthetic, 2-fold symmetric 70-residue peptide is described. The design strategy involves the generation of a 35-residue four-stranded beta-sheet peptide in which successive hairpins are nucleated by appropriately positioned (D)Pro-Xxx sequences. Oxidative dimerization using a single Cys residue positioned at the center of the C-terminal strand results in a disulfide-bridged eight-stranded structure. Nuclear Overhauser effects firmly establish an eight-stranded beta-sheet in methanol. In water, the outer strands are frayed, but a well-defined four-stranded beta-sheet stabilized by a disulfide bridge and a hydrophobic cluster is determined from NMR data. Comparison of the precursor peptide with the disulfide-bridged dimer reveals considerable enhancement of beta-sheet content in the latter, suggesting that the disulfide cross-link is an effective strategy for the stabilization of beta-sheets.     

Aggregation of polyalanine in a hydrophobic environment

The dimerization of polyalanine peptides in a hydrophobic environment was explored using replica exchange molecular dynamics simulations. A nonpolar solvent (cyclohexane) was used to mimic, among other hydrophobic environments, the hydrophobic interior of a membrane in which the peptides are fully embedded. Our simulations reveal that while the polyalanine monomer preferentially adopts a beta-hairpin conformation, dimeric phases exist in an equilibrium between random coil, alpha-helical, beta-sheet, and beta-hairpin states. A thermodynamic characterization of the dimeric phases reveals that electric dipole-dipole interactions and optimal side-chain packing stabilize alpha-helical conformations, while hydrogen bond interactions favor beta-sheet conformations. Possible pathways leading to the formation of alpha-helical and beta-sheet dimers are discussed.     

Light-triggered disassembly of amyloid fibrils

There is growing demand for novel methods that could render the controlled disassembly of higher-order structures formed, for example, by peptides. Herein, we demonstrate such a method based on the application of a photocaged variant of the amino acid lysine, namely, lys(Nvoc). Specifically, we introduce lys(Nvoc) into the primary sequence of the amyloidogenic peptide, Aβ(16-22), at a position where the native side chain is known to play a key role in fibril formation via hydrophobic interactions. Both AFM and infrared spectroscopic measurements indicate that the resultant Aβ(16-22) mutant is able to form fibrils whereas, more importantly, the fibrils thus formed can be completely disassembled upon irradiation with near-UV light, which cleaves the photolabile Nvoc moiety and triggers the restoration of the lysine side chain. These results suggest that the generation of a single charge in a highly hydrophobic region of the fibrils is sufficient to promote their dissociation. Thus, we envisage that the current approach will find useful applications wherein controlled structural disassembly or content release is required.     

Structural regulation of a peptide-conjugated graft copolymer: a simple model for amyloid formation

The self-assembly of peptides and proteins into beta-sheet-rich high-order structures has attracted much attention as a result of the characteristic nanostructure of these assemblies and because of their association with neurodegenerative diseases. Here we report the structural and conformational properties of a peptide-conjugated graft copolymer, poly(gamma-methyl-L-glutamate) grafted polyallylamine (1) in a water-2,2,2-trifluoroethanol solution as a simple model for amyloid formation. Atomic force microscopy revealed that the globular peptide 1 self-assembles into nonbranching fibrils that are about 4 nm in height under certain conditions. These fibrils are rich in beta-sheets and, similar to authentic amyloid fibrils, bind the amyloidophilic dye Congo red. The secondary and quaternary structures of the peptide 1 can be controlled by manipulating the pH, solution composition, and salt concentration; this indicates that the three-dimensional packing arrangement of peptide chains is the key factor for such fibril formation. Furthermore, the addition of carboxylic acid-terminated poly(ethylene glycol), which interacts with both of amino groups of 1 and hydrophobic PMLG chains, was found to obviously inhibit the alpha-to-beta structural transition for non-assembled peptide 1 and to partially cause a beta-to-alpha structural transition against the 1-assembly in the beta-sheet form. These findings demonstrate that the amyloid fibril formation is not restricted to specific protein sequences but rather is a generic property of peptides. The ability to control the assembled structure of the peptide should provide useful information not only for understanding the amyloid fibril formation, but also for developing novel peptide-based material with well-defined nanostructures.     

pH-induced reversible conformational and morphological regulation of polyleucine grafted polyallylamine assembly in solution

One of the essential parts in the molecular mechanism of biological properties is the structural changes of proteins induced by stimuli. An amphiphilic copolymer, poly(L-leucine) grafted polyallylamine as a simple model of proteins, has been prepared by NCA polymerization with free amino groups of polyallylamine as an initiator. Here, we report the pH-induced reversible conformational and morphological regulation of the amphiphilic copolymer, whose hydrophobic peptide graft chains have no pH-sensitive groups, in an aqueous solution containing 50 vol % trifluoroethanol. The conformation of the poly(L-leucine) graft chain was found to be strongly pH dependent. Under acidic conditions, where electrostatic repulsion existed between the neighboring protonated amine moieties of the polyallylamine main chain, the rapid aggregation of the poly(l-leucine) graft chains was disturbed, and the peptide graft chains formed a beta-sheet structure owing to the intramolecular hydrogen bonding among the graft chains. Under this condition, the amphiphilic polymer formed amyloid-like fibrils, and then the fibrils grew into a planer plate composed of staked beta-sheets. On the other hand, under basic conditions, the poly(L-leucine) graft chains showed conformational transitions from a beta-sheet structure to an alpha-helical conformation owing to a distortion of the regular arrangement of the peptide graft chains by the conformational change of the polyallylamine main chain, whose amino groups were deprotonated. The conformational transition resulted in a disturbance of the regular sheet assembly of the amphiphilic copolymer and induced morphological changes to the amorphous globular aggregates. The pH-induced conformational and morphological changes of the poly(L-leucine) graft polyallylamine were reversible and synchronized with the protonation of the polyallylamine main chain.