β-Sheet to Helical-Sheet Evolution Induced by Topochemical Polymerization: Cross-α-Amyloid-like Packing in a Pseudoprotein with Gly-Phe-Gly Repeats

Protein-mimics are of great interest for their structure, stability, and properties. We are interested in the synthesis of protein-mimics containing triazole linkages as peptide-bond surrogate by topochemical azide-alkyne cycloaddition (TAAC) polymerization of azide- and alkyne-modified peptides. The rationally designed dipeptide N₃-CH₂CO-Phe-NHCH₂CCH ( 1 ) crystallized in a parallel β-sheet arrangement and are head-to-tail aligned in a direction perpendicular to the β-sheet-direction. Upon heating, crystals of 1 underwent single-crystal-to-single-crystal polymerization forming a triazole-linked pseudoprotein with Gly-Phe-Gly repeats. During TAAC polymerization, the pseudoprotein evolved as helical chains. These helical chains are laterally assembled by backbone hydrogen bonding in a direction perpendicular to the helical axis to form helical sheets. This interesting helical-sheet orientation in the crystal resembles the cross-α-amyloids, where α-helices are arranged laterally as sheets.     

Synthesis and Reversible Hydration of a Pseudoprotein,a Fully Organic Polymeric Desiccant by Multiple Single‐Crystal‐to‐Single‐Crystal Transformations

A diphenylalanine derivative, N3‐Phe‐Phe‐NHCH2CCH, was designed for topochemical azide–alkyne cycloaddition (TAAC) polymerization. This dipeptide adopted β‐sheet arrangement as designed, in its crystals, but the azide and alkyne were not fitly aligned for their topochemical reaction. However, the voids present around these groups allowed them to attain a reactive geometry upon heating and their consequent TAAC polymerization to a pseudoprotein in a single‐crystal‐to‐single‐crystal (SCSC) fashion. This motion led to the creation of channels in the product crystal and it absorbed water from the surroundings to fill these channels as H‐bonded water wire. The pseudoprotein undergo reversible hydration/dehydration in SCSC fashion many times under mild conditions: hydration at low relative humidity and dehydration at low temperature. Vapor sorption analyses suggest that this fully organic polymer might be useful as an energy‐efficient desiccant material for controlling indoor humidity.     

Synthesis and Reversible Hydration of a Pseudoprotein,a Fully Organic Polymeric Desiccant by Multiple Single‐Crystal‐to‐Single‐Crystal Transformations

A diphenylalanine derivative, N3‐Phe‐Phe‐NHCH2CCH, was designed for topochemical azide–alkyne cycloaddition (TAAC) polymerization. This dipeptide adopted β‐sheet arrangement as designed, in its crystals, but the azide and alkyne were not fitly aligned for their topochemical reaction. However, the voids present around these groups allowed them to attain a reactive geometry upon heating and their consequent TAAC polymerization to a pseudoprotein in a single‐crystal‐to‐single‐crystal (SCSC) fashion. This motion led to the creation of channels in the product crystal and it absorbed water from the surroundings to fill these channels as H‐bonded water wire. The pseudoprotein undergo reversible hydration/dehydration in SCSC fashion many times under mild conditions: hydration at low relative humidity and dehydration at low temperature. Vapor sorption analyses suggest that this fully organic polymer might be useful as an energy‐efficient desiccant material for controlling indoor humidity.     

A Designed Three‐Stranded β‐Sheet in an α/β Hybrid Peptide

The incorporation of β‐amino acid residues into the antiparallel β‐strand segments of a multi‐stranded β‐sheet peptide is demonstrated for a 19‐residue peptide, Boc‐LV^βFV^DPGL^βFVVL^DPGLVL^βFVV‐OMe (BBH19). Two centrally positioned ^DPro–Gly segments facilitate formation of a stable three‐stranded β‐sheet, in which β‐phenylalanine (^βPhe) residues occur at facing positions 3, 8 and 17. Structure determination in methanol solution is accomplished by using NMR‐derived restraints obtained from NOEs, temperature dependence of amide NH chemical shifts, rates of H/D exchange of amide protons and vicinal coupling constants. The data are consistent with a conformationally well‐defined three‐stranded β‐sheet structure in solution. Cross‐strand interactions between ^βPhe3/^βPhe17 and ^βPhe3/Val15 residues define orientations of these side‐chains. The observation of close contact distances between the side‐chains on the N‐ and C‐terminal strands of the three‐stranded β‐sheet provides strong support for the designed structure. Evidence is presented for multiple side‐chain conformations from an analysis of NOE data. An unusual observation of the disappearance of the Gly NH resonances upon prolonged storage in methanol is rationalised on the basis of a slow aggregation step, resulting in stacking of three‐stranded β‐sheet structures, which in turn influences the conformational interconversion between type I′ and type II′ β‐turns at the two ^DPro–Gly segments. Experimental evidence for these processes is presented. The decapeptide fragment Boc‐LV^βFV^DPGL^βFVV‐OMe (BBH10), which has been previously characterized as a type I′ β‐turn nucleated hairpin, is shown to favour a type II′ β‐turn conformation in solution, supporting the occurrence of conformational interconversion at the turn segments in these hairpin and sheet structures.     

Crystal‐to‐Crystal Synthesis of Helically Ordered Polymers of Trehalose by Topochemical Polymerization

The synthesis of crystalline helical polymers of trehalose via topochemical azide–alkyne cycloaddition (TAAC) of a trehalose‐based monomer is presented. An unsymmetrical trehalose derivative having azide and alkyne crystallizes in two different forms having almost similar packing. Upon heating, both the crystals undergo TAAC reaction to form crystalline polymers. Powder X‐ray diffraction (PXRD) studies revealed that the monomers in both the crystals polymerize in a crystal‐to‐crystal fashion; circular dichroism (CD) studies of the product crystals revealed that the formed polymer is helically ordered. This solvent‐free, catalyst‐free polymerization method that eliminates the tedious purification of the polymeric product exemplifies the advantage of topochemical polymerization reaction over traditional solution‐phase polymerization.     

Designed Synthesis of a 1D Polymer in Twist‐Stacked Topology via Single‐Crystal‐to‐Single‐Crystal Polymerization

To synthesize a fully organic 1D polymer in a novel twist‐stacked topology, we designed a peptide monomer HC≡CCH₂‐NH‐Ile‐Leu‐N₃, which crystallizes with its molecules H‐bonded along a six‐fold screw axis. These H‐bonded columns pack parallelly such that molecules arrange head‐to‐tail, forming linear non‐covalent chains in planes perpendicular to the screw axis. The chains arrange parallelly to form molecular layers which twist‐stack along the screw axis. Crystals of this monomer, on heating, undergo single‐crystal‐to‐single‐crystal (SCSC) topochemical azide–alkyne cycloaddition (TAAC) polymerization to yield an exclusively 1,4‐triazole‐linked polymer in a twist‐stacked layered topology. This topologically defined polymer shows better mechanical strength and thermal stability than its unordered form, as evidenced by nanoindentation studies and thermogravimetric analysis, respectively. This work illustrates the scope of topochemical polymerizations for synthesizing polymers in pre‐decided topologies.     

Spontaneous Single‐Crystal‐to‐Single‐Crystal Evolution of Two Cross‐Laminated Polymers

Two cases of spontaneous evolution of monomers to linear polymers having novel cross‐laminated topology are reported. We synthesized two peptide monomers N₃‐Gly‐Gly‐NH‐CH₂‐CCH and N₃‐Gly‐Gly‐Gly‐CH₂‐CCH and solved their crystal structures by single‐crystal X‐ray diffraction. They adopt H‐bonded crisscrossed layered packing in their crystals such that: (a) the monomers are aligned head‐to‐tail in 1D‐chain‐like arrays and parallel arrangement of such arrays forms a layer; (b) the proximally placed azide and alkyne motifs are in an orientation apt for their regiospecific cycloaddition; (c) each monomer having x peptide bonds is H‐bonded with 2x monomers disposed in intersecting arrangement, which pre‐organize 1D‐chain‐like arrays in adjacent layers in perpendicular orientation. These crystals underwent spontaneous single‐crystal‐to‐single‐crystal (SCSC) polymerization via azide–alkyne cycloaddition reaction to form triazolyl‐polyglycines, at room temperature. The crisscrossed arrangement of monomers in adjacent layers ensured the formation of cross‐laminated polymers.     

A pH Switch for β‐Sheet Protein Folding

Protein design advancements have led to biotechnological strategies based on more stable and more specific structures. Herein we present a 6‐residue sequence (HPATGK) that acts as a stable structure‐nucleating turn at physiological and higher pH but is notably unfavorable for chain direction reversal at low pH. When placed into the turn of a β‐sheet, this leads to a pH switch of folding. Using a standard 3‐stranded β‐sheet model, the WW domain, it was found that the pH switch sequence insertion caused minimal change at pH 8 but a ca. 50 °C drop in the melting temperature (T_m) was observed at pH 2.5: ΔΔG_F ≥11.3 kJ mol⁻¹. Using the strategies demonstrated in this article, the redesign of β‐sheets to contain a global, or local, pH‐dependent conformational switch should be possible.     

Diphenylacetylene‐Linked Peptide Strands Induce Bidirectional β‐Sheet Formation

In the search for synthetic mimics of protein secondary structures relevant to the mediation of protein–protein interactions, we have synthesized a series of tetrasubstituted diphenylacetylenes that display β‐sheet structures in two directions. Extensive X‐ray crystallographic and NMR solution phase studies are consistent with these proteomimetics adopting sheet structures, displaying both hydrophobic and hydrophilic amino acid side chains.     

[Leu2]Gramicidin S preserves the structural properties of its parent peptide and forms helically aligned β‐sheets

For crystallographic analysis, Leu was substituted for Orn in Gramicidin S (LGS) to suppress interactions with hydrophilic solvent molecules, which increased the flexibility of the Orn side chains, leading to disorder within the crystals. The asymmetric unit (C₆₂H₉₄N₁₀O₁₀·1.296C₃H₈O·1.403H₂O) contains three LGS molecules (A, B and C) forming β‐turn and intramolecular β‐sheet structures. With the exception of one motif in molecule C, d ‐Phe‐Pro turn motifs (Phe is phenylalanine and Pro is proline) were classed as type II′ β‐turns. The peptide backbones twist slightly to the right along the long axis of the molecule. The puckering of Pro is in a Cγ‐endo or twisted Cγ‐endo–Cβ‐exo form. Flanking molecules are arranged such that the angles (A…B = 104°, B…C = 139° and C…A = 117°) form helical β‐sheets. Solvent molecules interact with the peptide backbones supporting the β‐sheets. The forms of the replacement Leu side chains are consistent with the e‐form of the Orn side chain in GS analogues. No hydrophilic region composed of solvent molecules, such as that observed in Gramicidin S hydrochloride (GS·HCl) crystals, was found. The perturbation of αH chemical shifts and coupling constants of CONH showed that the structural properties of GS·HCl and LGS are similar to each other in solution. CD spectra also supported the structural similarity. With the sequence cyclo(–Val–Leu–Leu–d ‐Phe–Pro–)₂ (Val is valine and Leu is leucine), LGS lacks the amphiphilicity and antimicrobial activity of parental Gramicidin S (GS). However, the structure of LGS reflects the structural characteristics of GS and no disordering inconvenient for structural analysis was found. Thus, LGS could be a novel scaffold useful for studying β‐turn and sheet structures.     

Quantum mechanical studies on model α‐pleated sheets

Pauling and Corey proposed a pleated‐sheet configuration, now called α‐sheet, as one of the protein secondary structures in addition to α‐helix and β‐sheet. Recently, it has been suggested that α‐sheet is a common feature of amyloidogenic intermediates. We have investigated the stability of antiparallel β‐sheet and two conformations of α‐sheet in solution phase using the density functional theoretical method. The peptides are modeled as two‐strand acetyl‐(Ala)₂‐N‐methylamine. Using stages of geometry optimization and single point energy calculation at B3LYP/cc‐pVTZ//B3LYP/6‐31G* level and including zero‐point energies, thermal, and entropic contribution, we have found that β‐sheet is the most stable conformation, while the α‐sheet proposed by Pauling and Corey has 13.6 kcal/mol higher free energy than the β‐sheet. The α‐sheet that resembles the structure observed in molecular dynamics simulations of amyloidogenic proteins at low pH becomes distorted after stages of geometry optimization in solution. Whether the α‐sheets with longer chains would be increasingly favorable in water relative to the increase in internal energy of the chain needs further investigation. Different from the quantum mechanics results, AMBER parm94 force field gives small difference in solution phase energy between α‐sheet and β‐sheet. The predicted amide I IR spectra of α‐sheet shows the main band at higher frequency than β‐sheet. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Polymerization and characterization of self‐assembled β‐cyclodextrin‐threaded chiral monomers

A helical inclusion complex polymer was fabricated through the polymerization of β‐cyclodextrin‐threaded chiral monomers. The photo induced polymerization of inclusion complex clusters caused shrinkage of the polymer and decreased the pitches, leading to the disappearance of spring‐like construction under TEM. From the results of circular dichroism of the inclusion complex polymer, the helical construction was confirmed, and an entanglement of the polymer chains is proposed. After removal of the β‐cyclodextrins from the pendant groups of the inclusion complex polymer, the helical structure was found to be maintained. The highly ordered molecular arrangement of β‐cyclodextrins removed from the inclusion complex polymer was confirmed using POM. Here we demonstrate the fabrication of helical polymer fibers composed of entangled polymers through self‐assembled β‐cyclodextrin‐threaded chiral monomers. The helical polymer construction was maintained by the entwisted polymer chains even after the removal of β‐cyclodextrins from the pendant groups of the inclusion complex polymer. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 2975–2981, 2010     

Impact of Strand Number on Parallel β‐Sheet Stability

We have examined whether parallel β‐sheet secondary structure becomes more stable as the number of β‐strands increases, via comparisons among peptides designed to adopt two‐ or three‐stranded parallel β‐sheet conformations in aqueous solution. Our three‐strand design is the first experimental model of a triple‐stranded parallel β‐sheet. Analysis of the designed peptides by nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy supports the hypothesis that increasing the number of β‐strands, from two to three, increases the stability of the parallel β‐sheet. We present the first experimental evidence for cooperativity in the folding of a triple‐stranded parallel β‐sheet, and we show how minimal model systems may enable experimental documentation of characteristic properties, such as CD spectra, of parallel β‐sheets.     

A Molecular Dynamics Study on Controlling the Self‐Assembly of β‐Sheet Peptides with Designer Nanorings

Recently, a rational approach for constructing β‐barrel protein mimics by the self‐assembly of peptide‐based building blocks has been demonstrated. We performed molecular dynamics simulations of nanoring formation by means of the self‐assembly of designed β‐sheet‐forming peptides. Several factors contributing to the stability of the nanoring structures with respect to size were investigated. Our simulations predicted that an optimal nanoring size may be achieved by minimizing repulsions due to steric hindrance between bulky groups while maintaining favorable hydrogen‐bond interactions between neighboring β‐sheet chains. It was shown that mutations in a test peptide, in which all or half of the tryptophan residues were replaced by phenylalanine, could enable the assembly of stable nanoring structures with smaller pore sizes. Insights into the fundamental factors driving the formation of peptide‐based nanostructures are expected to facilitate the design of novel functional bionanostructures.     

β‐Hairpins Generated from Hybrid Peptide Sequences Containing both α‐ and β‐Amino Acids

The incorporation of the β‐amino acid residues into specific positions in the strands and β‐turn segments of peptide hairpins is being systematically explored. The presence of an additional torsion variable about the C(α) C(β) bond (θ) enhances the conformational repertoire in β‐residues. The conformational analysis of three designed peptide hairpins composed of α/β‐hybrid segments is described: Boc‐Leu‐Val‐Val‐^DPro‐β Phe ‐Leu‐Val‐Val‐OMe ( 1 ), Boc‐Leu‐Val‐β Val ‐^DPro‐Gly‐β Leu ‐Val‐Val‐OMe ( 2 ), and Boc‐Leu‐Val‐β Phe ‐Val‐^DPro‐Gly‐Leu‐β Phe ‐Val‐Val‐OMe ( 3 ). 500‐MHz ¹H‐NMR Analysis supports a preponderance of β‐hairpin conformation in solution for all three peptides, with critical cross‐strand NOEs providing evidence for the proposed structures. The crystal structure of peptide 2 reveals a β‐hairpin conformation with two β‐residues occupying facing, non‐H‐bonded positions in antiparallel β‐strands. Notably, βVal(3) adopts a gauche conformation about the C(α) C(β) bond (θ=+65°) without disturbing cross‐strand H‐bonding. The crystal structure of 2 , together with previously published crystal structures of peptides 3 and Boc‐β Phe ‐β Phe ‐^DPro‐Gly‐β Phe ‐β Phe ‐OMe, provide an opportunity to visualize the packing of peptide sheets with local ‘polar segments' formed as a consequence of reversal peptide‐bond orientation. The available structural evidence for hairpins suggests that β‐residues can be accommodated into nucleating turn segments and into both the H‐bonding and non‐H‐bonding positions on the strands.     

2,3,4,6‐Tetra‐O‐acetyl‐α‐d‐glucopyranosyl azide

The Cu^I‐catalysed 1,3‐dipolar cycloaddition of an azide and a terminal alkyne is becoming an increasingly popular tool for synthetic chemists. This is the most representative of the so‐called `click reactions' and it is used to generate 1,4‐disubstituted triazoles in high yield. During studies on such cycloaddition reactions, a reduced reactivity of an α‐glucosyl azide with respect to the corresponding β‐anomer was observed. With the aim of understanding this phenomenon, the structure of the title compound, C₁₄H₁₉N₃O₉, has been determined at 140 K. The glucopyranosyl ring appears in a regular ⁴C₁ chair conformation with all the substituents in equatorial positions, except for the anomeric azide group, which adopts an axial orientation. The observed bond lengths are consistent with a strong anomeric effect, which is reflected in a change in dipolar character and hence reduced reactivity of the α‐glucosyl azide.     

Synthesis,Characterization, and thermoresponsive properties of Helical Polypeptides Derivatized from Poly(γ−4‐(3‐chloropropoxycarbonyl)benzyl‐L‐glutamate)

A series of side‐chain‐functionalized α‐helical polypeptides, i.e., poly(γ‐4‐(3‐chloropropoxycarbonyl)benzyl‐_L‐glutamate) (6) have been prepared from n‐butylamine initiated ring‐opening polymerization (ROP) of γ‐4‐(3‐chloropropoxycarbonyl)benzyl‐_L‐glutamic acid‐based N‐carboxyanhydride. Polypeptides bearing oligo‐ethylene‐glycol (OEG) groups or 1‐butylimidazolium salts were prepared from 6 via copper‐mediated [2+3] alkyne‐azide 1,3‐dipolar cycloaddition or nuleophilic substitution, respectively. CD and FTIR analysis revealed that the polymers adopt α‐helical conformations both in solution and the solid state. Polymers bearing OEG (m = 3) side‐chains showed reversible LCST‐type phase transition behaviors in water while polymers bearing 1‐butylimidazolium and I^? counter‐anions exhibited reversible UCST‐type transitions in water. Variable‐temperature UV‐vis analysis revealed that the phase transition temperatures (T_pts) were dependent on the main‐chain length and polymeric concentration. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53, 2469–2480     

Halbsandwich‐Komplexe von Ruthenium(II), Rhodium(III) und Iridium(III) mit Tripeptidestern aus α‐, β‐ und γ‐Aminosäuren als Liganden. — Peptidsynthese und Cyclisierung zu Cyclotripeptiden am Metallzentrum

Metal Complexes with Biological Important Ligands. CXLII. Half Sandwich Complexes of Ruthenium(II), Rhodium(III), and Iridium(III) with Tripeptide Esters from α‐, β‐, and γ‐Amino Acids as Ligands. — Peptide Synthesis and Cyclization to Cyclotripeptides at Metal Centers Halfsandwich complexes of ruthenium, rhodium and iridium with deprotonated N, N', N"‐tripeptide ester ligands were obtained from chloro bridged compounds and tripeptide methyl esters ( 1—6 ) or by peptide synthesis at a metal centre ( 9—15 ). For the peptide synthesis at the complex (C₆Me₆)Ru coordinated dipeptide methyl esters from glycine and β‐alanine or γ‐amino butyric acid were elongated by an a‐amino acid methylester. The tripeptide ester Ru(η⁶‐C₆Me₆) complexes with chiral amino acid components and an “asymmetric” metal atom are formed with high diastereoselectivity. The tripeptide esters Gly‐Gly‐β‐AlaOMe, Val‐Gly‐β‐AlaOMe and Phe‐Gly‐β‐AlaOMe can be condensated at the (C₆Me₆)Ru complex with sodium methanolate to give triple deprotonated cyclic tripeptides.     

pH‐Controlled Formation of a Stable β‐Sheet and Amyloid‐like Fibers from an Amphiphilic Peptide: The Importance of a Tailor‐Made Binding Motif for Secondary Structure Formation

The new amphiphilic peptide 1 is composed of alternating cyclohexyl side chains and guanidiniocarbonyl pyrrole (GCP) groups. In contrast to analogue 2 , which contains lysine instead of the GCP groups and only exists as a random coil owing to charge repulsion, peptide 1 forms a stable β‐sheet at neutral pH in aqueous medium. The weakly basic GCP groups (pK_a≈7) are key for secondary structure formation as they stabilize the β‐sheet through mutual interactions (formation of a “GCP zipper”). The β‐sheets further aggregate into left‐handed helically twisted fibers. However, β‐sheet formation is completely reversible as a function of pH. At low pH (ca. 4), peptide 1 is unstructured (random coil) as all GCP units are protonated. Only round colloidal particles are observed. The amyloid nature of the fibers formed at neutral pH was confirmed by staining experiments with Congo Red and thioflavin T. Furthermore, at millimolar concentrations, peptide 1 forms a stable hydrogel.     

Solid state self‐assembly of the single‐walled carbon nanotubes and poly(γ‐benzyl‐l‐glutamate)s with different conformations

A series of pyrenyl‐terminated poly(γ‐benzyl‐l ‐glutamate)s (py‐PBLGs) with controlled polymer molecular weight (M_W = 2.3–14.8 kg mol^?1) and molecular weight distribution (PDI = 1.17–1.55) have been prepared from 1‐pyrenemethylamine hydrochloride‐mediated ring‐opening polymerization (ROP) of γ‐benzyl‐l ‐glutamic acid based N‐carboxyanhydride (BLG‐NCA). FTIR analysis revealed that the py‐PBLG₉ was conformationally heterogeneous with 35.0% α‐helix, 55.6% β‐sheet, and 9.4% random coil conformations in the solid state, whereas the py‐PBLG₆₆ adopts 100% α‐helix conformation. Py‐PBLGs promote the dispersion of SWCNTs in organic solvents and in the PBLG solid through π–π interaction, as evidenced by the Raman spectroscopic studies. WAXD analysis revealed that the SWCNTs significantly affect the ordering of the py‐PBLG self‐assembly: the long range hexagonal packing of py‐PBLG₆₆ rods is notably enhanced by the addition of SWCNTs, whereas the lamellar packing of py‐PGLG₉ β‐sheets is weakened. In the hexagonal lattice, the SWCNTs are intercalated parallel to the py‐PBLG₆₆ rods, in contrast to the normal orientation of the SWCNTs with respect to the extended py‐PBLG₉ chains in the β‐sheets. The relative packing structure also affects the intermolecular interaction among the PBLGs: SWCNTs promote the interaction among the py‐PBLG₉ chains packed in a lamellar structure and weaken the intermolecular interaction among the py‐PBLG₆₆ columnar hexagonal array. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013 , 51, 4489–4497