N‐terminal diproline and charge group effects on the stabilization of helical conformation in alanine‐based short peptides: CD studies with water and methanol as solvent

Protein folding problem remains a formidable challenge as main chain, side chain and solvent interactions remain entangled and have been difficult to resolve. Alanine‐based short peptides are promising models to dissect protein folding initiation and propagation structurally as well as energetically. The effect of N‐terminal diproline and charged side chains is assessed on the stabilization of helical conformation in alanine‐based short peptides using circular dichroism (CD) with water and methanol as solvent. A1 (Ac–Pro–Pro–Ala–Lys–Ala–Lys–Ala–Lys–Ala–NH₂) is designed to assess the effect of N‐terminal homochiral diproline and lysine side chains to induce helical conformation. A2 (Ac–Pro–Pro–Glu–Glu–Ala–Ala–Lys–Lys–Ala–NH₂) and A3 (Ac–d Pro–Pro–Glu–Glu–Ala–Ala–Lys–Lys–Ala–NH₂) with N‐terminal homochiral and heterochiral diproline, respectively, are designed to assess the effect of Glu...Lys (i , i  + 4) salt bridge interactions on the stabilization of helical conformation. The CD spectra of A1 , A2 and A3 in water manifest different amplitudes of the observed polyproline II (PPII) signals, which indicate different conformational distributions of the polypeptide structure. The strong effect of solvent substitution from water to methanol is observed for the peptides, and CD spectra in methanol evidence A2 and A3 as helical folds. Temperature‐dependent CD spectra of A1 and A2 in water depict an isodichroic point reflecting coexistence of two conformations, PPII and β‐strand conformation, which is consistent with the previous studies. The results illuminate the effect of N‐terminal diproline and charged side chains in dictating the preferences for extended‐β, semi‐extended PPII and helical conformation in alanine‐based short peptides. The results of the present study will enhance our understanding on stabilization of helical conformation in short peptides and hence aid in the design of novel peptides with helical structures. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.     

Thermally induced cyclization of L‐isoleucyl‐L‐alanine in solid state: Effect of dipeptide structure on reaction temperature and self‐assembly

Thermal treatment of short‐chain oligopeptides is able to initiate the process of their self‐assembly with the formation of organic nanostructures with unique properties. On the other hand, heating can lead to a chemical reaction with the formation of new substances with specific properties and ability to form structures with different morphology. Therefore, in order to have a desired process, researcher needs to find its temperature range. In the present work, cyclization of _L‐isoleucyl‐_L‐alanine dipeptide in the solid state upon heating was studied. Kinetic parameters of this reaction were estimated within the approaches of the nonisothermal kinetics. The correlation between side chain structure of dipeptides and temperature of their cyclization in the solid state was found for the first time. This correlation may be used to predict the temperature, at which dipeptide self‐assembly changes to chemical reaction. The differences in self‐assembly of linear and cyclic dipeptides were demonstrated using atomic force microscopy. The effect of dipeptide concentration in a source solution and an organic solvent used on self‐assembly of dipeptides was shown. The new information obtained on the thermal properties and self‐assembly of linear and cyclic forms of _L‐isoleucyl‐_L‐alanine may be useful for the design of new nanomaterials based on oligopeptides, as well as for the synthesis of cyclic oligopeptides.     

Inner Surface Chirality of Single‐Handed Twisted Carbonaceous Tubular Nanoribbons

Single‐handed twisted 4,4′‐biphenylene‐bridged polybissilsesquioxane tubular nanoribbons and single‐layered nanoribbons were prepared by tuning the water/ethanol volume ratio in the reaction mixture at pH = 11.6 through a supramolecular templating approach. The single‐layered nanoribbons were formed by shrinking tubular nanoribbons after the removal of the templates. In addition, solvent‐induced handedness inversion was achieved. The handedness of the polybissilsesquioxanes could be controlled by changing the ethanol/water volume ratio in the reaction mixture. After carbonization at 900 °C for 4.0 h and removal of silica, single‐handed twisted carbonaceous tubular nanoribbons and single‐layered nanoribbons with micropores in the walls were obtained. X‐ray diffraction and Raman spectroscopy analyses indicated that the carbon is predominantly amorphous. The circular dichroism spectra show that the twisted tubular nanoribbons exhibit optical activity, while the twisted single‐layered nanoribbons do not. The results shown here indicate that chirality is transferred from the organic self‐assemblies to the inner surfaces of the 4,4′‐biphenylene‐bridged polybissilsesquioxane tubular nanoribbons and subsequently to those of the carbonaceous tubular nanoribbons. Chirality 27:809–815, 2015. © 2015 Wiley Periodicals, Inc.     

Optical Activity Governed by Local Chiral Structures in Two‐Dimensional Curved Metallic Nanostructures

Chiral nanostructures show macroscopic optical activity. Local optical activity and its handedness are not uniform in the nanostructure, and are spatially distributed depending on the shape of the nanostructure. In this study we fabricated curved chain nanostructures made of gold by connecting linearly two or more arc structures in a two‐dimensional plane. Spatial features of local optical activity in the chain structures were evaluated with near‐field circular dichroism (CD) imaging, and analyzed with the aid of classical electromagnetic simulation. The electromagnetic simulation predicted that local optical activity appears at inflection points where arc structures are connected. The handedness of the local optical activity was dependent on the handedness of the local chirality at the inflection point. Chiral chain structures have odd inflection points and the local optical activity distributed symmetrically with respect to structural centers. In contrast, achiral chain structures have even inflection points and showed antisymmetric distribution. In the near‐field CD images of fabricated chain nanostructures, the symmetric and antisymmetric distributions of local CD were observed for chiral and achiral chain structures, respectively, consistent with the simulated results. The handedness of the local optical activity was found to be determined by the handedness of the inflection point, for the fabricated chain structures having two or more inflection points. The local optical activity was thus governed primarily by the local chirality of the inflection points for the gold chain structures. The total effect of all the inflection points in the chain structure is considered to be a predominant factor that determines the macroscopic optical activity. Chirality 28:540–544, 2016. © 2016 Wiley Periodicals, Inc.     

Cationic oligopeptides with the repeating sequence L‐lysyl‐L‐alanyl‐L‐alanine: conformational and thermal stability study using optical spectroscopic methods

The infrared (IR), vibrational circular dichroism (VCD), and electronic circular dichroism (ECD) spectra of short cationic sequential peptides (L ‐Lys‐L ‐Ala‐L ‐Ala)_n (n = 1, 2, and 3) were measured over a range of temperatures (20–90 °C) in aqueous solution at near‐neutral pH values in order to investigate their solution conformations and thermally induced conformational changes. VCD spectra of all three oligopeptides measured in the amide I′ region indicate the presence of extended helical polyproline II (PPII)‐like conformation at room temperature. UV‐ECD spectra confirmed this conclusion. Thus, the oligopeptides adopt a PPII‐like conformation, independent of the length of the peptide chain. However, the optimized dihedral angles ? and ψ are within the range ?82 to ?107° and 143–154°, respectively, and differ from the canonical PPII values. At elevated temperatures, the observed intensity and bandshape variations in the VCD and ECD spectra show that the PPII‐like conformation of the Lys‐Ala‐Ala sequence is still preferred, being in equilibrium with an unordered conformer at near‐neutral pH values within the range of temperatures from 20 to 90 °C. This finding was obtained from analysis of the temperature‐dependent spectra using the singular value decomposition method. The study presents KAA‐containing oligopeptides as conformationally stable models of biologically important cationic peptides and proteins. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.     

Structure and chiroptical properties of supramolecular flower pigments

Research over the last 30 years has shown that at physiological concentrations of ca. 5 x 10(-3) M, flower pigments composed of anthocyanins, either alone or complexed with flavone copigments, and frequently with metals, are self-assembled into non-covalent, chiral supramolecular complexes. This serves several biological functions including color stability, protection against UV radiation and provision for specific colors to attract insects for pollination. Self-association of the monomers takes place under conditions of molecular crowding by precise matching of the pi-pi stacking interactions of the aromatic chromophores and intermolecular hydrogen bonding between the attached sugars. The resulting handedness is controlled by the chiral information provided by the sugars joined glycosidically at certain positions around the periphery of the aromatic nuclei. This review gives an overview of (i) the physicochemical evidence including circular dichroism, (1)H NMR, and X-ray analysis for the structure and supramolecular chirality of these amphiphilic complexes, (ii) the role of the sugars on directing the chirality of the resulting supramolecules, (iii) the energetics of monomer association, and (iv) the possible influence of stacking chirality on insect pollination.     

Solution structure of LC5, the CCR5‐ derived peptide for HIV‐1 inhibition

The synthetic peptide fragment (LC5: LRCRNEKKRHRAVRLIFTI) inhibits human immunodeficiency virus type 1 (HIV‐1) infection of MT‐4 cells. In this study, the solution structure of LC5 in SDS micelles was elucidated by using the standard ¹H two‐dimensional NMR spectroscopic method along with circular dichroism and fluorescence quenching. The peptide adopts a helical structure in the C‐terminal region (residues 13–16), whereas the N‐terminal part remains unstructured. The importance of Phe17 in maintaining the structure of LC5 was demonstrated by replacing Phe17 with Ala, which resulted in the dramatic conformational change of LC5. The solution structure of LC5 elucidated in the present work provides a basis for further study of the mechanism of the inhibition of HIV‐1 infection. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.     

Self‐assembly and chiroptical properties in supramolecular complexes of adenosine phosphates and guanidinium‐bispyrene

Supramolecular systems that respond to the hydrolysis of adenosine phosphates (APs) are attractive for biosensing and to fabricate bioinspired self‐assembled materials. Here, we report on the formation of supramolecular complexes between an achiral guanidinium derivative bearing two pyrene moieties, with each of the three adenosine phosphates: AMP, ADP, and ATP. By combining results from circular dichroism spectroscopy and molecular modeling simulations, we explore the induced chirality, the dynamics of the complexes, and the interactions at play, which altogether provide insights into the supramolecular self‐assembly between APs and the guanidinium‐bispyrene. Finally, we identify the chiroptical signals of interest in mixtures of the guanidinium derivative with the three APs in different proportions. This study constitutes a basis to evolve toward a chiroptical detection of the hydrolysis of APs based on organic supramolecular probes.     

Glycosaminoglycan and DNA Binding Induced Intra‐ and Intermolecular Exciton Coupling of the bis‐4‐Aminoquinoline Surfen

Despite the diverse biological activities of the glycosaminoglycan (GAG) antagonist surfen, the molecular details of its interaction with biomacromolecules remain poorly understood. Therefore, heparin and DNA binding properties of surfen were studied by circular dichroism (CD) and UV absorption spectroscopy methods. High‐affinity (K_a ~ 10⁷ M^‐1) association of surfen to the chiral heparin chain gives rise to a characteristic biphasic CD pattern due to the conformational twist of the aminoquinoline moieties around the central urea bridge. At higher drug loading, intermolecular stacking of surfen molecules alters the induced CD profile and also provokes strong UV hypochromism. In contrast to the right‐handed heparin template, binding of surfen to the left‐helicity chondroitin sulfate chains produces inverted CD pattern. Large UV hypochromism as well as polyphasic induced ellipticity bands indicate that surfen intercalates between the base pairs of calf‐thymus DNA. Extensive CD spectroscopic changes observed at higher drug binding ratios refer to cooperative binding interactions between the intercalated drug molecules. The inherent conformational flexibility of surfen demonstrated here for the first time is important in its binding to distinct macromolecular targets and should be considered for rational drug design of novel GAG antagonists. Chirality 27:605–612, 2015. © 2015 Wiley Periodicals, Inc.     

Helical Polybissilsesquioxane Bundles Prepared Using a Self‐Templating Approach

Polybissilsesquioxanes with single‐handed helical morphologies attracted much attention during the last decade, which could be applied as asymmetric catalysts and chiral stationary phases. Herein, a pair of chiral biphenylene‐bridged bissilsesquioxanes were synthesized. They self‐assembled into helical bundles in ethanol, behavior that was confirmed in field emission scanning electron microscopy images. Circular dichroism analysis indicated that the biphenylene groups twisted in a single‐handed fashion. Single‐handed helical polybissilsesquioxane bundles were prepared via polycondensation of the bissilsesquioxanes, using a self‐templating approach. Because of the shrinkage that occurred during polycondensation, the helical pitches of the bundles were shorter than those of their corresponding organic self‐assemblies. The wide‐angle X‐ray diffraction pattern indicated that there were no π–π interactions among the diphenylene groups. The circular dichroism spectra indicated that the chirality was successfully transferred from the bissilsesquioxane self‐assemblies to the polybissilsesquioxane. The polybissilsesquioxanes displayed a capacity for the adsorption of nitrobenzene and had potential application for enantioseparation. Chirality 28:44–48, 2016. © 2015 Wiley Periodicals, Inc.     

Difference in the structures of alanine tri‐ and tetra‐peptides with antiparallel β‐sheet assessed by X‐ray diffraction,solid‐state NMR and chemical shift calculations by GIPAW

Alanine oligomers provide a key structure for silk fibers from spider and wild silkworms.We report on structural analysis of l ‐alanyl‐l ‐alanyl‐l ‐alanyl‐l ‐alanine (Ala)₄ with anti‐parallel (AP) β‐structures using X‐ray and solid‐state NMR. All of the Ala residues in the (Ala)₄ are in equivalent positions, whereas for alanine trimer (Ala)₃ there are two alternative locations in a unit cell as reported previously (Fawcett and Camerman, Acta Cryst., 1975, 31, 658–665). (Ala)₄ with AP β‐structure is more stable than AP‐(Ala)₃ due to formation of the stronger hydrogen bonds. The intermolecular structure of (Ala)₄ is also different from polyalanine fiber structure, indicating that the interchain arrangement of AP β‐structure changes with increasing alanine sequencelength. Furthermore the precise ¹H positions, which are usually inaccesible by X‐ray diffraction method, are determined by high resolution ¹H solid state NMR combined with the chemical shift calculations by the gauge‐including projector augmented wave method. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 13–20, 2014.     

Solution conformation of a tetradecapeptide stabilized by two di‐n‐propyl glycine residues

The solution conformation of a designed tetradecapeptide Boc‐Val‐Ala‐Leu‐Dpg‐Val‐Ala‐Leu‐Val‐Ala‐Leu‐Dpg‐Val‐Ala‐Leu‐OMe (Dpg‐14) containing two di‐n‐propyl glycine (Dpg) residues has been investigated by ¹H NMR and circular dichroism in organic solvents. The peptide aggregates formed at a concentration of 3 mM in the apolar solvent CDCl₃ were broken by the addition of 12% v/v of the more polar solvent DMSO‐d₆. Successive N_iH N_i+1H NOEs observed over the entire length of the sequence in this solvent mixture together with the observation of several characteristic medium‐range NOEs support a major population of continuous helical conformations for Dpg‐14. Majority of the observed coupling constants ( ) also support ? values in the helical conformation. Circular dichroism spectra recorded in methanol and propan‐2‐ol give further support in favor of helical conformation for Dpg‐14 and the stability of the helix at higher temperature. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.     

Fine tuning of the catalytic activity of colicin E7 nuclease domain by systematic N‐terminal mutations

The nuclease domain of colicin E7 (NColE7) promotes the nonspecific cleavage of nucleic acids at its C‐terminal HNH motif. Interestingly, the deletion of four N‐terminal residues (446–449 NColE7 = KRNK) resulted in complete loss of the enzyme activity. R447A mutation was reported to decrease the nuclease activity, but a detailed analysis of the role of the highly positive and flexible N‐terminus is still missing. Here, we present the study of four mutants, with a decreased activity in the following order: NColE7  >> KGNK > KGNG ～ GGNK > GGNG. At the same time, the folding, the metal‐ion, and the DNA‐binding affinity were unaffected by the mutations as revealed by linear and circular dichroism spectroscopy, isothermal calorimetric titrations, and gel mobility shift experiments. Semiempirical quantum chemical calculations and molecular dynamics simulations revealed that K446, K449, and/or the N‐terminal amino group are able to approach the active centre in the absence of the other positively charged residues. The results suggested a complex role of the N‐terminus in the catalytic process that could be exploited in the design of a controlled nuclease.     

Sequence requirement and subtype specificity in the high‐affinity interaction between human frizzled and dishevelled proteins

Members of the Wnt family of lipoglycoproteins initiate signaling by binding to Frizzled (Fz) receptors, and the signal is then relayed by Disheveled (Dvl). The Dvl PDZ domain is known to interact directly with a peptide derived from the KTXXXW motif of Fz7, which is conserved in all known Fz subtypes. We found that an extended region spanning the KTXXXW motif on both its N‐terminal and C‐terminal sides dramatically influences the affinity of peptides derived from Fz7 for Dvl PDZ. An alanine scanning study identified the specific residues external to the KTXXXW motif that are important for high‐affinity binding. In a circular dichroism analysis, mutation of some of these critical residues resulted in peptide conformational changes, suggesting that the secondary structure of the peptides contributes to Fz‐Dvl PDZ binding. Of the 10 known Fz subtypes, peptides derived from only Fz1, Fz2, Fz3, Fz4, and Fz7 directly bound to Dvl PDZ domain in our study. Other Fz subtypes, including some known to be involved in Wnt/β‐catenin signaling (Fz5, Fz9), did not bind to Dvl, suggesting that direct interaction with Dvl PDZ does not determine the subtype‐specific functionality of Fz. Molecular modeling and circular dichroism studies indicated that the Fz peptides that bind to Dvl PDZ domain form specific conformations that are different from those of nonbinding peptides.     

The effect of temperature and salt concentration on the circular dichroism exhibited by unionized derivatives of L-alanine in aqueous solution

The circular dichroism of Ac–Ala–NHMe, cyclo(–Ala–Ala–), Ac–Ala–OMe, Ac–Ala–Ala–OMe, and Ac–Ala–Ala–Ala–OMe has been measured in water and in aqueous salt solutions as a function of temperature. Only cyclo(–Ala–Ala–) exhibits circular dichroism which is independent of temperature. Each of the linear derivatives of L -alanine exhibits a positive circular dichroism in the range 208–218 nm at 15°C in water. Heating reduces the intensity of the positive circular dichroism, and only Ac–Ala–OMe retains positive circular dichroism at 75°C in water. Isothermal addition of salts produces changes in the circular dichroism of linear derivatives of L -alanine which resemble those seen on heating. The relative effectiveness of the salts tested, at a concentration of 4M, is LiCl ? KCl = NaCl < MgCl₂ ? CaCl₂ ? NaClO₄. The circular dichroism of cyclo(–Ala–Ala–) is also affected by the salts. Extrapolation of the results obtained with Ac–Ala–OMe, Ac–Ala–Ala–OMe, and Ac–Ala–Ala–Ala–OMe to a long polypeptide with a –CH₂R side chain in the L -configuration leads to the conclusion that this polypeptide should exhibit a temperature-dependent salt-sensitive positive circular dichroism between 208 and 218 nm when it exists as a statstical coil.     

The effects of alpha-helix on the stability of Asn residues: deamidation rates in peptides of varying helicity

Asn deamidation was monitored in Ala-based octadecapeptides of varying alpha-helicity. Gly was substituted for Ala residues at positions 6 and 16 to create a peptide with less helicity. Ala --> Gly substitutions were made at three or more residues from the Asn to negate known primary sequence effects on deamidation rates. The extent of helicity and rate of Asn deamidation for alkaline aqueous solutions of each peptide was measured as a function of temperature by circular dichroism and reversed-phase high-performance liquid chromatography, respectively. The rate of deamidation in the peptides was inversely proportional to the extent of alpha-helicity. The results support the conclusion that Asn deamidation only occurs in the nonhelical population of conformers.     

Helicity of short E-R/K peptides

Understanding the secondary structure of peptides is important in protein folding, enzyme function, and peptide‐based drug design. Previous studies of synthetic Ala‐based peptides (>12 a.a.) have demonstrated the role for charged side chain interactions involving Glu/Lys or Glu/Arg spaced three (i, i + 3) or four (i, i + 4) residues apart. The secondary structure of short peptides (<9 a.a.), however, has not been investigated. In this study, the effect of repetitive Glu/Lys or Glu/Arg side chain interactions, giving rise to E‐R/K helices, on the helicity of short peptides was examined using circular dichroism. Short E‐R/K–based peptides show significant helix content. Peptides containing one or more E‐R interactions display greater helicity than those with similar E‐K interactions. Significant helicity is achieved in Arg‐based E‐R/K peptides eight, six, and five amino acids long. In these short peptides, each additional i + 3 and i + 4 salt bridge has substantial contribution to fractional helix content. The E‐R/K peptides exhibit a strongly linear melt curve indicative of noncooperative folding. The significant helicity of these short peptides with predictable dependence on number, position, and type of side chain interactions makes them an important consideration in peptide design.     

Nanofiber formation of amphiphilic cyclic tri‐β‐peptide

A novel amphiphilic cyclic peptide composed of two β‐glucosamino acids and one trans‐2‐aminocyclohexylcarboxylic acid was synthesized and investigated on assembly formation. The cyclic tri‐β‐peptide was self‐assembled into rodlike crystals or nanofibers depending on preparative conditions. The rodlike crystals showed a layer spacing of 4.8 Å along the long axis, and columnar spacings of 10.8 and 21.5 Å by electron diffraction analysis along the short axis. The former confirms the columnar structure upon molecular stacking, and the latter indicates triple bundle formation of the columnar assemblies. Fourier transform infrared (FT‐IR) measurement of the fibrous assembly showed formation of homogeneous hydrogen bonds among amide groups, also supporting the molecular stacking of cyclic β‐peptides. Straight nanofibers with uniform diameter were also uniquely obtained. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.