Helix‐coil and beta sheet‐coil transitions in a simplified,yet realistic protein model

A reduced model of polypeptide chains and protein stochastic dynamics is employed in Monte Carlo studies of the coil‐globule transition. The model assumes a high‐resolution lattice representation of protein conformational space. The interaction scheme is derived from a statistical analysis of structural regularities seen in known three‐dimensional protein structures. It is shown that model polypeptides containing residues that have strong propensities towards locally expanded conformations collapse to β‐like globular conformations, while polypeptides containing residues with helical propensities form globules of closely packed helices. A more cooperative transition is observed for β‐type systems. It is also demonstrated that hydrogen bonding is an important factor for protein cooperativity, although, for systems with suppressed hydrogen bond interactions, a higher cooperativity of β‐type proteins is also observed.     

RAFT polymerization kinetics and polymer characterization of P3HT rod–coil block copolymers

Here an in‐depth analysis of reversible addition–fragmentation chain transfer (RAFT) polymerization kinetics is reported in order to provide better definition of poly(3‐hexylthiophene) (P3HT) rod–coil block copolymers thru a more thorough understanding of the RAFT polymerization of the coil block. To this end, a new P3HT macroRAFT agent is synthesized and utilized to prepare rod–coil block copolymers with P3HT and poly(styrene), poly(tert‐butylacrylate), and poly(4‐vinylpyridine), and the RAFT polymerization kinetics of each system are fully detailed. This is achieved by a comprehensive analysis of characterization data from ¹H nuclear magnetic resonance spectroscopy, gel permeation chromatography, and matrix‐assisted laser desorption ionization time of flight spectroscopy, which are used as complementary techniques in order to address difficulties in accurately characterizing the synthesized polymer systems. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014 , 52, 3575–3585     

Alkaline Earth Metal Ion Induced Coil–Helix–Coil Transition of Lysine–Coumarin–Azacrown Hybrid Foldamers with OFF–OFF–ON Fluorescence Switching

A new metal‐ion‐responsive and fluorescent foldamer, OPLM₈ , composed of eight lysine–coumarin–azacrown units, has been designed and synthesized. The flexible OPLM₈ can be forced into a well‐defined helix structure only upon the addition of alkaline earth metal ions. The structural change is based on the crown ether moieties being positioned in the requisite arrangement along the peptide chain, that is, at i, i+4 spacing, such that the alkaline earth metal ions can mediate the formation of four sandwich complexes between them. Moreover, varying the chelator‐to‐metal‐ion ratio from 2:1 to 1:1 resulted in disassembly of the sandwich complexes leading to collapse of the helical structure to a random coil. These metal‐ion‐induced structural transitions could not only be monitored by the CD amplitude change but also easily probed by unique “OFF–OFF–ON” fluorescence intensity changes from 0.7‐fold to 14‐fold as the structure changed from the folded helix to a random coil. To further verify that the helix formation was indeed induced by metal‐ion complexation, two kinds of control octamers with only four metal‐ion chelators on the side chains were studied. One, which was capable of forming two sandwich complexes between the i and i+4 residues, displayed a negative Cotton couplet with the magnitude of its A value close to half that of OPLM₈ , and the second had four metal‐ion chelators positioned in the same turn, and hence was incapable of forming intramolecular metal complexes and showed different induced CD signals. Collectively, the photospectroscopic data and the results of the control studies suggest that alkaline earth metal ions can efficiently promote the flexible octamer OPLM₈ into a well‐organized helix by the formation of sandwich complexes between substituents at an i, i+4 spacing.     

A model for the helix–coil transition of DNA

The helix–coil phase transition of DNA is studied through a model equivalent to the one used in the theory of superconductivity. A distribution function for the excitations analogous to the usual Fermi function is obtained which depends on the parameter T₀, the maximum temperature at which all pairs of bases are bonded. The expression for the number of unbonded pairs of bases depends only on the two parameters, T₀ and T_c (critical temperature).     

Infrared study of the stability and folding kinetics of a 15-residue beta-hairpin

The thermal stability and folding kinetics of a 15-residue beta-hairpin (SESYINPDGTWTVTE) have been studied by using infrared (IR) spectroscopy coupled with laser-induced temperature-jump (T-jump) technique for rapid folding-unfolding initiation. An alternative method based on analyzing IR difference spectra was also introduced to obtain thermodynamic properties of beta-sheets, which complements the commonly used circular dichroism (CD) and fluorescence techniques. Equilibrium IR measurements indicate that the thermal unfolding of this beta-hairpin is fairly broad. However, it can be described by a two-state transition with a thermal melting temperature of approximately 29 degrees C. Time-resolved IR measurements following a T-jump, probed at 1634 cm(-1), indicate that the folding of this beta-hairpin follows first-order kinetics and is amazingly fast. At 300 K, the folding time is approximately 0.8 micros, which is only 2-3 times slower than that of alpha-helix formation. Additionally, the energetic barrier for folding is small (approximately 2 kcal mol(-1)). These results, in conjunction with results from other studies, support a view that the details of native contacts play a dominant role in the kinetics of beta-hairpin folding.     

Ordered nanostructures from self‐assembly of H‐shaped coil–rod–coil molecules

A new class of π‐conjugated, skewed H‐shaped oligomers, consisting of biphenyl, phenylene vinylene, and phenylene ethynylene units as the rigid segment, were synthesized via Sonogashira coupling and Wittig reactions. The coil segments of these molecules were composed of poly(ethylene oxide) (PEO) or PEO with lateral methyl groups between the rod and coil segment, respectively. The experimental results revealed that the lateral methyl groups attached to the surface of the rod and coil segments dramatically influenced the self‐assembling behavior of the molecules in the crystalline phase. H‐shaped rod–coil molecules containing a lateral methyl group at the surface of the rod and PEO coil segments self‐assemble into a two‐dimensional columnar or a three‐dimensional body‐centered tetragonal nanostructures in the crystalline phase, whereas molecules lacking a lateral methyl group based on the PEO coil chain self‐organize into lamellar or hexagonal perforated lamellar nanostructures. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53, 85–92     

Non-newtonian viscosity of polypeptides in the helix–coil transition region

The non-Newtonian intrinsic viscosities [η] of poly(γ-methyl L-glutamate) were measured in the helix–coil transition region under various conditions in this work. The helix content f_H, which represents the degree of conformational transition, was obtained by using a polarimeter. Our experimental results show that the non-Newtonian behavior of the polypeptide is markedly affected by its conformation; i.e., the non-Newtonian effect becomes larger as f_H increases. The effect of external pressure ΔP on [η] was studied carefully; [η] increases with f_H when ΔP < 1.5 psi, but it decreases when ΔP > 1.5 psi and f_H > 0.8. The reason for this result is considered in the text.     

Desorption kinetics of a xanthenol–dioxane clathrate

The host xanthenol compound forms a 1:1 clathrate with dioxane, namely 9‐(1‐naphthyl)‐9H‐xanthen‐9‐ol–1,4‐dioxane, C₂₃H₁₆O₂·C₄H₈O₂. The structure of this clathrate is reported, along with a study of the kinetics of desolvation and the determination of an activation energy. The guest mol­ecules are stabilized by O_host—H⋯O_guest hydrogen bonds [O—H = 0.968 (2) Å, O⋯O = 2.7532 (13) Å and O—H⋯O = 151.9 (4)°].     

Pressure–volume–temperature behavior of two polycyanurate networks

The pressure–volume–temperature (PVT) behavior was studied for two polycyanurate networks having different crosslink densities using a pressurizable dilatometer. The samples were studied at temperatures ranging from 60 to 180 °C and at pressures up to 170 MPa to yield PVT data in both rubbery and glassy states. The Tait equation is found to well describe the isobaric temperature scan and isothermal pressure scan data. The thermal expansion coefficients, instantaneous bulk moduli, and thermal pressure coefficients are extracted from the data and their dependence on crosslink density is examined. The time‐dependent viscoelastic bulk modulus (K(t)) is also calculated in the vicinity of the α‐relaxation from previously published pressure relaxation experimental data, and the strength and shape of the dispersion are found to be independent of crosslink density. The limiting bulk moduli depend strongly on temperature with those of the more loosely crosslinked sample being lower at a given temperature and pressure, although at T_g(P), the limiting moduli of the more loosely crosslinked sample are slightly higher than those of the more highly crosslinked sample. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2010     

Conjugation of arginine–glycine–aspartic acid peptides to thermoreversible N‐isopropylacrylamide polymers

Thermoreversible polymeric biomaterials are finding increased acceptance in tissue engineering applications. One drawback of the polymers is their synthetic nature, which does not allow direct interaction of mammalian cells with the polymers. This limitation may be alleviated by grafting arginine–glycine–aspartic acid (RGD) containing peptides onto the polymer backbone to facilitate interactions with cell‐surface integrins. Toward this goal, N‐isopropylacrylamide (NiPAM)‐based thermoreversible polymers containing amine‐reactive N‐acryloxysuccinimide (NASI) groups were synthesized. Conjugation of RGD‐containing peptides to polymers was demonstrated with ¹H NMR spectroscopy and reverse‐phase high‐pressure liquid chromatography. The conjugation reaction was optimal at 4 °C and pH of 8.0, and increased with the increasing NASI content of polymers. With a peptide grafting ratio of 0.25 mol %, there was no significant change in the lower critical solution temperature of the polymers. Finally, the NASI‐containing polymers, cast as films, on tissue culture polystyrene, were shown to conjugate to RGD‐containing peptides and support C2C12 cell attachment. We conclude that NASI‐containing thermoreversible polymers are amenable for grafting biomimetic peptides to impart cell adhesiveness to the polymers. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 3989–4000, 2003     

Synthesis and characterization of fluorene‐based rod–coil liquid crystal polymers

A series of fluorene‐based rod–coil liquid crystal polymers with different lengths of the coil segments on backbones were designed and synthesized by a palladium‐catalyzed Suzuki coupling‐reaction. The thermal stability, the UV–Vis absorption and fluorescence spectra in chloroform solution and thin film, the electrochemical properties, thermal behavior, and morphology of these rod–coil polymers were investigated. The thermal stability of these polymers steadily decreased on increasing the length of the coil segments on the backbone; their optical and electrochemical properties did not exhibit noticeable dependence on the weight fraction of the coil segments. However, the shoulder emission and the full width at the half‐maximum (FWHM) in PL spectra of the films increased, whereas the oxidation onset potentials and the corresponding HOMO energy levels decreased with the increase in the weight fraction of the coil segments, which was assigned to microphase separation and formation of folded chain conformation as the weight fraction of the coil segments increased. These polymers displayed a characteristic liquid crystalline texture. The variation of the weight fraction of the coil segments obviously affected the thermal behavior and morphology of these rod–coil polymers. Copyright © 2008 John Wiley & Sons, Ltd.     

Synthesis of a novel hybrid liquid‐crystalline rod–coil diblock copolymer

A series of novel rod–coil diblock copolymers on the basis of mesogen‐jacketed liquid‐crystalline polymer were successfully prepared by atom transfer radical polymerization from the flexible polydimethylsiloxane (PDMS) macroinitiator. The hybrid diblock copolymers, poly{2,5‐bis[(4‐methoxyphenyl)oxycarbonyl]styrene}‐block‐polydimethylsiloxane, had number‐average molecular weights (M_n's) ranging from 9500 to 30,900 and relatively narrow polydispersities (≤1.34). The polymerization proceeded with first‐order kinetics. Data from differential scanning calorimetry validated the microphase separation of the diblock copolymers. All block copolymers exhibited thermotropic liquid‐crystalline behavior except for the one with M_n being 9500. Four liquid‐crystalline diblock copolymers with PDMS weight fractions of more than 18% had two distinctive glass‐transition temperatures. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 1799–1806, 2003     

Hydration-dependent enthalpy changes in the helix–coil transition in tendon

The shrinkage phenomenon in bovine achilles heel tendon was studied calorimetrically as a function of water content of the tendon. The transition temperature was found to increase from 67°C to 98°C as the water content decreased from 53% by weight to 26% by weight. The enthalpy change was found to increase with increasing percentages of water. The data is interpreted by considering the possibility of water binding to the polar sites on the solute molecule which become free after the transition. A calculation is carried out in which the melting shifts are taken to be related to the free energy of binding. The increase in enthalpy with an increase in water content is shown to have a semiquantitative interpretation in terms of the structural aspects of water.     

Liposome fusion with orthogonal coiled coil peptides as fusogens: the efficacy of roleplaying peptides

Biological membrane fusion is a highly specific and coordinated process as a multitude of vesicular fusion events proceed simultaneously in a complex environment with minimal off-target delivery. In this study, we develop a liposomal fusion model system with specific recognition using lipidated derivatives of a set of four de novo designed heterodimeric coiled coil (CC) peptide pairs. Content mixing was only obtained between liposomes functionalized with complementary peptides, demonstrating both fusogenic activity of CC peptides and the specificity of this model system. The diverse peptide fusogens revealed important relationships between the fusogenic efficacy and the peptide characteristics. The fusion efficiency increased from 20% to 70% as affinity between complementary peptides decreased, (from K_F ≈ 10⁸ to 10⁴ M⁻¹), and fusion efficiency also increased due to more pronounced asymmetric role-playing of membrane interacting ‘K’ peptides and homodimer-forming ‘E’ peptides. Furthermore, a new and highly fusogenic CC pair (E₃/P1_K) was discovered, providing an orthogonal peptide triad with the fusogenic CC pairs P2_E/P2_K and P3_E/P3_K. This E₃/P1_k pair was revealed, via molecular dynamics simulations, to have a shifted heptad repeat that can accommodate mismatched asparagine residues. These results will have broad implications not only for the fundamental understanding of CC design and how asparagine residues can be accommodated within the hydrophobic core, but also for drug delivery systems by revealing the necessary interplay of efficient peptide fusogens and enabling the targeted delivery of different carrier vesicles at various peptide-functionalized locations.

We developed a liposomal fusion model system with specific recognition using a set of heterodimeric coiled coil peptide pairs. This study unravels important structure–fusogenic efficacy relationships of peptide fusogens.     

On the Helical Motif of the Complexes Created by Association of Helix‐Forming Schizophyllan (SPG) and Helix‐Forming Polythiophene Derivatives

π‐Conjugated polymers can finely tune their electrical and optical properties in response to their conformational changes. We believe that a deeper understanding of their higher‐order structures will stimulate further development of their applications. We had revealed that one helix‐forming natural polysaccharide (SPG) and one polythiophene derivative (PT‐1) formed a stable one‐dimensional complex and in the polythiophene main chain a helical conformation was induced through the dynamic conformational changes. The objective of our present research is to obtain a better mechanistic understanding on the interaction between SPG and polythiophenes. Here we have used particular left‐ and right‐handed helix‐forming polythiophene derivatives (D ‐ and L ‐POWTs, respectively) and studied their influence on the helical motif of the complexes. We observed that SPG interacts with both D ‐ and L ‐POWTs through their dynamic conformational changes and both D ‐ and L ‐POWTs form the right‐handed co‐helical complexes with SPG according to the inherent helical motif of SPG. In addition, it was confirmed that 1) the complexes do not coagulate in aqueous solution, and 2) the exchange in the helical motif can occur only when the polymers experience the denature–renature process. We believe, therefore, that the mechanism of the helical induction of the SPG/POWT complexes is very unique, being different from conventional equilibrium reactions.     

The kinetics of the bromate–sulfite reaction system

The kinetics of the reaction between BrO₃⁻ and sulfite was studied by measuring the concentrations of [Br⁻] and [H⁺] both in buffered and in unbuffered solutions. A mechanism was applied for simulation of the experimental observations. Rate constants k₁=(0.027±0.004) M⁻¹s⁻¹ and k₂=(85±5) M⁻¹s⁻¹ were determined for the following reactions: \halign{\hfill $#$\hfill &\hfill\qquad\qquad #\cr 3\ \rm HSO_{3}\!^{-}+BrO_{3}\!^{-}\longrightarrow 3\ SO_{4}\!^{2-}+Br^{-}+3\ H^{+}& (1)\cr 3\ \rm H_{2}SO_{3}(\hbox{or}\ SO_{2.}\hbox{aq})+BrO_{3}\!^{-}\longrightarrow 3\ SO_{4}\!^{2-}+Br^{-}+6\ H^{+}& (2)\cr } Rate constant k₁ was obtained directly from the experimental results on unbuffered reactions, where Reaction (1) was predominant. Rate constant k₂ was obtained by computer fitting of [Br⁻] to the experimental values for buffered reactions, where the rate of Reaction (2) was about four times higher than that of Reaction (1). © 1998 John Wiley & Sons, Inc. Int J Chem Kinet 30: 869–874, 1998     

Boc–Pro–Hyp–Gly–OBzl and Boc–Ala–Hyp–Gly–OBzl,two repeating triplets found in collagen

The protected tripeptides benzyl N‐{2‐[N‐(tert‐butoxy­carbon­yl)­prol­yl]‐4‐hydroxy­prol­yl}glycinate or Boc–Pro–Hyp–Gly–OBzl, C₂₄H₃₃N₃O₇, and benzyl N‐{2‐[N‐(tert‐butoxy­carbon­yl)­alan­yl]‐4‐hydroxy­prol­yl}glycinate or Boc–Ala–Hyp–Gly–OBzl, C₂₂H₃₁N₃O₇, are the minimum repeating triplets found in collagen. Within the crystal structure of each are two independent peptide mol­ecules with similar structures. The peptides are arranged anti­parallel to one another and inter­act through hydrogen bonds involving the main chains and the 4‐hydroxy­prolyl groups. The structures exhibit characteristics of a triple helix, but the peptides tend to assume a sheet‐like structure.