Flexible Main Chain Research Articles

Disulfide crosslinks to probe the structure and flexibility of a designed four-helix bundle protein.

The introduction of disulfide crosslinks is a generally useful method by which to identify regions of a protein that are close together in space. Here we describe the use of disulfide crosslinks to investigate the structure and flexibility of a family of designed 4-helix bundle proteins. The results of these analyses lend support to our working model of the proteins' structure and suggest that the proteins have limited main-chain flexibility.

Assignment of the protonated 13C resonances of apo-neocarzinostatin by 2D heteronuclear NMR spectroscopy at natural abundance

Nearly complete assignment of the protonated carbon resonances of apo-neocarzinostatin, a 113-amino acid antitumor antibiotic carrier protein, has been achieved at natural 13C abundance using heteronuclear 2D experiments. Most of the cross peaks in the proton-carbon correlation map were identified by the combined use of HMQC, HMQC-RELAY and HMQC-NOESY spectra, using already published proton chemical shifts. However, double-DEPT and triple-quantum experiments had to be performed for the edition of CH and CH2 side-chain groups, respectively, which were hardly visible on HMQC-type maps. The triple-quantum pulse sequence was adapted from its original scheme to be applicable to a natural abundance sample. The correlation between carbon chemical shifts and the apo-neocarzinostatin structure is discussed. In particular, 13C alpha secondary shifts correlate well with the backbone conformation. These shifts also yield information about the main-chain flexibility of the protein. Assignments reported herein will be used further for interpretation of carbon relaxation times in a study of the internal dynamics of apo-neocarzinostatin.

Self-order in flexible non-mesogenic macromolecules

Some very flexible linear poly(di-n-alkylsiloxane)s and cyclolinear oligo- and polyorganosiloxanes, which do not contain classical rigid rodlike or disclike mesogens, similar to other semi-organic polymers like polyphosphazenes and polysilanes, can form thermodynamically stable two-dimensionally ordered thermotropic mesophases. In many respects the mesophases in polysiloxanes resemble columnar liquid crystals which seems to be the result of the amphiphilic constitution of the polyorganosiloxanes. The origin of the mesomorphic state seems to be closely related to the competition between the interaction of the polar inorganic backbones and those of the organic side chains facilitated by the high flexibility of the inorganic main chain. Similarily to discotic liquid crystals, mesophases in polysiloxanes consist mostly of columns packed hexagonally (or closely so) with lateral long-range positional order, but with only short-range order along the columns. The unique feature of the columnar mesophases is that the axes of macromolecules lie along the column axes. The influence of molecular structure and molecular mass of linear macromolecules is discussed. It has been demonstrated that the temperature interval of mesophase stability is critically dependent on the length of the alkyl side chains. Both the process of formation of the mesophase from the isotropic melt and the crystallization of the mesophase are nucleation controlled processes, although the crystallization of the mesomorphic state is characterized by some specific features. The phase behaviour of cyclolinear polyorganosiloxanes is described with particular emphasis on the temperature stability as a function of molecular structure, tacticity, substituents and flexible spacers.

Influence of molecular structure on the nematic-nematic transition in polyethers based on 1-(4-hydroxyphenyl)-2-(2-R-4-hydroxyphenyl)ethane where R=CH3 and Cl, and flexible spacers with an odd number of methylene units

In a previous paper (reference 1b) we reported that flexible main chain liquid crystalline copolymers based on various molar ratios between the flexible mesogenic groups 1-(4-hydroxyphenyl)-2-(2-R-4-hydroxyphenyl)ethane (RBPE) where R=F, Cl, CH3 and several different molar ratios between flexible spacers containing odd numbers of methylenic units, i.e. 5, 7, and 9 display two enantiotropic uniaxial nematic mesophases. The homopolymers RBPE-X (where R=-CH3 and-Cl) and X=number of methylenic units in the flexible spacer, i.e. X=5, 7, 9, 11, and 13) display also two nematic (n1, n2) mesophases which are however, monotropic or virtual. This paper will discuss the dependence of the phase transition temperatures between these two nematic mesophases (Tn1n2), the isotropization temperature (Tin1), and of their associated thermodynamic parameters of the MBPE-X (M=CH3) and C1BPE-X homopolyethers as a function of spacer length X. These results will be compared with the predictions of the only available theory which predicts the existence of two uniaxial nematic mesophases in flexible main chain liquid crystalline polymers (reference 6).

The crystal structure of a mutant protein with altered but improved hydrophobic core packing.

The dense packing observed in protein interiors appears to be crucial for stabilizing the native structure--even subtle internal substitutions are usually destabilizing. Thus, steric complementarity of core residues is thought to be an important criterion for "inverse folding" predictive methods, which judge whether a newly determined sequence is consistent with any known folds. A major problem in the development of useful core packing evaluation algorithms, however, is that there are occasional mutations that are predicted to disrupt native packing but that yield an equally or more stable protein. We have solved the crystal structure of such a variant of lambda repressor, which, despite having three larger core substitutions, is more stable than the wild type. The structure reveals that the protein accommodates the potentially disruptive residues with shifts in its alpha-helical arrangement. The variant is apparently more stable because its packing is improved--the core has a higher packing density and little geometric strain. These rearrangements, however, cause repositioning of functional residues, which result in reduced DNA binding activity. By comparing these results with the predictions of two core packing algorithms, it is clear that the protein possesses a relatively high degree of main-chain flexibility that must be accounted for in order to predict the full spectrum of compatible core sequences. This study also shows how, in protein evolution, a particular set of core residue identities might be selected not because they provide optimal stability but because they provide sufficient stability in addition to the precise structure required for optimal activity.

Why do Polyethylene Glycol-Coated Liposomes Circulate So Long?: Molecular Mechanism of Liposome Steric Protection with Polyethylene Glycol: Role of Polymer Chain Flexibility

The hypothesis is suggested describing the molecular mechanism of protective action of poly(ethylene glycol) on liposomes in vivo on the basis of polymer properties in solvent. The protective layer of polymer on the liposome surface is considered as a “cloud” of possible conformations of macromolecules. If polymer is water-soluble and has flexible main chain, the density of this cloud is high enough to prevent the interaction of opsonins with liposome. At the same time, certain optimal concentration of the protective polymer can be found, when more loose areas in polymeric “clouds” can be used for the immobilization of antibodies on liposomes. As a result, long-circulating targeted liposomes can be obtained.

Orientational order in liquid crystal solutions of polyhexylisocyanate. II. Deuterium nuclear magnetic resonance

The concentration dependence of the order parameter was measured for liquid crystal solutions of deuterated samples of polyhexylisocyanate of two molecular weights in two solvents, chloroform and toluene. Trends in and values of order parameters determined from deuterium nuclear magnetic resonance (DNMR) spectroscopy for this semiflexible polymer were analyzed in terms of a recent modification [DuPré and Yang, J. Chem. Phys. 94, 7466 (1991)] of the Onsager theory that takes into account macromolecular flexibility and the higher solute densities characteristic of these polymer liquid crystals. Computer simulation of DNMR spectra with the consideration of internal flexibility of the polymer main chain was performed also to interpret unusual line shape features observed in liquid crystal solutions of this polymer.

Importance of main-chain flexibility and the insulin fold in insulin-receptor interactions.

We have investigated the effects of altering the disposition between the COOH-terminal B chain domain of insulin and the core of the insulin molecule on ligand interactions with the hepatocyte insulin receptor. Analogues include those in which ArgB22 of des-octapeptide(B23-B30)-insulin is extended by one to three residues of glycine prior to termination in Phe-NH2, by one to five residues of glycine prior to termination in Phe-Phe-NH2, or by an additional residue of glycine prior to termination in more extended sequences derived from insulin or [GlyB24]insulin. Analogues were also examined with respect to their abilities to form hexamers in solution in the presence of Co2+, phenol, and NaSCN. Overall, our studies of ligand-receptor interactions identify that (a) the energetic penalty for the introduction of a single residue of glycine is uniform in all classes of analogues for up to three residues of glycine but diminishes somewhat for analogues with longer insertions and (b) the COOH-terminal residues of the B chain retain their importance for all classes of analogues, no matter the number of glycine residues introduced. Analogues with glycine insertions, but not those with glycine substitutions, readily form thiocyanate-stabilized complexes with Co2+ in the presence of phenol.(ABSTRACT TRUNCATED AT 250 WORDS)

The crystallographic structure of the protease from human immunodeficiency virus type 2 with two synthetic peptidic transition state analog inhibitors

The crystal structure of human immunodeficiency virus (HIV) type 2 protease has been determined in complexes with peptidic inhibitors Noa-His-Cha psi [CH(OH)CH(OH)]Val-Ile-Amp (U75875) and Qnc-Asn-Cha psi [CH(OH)CH2]Val-Npt(U92163) (where Noa is naphthyloxyacetyl, Cha is cyclohexylalanine, Amp is 2-aminomethylpyridine, Qnc is quinoline-2-carbonyl, and Npt is neopentylamine), which have dihydroxyethylene and hydroxyethylene moieties, respectively, in place of the normal scissile bond of the natural ligand. The complexes crystallize in space group P2(1)2(1)2(1), with one dimer-inhibitor complex per asymmetric unit and average cell dimensions of a = 33.28 A, b = 45.35 A, c = 135.84 A. Data were collected to approximately 2.5-A resolution. The model structures were refined with resulting R-factors of around 0.19. As expected, the HIV-2 protease structure is approximately C2-symmetric with a gross structure very similar to that of the HIV-1 enzyme. The inhibitors bind in an extended conformation positioned lengthwise in the binding cleft in a manner similar to that found in the HIV-1 protease-inhibitor complexes previously reported. The substitution of the bulkier Ile82 side chain in the HIV-2 protease may help explain the better ability of HIV-2 protease to bind and hydrolyze ligands with small P1 and P1' side groups. It appears that differences in specificity between the proteases of HIV-1 and HIV-2 are not merely a result of simple side chain substitutions, but may be complicated by differences in main chain flexibility as well.

Molecular Motion and Dielectricity in Polymers with Cyanoethyl Group

The molecular motion of side chain with cyanoethyl groups in polymers having rigid and flexible main chains was investigated by dielectric measurement. Cyanoethylated polysaccharides with a rigid main chain showed a large dielectric relaxation (β) at low temperature (-50°C), β relaxation was enhanced by adding tricresylphosphate as a plasticizer. This β relaxation originates from the molecular motion of cyano group in the side chain. The β relaxation in cyanoethylated hydroxypropylcellulose, internal-plasticized cellulose, was very small and the α relaxation due glass transition was clearly observed. In cyanoethylated ployvinylalcohol and polyhydroxymethylene having a flexible main chain, the small β relaxation was observed just below each glass transition temperature (Tg). The relationship between the dielectric relaxation strength of the side chain and main chain structures was evaluated from the ratio of Tg to Ts (β relaxation temperature), corresponding to the magnitude of the chain mobility. It was revealed that cyanoethyl group connected with a rigid main chain was appropriate for a large dielectric relaxation strength in β relaxation.

Effect of articulated side groups on the main-chain flexibility of polycarbonates

Conformational energies were calculated for a series of polycarbonates with articulated side groups attached to the central C α atom. In all the cases considered here, the placement of a CH 2 spacer for the articulated side chain increases the main-chain rigidity as compared to that of Bisphenol-A polycarbonate (BPAPC) although the energies of the segment at the minima are lowered. The minima also become localized, thus impeding the synchronous rotation of the phenyls within a low energy barrier. A new steric factor σ s based on the conformational partition function is used for comparing the chain flexibilties

Gas transport and sub- Tg relaxations in unmodified and nitrated polyarylethersulfones

Aromatic nitration has been used to modify the polymer main chain of polysulfone and polyethersulfone. Alteration in the gas separation characteristics of homogeneous membrane made out of these polymers could be observed upon nitration. Generally, separation factors for gas mixtures of CO 2/CH 4 increased while the permeability decreased. Remarkably, a decreasing diffusivity for both gases upon nitration could not be correlated with an increasing free-volume but was interpreted as an drastically decreased main-chain flexibility. The decrease of main-chain segmental mobility could be verified experimentally by a diminished amount of β-relaxations determined by torsional braid analysis.

Catalysis by surfactant aggregates in aqueous solutions

Abstract

Aggregation state and mesophase structure of comb-shaped polymers with fluorocarbon side groups

The aggregation states of a series of comb-shaped polymers with perfluoroalkyl side chains were investigated. The main chains of the comb-shaped polymers were poly(fumarate), poly(acrylate) and poly(methacrylate). D.s.c. and w.a.x.d. measurements and p.o.m. observations over a wide temperature range showed that all the poly(fluoroalkylfumarates) (PFAF) investigated were amorphous polymers, but poly(fluoroalkylacrylate) (PFAA) and poly(fluoroalkylmethacrylate) (PFAMA) having a heptadecafluorodecyl (C 8F 17) group in the side chain were in a mesomorphic state at room temperature. The type of mesophases can be most likely classified as an ordered smectic liquid crystalline (LC) structure in the Smectic B (S B) modification for PFAA and an unordered smectic LC structure in the Smectic A (S A) modification for PFAMA. Increasing the main chain flexibility in going from poly(fumarate) to poly(methacrylate) and poly(acrylate) enhances the probability of ordered structure formation.

Phase transitions in narrow-molar-mass samples of side-chain liquid-crystalline polymers: molar-mass dependence

The molar-mass dependence of phase transitions in narrow-molar-mass samples of smectic side-chain poly(vinyl ether)s is discussed with reference to earlier data by Stevens et al. and Percec et al. on narrow fractions of smectic side-chain polysiloxanes and polymethacrylates. The constant heat of isotropization ( Δh i) and the proportionality between the glass transition temperature ( T g) and the reciprocal degree of polymerization ( DP) observed for polysiloxanes and polymethacrylates indicate that the order within the smectic layers and the penetration of the flexible main chains of the smectic layers was not appreciably affected by changes in DP. The poly(vinyl ether)s on the other hand exhibited a pronounced decrease in Δh i with increasing DP and a more complex correlation between T g and DP indicative of an increasing disturbance by the flexible main chains of the smectic layers with increasing DP. These differences between polysiloxanes/polymethacrylates and poly(vinyl ether)s were also found to have profound effects on the DP dependence of the isotropization temperature.

Relationship between nuclear magnetic resonance chemical shift and protein secondary structure

An analysis of the 1H nuclear magnetic resonance chemical shift assignments and secondary structure designations for over 70 proteins has revealed some very strong and unexpected relationships. Similar studies, performed on smaller databases, for 13C and 15N chemical shifts reveal equally strong correlations to protein secondary structure. Among the more interesting results to emerge from this work is the finding that all 20 naturally occurring amino acids experience a mean αa- 1H upfield shift of 0.39 parts per million (from the random coil value) when placed in a helical configuration. In a like manner, the α- 1H chemical shift is found to move downfield by an average of 0.37 parts per million when the residue is placed in a β-strand or extended configuration. Similar changes are also found for amide 1H, carbonyl 13C, α- 13C and amide 15N chemical shifts. Other relationships between chemical shift and protein conformation are also uncovered; in particular, a correlation between helix dipole effects and amide proton chemical shifts as well as a relationship between α-proton chemical shifts and main-chain flexibility. Additionally, useful relationships between α-proton chemical shifts and backbone dihedral angles as well as correlations between amide proton chemical shifts and hydrogen bond effects are demonstrated.

Single Ionic Conduction Based on Poly(Siloxane-g-Ethylene Oxide) Effect of Sterically Hindered Groups on Ion Dissociation

Abstract We have synthesized and characterized poly(siloxane-g-ethylene oxide) containing Li, Na and K 2,6-di-t-butyl phenolates, and studied the effect of steric hindrance on the ionic conductivities. These polymers have a flexible siloxane main chain and the anion source bonded on it, such that only the cation can migrate. The ionic conductivity of lithium, sodium and potassium phenolate was found to be 10−7 − 10−5 s/cm at 30°C. The conductivity of Na and K salts was approximately 102 greater than that of the Li salts. This was accounted for by the improved ion pair separation in the Na and K phenolates due to the steric hindrance of the t-butyl groups. The temperature dependence of ionic conductivity suggests that the migration of ions is controlled by segmental motion of the polymer, since linear curves were obtained in VTF plots.

Synthesis, polymerization and cation conductive properties of (ω‐carboxy)‐oligo(oxyethylene) methacrylate

AbstractAlkali‐metal salts of (ω‐carboxy)oligo(oxyethylene) methacrylate (CME12M, M = Li or Cs) have been synthesized and polymerized to prepare solid polymer electrolytes. These types of solid polymer electgrolytes provide a homogeneous phase, since these polymers have a flexible main chain, an oligo(oxyethylene) side chain for ion conduction, and a carrier ion source in one repeating unit. The AC conductivity of P(CME12Li) homopolymer is 8.9 × 10−9 S cm−1 at 30°C, while that of P(CME12Cs) is 3.3 × 10−6 S cm−1 at 30°C, which is the highest value among single ion conductors, have been reported as polyelectrolyte “homopolymer” without any additives. High ionic conduction of P(CME12Cs) is due to low glass transition temperature (Tg = −54°C) and weaker ion–ion and ion–dipole interaction of Cs+ than that of Li+.

Phase behaviour of amphiphilic side-chain polymers

Abstract The present study describes the phase behaviour of a low-molar-mass 1,3-diol with a linear alkyl chain in aqueous solution. From the combined results of differential scanning calorimetry and optical polarizing microscopy a phase diagram was constructed. The low-molar-mass diol forms a lamellar mesophase only in the presence of water. The influence of the linkage of the amphiphilic molecule to different polymer backbones on the stability of the mesophase was investigated. It is evident that amphiphilic side-chain polymers show a distinct stabilization of the mesophase. Moreover, comparison between the polyacrylate, polymethacrylate and polysiloxane indicates a strong influence of the main-chain flexibility on the stability of the liquid-crystalline phase. The type of the liquid-crystalline phase of the side-chain polyacrylate in the water-saturated state was identified by X-ray investigations as lamellar. The hydration behaviour of the polymers was investigated by 2H-N.M.R. and isopiestic measurem...

Structure and properties of Langmuir-Blodgett films made from polyamides

Amphiphilic polyamides were synthesized from amphiphilic diamines and diacid derivatives to yield polymer chains with different flexebilities. Monolayers from most of these polycondensates could successfully be transferred onto substrates by the Langmuir-Blodgett method. The properties of the films obtained are strongly dependent on the chemical structure of the compounds. Thus the orientation of the alkyl chains changes from highly ordered to almost random when the flexibility of the polymer main chain is varied from highly flexible to stiff.