Unordered Chain Research Articles

Physics of agarose fluid gels: Rheological properties and microstructure

Agarose, a strongly gelling polysaccharide, is a common ingredient used to optimize the viscoelastic properties of a multitude of food products. Through aggregation of double helices via hydrogen bonds while cooling under quiescent conditions it forms firm and brittle gels. However, this behavior can be altered by manipulating the processing conditions viz shear. For example, gelation under shear leads to microgel particles with large surface area, which in turn leads to completely different rheological properties and texture. Such fluid gels are shown to play an important role in texture modification of foods and beverages for dysphagia patients. In this study, different concentration of agarose fluid gel (0.5 % wt, 1 % wt and 2 % wt) were considered. Rheological measurements of the microgel particles showed an increase of storage and loss modulus with increasing concentration. However, 1 % wt fluid gel exhibited the lowest viscosity in the low shear range and the shortest LVE range. Furthermore, the effect on the microstructure and size of gel particles were also investigated by using light microscopy and particle size analysis. It was observed that as the concentration of agarose increased the particle size and unordered chains present at the particle surface decreases. Based on our results, we propose specific models suggesting the impact of the particle size, the concentration and the “hairy” projections on the rheological and tribological properties that could help in understanding the differences in characteristics of fluid gels.

Structural Analysis of Nonapeptides Derived from Elastin

Elastin-derived peptides are released from the extracellular matrix remodeling by numerous proteases and seem to regulate many biological processes, notably cancer progression. The canonical elastin peptide is VGVAPG, which harbors the XGXXPG consensus pattern, allowing interaction with the elastin receptor complex located at the surface of cells. Besides these elastokines, another class of peptides has been identified. This group of bioactive elastin peptides presents the XGXPGXGXG consensus sequence, but the reason for their bioactivity remains unexplained. To better understand their nature and structure-function relationships, herein we searched the current databases for this nonapeptide motif and observed that the XGXPGXGXG elastin peptides define a specific group of tandemly repeated patterns. Further, we focused on four tandemly repeated human elastin nonapeptides, i.e., AGIPGLGVG, VGVPGLGVG, AGVPGLGVG, and AGVPGFGAG. These peptides were analyzed by means of optical spectroscopies and molecular dynamics. Ultraviolet-circular dichroism and Raman spectra are consistent with a mixture of β-turn, β-strand, and random-chain secondary elements in aqueous media. Quantitative analysis of their conformations suggested that turns corresponded to half of the total population of structural elements, whereas the remaining half were equally distributed between β-strand and unordered chains. These distributions were confirmed by molecular dynamics simulations. Altogether, our data suggest that these highly dynamic peptides harbor a type II β-turn located in their central part. We hypothesize that this structural element could explain their specific bioactivity.

Disorder-to-Order Markers of a Cyclic Hexapeptide Inspired from the Binding Site of Fertilin β Involved in Fertilization Process.

Synthetic peptides mimicking the binding site of fertilin β to its receptor, integrin α6β1, were shown to inhibit sperm–egg fusion when added to in vitro media. In contrast, the synthetic cyclic hexapeptide, cyclo(Cys1-Ser2-Phe3-Glu4-Glu5-Cys6), named as cFEE, proved to stimulate gamete fusion. Owing to its biological specificity, this hexapeptide could help improve the in vitro fertilization pregnancy rate in human. In an attempt to establish the structure–activity relationship of cFEE, its structural dynamics was herein analyzed by means of ultraviolet circular dichroism (UV-CD) and Raman scattering. The low concentration CD profile in water, containing mainly a deep minimum at ∼202 nm, is consistent with a rather unordered chain. However, an ordering trend of the peptide loop has been observed in a less polar solvent such as methanol, where the UV-CD signal shape is formed by a double negative marker at ∼202/215 nm, indicating the presence of a type-II′ β-turn. Raman spectra recorded in aqueous samples upon a 100-fold concentration increase, still showed an important population (∼30%) of the disordered structure. The structural flexibility of the disulfide bridge was confirmed by the Raman markers arising from the Cys1-Cys6 disulfide bond-stretch motions. Density functional theory calculations highlighted the formation of the type-II′ β-turn on the four central residues of cFEE (i.e., -Ser2-Phe3-Glu4-Glu5-) either with a left- or with a right-handed disulfide. The structure with a left-handed S–S bond, however, appears to be more stable.

Dynamical Behavior of Somatostatin-14 and Its Cyclic Analogues as Analyzed in Bulk and on Plasmonic Silver Nanoparticles.

Primarily known as the inhibitor of growth hormone release, the role of somatostatin in many other inhibiting activities upon binding to its five G-protein-coupled receptors has been elucidated. Because of the short half-life of somatostatin, a number of synthetic analogues were elaborated for this peptide hormone. Herein, after recalling the main somatostatin therapeutic interests, we present the dynamical behavior of somatostatin-14 and its two currently used synthetic cyclic analogues, octreotide and pasireotide. Physical techniques, such as fluorescence, UV-visible absorption, circular dichroism, Raman spectroscopy, surface-enhanced Raman spectroscopy, and transmission electron microscopy, were jointly used in order to get information on the solution structural features, as well as on the anchoring sites of the three peptides on silver colloids. While somatostatin-14 adopts a rather unordered chain within the submillimolar concentration range, its cyclic analogues were revealed to be ordered, i.e., stabilized either in a type-II' β-turn (octreotide) or in a face-to-face γ-turn/type-I β-turn (pasireotide) structure. Nevertheless, a progressive structuring trend was observed in somatostatin-14 upon increasing concentration to the millimolar range. Because of their cationic character, the three peptides have revealed their capability to bind onto negatively charged silver nanoparticles. The high affinity of the peptides toward metallic particles seems to be extremely promising for the elaboration of somatostatin-based functionalized plasmonic nanoparticles that can be used in diagnosis, drug delivery, and therapy.

Effect of mechanical deformation on the structure of regenerated Bombyx mori silk fibroin films as revealed using Raman and infrared spectroscopy.

To better understand the effect of mechanical stress during the spinning of silk, the protein orientation and conformation of Bombyx mori regenerated silk fibroin (RSF) films have been studied as a function of deformation in a static mode or in real time by tensile-Raman experiments and polarization modulation infrared linear dichroism (PM-IRLD), respectively. The data show that either for step-by-step or continuous stretching, elongation induces the progressive formation of β-sheets that align along the drawing axis, in particular above a draw ratio of ~2. The formation of β-sheets begins before their alignment during a continuous drawing. Unordered chains were, however, never found to be oriented, which explains the very low level of orientation of the amorphous phase of the natural fiber. Stress-perturbed unordered chains readily convert into β-sheets, the strain-induced transformation following a two-state process. The final level of orientation and β-sheet content are lower than those found in the native fiber, indicating that various parameters have to be optimized in order to implement a spinning process as efficient as the natural one. Finally, during the stress relaxation period in a step-by-step drawing, there is essentially no change of the content and orientation of the β-sheets, suggesting that only unordered structures tend to reorganize.

Poset-ting the Phronetic: Coming to Rowing Terms in Robert Morris's Doubles and Pairs

POSET-TING THE PHRONETIC: COMING TO ROWING TERMS IN ROBERT MORRIS’S DOUBLES AND PAIRS DAVID HENNING PLYLAR I calmly write: “In the beginning was the deed!”1 And the deed stipulated the terms and conditions of occupancy.2 I N HIS ESSAY/TALK “COMPOSING EACH TIME,” Robert Morris refers simultaneously to his composition Each Time and the renewed act of composing each time he does so. I had the pleasure of hearing the talk and later reading it in his collection of essays, The Whistling Blackbird. There are many insights to be gained from the study of the rich body of Morris’s work (in which I include his musical compositions, his writings I Poset-ting the Phronetic 227 and his considered remarks in conversation. Off-the-cuff statements or jokes are ornaments that reflect his improvisatory interests). “Composing Each Time” eloquently addresses some issues concerning the compositional process, and Morris’s addition of a short preface to the printed edition of the talk led to an unordered chain of ideas that resulted in my writing this brief text. Morris invokes the weight and wisdom of one of history’s great thinkers in this preface, a member of only the third generation to benefit from and appreciate the fruits of a dominant Platonic relationship: Aristotle. Drawing on this part of the Hellenic tradition struck me as a move calculated to show that, among other things, modern problems of art creation and reception are not historically unique. At various points in the compositional process, Morris adjusts his Aris-throttle to make artistically viable decisions as the aesthetic situation demands. II Labels of styles or movements, while expedient, have the unfortunate side effect of packaging a world-view in a conveniently disposable thought-crumple. Some members of the musical community at large may seize on such a label and, politike in praxis, throw out the bathtub with the baby.3 Morris, however, is not an apologist and does not need to be. Any attentive listener can hear that there is substantial depth and diversity in the music of Robert Morris. I do not hear his music in the same way that you or he does, and thankfully so. One of Morris’s great pedagogical strengths (in and out of the classroom) is his encouragement of a pluralistic approach to reception and analysis. Sometimes Morris’s commentary is Greek to me; but his application of some tenets of pre-modern philosophy to his own compositional process is actually a rallying cry to those who see the value in the merger of thought and the poetic—or rather, to those who suspect there never was such a division in the first place. While the wanderings of my own prose may be comparably parapathetic, may you temporarily chart your course with stoic resolve through a garden rife with mixed metaphor,4 as we come to rowing terms in doubles and pairs. We can do this working together (as it happens, not in harmony: Example 1A) . . . . . . Or while not quite in sync (Examples 1B and 1C). 228 Perspectives of New Music T9I: 93614TE75208 m. 64: T9I rotated and manipulated: E 893614T572(7272)0 T9I: 93614T E75208 EXAMPLE 1A: ROBERT MORRIS, DOUBLES AND PAIRS, M. 64 RT9I: 80257ET41639 mm. 39–40: RT9I rotated and manipulated: 57ET4163 8 (0392) EXAMPLE 1B: ROBERT MORRIS, DOUBLES AND PAIRS, MM. 39–40 Poset-ting the Phronetic 229 III Many of life’s experiences tend to be cyclical in nature, though certain trajectories trace a more linear path,5 such as an individual’s life cycle (the cycle here applies to the disembodied perception of one observing a population, or various religious doctrines the cycles of which generally still have an ultimate terminus). Heraclitean rivers may not be the same for every footstep they receive, but there may be intersubjective agreement that the river exists, possesses certain characteristics, and at least for the time being follows a particular path. It is important to note that this non-comprehensive suggestion refers to perception and not assertions of actuality. Heraclitus’s river here represents the flow of historical time, as perceived by the multiplicity of streams of consciousnesses . We may not agree on...

Study of the Ribonuclease S-Peptide/S-Protein Complex by Means of Raman Difference Spectroscopy

The isolated S-peptide (enzymatically cleaved 1−20 fragment of the ribonuclease, RNase S) is partly helical in solution. Both S-peptide and its truncated 1−15 analogue pep01 can combine with S-protein (residual part of RNase S without S-peptide), restoring a RNase S‘ complex. Part 3−13 of the peptides forms an α-helix when within the RNase S‘ complex. To compare the solvated forms of both peptides with their structures when complexed with the S-protein, we have measured the Raman spectra of these forms by means of difference spectroscopy. The spectra of the peptides in water solutions are characterized by much wider vibrational bands than the spectrum of the peptides within the RNase S‘ complexes. This shows that the structure of the solvated peptides consists of a heterogeneous mixture of interconverting species. Only two main bands characteristic for the exposed α-helix (in D2O) and for an unordered chain are observed for amide-I regions of the dissolved peptides spectra. Relative intensities of the ban...

Backbone folding of the polypeptide cardiac stimulant anthopleurin-A determined by nuclear magnetic resonance, distance geometry and molecular dynamics

The solution conformation of the cardiac stimulatory sea anemone polypeptide anthopleurin-A has been characterised using distance geometry and restrained molecular dynamics calculations. A set of 253 approximate interproton distance restraints and 14 peptide backbone torsion angle restraints derived from two-dimensional 1H-NMR spectra at 500 MHz were used as input for these calculations. 13 structures generated by either metric matrix or variable target function distance geometry calculations were refined using energy minimisation and restrained molecular dynamics. The resulting structures contain a region of twisted antiparellel beta-sheet to which two separate regions of unordered chain are linked by three disulphide bonds. Two loops, one including Pro-41 and the other encompassing residues 10-18, are poorly defined by the NOE data.

Vibrational circular dichroism spectra of three conformationally distinct states and an unordered state of poly(L-lysine) in deuterated aqueous solution.

AbstractFourier transform ir vibrational circular dichroism (VCD) spectra in the amide I′ region of poly(L‐lysine) in D2O solutions have confirmed the existence of three distinct conformational states and an unordered conformational state in this homopolypeptide. Characteristic VCD spectra are presented for the right‐handed α‐helix, the antiparallel β‐sheet, an extended helix conformation previously referred to as the so‐called “random coil,” and a completely unordered conformation characterized by the absence of any amide I′ VCD. VCD for the antiparallel β‐sheet in solution and the unordered chain conformation are presented for the first time. Each of the four different VCD spectra is unique in appearance and lends weight to the view that VCD has the potential to become a sensitive new probe of the secondary structure of proteins in solution.

Molecular motion of polycarbonate in the vicinity of −60°C as revealed by broad-line n.m.r., magic angle spinning n.m.r. and conformational analysis

On the basis of correlation of data obtained by broad-line n.m.r. and magic angle spinning n.m.r. analysis as well as conformational analysis, conclusions have been drawn concerning the nature of molecular motion occurring in a polycarbonate chain in the vicinity of −60°C. It is postulated that this motion is connected with conformational reorientation of bisphenol in unordered chains with a random conformation.

Identification of β,β-turns and unordered conformations in polypeptide chains by vacuum ultraviolet circular dichroism

Different conformations of polypeptides were characterized by measurements of the circular dichroism (CD) extended into the vacuum ultraviolet region. (i) The linear beta-pleated sheet structure was characterized in a broad ultraviolet region down to 165 nm by examination of copolypeptides composed of alternating hydrophobic and hydrophilic amino-acid residues, e.g., poly(Lys-Leu-Lys-Leu). A short-wavelength intense band was found at about 169 nm, which is characteristic of beta-pleated sheet conformation. (ii) The beta-turns were experimentally measured using poly(Ala(2)-Gly(2)) in a broad spectral region down to 165 nm with accuracy. The observed CD spectrum is in excellent qualitative agreement with the theoretical curve calculated by Woody for the beta-turns of type II and/or I of Venkatachalam. The similarity in shape between the theoretical curve and the observed CD spectra suggests a dominance of beta-turn segments in the poly(Ala(2)-Gly(2)) structure. The presence of beta-turns in poly(Ala(2)-Gly(2)) is also in agreement with the characterization of this polypeptide by solid state methods (electron microscopy and x-ray diffraction). The CD spectrum of beta-turns is characterized by a very intense band at 207.5 nm and strong negative bands at 191 and 169 nm. Copolypeptides such as poly(Ala(2)-Gly(3)) and poly(Ala(3)-Gly(3)) yielded a similar type of CD spectrum, analysis of which indicates that a large fraction of their residues is contained in beta-turn regions. (iii) The CD spectrum of the unordered chain of these alternating copolypeptides in salt-free solution is observed in the vacuum ultraviolet region.

Effect of temperature on the circular dichroism spectra of polypeptides in the extended state.

AbstractThe circular dichroism (CD) spectra of poly‐L‐proline and of poly‐L‐glutamic acid and poly‐L‐lysine in their charged states have been studied as a function of temperature. The variation of CD spectra with temperature is inconsistent with the assignment of the spectrum of such charged polypetides to an unordered chain conformation, but does support our earlier assignment to a locally ordered structure—what we have called the extended helix conformation. These results also strengthen our previous assignment of the CD spectrum of an unordered chain, and indicate that three conformational states (α‐helix, extended helix, and unordered) should be incorporated in our thinking about conformational transitions in polypeptides.