Dynamics Study of the Influence of Temperature on Konjac Glucomannan Saline Solution’s Viscosity

Molecular dynamics (MD) method is adopted to simulate the conformation variations of konjac glucomannan (KGM) saline solution at different temperatures, and structurally analyze the trends and reasons of viscosity change in KGM saline solution with temperature. The experimental results have been analyzed to find out that the sum of formative hydrogen bonds decreases with the rise of temperature and the amount of intramolecular hydrogen bonds suddenly increases at 323 K. Besides, in terms of molecular orbital data obtained from simulation, we can know that hydrogen bonding energy also decreases with the rise of temperature. Therefore, we can predict the viscosity of KGM saline solution decreases gradually when rising the temperature.     

Dynamics Study of the Influence of Temperature on Konjac Glucomannan Saline Solution＇s Viscosity

Molecular dynamics （MD） method is adopted to simulate the conformation variations of konjac glucomannan （KGM） saline solution at different temperatures, and structurally analyze the trends and reasons of viscosity change in KGM saline solution with temperature. The experimental results have been analyzed to find out that the sum of formative hydrogen bonds decreases with the rise of temperature and the amount of intramolecular hydrogen bonds suddenly increases at 323 K. Besides, in terms of molecular orbital data obtained from simulation, we can know that hydrogen bonding energy also decreases with the rise of temperature. Therefore, we can predict the viscosity of KGM saline solution decreases gradually when rising the temperature.     

Molecular Dynamics Simulations of the Interactions between Konjac Glucomannan and Carrageenan

The interactions between konjac glucomannan and carrageenan were studied with the method of molecular dynamics simulation. Part representative structure segments of KGM and two unit structures of κ-carrageenan （Fig. 2） were used as mode, and the force-field was AMBER2. The stability and sites of konjac glucomannan/carrageenan interactions in water were researched at 373 K with the following results： the potential energy （EPOT） of the mixed gel was dropped, while those of single-konjac glucomannan gel and single carrageenan were increased. The surface area （SA） of KGM in the mixed system was decreased to 1002.2A^°^2, and that of carrageenan to 800.9 A^°^2. The variations of two parameters showed that the stability of compound gel konjac glucomannan/carrageenan was improved, which is consistent with the previous studies. The sites of interactions in the mixed gel were the -OH groups on C（2）, C（4） and C（6）, the acetyl group in KGM mannose, and the -OH group on C（6） in carrageenan. The hydrogen bond was formed directly or indirectly by the bridge of waters.     

Formation Mechanism and Stability Study of Konjac Glucomannan Helical Structure

The formation mechanism and stability of konjac glucomannan (KGM) helical structure were investigated by molecular dynamic simulation and experimental method. The results indicate that the molecular conformation of KGM is a non-typical helical structure. In detail, helical structure of KGM is mainly sustained by acetyl group, whose size and stability are affected by the molecular polymerization degree of KGM. In vacuum among the non-bonding interactions, electrostatic force is the greatest factor affecting its helical structure, but in water solution, hydrogen bond affects the helical arrangement greatly. To our interest, temperature exhibits a reversible destroying effect to some extent; the helical structure will disappear completely and present a ruleless clew-like arrangement till 341 K. This work suggests that the method of combining molecular dynamic simulation and experiment tools can be effective in the study of KGM helical structure.     

Effect of Plasma Treatment on the Structures and Properties of Konjac Glucomannan Film

To understand the effect of plasma treatment on the Konjac glucomannan film, the nitrogen plasma was injected into the film by ion beam injection machine in this study. The structures and properties of Konjac glucomannan film after plasma treatment were analyzed by Infrared spectroscopy, Raman spectrum, X-ray, ect. The result showed that nitrogen groups appeared in the KGM molecular chain and part of this chain fractured, and the number of hydrogen bonds increased after the treatment of plasma. The form of KGM molecule remained amorphous non-crystalline state, but the crystalline region was increased and became more ordered. The mechanical property of tensile strength and breaking elongation was improved, while the WVP was decreased. The nitrogen groups were grafted on the KGM molecular chain after plasma treatment, which led to the improvement of the properties of KGM film.     

Conformational Studies on Polytripeptides as a Model of Collagen

To study the role of glycine residues in stabilizing the collagen triple helix, the glycine residues in the polytripeptide (Pro-Ala-Gly)_n were partially replaced by alanine. The proline content was kept constant. The stability of the helical conformation of these polypeptides was studied by IR- and X-ray measurements in the solid state and by ORD, CD and viscometry in solution. The renaturation was followed as a function of time. All the polytripeptides studied, with the exception of (-Pro-Ala-Ala-)_n attained the polyproline II conformation. However the stability decreased with increasing alanine content. Obviously the molecules of (-Pro-Ala-Gly-) are highly associated by intermolecular hydrogen bonds and one may therefore suppose that a triple-stranded helix aggregation occurs. The results of the refolding process show that the stability of the helices seems to also affect the refolding rate in terms of the optical rotation, Two transitions appeared: the first one is responsible for a rapid reversible change in conformation and the second one for a further slow and irreversible change in the hydrodynamic shape. The latter seems to be due to the partial helical nature, leading to higher chain mobility.     

The Effects of Various Alcohols on the Stability of Melittin: A Molecular Dynamics Study

In this study, 200 ps molecular dynamics simulations were conducted to investigate the effects of various alcohols on the structural stability of melittin. The averaged helicity of melittin remained 80% in pure butanol, whereas it was below 60% both in pure water and in pure methanol. The α‐helix propensity of melittin increased with the aliphatic chain length of the alcohol. Charge‐charge interaction between Lys21 and Arg24 and polar‐nonpolar interaction between Trp19 and Arg22 are probably responsible for the higher structural integrity of the C‐terminal α‐helix over the N‐terminal one. The weaker dielectric constant of longer aliphatic chain length of alcohol possibly reduces the hydrogen bonding between amide protons and surrounding solvent molecules and simultaneously promotes the intramolecular hydrogen bonding in melittin and therefore stabilizes the secondary structure of melittin. The effect of various alcohols on stabilizing melittin is most likely due to their ability to form clusters on the surface of melittin effectively, favoring the formation of intramolecular hydrogen bonds instead of intermolecular hydrogen bonds and promoting the formation of stable α‐helices.     

A novel type of optically active helical polymers: Synthesis and characterization of poly(N‐propargylureas)

This article presents two novel artificial helical polymers, substituted polyacetylenes with urea groups in side chains. Poly( 4 ) and poly( 5 ) can be obtained in high yields (≥97%) and with moderate molecular weights (11,000–14,000). Poly( 4 ) contains chiral centers in side chains, and poly( 5 ) is an achiral polymer. Both of the two polymers adopted helical structures under certain conditions. More interestingly, poly( 4 ) exhibited large specific optical rotations, resulting from the predominant one‐handed screw sense. The helical conformation in poly( 5 ) was stable against heat, while poly( 4 ) underwent conformational transition from helix to random coil upon increasing temperature from 0 to 55 °C. Solvents had considerable influence on the stability of the helical conformation in poly( 4 ). The screw sense adopted by the helices was also largely affected by the nature of the solvent. Poly( 4 ‐co‐ 5 )s formed helical conformation and showed large optical rotations, following the Sergeants and Soldiers rule. By comparing the present two polymers (with one ? N? H groups) with the three polymers previously reported (with two ? N? H groups in side chains), the nature of the hydrogen bonds formed between the neighboring urea groups played big roles in the formation of stable helical conformation. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4112–4121, 2008     

Multiple conformational states in crystals and in solution in alphagamma hybrid peptides. Fragility of the C12 helix in short sequences

The conformational properties of foldamers generated from alphagamma hybrid peptide sequences have been probed in the model sequence Boc-Aib-Gpn-Aib-Gpn-NHMe. The choice of alpha-aminoisobutyryl (Aib) and gabapentin (Gpn) residues greatly restricts sterically accessible conformational space. This model sequence was anticipated to be a short segment of the alphagamma C12 helix, stabilized by three successive 4-->1 hydrogen bonds, corresponding to a backbone-expanded analogue of the alpha polypeptide 3(10)-helix. Unexpectedly, three distinct crystalline polymorphs were characterized in the solid state by X-ray diffraction. In one form, two successive C12 hydrogen bonds were obtained at the N-terminus, while a novel C17 hydrogen-bonded gamma alpha gamma turn was observed at the C-terminus. In the other two polymorphs, isolated C9 and C7 hydrogen-bonded turns were observed at Gpn (2) and Gpn (4). Isolated C12 and C9 turns were also crystallographically established in the peptides Boc-Aib-Gpn-Aib-OMe and Boc-Gpn-Aib-NHMe, respectively. Selective line broadening of NH resonances and the observation of medium range NH(i) <--> NH(i+2) NOEs established the presence of conformational heterogeneity for the tetrapeptide in CDCl3 solution. The NMR results are consistent with the limited population of the continuous C12 helix conformation. Lengthening of the (alphagamma) n sequences in the nonapeptides Boc-Aib-Gpn-Aib-Gpn-Aib-Gpn-Aib-Gpn-Xxx (Xxx = Aib, Leu) resulted in the observation of all of the sequential NOEs characteristic of an alphagamma C12 helix. These results establish that conformational fragility is manifested in short hybrid alphagamma sequences despite the choice of conformationally constrained residues, while stable helices are formed on chain extension.     

The molecular and crystal structure of tert-butyl Nalpha-tert-butoxycarbonyl-L-(S-trityl)cysteinate and the conformation-stabilizing function of weak intermolecular bonding

The title compound, C31H37NO4S [systematic name: (R)-tert-butyl-2-[(tert-butoxycarbonyl)amino]-3-(tritylsulfanyl)propanoate] is an L-cysteine derivative with three functions: NH2, COOH and SH, blocked by protecting groups tert-butoxycarbonyl, tert-butyl and trityl, respectively. The main chain of the molecule adopts the extended, nearly all-trans C5 conformation with the intramolecular N-H...O=C hydrogen bond. The urethane group is not involved in any intermolecular hydrogen bonding. Only weak intermolecular hydrogen bonds and hydrophobic contacts are observed in the crystal structure. These are C-H...O hydrogen bonds and CH/pi interactions with donor...acceptor distances, C...O ca. 3.5 A and C...C ca. 3.7 A, respectively. The first type of interaction links phenyl H-atoms and carbonyl groups. The second type of interaction is formed between a methyl group of the tert-butyl fragment and a trityl phenyl ring. The resulting molecular conformation in the crystal is very close to an ab initio minimum energy conformer of the isolated molecule. The extended C5 conformation of the main peptide chain is the same and there is slight discrepancy in the disposition of trityl phenyl rings. Their small dislocation creates the possibility of forming the entire network above of extensive, specific, weak intermolecular interactions; these constrain the molecule and permit it to retain the minimum energy C5 conformation of its main chain in the solid state. In contrast, in n-hexane solution, where such specific interactions cannot occur, only a small population of the molecules adopts the extended C5 conformation.     

Low-frequency vibrational spectrum of water in the hydration layer of a protein: a molecular dynamics simulation study

An atomistic molecular dynamics simulation has been carried out to understand the low-frequency intermolecular vibrational spectrum of water present in the hydration layer of the protein villin headpiece subdomain or HP-36. An attempt is made to explore how the heterogeneous rigidity of the hydration layers of different segments (three alpha helices) of the protein, strength of the protein-water hydrogen bonds, and their differential relaxation behavior influence the distribution of the intermolecular vibrational density of states of water in the hydration layers. The calculations revealed that compared to bulk water these bands are nonuniformly blue-shifted for water near the helices, the extent of shifts being more pronounced for water molecules hydrogen bonded to the protein residues. It is further noticed that the larger blue shift observed for the water molecules hydrogen bonded to helix 2 residues correlates excellently with the slowest structural relaxation of these hydrogen bonds. These results can be verified by suitable experimental measurements.     

Studies on Single Chain Structure of Konjac Glucomannan

1INTRODUCTION The single chain structure of KGM is the ele-mentary acting unit of its biological function and viscoelasticity of mechanical properties.The re-search method of saccharide chain and the com-plexity of its structure have restricted the study on structure-activity relationship.Therefore,the studies concerning KGM both at home and abroad mainly focus on its application,whereas less on its structure.Previous researches were only related to the determination and distribution as…     

Probing the role of the C-H...O hydrogen bond stabilized polypeptide chain reversal at the C-terminus of designed peptide helices. Structural characterization of three decapeptides

The structural characterization in crystals of three designed decapeptides containing a double d-segment at the C-terminus is described. The crystal structures of the peptides Boc-Leu-Aib-Val-Xxx-Leu-Aib-Val-(D)Ala-(D)Leu-Aib-OMe, (Xxx = Gly 2, (D)Ala 3, Aib 4) have been determined and compared with those reported earlier for peptide 1 (Xxx = Ala) and the all l analogue Boc-Leu-Aib-Val-Ala-Leu-Aib-Val-Ala-Leu-Aib-OMe, which yielded a perfect right-handed alpha-helical structure. Peptides 1 and 2 reveal a right-handed helical segment spanning residues 1 to 7, ending in a Schellman motif with (D)Ala(8) functioning as the terminating residue. Polypeptide chain reversal occurs at residue 9, a novel feature that appears to be the consequence of a C-H.O hydrogen bond between residue 4 C(alpha)H and residue 9 CO groups. The structures of peptides 3 and 4, which lack the pro R hydrogen at the C(alpha) atom of residue 4, are dramatically different. Peptide 3 adopts a right-handed helical conformation over the 1 to 7 segment. Residues 8 and 9 adopt alpha(L) conformations forming a C-terminus type I' beta-turn, corresponding to an incipient left-handed twist of the polypeptide chain. In peptide 4, helix termination occurs at Aib(6), with residues 6 to 9 forming a left-handed helix, resulting in a structure that accommodates direct fusion of two helical segments of opposite twist. Peptides 3 and 4 provide examples of chiral residues occurring in the less favored sense of helical twist; (D)Ala(4) in peptide 3 adopts an alpha(R) conformation, while (L)Val(7) in 4 adopts an alpha(L) conformation. The structural comparison of the decapeptides reported here provides evidence for the role of specific C-H.O hydrogen bonds in stabilizing chain reversals at helix termini, which may be relevant in aligning contiguous helical and strand segments in polypeptide structures.     

Construction of Helically Stacked π-Electron Systems in Poly(quinolylene-2,3-methylene) Stabilized by Intramolecular Hydrogen Bonds

π-Stacked polymers, which consist of layered π-electron systems in a polymer, can be expected to be used in molecular electronic devices. However, the construction of a stable π-stacked structure in a polymer is considerably challenging because it requires sophisticated designs and precise synthetic methods. Herein, we present a novel π-stacked architecture based on poly(quinolylene-2,3-methylene) bearing alanine derivatives as the side chain, obtained through the living cyclo-copolymerization of an o-allenylaryl isocyanide. In the resulting polymer, the neighboring quinoline rings of the main chain form a layered structure with π–π interactions, which is stabilized by intramolecular hydrogen bonds. The vicinal quinoline units form two independent helices and the whole molecule is a twisted-tape structure. This structure is established on the basis of UV/CD spectra, theoretical calculations, and atomic-force microscopy.     

alpha and piDL helical states of alternating poly(gamma-benzyl D-L-glutamate) in solution.

As in solid state, strictly alternating poly(gamma-benzyl D-L-glutamate) in solution can adopt two different helical conformations. Besides the alpha helix, a second helical conformation is found at higher temperatures in dioxane and chloroform, the properties of which correspond to that of the piDL4 helix. As the molecules have a finite length a screw sense is favored for both helical forms thus giving rise to optical activity allowing the study of the transconformation by optical rotatory dispersion and circular dichroism besides infrared and dielectric measurements. Thus, as the temperature is raised the equilibria right-left handed alpha helices and alpha-piDL helical forms can be followed. The favored screw senses are determined by the number of interacting side chains for the alpha helix and by the number of hydrogen bonds which are formed in the piDL helical conformation. The side chain-side chain interactions in the alpha helix are experimentally shown to be attractive.     

Studies on Hydrogen Bonding Network Structures of Konjac Glucomannan

In this paper, the hydrogen bonding network models of konjac glucomannan （KGM） are predicted in the approach of molecular dynamics （MD）. These models have been proved by experiments whose results are consistent with those from simulation. The results show that the hydrogen bonding network structures of KGM are stable and the key linking points of hydrogen bonding network are at the O（6） and O（2） positions on KGM ring. Moreover, acety has significant influence on hydrogen bonding network and hydrogen bonding network structures are more stable after deacetylation.     

Chain conformation in polyretropeptides. II. Quantum mechanical and empirical force field calculations on 2,5,9,11-Tetraoxo-3,6,8,12-tetraza-tridecane,a model compound for the terpolymer of glycine and its retropeptides

A conformational study of the terpolymer of glycine and its retropeptides monomethylen-diamine (gGly) and malonyl (mGly) with sequence: (-Gly-gGly-mGly-), is presented. First, we investigated the conformational preferences of the model molecule 2,5,9,11-tetraoxo-3,6,8,12-tetraza-tridecane using quantum mechanical calculations. The results indicated that the compound has a strong tendency to fold, giving intramolecular hydrogen bonds. Interestingly, the C₁₃ (intramolecular 13-membered ring hydrogen-bonded system) conformation, which is the pattern of an α-helix conformation, was characterized as a minimum. Force-field calculations in an infinite chain model showed that there are two preferred conformations to this regular polyretropeptide. These correspond to an α-helix and a 6-fold helix stabilized by intramolecular and intermolecular hydrogen bonds, respectively. © 1996 John Wiley & Sons, Inc.     

Theoretical study of intramolecular interaction energies during dynamics simulations of oligopeptides by the fragment molecular orbital-Hamiltonian algorithm method

We analyzed the interaction energies between residues (fragments) in an oligopeptide occurring during dynamic simulations by using the fragment molecular orbital-Hamiltonian algorithm (FMO-HA) method, an ab initio MO-molecular dynamics technique. The FMO method enables not only calculation of large molecules based on ab initio MO but also easy evaluation of interfragment interaction energies. The glycine pentamer [(Gly)(5)] and decamer [(Gly)(10)] were divided into five and ten fragments, respectively. alpha-helix structures of (Gly)(5) and (Gly)(10) were stabilized by attractive interaction energies owing to intramolecular hydrogen bonds between fragments n and n+3 (and n+4), and beta-strand structures were characterized by repulsive interaction energies between fragments n and n+2. We analyzed interfragment interaction energies during dynamics simulations as the peptides' geometries changed from alpha helix to beta strand. Intramolecular hydrogen bonds between fragments 2-4 and 2-5 control the geometrical preference of (Gly)(5) for the beta-strand structure. The pitch of one turn of the alpha helix of (Gly)(10) elongated and thus weakened during dynamics due to a shifting of the intramolecular hydrogen bonds, and enabled the beta-strand structure to form. Changes in interaction energies due to the intramolecular hydrogen bonds controlled the tendency toward alpha-helix or beta-strand structure of (Gly)(5) and (Gly)(10). Evaluation of interfragment interaction energies during dynamics simulations thus enabled detailed analysis of the process of the geometrical changes occurring in oligopeptides.     

Aromatic δ-peptides: design, synthesis and structural studies of helical, quinoline-derived oligoamide foldamers

Oligoamides of 8-amino-4-isobutoxy-2-quinolinecarboxylic acid were designed and synthesized, and their helical structures were characterized in the solid state by single crystal X-ray diffraction, and in solution by ¹H NMR. The monomer methyl 4-isobutoxy-8-nitro-2-quinolinecarboxylate is easily prepared in three steps from 2-nitroaninile and dimethyl acetylene dicarboxylate. Successive hydrogenations of nitro groups, saponifications of esters and couplings of amines and acids via the acid chlorides gave a dimer, tetramer, hexamer, octamer, and decamer in a convergent fashion. The oligomers were shown to adopt a bent conformation stabilized by intramolecular hydrogen bonds between amide hydrogens and adjacent quinoline nitrogens. In the solid, the dimer adopts a planar crescent shape and the octamer a helical conformation. All NMR data are consistent with similar conformations in solution. The helices are apparently remarkably stable. Some of them remain helical even at 120°C in deuterated DMSO. The structural studies confirm the predictions made by computer and demonstrate the high potency of the design principles.     

Origin of the pKa perturbation of N-terminal cysteine in alpha- and 3(10)-helices: a computational DFT study

It is well documented that helices in proteins can decrease the pKa of residues located at the N-terminus, but the real nature of this perturbation remains unclear. In the present work, the origin of the effect of 3(10)- and alpha-polyalanine helices on the pKa of an N-terminal cysteine residue is examined in gas phase as well as in aqueous solution by means of density functional theory. In a systematic study of the helix dipole, the proton affinity (PA), and the pKa of the N-terminal cysteine, in relation to both the helix length and the strength of the hydrogen bonds between the helix backbone amides and the Sgamma of the N-terminal cysteine, a direct relation between the terminal hydrogen bonds and the pKa perturbation is revealed.