Helix In Aqueous Solution Research Articles

Molecular dynamics simulation: Effect of sulfation on the structure of curdlan triple helix in aqueous solution

In this work, by using molecular dynamics simulations, we elucidate the effect of sulfation substitution on the stability of the curdlan triple helix structure. The simulation results indicate that the stability of the triple helix structure is significantly influenced by the sites of sulfation substitution. The substitution at the O2 site directly disrupts the hydrogen bonding network between the triple helix chains, significantly destroying the triple helix conformation. When substitutions occur at both the O4 and O6 sites simultaneously (O4,6), the electrostatic repulsion between numerous sulfate groups introduces considerable energy perturbation to the triple helix, leading to alterations in the glucan chain conformation and consequent destabilization of the triple helix structure. Meanwhile, we find that even if the sulfation substitution is performed at the same substitution sites, the difference in the degree of substitution also has an impact on the triple helix stability. The resistance of the triple helix to sulfation substitution at O2 is weak, and low degree of substitution can lead to the unwinding of the triple helix. However, it demonstrates higher resistance to substitution at O4,6 where only higher degree of substitution results in triple helix destabilization.

Circularly polarized luminescence of polymers with coil to helix transformation in water system triggered via metal coordination

Circularly polarized luminescence (CPL) of conjugated polymers is promising functional materials for a wide range application, particularly in the field of chiral optoelectronic devices. It is critical yet challenging to endow these materials against varied environment change, such as polarity of water, due to the destruction of the induced helicity of conjugated polymers by water hydrogen bonding. In this contribution, a series of aqueous phase CPL-active materials are constructed through the synergistic effect of hydrogen bonding and metal coordination. The fluorescent random coil amino acid-based poly( N -propargylamide) exhibiting obvious CD and CPL effects are induced by metal ions in aqueous solution. The conformational transition from coil to helix and the CPL performance are distinctly depicted via the CD, CPL signals and noticeably red-shifted UV–vis absorption. Moreover, the luminescence dissymmetry factor (| g lum |) values of the induced helical polymers were up to 8.07 × 10 −3 and 2.73 × 10 −2 , respectively, in aqueous solution and thin films. It was found that the successful induction of aqueous phase CPL-active polymer attribute to chiral amplification and aggregation-enhanced emission (AEE) effect of contracted cis-cisoidal helical main chain. These results indicated a general and simple approach for the construction of aqueous phase CPL materials, and a possible relationship between geometric structure of helical conformation and the CPL-activity induction of optically inactive polymers are simultaneously established. This contribution broadens practically chiroptical applications of CPL materials in water environment and enriches the synthetic types of CPL materials. • The CPL-active polymer based on cis-cisoid helix in aqueous solution and thin films states is prepared. • The | g lum | value of the prepared polymer in aqueous solution and films are as high as to 8.07 × 10 −3 and 2.73 × 10 −2 , respectively. • The successful trigger of CPL-activity attribute to chiral amplification and aggregation-enhanced emission (AEE) effect of one-handed helical structure.

Discrete Stacked Dimers of Aromatic Oligoamide Helices.

Tight binding was observed between the C‐terminal cross section of aromatic oligoamide helices in aqueous solution, leading to the formation of discrete head‐to‐head dimers in slow exchange on the NMR timescale with the corresponding monomers. The nature and structure of the dimers was evidenced by 2D NOESY and DOSY spectroscopy, mass spectrometry and X‐ray crystallography. The binding interface involves a large hydrophobic aromatic surface and hydrogen bonding. Dimerization requires that helices have the same handedness and the presence of a C‐terminal carboxy function. The protonation state of the carboxy group plays a crucial role, resulting in pH dependence of the association. Dimerization is also influenced by neighboring side chains and can be programmed to selectively produce heteromeric aggregates.

Diskrete gestapelte Dimere von aromatischen Oligoamid‐Helices

AbstractEine starke Bindung wurde zwischen den C‐terminalen Querschnitten von aromatischen Oligoamid‐Helices in wässriger Lösung beobachtet. Diese führt zur Bildung von diskreten Kopf‐an‐Kopf‐Dimeren, die im langsamen Austausch mit den entsprechenden Monomeren auf der NMR‐Zeitskala stehen. Die Art und Struktur der Dimere wurde durch 2D‐NOESY‐ und DOSY‐Spektroskopie, Massenspektrometrie und Röntgenkristallographie nachgewiesen. An der Bindungsschnittstelle beteiligt sind eine große hydrophobe aromatische Oberfläche und Wasserstoffbrückenbindungen. Die Dimerisierung setzt voraus, dass die Helices die gleiche Händigkeit aufweisen und eine C‐terminale Carboxyfunktion vorhanden ist. Der Protonierungszustand der Carboxygruppe spielt eine entscheidende Rolle und führt zu einer pH‐Abhängigkeit der Assoziation. Die Dimerisierung wird auch durch benachbarte Seitenketten beeinflusst und kann programmiert werden, um selektiv heteromere Aggregate zu bilden.

Liquid crystal phase behavior of a DNA dodecamer and the chromonic dye Sunset Yellow

Sunset Yellow (SSY) is an aromatic heterocycle nano-sheet functionalized by hydrophilic sulphanate groups. SSY forms chromonic stacks and liquid crystal (LC) phases in aqueous solution. The DNA oligomer 5\ensuremath{'}-GCGCTTAAGCGC-3\ensuremath{'} is a self-complementary strand which forms duplexed B-form helices in aqueous solution, which, similarly, aggregate into chromonic stacks and form LC phases. Binary aqueous solutions of these two molecules were investigated using polarized optical microscopy, x-ray diffraction, and spectroscopy. At lower solute concentrations and/or higher temperatures these solutions form uniformly mixed single phases, including isotropic, chiral nematic, and hexagonal columnar LCs. At higher solute concentrations and/or lower temperatures, the uniform columnar solution separates into two columnar phases, one containing SSY with trace DNA and the other containing both SSY and DNA aggregates. The study of these solutions indicates that the mixed and unmixed phases are composed of single component SSY or DNA chromonic stacks, with the DNA stacks containing a small fraction of intercalated SSY, evidenced by structurally induced circular dichroism in the SSY absorption band. In the columnar monophase, the hexagonal lattice sites are occupied randomly by either DNA or SSY columns, with the column spacing varying continuously with the SSY-DNA mass ratio. The results demonstrate significant selectivity in the chromonic stacking of both molecules. The binding mode of these chromonic LCs may have applications to adaptive optics and nucleic acid chemistry.

The isolated, twenty-three-residue-long, N-terminal region of the glutamine synthetase inactivating factor binds to its target

Glutamine synthetase (GS) catalyzes the ATP-dependent formation of glutamine from glutamate and ammonia. The activity of Synechocystis sp. PCC 6803 GS type I is regulated by protein-protein interactions with a 65-residue-long protein (IF7). IF7 binds initially to GS through residues at its N terminus. In this work, we studied the conformational preferences of the N-terminal region of IF7 (IF7pep, residues Ala7-Ala29), its binding to GS and its functional properties. Isolated IF7pep populated a nascent helix in aqueous solution. IF7pep was bound to GS with an affinity constant of 0.4μM, and a 1:1 stoichiometry. IF7pep did not inactivate GS, suggesting that there were other IF7 regions important to carry out the inactivating function. Binding of IF7pep to GS was electrostatically-driven and it did not follow a kinetic two-state model.

Structural dissection of the C-terminal sterile alpha motif (SAM) of human p73

The alpha splice variant of p73 (p73α), a homologue of the tumour suppressor p53, has at its C terminus a sterile alpha motif (SAM); this domain, SAMp73, is involved in lipid binding and it is thought to mediate in protein–protein interactions. SAMp73 is composed of five helices (α1–α5). In this work, we dissected SAMp73 in fragments encompassing the different helices, to study the conformational stability of the isolated elements of secondary structure. There was no evidence of stable residual helical structure in the isolated α1, α4 and α5 helices in aqueous solution, as shown by 2D-1H NMR and far-UV CD spectroscopies; those helices acquired native-like helical structure in the presence of 40% trifluoroethanol (TFE). The population of helical structure in α5 seemed to be driven by the indole moiety of Trp542, and it was enhanced by the presence of α4. On the other hand, helices α2 and 310(α3) had a tendency to self-associate even in TFE–water solutions. However, the short, aggregation-prone 310(α3) helix was key to attain the native-like fold of SAMp73, as suggested by experiments with non-covalent complexes among the peptides.

Probing polyproline structure and dynamics by photoinduced electron transfer provides evidence for deviations from a regular polyproline type II helix.

Polyprolines are well known for adopting a regular polyproline type II helix in aqueous solution, rendering them a popular standard as molecular ruler in structural molecular biology. However, single-molecule spectroscopy studies based on Förster resonance energy transfer (FRET) have revealed deviations of experimentally observed end-to-end distances of polyprolines from theoretical predictions, and it was proposed that the discrepancy resulted from dynamic flexibility of the polyproline helix. Here, we probe end-to-end distances and conformational dynamics of poly-l-prolines with 1-10 residues using fluorescence quenching by photoinduced-electron transfer (PET). A single fluorophore and a tryptophan residue, introduced at the termini of polyproline peptides, serve as sensitive probes for distance changes on the subnanometer length scale. Using a combination of ensemble fluorescence and fluorescence correlation spectroscopy, we demonstrate that polyproline samples exhibit static structural heterogeneity with subpopulations of distinct end-to-end distances that do not interconvert on time scales from nano- to milliseconds. By observing prolyl isomerization through changes in PET quenching interactions, we provide experimental evidence that the observed heterogeneity can be explained by interspersed cis isomers. Computer simulations elucidate the influence of trans/cis isomerization on polyproline structures in terms of end-to-end distance and provide a structural justification for the experimentally observed effects. Our results demonstrate that structural heterogeneity inherent in polyprolines, which to date are commonly applied as a molecular ruler, disqualifies them as appropriate tool for an accurate determination of absolute distances at a molecular scale.

Solution NMR structure of an immunodominant epitope of myelin basic protein

Using solution NMR spectroscopy, three-dimensional structures have been obtained for an 18-residue synthetic polypeptide fragment of 18.5 kDa myelin basic protein (MBP, human residues Q81-T98) under three conditions emulating the protein's natural environment in the myelin membrane to varying degrees: (a) an aqueous solution (100 mM KCl pH 6.5), (b) a mixture of trifluoroethanol (TFE-d2) and water (30 : 70% v/v), and (c) a dispersion of 100 mM dodecylphosphocholine (DPC-d38, 1 : 100 protein/lipid molar ratio) micelles. This polypeptide sequence is highly conserved in MBP from mammals, amphibians, and birds, and comprises a major immunodominant epitope (human residues N83-T92) in the autoimmune disease multiple sclerosis. In the polypeptide fragment, this epitope forms a stable, amphipathic, alpha helix under organic and membrane-mimetic conditions, but has only a partially helical conformation in aqueous solution. These results are consistent with recent molecular dynamics simulations that showed this segment to have a propensity to form a transient alpha helix in aqueous solution, and with electron paramagnetic resonance (EPR) experiments that suggested a alpha-helical structure when bound to a membrane [I. R. Bates, J. B. Feix, J. M. Boggs & G. Harauz (2004) J Biol Chem, 279, 5757-5764]. The high sensitivity of the epitope structure to its environment is characteristic of intrinsically unstructured proteins, like MBP, and reflects its association with diverse ligands such as lipids and other proteins.

The complete chirospectroscopic signature of the peptide 3(10)-helix in aqueous solution.

We synthesized by solution methods a water-soluble, terminally blocked heptapeptide based on five markedly helicogenic, C(alpha)-tetrasubstituted alpha-amino acids C(alpha)-methyl-L-norvalines and two strongly hydrophilic 2-amino-3-[1-(1,4,7-triazacyclononane)]-L-propanoic acid residues at positions 2 and 5. A Fourier transform infrared absorption and NMR analysis in deuterated chloroform and aqueous solutions of the heptapeptide and two side-chain protected synthetic precursors confirmed our working hypothesis that all oligomers are folded in the 3(10)-helical conformation. Based on these findings, we exploited this heptapeptide as a chiral reference compound for detailed electronic CD, vibrational CD, and Raman optical activity characterizations of the 3(10)-helix in aqueous solution.

Tat cell-penetrating peptide has the characteristics of a poly(proline) II helix in aqueous solution and in SDS micelles.

Tat cell-penetrating peptide (GRKKRRQRRRPPQG) is able to translocate and carry molecules across cell membranes. Using CD spectroscopy the conformation of this synthetic peptide was studied in aqueous and membrane-mimicking, micellar SDS solutions at different temperatures. The CD spectrum of the Tat cell-penetrating peptide in SDS micellar solution was virtually unchanged from that in aqueous solution, and at low temperature it was close to that of a poly(proline) II helix.

The Influence of a Chiral Amino Acid on the Helical Handedness of PNA in Solution and in Crystals

The X-ray structure of a self-complementary PNA hexamer (H-CGTACG-L-Lys-NH2) has been determined to 2.35 Å resolution. The introduction of an L-lysine moiety has previously been shown to induce a preferred left-handedness of the PNA double helices in aqueous solution. However, in the crystal structure an equal amount of interchanging right- and left-handed helices is observed. The lysine moieties are pointing into large solvent channels and no significant interactions between this moiety and the remaining PNA molecule are observed. In contrast, molecular mechanics calculations show a preference for the left-handed helix of this hexameric PNA in aqueous solution as expected. The calculations indicate that the difference in the free energy of solvation between the left-handed and the right-handed helix is the determining factor for the preference of the left-handed helix in aqueous solution.

The structure and dynamics of DNA in the gas phase.

The impact of the transfer from water to the vacuum in the duplex DNA has been explored by using long molecular dynamic simulations. In opposition to chemical intuition, it is found that vaporization of DNA, even at high temperatures, does not lead to a total disruption of the double helix. Rather, the DNA duplex preserves gross structural, energetic, and dynamic features of the conformation of the double helix in aqueous solution. Thus, the two strands remain bound, the global structure has a slight helicity, and the total number of DNA-DNA interactions is not dramatically different from that found in solution. The results provide detailed structural and dynamic information useful to complement current mass spectroscopy studies of DNA structures.

Stabilizing interactions between aromatic and basic side chains in alpha-helical peptides and proteins. Tyrosine effects on helix circular dichroism.

Here we investigate the structures and energetics of interactions between aromatic (Phe or Tyr) and basic (Lys or Arg) amino acids in alpha-helices. Side chain interaction energies are measured using helical peptides, by quantifying their helicities with circular dichroism at 222 nm and interpreting the results with Lifson-Roig-based helix/coil theory. A difficulty in working with Tyr is that the aromatic ring perturbs the CD spectrum, giving an incorrect helicity. We calculated the effect of Tyr on the CD at 222 nm by deriving the intensities of the bands directly from the electronic and magnetic transition dipole moments through the rotational strengths corresponding to each excited state of the polypeptide. This gives an improved value of the helix preference of Tyr (from 0.48 to 0.35) and a correction to the helicity for the peptides containing Tyr. We find that Phe-Lys, Lys-Phe, Phe-Arg, Arg-Phe, and Tyr-Lys are all stabilizing by -0.10 to -0.18 kcal.mol-1 when placed i, i + 4 on the surface of a helix in aqueous solution, despite the great difference in polarity between these residues. Interactions between these side chains have previously been attributed to cation-pi bonds. A survey of protein structures shows that they are in fact predominantly hydrophobic interactions between the CH2 groups of Lys or Arg and the aromatic rings.

Hybrid SCC-DFTB/molecular mechanical studies of H-bonded systems and ofN-acetyl-(L-Ala)nN?-methylamide helices in water solution

A hybrid quantum mechanical (QM) and molecular mechanical (MM) approach has been developed and used to study the aqueous solvation effect on biological systems. The self-consistent charge density functional tight-binding (SCC-DFTB) method is employed to perform the quantum mechanical calculations in the QM part, while the AMBER 4.1 force field is used to perform the molecular mechanical calculations in the MM part. The coupling terms between these two parts include electrostatic and van der Waal's interactions. As a test of feasibility, this approach has been first applied to some small systems H-bonded with water molecule(s), and very good agreement with the ab initio results has been achieved. The hybrid potential was then used to investigate the solvation effect on the capped (L-Ala)n helices with n=4, 5, 8 and 11. (L-Ala)n was treated with the SCC-DFTB method and the water molecules with the TIP3P water model. It has been shown that, in gas phase, the α helices of (L-Ala)n are less stable than the corresponding 310 helices. In water solution, however, the α helices are stabilized and, compared with 310 helices, the α helices have stronger charge–charge interactions with the surrounding water molecules. This may be explained by the larger dipole moment of α helices in aqueous solution, which will influence and organize the orientations of the surrounding water molecules. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 78: 459–479, 2000

Formation of Short, Stable Helices in Aqueous Solution by β-Amino Acid Hexamers

Formation of Short, Stable Helices in Aqueous Solution by β-Amino Acid Hexamers

Solution structures of human immunodeficiency virus type 1 (HIV-1) and moloney murine leukemia virus (MoMLV) capsid protein major-homology-region peptide analogs by NMR spectroscopy.

The capsid domain of retroviral Gag proteins possesses a single highly conserved subdomain termed the major homology region (MHR). While the mutagenesis of residues in the MHR will impair virus infectivity, the precise solution structure and function of the MHR is not known. To aid the structure/function characterization of the MHR, the structures of synthetic peptides encompassing the MHR of the human immunodeficiency virus type I (HIV-1) and Moloney murine leukemia virus (MoMLV) capsid proteins were investigated by several techniques. Homology-based secondary-structure prediction suggested that the HIV-1 and MoMLV peptides could form 50% and 38% alpha-helix, respectively. CD studies indicated that, in the presence of 50% trifluoroethanol, the HIV-1 peptide adopts an alpha-helical structure over half of its length, while the MoMLV peptide is over one third alpha-helix. Further analysis by 1H-NMR suggested that the C-terminal portion of the MHR of each virus forms a helix in aqueous solution. Distance-geometry structures of each peptide were calculated from NOE distance restraints and were refined by restrained molecular dynamics. The C-terminal halves of both peptides were observed to be in an alpha-helical conformation, while the N-terminal halves were disordered. Furthermore, both helices were amphipathic with high conservation of amino acid side-chain character, suggesting that a conserved helical MHR C-terminus is essential to retroviral capsid protein function.

Bactericidal Activity and Poly-l-proline II Conformation of the Tandem Repeat Sequence of Human Salivary Mucin Glycoprotein (MG2)

The tandem repeat 23-residue sequence [TRS23 (145–167): T-T-A-A-P-P-T-P-S-A-T-T-P-A-P-P-S-S-S-A-P-P-E] of human salivary mucin glycoprotein MG2 was examined for itsin vitrobactericidal activity against four oral microorganisms,Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Streptococcus gordonii, andStreptococcus mutans.The conformational features of the proline-rich peptide were determined by circular dichroism (CD) and 600 MHz two-dimensional (2D) nuclear magnetic resonance (NMR) in aqueous solution. The strains ofP. gingivalis(W50 and 381),A. actinomycetemcomitans(Y4 and 67),S. gordonii(DL1), andS. mutans(GS5) are highly sensitive to this peptide at 1.5–3.0 μM concentrations, suggesting that the proline-rich repeat sequence is a potent bactericidal agent for oral pathogens. The assignment of backbone and side-chain proton resonances was accomplished by the combined analysis of 2D total correlated spectroscopy and nuclear Overhauser effect spectroscopy. The temperature dependence of amide NH chemical shifts and the1H–2H exchange effect on amide NH resonances suggest the absence of intramolecularly hydrogen-bonded NH groups. The coupling constant (JNH–CαH) values, conformational restriction offered by the proline residues (φ = −60° ± 15°), the set of medium- and short-range nuclear Overhauser effects observed for this sequence, and the results of restrained structure calculation using DIANA, the distance geometry algorithm for NMR applications, provide evidence for the existence of a significant population of poly-l-proline II-type helices in aqueous solution. The CD spectra of the peptide in phosphate buffer (pH 7.2) and in methanol are reminiscent of the CD spectrum of the poly-l-proline II helical conformation and are consistent with the NMR data. The bactericidal activity of the proline-rich repeat sequence suggests that bacterial colonization, facilitated by the adsorbed salivary mucins on tooth surface, could be partly controlled and cleared by proteolytically degraded proline-rich peptides of MG2 in saliva before the colonized organisms turn into pathogens. It appears that the poly-l-proline II helix is the biologically active backbone conformation for bactericidal activity of the tandem repeat sequences of salivary MG2.

Molecular Dynamics Simulation of a PNA·DNA·PNA Triple Helix in Aqueous Solution

Molecular dynamics simulations have been used to explore the conformational flexibility of a PNA·DNA·PNA triple helix in aqueous solution. Three 1.05 ns trajectories starting from different but reasonable conformations have been generated and analyzed in detail. All three trajectories converge within about 300 ps to produce stable and very similar conformational ensembles, which resemble the crystal structure conformation in many details. However, in contrast to the crystal structure, there is a tendency for the direct hydrogen-bonds observed between the amide hydrogens of the Hoogsteen-binding PNA strand and the phosphate oxygens of the DNA strand to be replaced by water-mediated hydrogen bonds, which also involve pyrimidine O2 atoms. This structural transition does not appear to weaken the triplex structure but alters groove widths and so may relate to the potential for recognition of such structures by other ligands (small molecules or proteins). Energetic analysis leads us to conclude that the reason that the hybrid PNA/DNA triplex has quite different helical characteristics from the all-DNA triplex is not because the additional flexibility imparted by the replacement of sugar−phosphate by PNA backbones allows motions to improve base-stacking but rather that base-stacking interactions are very similar in both types of triplex and the driving force comes from weak but definate conformational preferences of the PNA strands.

Pulsed Electric Linear Dichroism of Poly(dA)·Poly(dT)·Poly(dT) and Poly(rA)·Poly(rU)·Poly(rU) in Solutions

Abstract The dependence of reduced dichroism (Δε/ε) of sonicated rodlike title triplexes with the counterion Mg2+, (dA)n·(dT)n·(dT′)n and (rA)n·(rU)n·(rU′)n, on the wavelength (190—300 nm) and on the applied-field strength (3.8—23.1 kV cm−1) was studied in aqueous ionic solutions at 7 °C. The sonicated samples were fractionated and well-characterized by the gel-permeation chromatography/low-angle laser light-scattering method. The reduced dichroism saturated at infinitely high electric fields ((Δε/ε)s) was estimated to be −1.22 for (dA)n·(dT)n·(dT′)n and −1.09 for (rA)n·(rU)n·(rU′)n, by fitting the observed Δε/ε values at 260 nm to a theoretical orientation function. The electric linear dichroism (ELD) spectra, i.e., the dependence of (Δε/ε)s on the wavelength, of (dA)n·(dT)n·(dT′)n and (rA)n·(rU)n·(rU′)n were determined. The measured ELD spectra were simulated by assigning the appropriate roll (θR) and tilt (θT) angles to the constituent bases. The most probable θR and θT values, determined for each triplex, indicate that the structures of triple helices both belong to an “A-form” family. The constituent bases in base-triple do not lie on a common plane. From an analysis of transient decay signals, the translation per base-triple (h) was estimated for each triplex. The structures of the present high molecular-weight triple-stranded helices in aqueous solution were determined for the first time and the plausible structural models were constructed from the experimentally evaluated sets of θR and θT.