Theoretical conformational analysis of phospholipids: I. Study of the interactions between phospholipid molecules by use of semi-empirical methods with the explicit introduction of polar headgroup interactions

We present a theoretical conformational analysis of a system composed of seven dipalmitoylphosphatidylethanolamine molecules in interaction. The combined use of classical semi-empirical methods for the polar headgroup region with mechanical statistical calculations for the aliphatic chains permits the evaluation of the free energy for a phospholipids molecule. The free energy variation in function of the mean intermolecular interchain distance gives information about the main lipid bilayer phase transition. It appears, however, necessary to take into account the hydration of the polar headgroups.     

Carrier design: Synthesis and conformational studies of poly (L-lysine) based branched polypeptides with hydroxyl groups in the side chains

In the present study the development of a new series of branched polypeptides that contain hydroxyl groups in side chains is reported. Serine or threonine were attached by 1-hydroxy-benzotriazole catalyzed active ester method to the N-terminals of oligo (DL -alanine) chains grafted to a polylysine backbone resulted in poly[Lys-(Ser₁-DL -Ala_m)] (SAK) and poly-[Lys-(Thr_i-DL -Ala_m)] (TAK). Ser was coupled also directly to the η-amino groups of polylysine followed by polymerization of N-carboxy-DL -alanine anhydride resulting oligo (DL -Ala) chain terminals. In this way a reverse sequence was built up in the side chain corresponding to the poly[Lys-(DL -Ala_m-Ser_i)] (ASK). The number of hydroxyl groups in the polymer was increased by the synthesis of a branched polypeptide with oligo (DL -serine) branches instead of oligo (DL -alanine) ones—poly[Lys-(DL -Ser_m)] (SK). Classification of solution conformations of branched polypeptides was carried out by CD spectroscopy performed in water solution of various pH values and ionic strengths. Incorporation of single Ser residues in poly[Lys-(X_i)]-type polypeptides markedly promotes the formation of ordered structure without resulting precipitation even in high salt concentration. The presence of branches with multiple DL -Ser residues resulted in a slightly decreased ability of the polypeptide backbone to adopt an ordered conformation. Comparison of the CD properties of the SAK-ASK pair demonstrates that these compounds are similar, showing an increased tendency to form an ordered spatial arrangement in solution at elevated pH or ionic strength; however, differences in their CD spectra suggest that SAK has higher capability to form regular conformation under comparable conditions. The replacement of Ser by the Thr residue in poly[Lys-(X_i-DL -Ala_m)] induced a conformational transition and TAK exhibited a more helical structure. These results might indicate that not only hydrophobic or ionic attraction, but also H-bond interaction, can play a role in the formation and/or stabilization of ordered conformation of branched polypeptides. Findings with the hydroxyl group containing polymers reported in this paper can also explain their prolonged shelf stability and high water solubility. © 1997 John Wiley & Sons, Inc. Biopoly 42: 719–730, 1997     

Self assembly of poly(o-methoxy aniline) with RNA and RNA/DNA hybrids: Physical properties and conformational change of poly(o-methoxy aniline)

Biomolecular hybrids of a conducting polymer [poly(o-methoxy aniline) (POMA)] and RNA are prepared at the three different compositions by mixing aqueous solutions of diethyl, 2-hydroxy ethyl, ammonium salt of RNA (type IX from Torula Yeast) and POMA (ES, emeraldine salt; doping level [Cl]/[N] = 0.52). A slow increase of pH up to 30 h of aging occurs in the mixture till it levels up. The TEM micrographs indicate a fibrillar network structure in all the hybrid compositions (POMA: RNA = 1:3, 1:1, 3:1, by weight). In the complexes three types of supramolecular interactions, viz. (i) electrostatic, (ii) H-bonding and (iii) π–π interactions, are evident from the FTIR spectroscopy. The CD spectra indicate a small distortion of A-RNA conformation towards its B form during the hybrid formation. Time and temperature dependent UV–vis spectral studies indicate a slow red shift of the π-band to polaron band transition peak (λ_max) for the uncoiling of the POMA (P) chain on the RNA (R) surface. The repulsive interaction between the radical cations of POMA (ES) absorbed on the RNA surface is attributed to the conformational change causing the uncoiling of POMA chain. UV–vis spectral study indicates that the uncoiling and attachment of POMA on RNA surface is much faster than that on DNA (D). In POMA–RNA–DNA (PRD) hybrid solutions slower red shift of λ_max indicates more disordered array of the phosphate groups than that in PR and PD systems. The conductivity values of the PR hybrids (10^− 6 S/cm^− 1) are three orders higher than that of RNA, rendering the PR hybrids to be useful for fabricating good biosensors. In the PRD hybrids conductivity decreases by two orders than those of PR and PD hybrids suggesting a disorder arrangement of POMA chains in the PRD hybrids. The I–V characteristic curves of the PR and PRD hybrids indicate a semiconducting nature of the hybrids.     

A conformational model of per-O-acetyl-cyclomaltoheptaose (-beta-cyclodextrin) in solution: detection of partial inversion of glucopyranose units by NMR spectroscopy

The stereochemical features of per-O-acetyl-cyclomaltoheptaose (-beta-cyclodextrin) have been investigated in solution by NMR spectroscopy, and the deviation of functionalised glucopyranose rings from 4C(1) chairs to skew-type conformations has been detected.     

NMR spectroscopy: a powerful tool for detecting the conformational features of symmetrical persubstituted mixed cyclomaltoheptaoses (beta-cyclodextrins)

The conformation in solution of exhaustively derivatized mixed cyclomaltooligosaccharides (cyclodextrins) has been defined by NMR spectroscopy. Both tilting of glucopyranose units about the glycosidic linkages and ring deviations from the 4C1 chair conformation are detected, the entities of which are strongly dependent on the nature of the derivatizing groups.     

Human telomere d[(TTAGGG)4] undergoes a conformational transition to the Na+-form upon binding with sanguinarine in presence of K+

Guanine-rich telomeric sequences fold into G-quadruplex conformation and are known to bind a variety of ligands including potential drug candidates. By means of CD spectroscopy and fluorescence lifetime measurements we demonstrate that putative anticancer therapeutic sanguinarine (SGR) exhibits two distinct interactions with human telomere d[(TTAGGG)₄] (H24) in presence of K⁺. Up to about 1:2 M ratio of H24:SGR (10 μM H24), two molecules of SGR bind H24. Above this molar ratio, SGR induces a conformational transition in H24 from the K⁺-form to the Na⁺-form. The demonstration of SGR-induced conformational transition in a G-quadruplex formed by a human telomeric sequence could provide new insights into interaction of drugs with quadruplex DNA structure.     

Synthesis of the four 1-(1-deoxy-D-pentitol-1-yl)thymines and conformational properties of the acyclic sugar chain

Acetylated D-pentose diethyl dithioacetals were coupled by way of 1-bromo-1-ethylthio derivatives with 2,4-bis(trimethylsilyl)thymine to afford diastereomeric pairs of acyclic-sugar nucleoside analogues bearing a thymin-1-yl and an ethylthio group at C-1. Free-radical desulfurization by the action of tributylstannane removed the ethylthio group to afford the corresponding acetylated 1-(1-deoxy-d-pentitol-1-yl)thymines and subsequently the free title compounds in the arabino, lyxo, ribo, and xylo series. Conformations of the intermediates and products were studied in detail and the final products were evaluated for their potential as agents active against plant viruses and rice blast fungus.     

Phase behavior in multilamellar vesicles of DPPC containing ganglioside GM3 with a C18:1 sphingoid base and a 24:0 acyl chain (GM3(18,24)) observed by X-ray diffraction

Structures and phase behavior of multilamellar vesicles of 1,2-dipalmitoyl-L-phosphatidylcholine (DPPC) containing various amount of ganglioside GM3 with a C18:1 sphingoid base and a 24:0 acyl chain (GM3(18,24)) were investigated by small-angle X-ray diffraction. Below 3.5 mol% GM3 content, the phase behavior was similar to that of pure DPPC except for a slight increase of lamellar repeat distance in the L(beta'), the P(beta') and the L(alpha) phases and a decrease of the pretransition temperature. In the range of 4-12 mol% GM3 content, another phase which has larger repeat distances coexisted with the phase observed below 3.5 mol% GM3 content. This has been interpreted that the phase separation into GM3-poor phase (denoted as A-phase) and GM3-rich phase (denoted as B-phase) took place. Above 13 mol% GM3 content, the B-phase became dominant. This phase separation may be related to the formation of GM3-enriched microdomains that had been observed on the cell surfaces which express large amounts of GM3, such as murine B16 melanoma (J. Biol. Chem. 260 (1985) 13328).     

Conformational behaviour of glycomimetics: NMR and molecular modelling studies of the C-glycoside analogue of the disaccharide methyl beta-D-galactopyranosyl-(1-->3)-beta-D-glucopyranoside

The conformational behaviour of the C-glycoside beta-C-Gal-(1-->3)-beta-Glc-OMe (1) has been studied using a combination of molecular mechanics and NMR spectroscopy (proton-proton coupling constants and nuclear Overhauser effects). It is shown that the C-disaccharide populates two distinctive conformational families in solution, the normal syn-psi conformation, which is the predominating conformation of parent O-glycoside 2, and the anti-psi conformation, which has not been detected for the O-disaccharide.     

Human UP1 as a model for understanding purine recognition in the family of proteins containing the RNA recognition motif (RRM)

Heterogeneous ribonucleoprotein A1 (hnRNP A1) is a prototype for the family of eukaryotic RNA processing proteins containing the common RNA recognition motif (RRM). The region consisting of residues 1-195 of hnRNP A1 is referred to as UP1. This region has two RRMs and has a high affinity for both single-stranded RNA and the human telomeric repeat sequence d(TTAGGG)(n). We have used UP1's novel DNA binding to investigate how RRMs bind nucleic acid bases through their highly conserved RNP consensus sequences. Nine complexes of UP1 bound to modified telomeric repeats were investigated using equilibrium fluorescence binding and X-ray crystallography. In two of the complexes, alteration of a guanine to either 2-aminopurine or nebularine resulted in an increase in K(d) from 88nM to 209nM and 316nM, respectively. The loss of these orienting interactions between UP1 and the substituted base allows it to flip between syn and anti conformations. Substitution of the same base with 7-deaza-guanine preserves the O6/N1 contacts but still increases the K(d) to 296nM and suggests that it is not simply the loss of affinity that gives rise to the base mobility, but also the stereochemistry of the specific contact to O6. Although these studies provide details of UP1 interactions to nucleic acids, three general observations about RRMs are also evident: (1) as suggested by informatic studies, main-chain to base hydrogen bonding makes up an important aspect of ligand recognition (2) steric clashes generated by modification of a hydrogen bond donor-acceptor pair to a donor-donor pair are poorly tolerated and (3) a conserved lysine position proximal to RNP-2 (K(106)-IFVGGI) orients the purine to allow stereochemical discrimination between adenine and guanine based on the 6-position. This single interaction is well-conserved in known RRM structures and appears to be a broad indicator for purine preference in the larger family of RRM proteins.     

Structural characterization of Burkholderia pseudomallei adenylate kinase (Adk): Profound asymmetry in the crystal structure of the ‘open’ state

In all organisms adenylate kinases (Adks) play a vital role in cellular energy metabolism and nucleic acid synthesis. Due to differences in catalytic properties between the Adks found in prokaryotes and in the cytoplasm of eukaryotes, there is interest in targeting this enzyme for new drug therapies against infectious bacterial agents. Here we report the 2.1 Å resolution crystal structure for the 220-residue Adk from Burkholderia pseudomallei (BpAdk), the etiological agent responsible for the infectious disease melioidosis. The general structure of apo BpAdk is similar to other Adk structures, composed of a CORE subdomain with peripheral ATP-binding (ATP_bd) and LID subdomains. The two molecules in the asymmetric unit have significantly different conformations, with a backbone RMSD of 1.46 Å. These two BpAdk conformations may represent ‘open’ Adk sub-states along the preferential pathway to the ‘closed’ substrate-bound state.     

Molecular dynamics simulations of a cyclic-beta-(1-->2) glucan containing an alpha-(1-->6) linkage as a 'molecular alleviator' for the macrocyclic conformational strain

The conformational preferences of a cyclic osmoregulated periplasmic glucan of Ralstonia solanacearum (OPGR), which is composed of 13 glucose units and linked entirely via beta-(1-->2) linkages excluding one alpha-(1-->6) linkage, were characterized by molecular dynamics simulations. Of the three force fields modified for carbohydrates that were applied to select a suitable one for the cyclic glucan, the carbohydrate solution force field (CSFF) was found to most accurately simulate the cyclic molecule. To determine the conformational characteristics of OPGR, we investigated the glycosidic dihedral angle distribution, fluctuation, and the potential energy of the glucan and constructed hypothetical cyclic (CYS13) and linear (LINEAR) glucans. All beta-(1-->2)-glycosidic linkages of OPGR adopted stable conformations, and the dihedral angles fluctuated in this energy region with some flexibility. However, despite the inherent flexibility of the alpha-(1-->6) linkage, the dihedral angles have no transition and are more rigid than that in a linear glucan. CYS13, which consists of only beta-(1-->2) linkages, is somewhat less flexible than other glycans, and one of its linkages adopts a higher energy conformation. In addition, the root-mean-square fluctuation of this linkage is lower than that of other linkages. Furthermore, the potential energy of glucans increases in the order of LINEAR, OPGR, and CYS13. These results provide evidence of the existence of conformational constraints in the cyclic glucan. The alpha-(1-->6)-glycosidic linkage can relieve this constraint more efficiently than the beta-(1-->2) linkage. The conformation of OPGR can reconcile the tendency for individual glycosidic bonds to adopt energetically favorable conformations with the requirement for closure of the macrocyclic ring by losing the inherent flexibility of the alpha-(1-->6)-glycosidic linkage.     

Kinetic studies of the reactions of pentacyanonitrosylferrate(2−) with ligands containing acidic methylene groups

The kinetic studies of the addition reactions of pentacyanonitrosylferrate(2−) (NP) with acidic methylene ligands of the form CH₂LL′ (L, L′ = -CN, -CONH₂; -CN, -CN; CH₃CO-, CH₃CO-) have been carried out in basic solutions. The increase in the second order rate constants for the formation of Fe(CN)₅N(O)CLL′⁴⁻ complexes with the increase of OH⁻ concentration indicated that ^?CHLL′ is the reactive species of the reactions. In addition to the pK_a, the lability of the methylene protons of the ligands in aqueous solution also governs the reactivity of the reactions. The nitrosation products were rather unstable with respect to the dissociation into and oxime compounds. The kinetic measurements showed that the rates of dissociation were first order and were rather insensitive to the hydroxide concentration for the ligands under study.     

Role of charges and solvent on the conformational properties of poly(galacturonic acid) chains: a molecular dynamics study

Pectin shares with many other polysaccharides an intrinsic chemical and physical complexity. The widespread industrial applications have made it one of the most studied polysaccharides. This work presents a theoretical model of poly(galacturonic acid), the major constituent of pectin, suitable to study its structural and dynamical properties. In particular, the effects of solvent and charge status are studied. The dynamics is shown to be severely affected by the presence of charged groups on each residue, making the charged chain much more rigid than the uncharged one. A key structural property for a semirigid polymer, the asymptotic persistence length, is calculated for relatively short charged and uncharged chains in molecular water solvent using a new method. The influence of charge on structural properties of poly(galacturonic acid) is shown to be strong and solvent-dependent. In fact, a large difference is found between continuum solvent adiabatic map calculations and molecular dynamics with explicit solvent, with the latter showing a much larger persistence length.     

Interaction of biologically active molecules with phospholipid membranes: I. Fluorescence depolarization studies on the effect of polymeric biocide bearing biguanide groups in the main chain

Interaction of poly(hexamethylene biguanide hydrochloride) (PHMB), which is a polymeric biocide bearing biguanide groups in its main chain, with phospholipid bilayers was studied by the fluorescence depolarization method. A strong interaction of PHMB with negatively charged bilayers composed of phosphatidylglycerol(PG) alone or of PG and phosphatidylcholine (PC) was observed, whereas neutral PC bilayers were not affected. On adding PHMB, the fluorescence polarization of diphenylhexatriene embedded in the negatively charged bilayers was reduced to a great extent, especially in the gel phase. This was interpreted in terms of PHMB-induced expansion and fluidization of the bilayer, which enables the probe molecule to undergo less-hindered torsional motion. Similarity between PHMB and polymyxin B in the structure, the mode of action against bacteria and the interaction with lipid membranes is discussed.     

Theoretical study of the experimental coordination behavior of N-(2-aminophenyl)-D-glycero-D-gulo-heptonamide to Hg(II) ion

The reactivity of N-(2-aminophenyl)-d-glycero-d-gulo-heptonamide (adgha), with the group 12 cations, Zn(II), Cd(II), and Hg(II), was studied in DMSO-d₆ solution. The studied system showed a selective coordination to Hg(II), and the products formed were characterized by ¹H and ¹³C NMR in DMSO-d₆ solution and fast atom bombardment (FAB⁺) mass spectra. The expected coordination compounds, [Hg(adgha)](NO₃)₂ and [Hg(adgha)₂](NO₃)₂, were observed as unstable intermediates that decompose to bis-[2-(d-glycero-d-gulo-hexahydroxyhexyl)-benzimidazole-κN]mercury(II) dinitrate, [Hg(ghbz)₂](NO₃)₂. The chemical transformation of the complexes was followed by NMR experiments, and the nature of the species formed is sustained by a theoretical study done using DFT methodology. From this study, we propose the structure of the complexes formed in solution, the relative stability of the species formed, and the possible role of the solvent in the observed transformations.     

The roles of cytoplasmic poly(A)-binding proteins in regulating gene expression: a developmental perspective.

Poly(A)-binding proteins (PABPs) are central to the regulation of messenger RNA (mRNA) translation and stability; however, the roles and contributions of different PABP family members in controlling gene expression are not yet fully understood. In this paper, the current state of knowledge of the different cytoplasmic PABP proteins and their function in animal cells will be summarised, with particular reference to their roles in development. Possible regulatory mechanisms and potential new roles for these proteins in the control of specific mRNAs are also highlighted.     

Mercaptoethanesulfonic acid (CoM imitator) interaction studies with nickel(II) complexes of pyridyl groups containing tetradentate ligands: Synthesis, structure, spectra and redox properties

Nickel(II) complexes of N,N′-dimethyl-N,N′-bis(pyridyl-2yl-methyl)ethylene-diamine (L¹), N,N′-dimethyl-N,N′-bis(pyridyl-2-ylmethyl)-1,2-diaminopropane (L²) and N,N′-dimethyl-N,N′-bis(pyridyl-2-ylmethyl)-1,3-diaminopropane (L³) were prepared and their spectroscopic and redox properties studied. The distorted octahedral structure was determined for [NiL³ClCH₃OH](ClO₄) by using X-ray crystallography. The electronic spectral behavior of the complexes at different pHs was analyzed; it is shown that a new band grew at the expense of the other band intensity in acid media. The redox properties of ligands and their complexes show the peaks of Ni(II) → Ni(III) and Ni(II) → Ni(0) as these were detected at low concentration while Ni(II) → Ni(I) process was detectable clearly at high concentration. Furthermore, the interaction studies of 2-mercaptoethanesulfonic acid as a simulator of coenzyme M reductase (CoM) with NiN₄ chromophores are discussed.     

Binding of moesin and ezrin to membranes containing phosphatidylinositol (4,5) bisphosphate: a comparative study of the affinity constants and conformational changes

The plasma membrane-cytoskeleton interface is a dynamic structure participating in a variety of cellular events. Moesin and ezrin, proteins from the ezrin/radixin/moesin (ERM) family, provide a direct linkage between the cytoskeleton and the membrane via their interaction with phosphatidylinositol 4,5-bisphosphate (PIP(2)). PIP(2) binding is considered as a prerequisite step in ERM activation. The main objective of this work was to compare moesin and ezrin interaction with PIP(2)-containing membranes in terms of affinity and to analyze secondary structure modifications leading eventually to ERM activation. For this purpose, we used two types of biomimetic model membranes, large and giant unilamellar vesicles. The dissociation constant between moesin and PIP(2)-containing large unilamellar vesicles or PIP(2)-containing giant unilamellar vesicles was found to be very similar to that between ezrin and PIP(2)-containing large unilamellar vesicles or PIP(2)-containing giant unilamellar vesicles. In addition, both proteins were found to undergo conformational changes after binding to PIP(2)-containing large unilamellar vesicles. Changes were evidenced by an increased sensitivity to proteolysis, modifications in the fluorescence intensity of the probe attached to the C-terminus and in the proportion of secondary structure elements.