Implicit two-phase solvation model as a tool to assess conformation and energetics of proteins in membrane-mimetic media

 A heterogeneous implicit membrane-mimetic model is applied to simulations of membrane proteins. The model employs atomic solvation parameters for gas–water and gas–cyclohexane transfer. It is used to analyze structure, energetics, and orientation with respect to the bilayer of two polypeptides with different modes of membrane binding – hydrophobic segment of human glycophorin A (GpA) and cytotoxin II from Naja naja oxiana snake venom (CTX). The native state of GpA represents a transmembrane (TM) α helix, while CTX is a water-soluble protein, which is able to interact with the cell membrane. The conformational space of the polypeptides was explored in Monte Carlo simulations. The results show that the most stable conformers of GpA represent a TM α helix. They are additionally stabilized by an applied TM voltage. The results also show that CTX inserts with its three loops, does not cross the hydrophobic layer, and stays partially immersed in the membrane. This agrees well with the experimental data, thus confirming the validity of the solvation model. Received: 13 June 2000 / Accepted: 15 September 2000 / Published online: 19 January 2001     

Enantioselective Total Synthesis of Brevetoxin A: Unified Strategy for the B,E, G,and J Subunits

Brevetoxin A is a decacyclic ladder toxin that possesses 5‐, 6‐, 7‐, 8‐, and 9‐membered oxacycles, as well as 22 tetrahedral stereocenters. Herein, we describe a unified approach to the B, E, G, and J rings based upon a ring‐closing metathesis strategy from the corresponding dienes. The enolate technologies developed in our laboratory allowed access to the precursor acyclic dienes for the B, E, and G medium‐ring ethers. The strategies developed for the syntheses of these four monocycles ultimately provided multigram quantities of each of the rings, supporting our efforts toward the completion of a convergent synthesis of brevetoxin A.     

Blood appearance of rat alkaline phosphatase originating from the duodenum in vitro

The major source of rat serum alkaline phosphatase (ALP) is well known to be from the intestinal enzyme, but it is still unclear whether it is from the duodenal or the ileal enzyme. The organic origin was investigated by means of two-dimensional electrophoresis. Major isoelectric points and molecular masses for activities of duodenal enzyme treated with both phosphatidylinositol-specific phospholipase C and neuraminidase were identified apparently with those of the major serum enzyme. In organ culture, the normal duodenal enzyme was released in the highest amounts to the culture medium. These results indicate that the major source of serum ALP in adult rats is basically from the duodenal enzyme. On the other hand, lectin affinity chromatography for ALPs showed that the ALP in the medium from culture duodenum and liver had the same complex-type sugar chain as with the ALP in the duodenal tissue. Although the duodenal ALP induced by glucosamine in vitro had the hybrid-type chain, sugar chains of the induced ALP in the culture medium were of the complex type, indicating that medial ALPs possessing the same sugar chain as the native duodenal enzyme, complex type, are mainly released from their tissues in normal conditions.     

Multidimensional umbrella sampling and replica‐exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers

Structural information of a transmembrane (TM) helix dimer is useful in understanding molecular mechanisms of important biological phenomena such as signal transduction across the cell membrane. Here, we describe an umbrella sampling (US) scheme for predicting the structure of a TM helix dimer in implicit membrane using the interhelical crossing angle and the TM–TM relative rotation angles as the reaction coordinates. This scheme conducts an efficient conformational search on TM–TM contact interfaces, and its robustness is tested by predicting the structures of glycophorin A (GpA) and receptor tyrosine kinase EphA1 (EphA1) TM dimers. The nuclear magnetic resonance (NMR) structures of both proteins correspond to the global free‐energy minimum states in their free‐energy landscapes. In addition, using the landscape of GpA as a reference, we also examine the protocols of temperature replica‐exchange molecular dynamics (REMD) simulations for structure prediction of TM helix dimers in implicit membrane. A wide temperature range in REMD simulations, for example, 250–1000 K, is required to efficiently obtain a free‐energy landscape consistent with the US simulations. The interhelical crossing angle and the TM–TM relative rotation angles can be used as reaction coordinates in multidimensional US and be good measures for conformational sampling of REMD simulations. © 2013 Wiley Periodicals, Inc.     

孪尾疏水缔合水溶性共聚物聚(丙烯酰胺/丙烯酸钠/N,N-二己基丙烯酰胺)/十二烷基硫酸钠水溶液的粘度行为

水溶性三元共聚物;孪尾疏水缔合水溶性共聚物聚(丙烯酰胺/丙烯酸钠/N;N-二己基丙烯酰胺)/十二烷基硫酸钠水溶液的粘度行为     

Design and synthesis of simplified polycyclic ethers and evaluation of their interaction with an α-helical peptide as a model of target proteins

Two simplified pentacyclic ethers, having 6/7/6/6/7 and 6/7/6/7/7 ring systems, were synthesized. A convergent route based on the Suzuki-Miyaura cross-coupling strategy was applied to synthesize these two compounds. Interactions between α-helical peptide, melittin, and synthesized pentacyclic ethers were evaluated by circular dichroism (CD) spectroscopy. Interestingly, only the polycyclic ether having a 6/7/6/7/7 ring stabilized the α-helical structure of melittin. This result indicated that a ring fusion manner of the polycyclic structure is important to recognize membrane proteins.     

Computational design of a β-peptide that targets transmembrane helices

The design of β-peptide foldamers targeting the transmembrane (TM) domains of complex natural membrane proteins has been a formidable challenge. A series of β-peptides was designed to stably insert in TM orientations in phospholipid bilayers. Their secondary structures and orientation in the phospholipid bilayer was characterized using biophysical methods. Computational methods were then devised to design a β-peptide that targeted a TM helix of the integrin α(IIb)β(3). The designed peptide (β-CHAMP) interacts with the isolated target TM domain of the protein and activates the intact integrin in vitro.     

Mono-, bis-, and tris(crown ether)s assembled around 1,3,5-triaroylbenzene scaffolds

A concise and experimentally straightforward method for assembling multiple benzo(crown ether) units around 1,3,5-triaroylbenzene scaffolds has been developed. Symmetrical tris(crown ether)s possessing three benzo(15-crown-5) or three benzo(18-crown-6) peripheral substituents have been prepared in good yield via cyclotrimerization of monomeric enaminones. Efficient cross-cyclotrimerizations have also been demonstrated through construction of unsymmetrical triaroylbenzenes functionalized with only one or two benzo(15-crown-5) moieties. The alkali cation-binding abilities of these mono- and polytopic crown ethers have been probed through picrate extraction experiments and isothermal titration calorimetry. Thermodynamic binding parameters uncovered using the latter technique reveal increasing K+/Na+ selectivity in the benzo(15-crown-5) series of compounds as a function of increasing numbers of benzo(crown) units. The data also indicate that the triaroylbenzene-derived bis- and tris-crown ethers do not engage in intramolecular chelation of cations too large to be accommodated by individual crown macrorings. Instead, cation/triaroylbenzene stoichiometries and binding profiles indicate formation of alkali metal-bridged dimers.     

Statistical analysis and exposure status classification of transmembrane beta barrel residues

Several computational methods exist for the identification of transmembrane beta barrel proteins (TMBs) from sequence. Some of these methods also provide the transmembrane (TM) boundaries of the putative TMBs. The aim of this study is to (1) derive the propensities of the TM residues to be exposed to the lipid bilayer and (2) to predict the exposure status (i.e. exposed to the bilayer or hidden in protein structure) of TMB residues. Three novel propensity scales namely, BTMC, BTMI and HTMI were derived for the TMB residues at the hydrophobic core region of the outer membrane (OM), the lipid-water interface regions of the OM, and for the helical membrane proteins (HMPs) residues at the lipid-water interface regions of the inner membrane (IM), respectively. Separate propensity scales were derived for monomeric and functionally oligomeric TMBs. The derived propensities reflect differing physico-chemical properties of the respective membrane bilayer regions and were employed in a computational method for the prediction of the exposure status of TMB residues. Based on the these propensities, the conservation indices and the frequency profile of the residues, the transmembrane residues were classified into buried/exposed with an accuracy of 77.91% and 80.42% for the residues at the membrane core and the interface regions, respectively. The correlation of the derived scales with different physico-chemical properties obtained from the AAIndex database are also discussed. Knowledge about the residue propensities and burial status will be useful in annotating putative TMBs with unknown structure.     

Design of a functional membrane protein by engineering a heme-binding site in glycophorin A

We have designed a functional model membrane protein by engineering a bis-Histidine heme-binding site into a natural membrane protein, glycophorin A (GpA), structurally characterized by the dimerization of a single transmembrane helix. Out of the 32 residues comprising the transmembrane helix of GpA, five amino acids were mutated; the resulting protein, ME1, has been characterized in dodecyl phosphocholin (DPC) micelles by UV-vis, CD spectroscopy, gel electrophoresis, and analytical ultracentrifugation. ME1 binds heme with sub-micromolar affinity and maintains the highly helical secondary structure and dimeric oligomerization state of GpA. The ME1-Heme complex exhibits a redox potential of -128 +/- 2 mV vs SHE, indicating that the heme resides in a hydrophobic environment and is well shielded from the aqueous phase. Moreover, ME1 catalyzes the hydrogen peroxide dependent oxidation of organic substrates such as TMB (2,2',5,5'-tetramethyl-benzidine). This protein may provide a useful framework to investigate how the protein matrix tunes the cofactor properties in membrane proteins.     

Dithiaporphyrin derivatives as photosensitizers in membranes and cells

We synthesized a series of analogues of 5,20-diphenyl-10,15-bis(4-carboxylatomethoxy)phenyl-21,23-dithiaporphyrin (I) as potential photosensitizers for photodynamic therapy (PDT). The photosensitizers differ in the length of the side chains that bind the carboxyl to the phenol at positions 10 and 15 of the thiaporphyrin. The spectroscopic, photophysical, and biophysical properties of these photosensitizers are reported. The structural changes have almost no effect on the excitation/emission spectra with respect to I's spectra or on singlet oxygen generation in MeOH. All of the photosensitizers have a very high, close to 1.00, singlet oxygen quantum yield in MeOH. On the contrary, singlet oxygen generation in liposomes was considerably affected by the structural change in the photosensitizers. The photosensitizers possessing short side chains (one and three carbons) showed high quantum yields of around 0.7, whereas the photosensitizers possessing longer side chains showed smaller quantum yield, down to 0.14 for compound X (possessing side-chain length of 10 carbons), all at 1 microM. Moreover a self-quenching process of singlet oxygen was observed, and the quantum yield decreased as the photosensitizer's concentration increased. We measured the binding constant of I to liposomes and found Kb = 23.3 +/- 1.6 (mg/mL)-1. All the other photosensitizers with longer side chains exhibited very slow binding to liposomes, which prevented us from assessing their Kb's. We carried out fluorescence resonance energy transfer (FRET) measurements to determine the relative depth in which each photosensitizer is intercalated in the liposome bilayer. We found that the longer the side chain the deeper the photosensitizer core is embedded in the bilayer. This finding suggests that the photosensitizers are bound to the bilayer with their acid ends close to the aqueous medium interface and their core inside the bilayer. We performed PDT with the dithiaporphyrins on U937 cells and R3230AC cells. We found that the dark toxicity of the photosensitizers with the longer side chain (X, VI, V) is significantly higher than the dark toxicity of sensitizers with shorter side chains (I, III, IV). Phototoxicity measurements showed the opposite direction; the photosensitizers with shorter side chains were found to be more phototoxic than those with longer side chains. These differences are attributed to the relationship between diffusion and endocytosis in each photosensitizer, which determines the location of the photosensitizer in the cell and hence its phototoxicity.     

Bilayer vesicles of amphiphilic cyclodextrins: host membranes that recognize guest molecules

A family of amphiphilic cyclodextrins (6, 7) has been prepared through 6-S-alkylation (alkyl=n-dodecyl and n-hexadecyl) of the primary side and 2-O-PEGylation of the secondary side of alpha-, beta-, and gamma-cyclodextrins (PEG=poly(ethylene glycol)). These cyclodextrins form nonionic bilayer vesicles in aqueous solution. The bilayer vesicles were characterized by transmission electron microscopy, dynamic light scattering, dye encapsulation, and capillary electrophoresis. The molecular packing of the amphiphilic cyclodextrins was investigated by using small-angle X-ray diffraction of bilayers deposited on glass and pressure-area isotherms obtained from Langmuir monolayers on the air-water interface. The bilayer thickness is dependent on the chain length, whereas the average molecular surface area scales with the cyclodextrin ring size. The alkyl chains of the cyclodextrins in the bilayer are deeply interdigitated. Molecular recognition of a hydrophobic anion (adamantane carboxylate) by the cyclodextrin vesicles was investigated by using capillary electrophoresis, thereby exploiting the increase in electrophoretic mobility that occurs when the hydrophobic anions bind to the nonionic cyclodextrin vesicles. It was found that in spite of the presence of oligo(ethylene glycol) substituents, the beta-cyclodextrin vesicles retain their characteristic affinity for adamantane carboxylate (association constant K(a)=7.1 x 10(3) M(-1)), whereas gamma-cyclodextrin vesicles have less affinity (K(a)=3.2 x 10(3) M(-1)), and alpha-cyclodextrin or non-cyclodextrin, nonionic vesicles have very little affinity (K(a) approximately 100 M(-1)). Specific binding of the adamantane carboxylate to beta-cyclodextrin vesicles was also evident in competition experiments with beta-cyclodextrin in solution. Hence, the cyclodextrin vesicles can function as host bilayer membranes that recognize small guest molecules by specific noncovalent interaction.     

Perfluoroalkylated 4,13-diaza-18-crown-6 ethers: synthesis, phase-transfer catalysis, and recycling studies

A series of N,N'-dialkyl-4,13-diaza-18-crown-6 lariat ethers possessing two C8H17 (2), (CH2)3C8F17 (3), (CH2)3C10F21 (4), and (CH2)2C8F17 (5) side arms were synthesized in good yields by N-alkylation of 4,13-diaza-18-crown-6. Potassium picrate could be extracted from an aqueous solution into an organic phase by all of the perfluoroalkylated macrocycles demonstrating their potential to be used as phase-transfer catalysts, and preliminary studies on a classical nucleophilic substitution established that they each gave higher catalytic activities under solid-liquid than under liquid-liquid phase-transfer conditions. The light fluorous macrocycles gave similar, if not better, catalytic activity compared to the parent, non-fluorinated phase-transfer catalyst 2 under solid-liquid conditions in conventional organic solvents in both an aliphatic and an aromatic nucleophilic substitution. N,N'-Bis(1H,1H,2H,2H,3H,3H-perfluoroundecyl)-4,13-diaza-18-crown-6 (3) was recycled six times in the iodide displacement reaction of 1-bromooctane and four times in the fluoride displacement reaction of 2,4-dinitrochlorobenzene using fluorous solid-phase extraction without any loss in activity.     

Hydrangenone, a new isoprenoid with an unprecedented skeleton from Salvia hydrangea

Hydrangenone, a new heptacyclic isoprenoid with a 6/7/6/5/5 membered carbon ring skeleton, was isolated from the aerial parts of Salvia hydrangea. The structure was established by extensive NMR spectroscopic methods. The relative and absolute configuration of 1 was assigned by NOESY and X-ray crystallographic analysis and by comparison of experimental and calculated electronic circular dichroism (ECD) spectra. Compound 1 showed in vitro antiplasmodial activity, with an IC(50) value of 1.4 μM against P. falciparum. A plausible biosynthetic pathway of 1 was also proposed.     

SELF ASSEMBLED POLYMER-SURFACTANT SYSTEMS

The influence of noncharged and especially charged polymers on structure formation in mesoscopic organized surfactant/alcohol/water systems is investigated. Cationic polyelectrolytes can be incorporated into the liquid crystalline SDS/decanol/water system keeping up the lamellar phase.

The “usual” swelling of the bilayer can suppressed and an adsorption of the polycation at the head groups of the SDS bilayer is assumed. The incorporation of poly-anions is more complicated and macroscopic phase separation can be observed. A characteristic feature of a system with two polymers is the appearance of two coexisting lamellar phases, i. e. a swellable and non-swellable one.

In the SDS/pentanol/water/xylene system the addition of a hydrophobic polymer can induce the formation of a bicontinuous phase channel.

Surprisingly, the addition of a cationic polyelectrolyte to the SDS based w/o-microemulsion does not lead to a macroscopic phase separation.     

Head-to-head right-handed cross-links of the antitumor-active bis(mu-N,N'-di-p-tolylformamidinato)dirhodium(II,II) unit with the dinucleotides d(GpA) and d(ApG)

Reactions of cis-[Rh(2)(DTolF)(2)(NCCH(3))(6)](BF(4))(2) with the dinucleotides d(GpA) and d(ApG) proceed to form [Rh(2)(DTolF)(2){d(GpA)}] and [Rh(2)(DTolF)(2){d(ApG)}], respectively, with bridging purine bases spanning the Rh-Rh unit in the equatorial positions. Both dirhodium adducts exhibit head-to-head (HH) arrangement of the bases, as indicated by the presence of H8/H8 NOE cross-peaks in the 2D ROESY NMR spectra. The guanine bases bind to the dirhodium core at positions N7 and O6, a conclusion that is supported by the absence of N7 protonation at low pH values and the notable increase in the acidity of the guanine N1H sites (pK(a) approximately 7.4 in 4:1 CD(3)CN/D(2)O), inferred from the pH-dependence titrations of the guanine H8 proton resonances. In both dirhodium adducts, the adenine bases coordinate to the metal atoms through N6 and N7, which induces stabilization of the rare imino tautomer of the bases with a concomitant substantial decrease in the basicity of the N1H adenine sites (pK(a) approximately 7.0-7.1 in 4:1 CD(3)CN/D(2)O), as compared to the imino form of free adenosine. The presence of the adenine bases in the rare imino form is further corroborated by the observation of DQF-COSY H2/N1H and ROE N1H/N6H cross-peaks in the 2D NMR spectra of [Rh(2)(DTolF)(2){d(GpA)}] and [Rh(2)(DTolF)(2){d(ApG)}] in CD(3)CN at -38 degrees C. The 2D NMR spectroscopic data and the molecular modeling results suggest the presence of right-handed variants, HH1R, in solution for both adducts (HH1R refers to the relative base canting and the direction of propagation of the phosphodiester backbone with respect to the 5' base). Complete characterization of [Rh(2)(DTolF)(2){d(GpA)}] and [Rh(2)(DTolF)(2){d(ApG)}] by 2D NMR spectroscopy and molecular modeling supports anti-orientation of the sugar residues for both adducts about the glycosyl bonds as well as N- and S-type conformations for the 5'- and 3'-deoxyribose residues, respectively.     

Directed assembly of surface-supported bilayers with transmembrane helices

The lateral assembly of transmembrane (TM) helices gives rise to membrane proteins with complex folds, which play important roles in biochemical processes. Therefore, the assembly of surface-supported bilayers containing TM helices is the first step toward the development of functional biomembrane mimetics. Here we report novel directed assembly of surface-supported lipid bilayers with laterally mobile TM helices. The TM helices were incorporated into lipid monolayers at the air/water interface, and the monolayers were then transferred onto glass substrates using Langmuir-Blodgett (LB) deposition. Finally, bilayers were assembled using lipid vesicle fusion on top of the LB monolayers. The novelty is the incorporation of the peptides into the monolayer at the first step of bilayer assembly, which allows control over the peptide concentration and orientation. The transmembrane orientation of the peptides was confirmed using oriented circular dichroism (OCD), lateral mobility was assessed using fluorescence recovery after photobleaching (FRAP), and diffusion coefficients were determined using a novel boundary profile evolution (BPE) method. The described directed-assembly approach can be used to develop versatile bilayer platforms for studying membrane proteins interactions in native bilayer environments.     

Anisotropic solvent model of the lipid bilayer. 2. Energetics of insertion of small molecules, peptides, and proteins in membranes

A new computational approach to calculating binding energies and spatial positions of small molecules, peptides, and proteins in the lipid bilayer has been developed. The method combines an anisotropic solvent representation of the lipid bilayer and universal solvation model, which predicts transfer energies of molecules from water to an arbitrary medium with defined polarity properties. The universal solvation model accounts for hydrophobic, van der Waals, hydrogen-bonding, and electrostatic solute-solvent interactions. The lipid bilayer is represented as a fluid anisotropic environment described by profiles of dielectric constant (ε), solvatochromic dipolarity parameter (π*), and hydrogen bonding acidity and basicity parameters (α and β). The polarity profiles were calculated using published distributions of quasi-molecular segments of lipids determined by neutron and X-ray scattering for DOPC bilayer and spin-labeling data that define concentration of water in the lipid acyl chain region. The model also accounts for the preferential solvation of charges and polar groups by water and includes the effect of the hydrophobic mismatch for transmembrane proteins. The method was tested on calculations of binding energies and preferential positions in membranes for small-molecules, peptides and peripheral membrane proteins that have been experimentally studied. The new theoretical approach was implemented in a new version (2.0) of our PPM program and applied for the large-scale calculations of spatial positions in membranes of more than 1000 peripheral and integral proteins. The results of calculations are deposited in the updated OPM database ( http://opm.phar.umich.edu ).     

Intercation spacing and side chain effects on phosphonium polymers: Thermal,supramolecular, and bactericidal properties

The properties of phosphonium polyelectrolytes (PELs) were evaluated in an effort to assess the influence of both side chain and main chain composition. The influence of side chain was examined by comparing properties of a series of PELs having hydrophobic octyloxy side chains to those of structural analogues lacking the side chains. The influence exerted by backbone flexibility/length of spacer between charges was revealed by comparing properties of two series of polymers with a variable number of methylene units between phosphonium charge‐bearing sites. Side chain composition and spacing between phosphonium units lead to noteworthy influence on thermal stability, glass transition, and crystallinity. The molecular structure of PELs also correlates with trends in film morphology and critical surface energy of PEL dip‐cast films. Sensitivity of morphology to humidity or water in the casting solvent was observed. Supramolecular assembly of films via layer‐by‐layer deposition of PELs alternating with anionic polythiophene derivative layers was also undertaken. The linearity of film growth, amount of material deposited in each bilayer, polycation:polyanion ratio, and film roughness all show noteworthy trends that depend on both the presence/absence of side chains and on spacing between ionic centers. The relationship between side chain and spacer on bactericidal activity against Staphylococcus aureus and Escherichia coli was assessed. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019 , 57, 24–34