Tuck C. Wong

Membrane Structure of the Human Immunodeficiency Virus gp41 Fusion Domain by Molecular Dynamics Simulation

The structures of the 16-residue fusion domain (or fusion peptide, FP) of the human immunodeficiency virus gp41 fusion protein, two of its mutants, and a shortened peptide (5-16) were studied by molecular dynamics simulation in an explicit palmitoyloleoylphosphoethanolamine bilayer. The simulations showed that the active wild-type FP inserts into the bilayer approximately 44 degrees +/- 6 degrees with respect to the bilayer normal, whereas the inactive V2E and L9R mutants and the inactive 5 to 16 fragment lie on the bilayer surface. This is the first demonstration by explicit molecular dynamics of the oblique insertion of the fusion domain into lipid bilayers, and provides correlation between the mode of insertion and the fusogenic activity of these peptides. The membrane structure of the wild-type FP is remarkably similar to that of the influenza HA(2) FP as determined by nuclear magnetic resonance and electron spin resistance power saturation. The secondary structures of the wild-type FP and the two inactive mutants are quite similar, indicating that the secondary structure of this fusion domain plays little or no role in affecting the fusogenic activity of the fusion peptide. The insertion of the wild-type FP increases the thickness of the interfacial area of the bilayer by disrupting the hydrocarbon chains and extending the interfacial area toward the head group region, an effect that was not observed in the inactive FPs.

Molecular Dynamics Study of Substance P Peptides Partitioned in a Sodium Dodecylsulfate Micelle

Two neuropeptides, substance P (SP) and SP-tyrosine-8 (SP-Y8), have been studied by molecular dynamics (MD) simulation in an explicit sodium dodecylsulfate (SDS) micelle. Initially, distance restraints derived from NMR nuclear Overhauser enhancements (NOE) were incorporated in the restrained MD (RMD) during the equilibration stage of the simulation. It was shown that when SP-Y8 was initially placed in an insertion (perpendicular) configuration, the peptide equilibrated to a surface-bound (parallel) configuration in approximately 450 ps. After equilibration, the conformation and orientation of the peptides, the solvation of both the backbone and the side chain of the residues, hydrogen bonding, and the dynamics of the peptides were analyzed from trajectories obtained from the RMD or the subsequent free MD (where the NOE restraints were removed). These analyses showed that the peptide backbones of all residues are either solvated by water or are hydrogen-bonded. This is seen to be an important factor against the insertion mode of interaction. Most of the interactions come from the hydrophobic interaction between the side chains of Lys-3, Pro-4, Phe-7, Phe-8, Leu-10, and Met-11 for SP, from Lys-3, Phe-7, Leu-10, and Met-11 in SP-Y8, and the micellar interior. Significant interactions, electrostatic and hydrogen bonding, between the N-terminal residues, Arg-Pro-Lys, and the micellar headgroups were observed. These latter interactions served to affect both the structure and, especially, the flexibility, of the N-terminus. The results from simulation of the same peptides in a water/CCl4 biphasic cell were compared with the results of the present study, and the validity of using the biphasic system as an approximation for peptide-micelle or peptide-bilayer systems is discussed.

Molecular Dynamics Study of Substance P Peptides in a Biphasic Membrane Mimic

Two neuropeptides, substance P (SP) and SP-tyrosine-8 (SP-Y8), have been studied by molecular dynamics (MD) simulation in a TIP3P water/CCl4 biphasic solvent system as a mimic for the water-membrane system. Initially, distance restraints derived from NMR nuclear Overhauser enhancements (NOE) were incorporated in the restrained MD (RMD) in the equilibration stage of the simulation. The starting orientation/position of the peptides for the MD simulation was either parallel to the water/CCl4 interface or in a perpendicular/insertion mode. In both cases the peptides equilibrated and adopted a near-parallel orientation within approximately 250 ps. After equilibration, the conformation and orientation of the peptides, the solvation of both the backbone and the side chain of the residues, hydrogen bonding, and the dynamics of the peptides were analyzed from trajectories obtained in the RMD or the subsequent free MD (where the NOE restraints were removed). These analyses showed that the peptide backbone of nearly all residues are either solvated by water or are hydrogen-bonded. This is seen to be an important factor against the insertion mode of interaction. Most of the interactions with the hydrophobic phase come from the hydrophobic interactions of the side chains of Pro-4, Phe-7, Phe-8, Leu-10, and Met-11 for SP, and Phe-7, Leu-10, Met-11 and, to a lesser extent, Tyr-8 in SP-Y8. Concerted conformational transitions took place in the time frame of hundreds of picoseconds. The concertedness of the transition was due to the tendency of the peptide to maintain the necessary secondary structure to position the peptide properly with respect to the water/CCl4 interface.

Molecular dynamics simulation of adrenocorticotropin (1-10) peptide in a solvated dodecylphosphocholine micelle.

Adrenocorticotropin (ACTH) (1-10), an adrenocorticotropin hormone fragment, has been studied by molecular dynamics (MD) simulation in an NPT ensemble in an explicit dodecylphosphocholine (DPC) micelle. Two starting configurations of the peptide/micelle system, corresponding to the insertion and surface-binding modes, were used. A common equilibrated configuration, in which the peptide lies parallel to the micellar surface, was reached from both simulations. In the initial part of the simulations, distance restraints derived from NMR nuclear Overhauser enhancements were incorporated before the peptide reached an equilibrium configuration with respect to the micelle. Analyses of the trajectories from the subsequent free (unrestrained) MD simulation showed that ACTH (1-10) does not conform strictly to a helical structure. The loss of the helical structure is due to decreased intramolecular hydrogen bonding accompanied by an increase of hydrogen bonding between the amide protons of the peptide and the micellar head groups. However, the extent of the latter interaction is less pronounced than in the negatively charged SDS micelle. The final structure enhances the amphipathic nature of the peptide, facilitating better interactions at the water-hydrophobic interface. The primary hydrophobic interactions with the micelle came from the side chains of Met4, Phe7, and Trp9. All peptide bonds were either hydrated or were involved in intramolecular hydrogen bonding. The interactions with the DPC micelle, the conformation of the bound peptide, and the dynamics of the peptide, as revealed by the time correlation functions of the N-H bonds, were compared with those of the ACTH (1-10)/SDS system studied previously by MD simulations.

The temperature dependence and thermodynamic functions of partitioning of substance P peptides in dodecylphosphocholine micelles

The temperature dependence of the partition of a neuropeptide, Substance P (SP), and its [Tyr8] analogue in a widely used membrane mimic, dodecylphosphocholine micelles, was studied by using a pulsed field gradient nmr diffusion technique. The partition coefficient was found to decrease when the temperature is increased, indicating a favorable (negative) enthalpy change upon partitioning of the peptides. Thermodynamic functions of the partitioning were determined. The enthalpy of partition ΔHpart, was found to be in the −2.5 to −3.0 kcal/mol range, which is between 2 and 3 times higher than the entropic term −TΔSpart. The free energy of partitioning is consistent with a model in which the SP peptides interact with the micelles mainly through the hydrophobic side chains of the residues Phe7, Phe8 (or Tyr8), Leu10, and Met11, and without the insertion of a major portion of the peptide into the hydrophobic core of the micelles.

NMR studies of adrenocorticotropin hormone peptides in sodium dodecylsulfate and dodecylphosphocholine micelles: proline isomerism and interactions of the peptides with micelles.

Three adrenocorticotropin hormone (ACTH) fragments (1-10, 1-24, and 11-24) have been studied in water and in sodium dodecylsulfate (SDS) and dodecylphosphocholine (DPC) micelles by nuclear magnetic resonance spectroscopy. The trans-cis isomerism at all three proline sites (at positions 12, 19, and 24) was found in the 11-24 segment of the peptide. The population of the cis isomers changes with the environment of the peptide. Specifically, the presence of the DPC micelle does not affect the trans-cis equilibrium in the 11-24 segment from that in water. In contrast, the presence of the SDS micelles decreases the population of the cis isomer at Pro(24), but increases its population at Pro(12) and Pro(19). The effect of SDS micelles on the trans-cis equilibrium at these proline sites was discussed. Intermolecular nuclear Overhauser effect (NOE) correlations between the ACTH peptides and the micelles were observed. These correlations occurred only in the 1-10 segment of the peptides, and the hydrophobic side chains contributed most to the intermolecular NOE. The intermolecular NOE pattern corroborates the suggestion that the 1-10 segment of the ACTH peptides bind to these micelles via a surface-binding mode, with most of the interactions coming from the insertion of the hydrophobic side chains.

The study of the conformation and interaction of two tachykinin peptides in membrane mimicking systems by NMR spectroscopy and pulsed field gradient diffusion.

Pulsed-field gradient diffusion has been used to study the binding of two tachykinin peptides, [Tyr(8)]-substance P (SP) and [Tyr(0)]-neurokinin A (NKA) to two membrane-mimicking micelles, dodecylphosphocholine, and sodium dodecylsulfate. The structure of these peptides bound to the micelles have also been studied by using two-dimensional nmr and restrained simulated annealing calculations. No major difference in the structures of each peptide in the two micellar media was found. The difference between the micelle-bound structure of [Tyr(8)]SP and that of SP was also minor. The longer helical conformation on the C-terminus for [Tyr(0)]NKA was observed, compared with that for NKA. The relationship between the difference in the biological potencies of [Tyr(8)]SP and SP and the differences in their structure, especially the interaction of the side chains of the two aromatic residues, and the difference in their binding affinities to membrane was discussed. In addition, differences between the result of restrained molecular dynamics simulations of [Tyr(8)]SP in the presence of an explicit micelle and the present results were observed and discussed.

Regioselective synthesis and characterization of 6-O-alkanoylgluconolactones

6-O-Alkanoylgluconolactones, a novel class of carbohydrate ester-linked surfactants containing a lactone head group, have been synthesized enzymatically from the unprotected aldonolactone. The synthesis was accomplished by regioselective esterification of glucono-1,5-lactones at C-6 by porcine pancreatic lipase in the solvent pyridine. These compounds were found to exhibit a sharp increase in solubility at 90–96°C but remained soluble well below their initial dissolution temperature, precipitating at 30–37°C. To determine the cause of this unusual solubility behavior, the composition of the precipitate was characterized by 1H and 13C NMR, and GC-MS. Analysis of the precipitates identified the material as a hydrolysate containing alkanoylglucono-1,5-lactone, alkanoylglucono-1,4-lactone and alkanoylgluconic acid. The hydrolysis and isomerization of the lactone gave a mixture of compounds that are more soluble than the corresponding pure alkanoylglucon-δ-lactone.

Molecular motion in a magnetically aligned lyotropic liquid crystal system

A study of the dynamics of the lipid molecules in the nematic lyotropic liquid crystal system composed of 30 per cent (by weight) potassium laurate-αd 2, 6 per cent decanol, 4 per cent potassium chloride and 60 per cent water was carried out using deuteron N.M.R. The quadrupolar splitting v Q of the N.M.R. spectrum, the decay T 2e of the quadrupolar echo the decay T 1Q of the quadrupolar energy and the return T 1Z of the Zeeman energy were measured as functions of temperature throughout the nematic region. The v Q values show that the order parameter for the α position of the laurate chain decreases from 0·17 to 0·11 with increasing temperature. There are two contributions to the observed values of T 2e. The time averaged dipolar interaction between the α deuterons and neighbouring protons results in a roughly constant contribution while the time dependent quadrupolar interaction causes a marked decrease in T 2e near the low temperature phase boundary. An analysis of the quadrupolar contribution suggests ...

Carbon-13 nuclear magnetic resonance studies of some organoselenium compounds containing carbon–selenium double bonds

Carbon-13 n.m.r. spectra were obtained for eight compounds having C = Se double bonds. These comprised five selenoketones, 2,2,4,4-tetramethylpentane-2-selone (1-Se), 1-thia-3,3,5,5-tetramethylcyclohexane-4-selone (2-Se), 1,1,3,3-tetra methylindane-2-selone (3-Se), 2,2,5,5-tetra methylcyclopent-3-ene-1-selone (4-Se), and selenofenchone (5-Se), one selenoester, ethyl selenobenzoate (6-Se), and two selenoamides, NN-dimethylselenobenzamide (7-Se) and NN-dimethyl-2,2-dimethylselenopropanamide (8-Se). Coupling constants, 1J(13C–77Se), were measured for (1) and (3)–(7). A comparison was made among the chemical shifts of (1)–(8), their oxygen analogues, and the sulphur analogues of (1), (5), and (7). The selenocarbonyl carbon atoms were shifted 34–72 p.p.m. downfield and the α-carbon atoms 10–19 p.p.m. downfield from their oxygen analogues. The differences, δΔSe, O, for the remaining carbons are only a few p.p.m. Values of 1J(13C–77Se) were 209–221 Hz, much larger than any previously observed 13C–77Se coupling constants.