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At least 505 records · Page 28Linked to original sources
PubMed2005

Molecular dynamics simulations of the endocannabinoid N-arachidonoylethanolamine (anandamide) in a phospholipid bilayer: probing structure and dynamics.

The phospholipid bilayer plays a central role in the lifecycle of the endogenous cannabinoid N-arachidonoylethanolamine (anandamide, 1). Compound 1 has been shown to be synthesized from lipids, to interact with the membrane-embedded cannabinoid CB1 receptor, to be transported to intracellular compartments, possibly via caveolae-related endocytosis, and finally, to be degraded by fatty acid amide hydrolase (FAAH), an integral membrane protein which has an active site that is accessed by 1 possibly via the bilayer. Because the anandamide system is intimately associated with the lipid milieu, information concerning the location of 1 in the phospholipid bilayer and the conformations it can adopt is important to our understanding of the mechanism of cannabinoid action at the molecular level. We report here an exploration of the properties of 1 in a 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) phospholipid bilayer via multi-nanosecond molecular dynamics simulations. Our results suggest that the polar headgroup of 1 resides at the lipid-water interface, specifically in the polar phospholipid headgroup region, whereas the nonpolar acyl chain of 1 extends into the hydrocarbon core of the membrane. Our analysis also indicates that (i) an elongated conformation of 1 is preferred in the DOPC bilayer environment; however, many other conformations of 1 are observed; (ii) hydrogen-bonding between the lipid (DOPC) and the headgroup of 1, although extensive, is quite short-lived; and (iii) the C-H bond order parameters for the acyl chain of 1 are low compared to order parameters typically seen for saturated acyl chains of fatty acids, and these order parameters decrease toward the bilayer center. The bilayer location for 1 revealed by these studies may be important for the interaction of 1 with membrane-embedded proteins such as the cannabinoid CB1 receptor and membrane-associated proteins such as FAAH.

Arachidonic Acids↗
PubMed2005

Molecular dynamics simulations of GlpF in a micelle vs in a bilayer: conformational dynamics of a membrane protein as a function of environment.

Octyl glucoside (OG) is a detergent widely employed in structural and functional studies of membrane proteins. To better understand the nature of protein-OG interactions, molecular dynamics simulations (duration 10 ns) have been used to explore an alpha-helical membrane protein, GlpF, in OG micelles and in DMPC bilayers. Greater conformational drift of the extramembraneous protein loops, from the initial X-ray structure, is seen for the GlpF-OG simulations than for the GlpF-DMPC simulation. The mobility of the transmembrane alpha-helices is approximately 1.3x higher in the GlpF-OG than the GlpF-DMPC simulations. The detergent is seen to form an irregular torus around the protein. The presence of the protein leads to a small perturbation in the behavior of the alkyl chains in the OG micelle, namely an approximately 15% increase in the trans-gauche(-)-gauche(+) transition time. Aromatic side chains (Trp, Tyr) and basic side chains (Arg, Lys) play an important role in both protein-detergent (OG) and protein-lipid (DMPC) interactions.

Aquaporins↗
PubMed2005

Ultrafast dynamics of the azobenzene-coumarin complex: investigation of cooling dynamics measured by an integrated molecular thermometer.

The energy dissipation mechanism from photoexcited azobenzene (Az) was studied by femtosecond time-resolved UV absorption spectroscopy using 7-amino-4-trifluoromethylcoumarin (ATC) as a probe. The distance between the probe molecule and Az was fixed by covalently linking them together through a rigid proline spacer. Picosecond dynamics in THF solutions were studied upon excitation into the S1 state by a 100 fs laser pulse at 480 nm. Transient absorption spectra obtained for Az-Pro-ATC combined the S1 state absorption and vibrationally excited ground-state absorption of ATC. Correction of the transient spectrum of Az-Pro-ATC for the S1 absorption provided the time-resolved absorption spectrum of the ATC hot band. Three major components were observed in the transient kinetics of Az-Pro-ATC vibrational cooling. It is proposed that in ca. 0.25 ps after the excitation, the S1 state of azobenzene decays to form an initial vibrationally excited nonthermalized ground state of Az-Pro-ATC that involves vibrational modes of both azobenzene and coumarin. This hot ground state decays in ca. 0.32 ps to the next, vibrationally equilibrated, transient state by redistributing the energy within the molecule. Subsequently, the latter state cools by transferring its energy to the closest solvent molecules in ca. 5 ps; then, the energy diffuses to the bulk solvent in 13 ps.

Azo Compounds↗
PubMed2006

Insights into photodissociation dynamics of propionyl chloride from ab initio calculations and molecular dynamics simulations.

The potential energy surfaces of isomerization, dissociation, and elimination reactions for CH3CH2COCl in the S0 and S1 states have been mapped with the different ab initio calculations. Mechanistic photodissociation of CH3CH2COCl at 266 nm has been characterized through the computed potential energy surfaces, the optimized surface crossing structure, intrinsic reaction coordinate, and ab initio molecular dynamics calculations. Photoexcitation at 266 nm leads to the CH3CH2COCl molecules in the S1 state. From this state, the C-Cl bond cleavage proceeds in a time scale of picosecond in the gas phase. The barrier to the C-Cl bond cleavage on the S1 surface is significantly increased by effects of the matrix and the internal conversion to the ground state prevails in the condensed phase. The HCl eliminations as a result of internal conversion to the ground state become the dominant channel upon photodissociation of CH3CH2COCl in the argon matrix at 10 K.

Journal Article↗
PubMed2005

Dynamic mechanism of E2020 binding to acetylcholinesterase: a steered molecular dynamics simulation.

The unbinding process of E2020 ((R,S)-1-benzyl-4-[(5,6-dimethoxy-1-indanon)-2-yl]-methylpiperidine) leaving from the long active site gorge of Torpedo californica acetylcholinesterase (TcAChE) was studied by using steered molecular dynamics (SMD) simulations on a nanosecond scale with different velocities, and unbinding force profiles were obtained. Different from the unbinding of other AChE inhibitors, such as Huperzine A that undergoes the greatest barrier located at the bottleneck of the gorge, the major resistance preventing E2020 from leaving the gorge is from the peripheral anionic site where E2020 interacts intensively with several aromatic residues (e.g., Tyr70, Tyr121, and Trp279) through its benzene ring and forms a strong direct hydrogen bond and a water bridge with Ser286 via its O24. These interactions cause the largest rupture force, approximately 550 pN. It was found that the rotatable bonds of the piperidine ring to the benzene ring and dimethoxyindanone facilitate E2020 to pass the bottleneck through continuous conformation change by rotating those bonds to avoid serious conflict with Tyr121 and Phe330. The aromatic residues lining the gorge wall are the major components contributing to hydrophobic interactions between E2020 and TcAChE. Remarkably, these aromatic residues, acting in three groups as "sender" and "receiver", compose a "conveyer belt" for E2020 entering and leaving the TcAChE gorge.

Acetylcholinesterase↗
PubMed2006

Energy-flow dynamics in the molecular channel of propanal photodissociation, C2H5CHO --> C2H6 + CO: direct ab initio molecular dynamics study.

Direct ab initio molecular dynamics calculations have been carried out for the molecular channel of the photodissociation of propanal, C2H5CHO --> C2H6 + CO, at the RMP2(full)/cc-pVDZ level of ab initio molecular orbital theory. The initial conditions were generated using the microcanonical sampling to put the excess energy randomly into all vibrational modes of the TS. Starting from the TS, a total of approximately 700 trajectories were numerically integrated for 100 fs. The obtained final energy distributions for the C2H6 and CO fragments and their relative translational motion were found to be quite similar to those obtained for the acetaldehyde reaction, CH3CHO --> CH4 + CO, in our previous study (Chem. Phys. Lett. 2006, 421, 549) despite the fact that the number of degree of freedom for C2H6 is larger than that for CH4. The coupling between the intrinsic reaction coordinate and one of the generalized normal modes orthogonal to it was predicted substantially strong around s = 1.4 amu(1/2) bohr, and it is expected that the energy flow out of C2H6 proceeds through this coupling. However, the obtained energy distributions strongly suggest that the coupling among the modes in C2H6 is quite small and the intramolecular energy redistribution does not occur efficiently in this molecule.

Journal Article↗
PubMed1982

Biochemical and dynamic responses to single and repeated doses of methyldopa and propranolol during dynamic physical activity.

Our purpose was to describe changes in potassium disposition with antirenin antihypertensives during dynamic physical activity in normal subjects receiving methyldopa and propranolol. Before the study, 2 hr after dosing and coincident with immediate preexercise on treadmill (at graded increases of exercise), and 2 hr after exercise, blood was sampled for determination of potassium, renin, aldosterone, and catecholamine levels. Blood pressure and heart rate were measured. The results demonstrate no greater increase in potassium after single or multiple doses of methyldopa than after placebo. After the first dose of propranolol there was a greater rise in potassium over that with placebo, but it was not observed after multiple doses, which may be related to the low doses. There were minor, but significant, changes in norepinephrine, renin, and systolic pressure with multiple-dose methyldopa and in renin, heart rate, and systolic and diastolic pressure with propranolol. Overall, the adrenergic responses to exercise win methyldopa and propranolol were biochemically altered rather than functionally impaired. The latter is related to dose and the underlying age and state of health of our subjects. Methyldopa (or clonidine) may be useful in patients with hypertension who exercise and are predisposed to pertubations in potassium disposition.

Adult↗
PubMed2004

Photodissociation dynamics of pyrrole: evidence for mode specific dynamics from conical intersections.

The H and D atom elimination mechanisms in the photodissociation of jet cooled pyrrole and pyrrole-d1 have been studied by photofragment velocity map imaging. The molecules were excited to the 1 1A2 (pi sigma*) state at lambda = 243 nm and to the 1 1B2 (pi pi*) state at lambda = 217 nm. H/D atoms were detected by (2 + 1) resonance enhanced multiphoton ionization (REMPI) at lambda = 243 nm. The analysis of the images and the resulting translational energy distributions from the 1 1A2 state demonstrates the existence of two decay pathways, fast mode-specific cleavage of the NH bond in the excited state (channel A) and internal conversion (IC) to the electronic ground state (S0) followed by unimolecular decomposition of the vibrationally hot S0 molecules (channel B). The angular distributions of the H/D atoms from the direct dissociation in the excited state are strongly anisotropic, whereas the decay of the S0 molecules leads to spatially isotropic distributions. The results at lambda = 217 nm indicate that the 1 1B2 state undergoes an ultrafast radiationless transition to 1 1A2 followed by the abovementioned direct mode-specific NH bond fission on the 1 1A2 potential energy surface (channel A') or conversion to S0 and subsequent unimolecular decomposition (channel B'). The latter pathway may also be initiated by a direct relaxation from 1 1B2 to S0. The anisotropy parameter of beta approximately -1 for the direct NH bond fission at lambda = 217 nm is in accordance with the expectations for a perpendicular electronic excitation and a dissociation lifetime that is short compared to the rotational period of the molecules. The fast decay dynamics of both excited electronic states can be rationalized with reference to the theoretically predicted conical intersections between the pi pi*, pi sigma*, and S0 potential energy surfaces and the antibonding nature of the pi sigma* potential energy surface with respect to the NH bond [A. L. Sobolewski, W. Domcke. C. Dedonder-Lardeux and C. Jouvet, Phys. Chem. Chem. Phys. 2002, 4, 1093].

Photochemistry↗
PubMed2006

On the role of the counter-ion in defining water structure and dynamics: order, structure and dynamics in hydrophilic and hydrophobic gadolinium salt complexes.

The crystal structures of the hydrated salts of [Gd.DOTAM]3+ and its more hydrophobic derivative [Gd.]3+, bearing 4 alpha-phenylethyl groups, (both Gd and Yb salts) are reported and compared. The nature of the anion determines the degree of ordering in the lattice and the extent of hydration. These effects are correlated with the results of 17O and 1H NMR measurements of water exchange dynamics in solution. With [Gd.DOTAM]3+, structural ordering or the extent of hydration in the hydrated lattice follows the sequence Cl->Br->I- and this order also defines the water exchange rate in solution: 7.3, 19.5, 33.3x10(4) s-1 (298 K), respectively. For [Gd.]3+ salts, the measured relaxivity is determined purely by the outer sphere term and the water exchange rate at 298 K is very similar (typically 1x10(4) s-1) for chloride, bromide, iodide, acetate, triflate and nitrate salts, notwithstanding the different nature and extent of hydration found in the crystalline lattice.

Journal Article↗
PubMed2004

Water network dynamics at the critical moment of a peptide's beta-turn formation: a molecular dynamics study.

All-atom molecular dynamics simulations for a single molecule of Leu-Enkephalin in aqueous solution have been used to study the role of the water network during the formation of beta-turns. We give a detailed account of the intramolecular hydrogen bonding, the water-peptide hydrogen bonding, and the orientation and residence times of water molecules focusing on the short critical periods of transition to the stable beta-turns. These studies suggest that, when intramolecular hydrogen bonding between the first and fourth residue of the beta-turn is not present, the disruption of the water network and the establishment of water bridges constitute decisive factors in the formation and stability of the beta-turn. Finally, we provide possible explanations and mechanisms for the formations of different kinds of beta-turns.

Computer Simulation↗
PubMed2004

Local order and dynamics in supercooled water: a study by IR spectroscopy and molecular dynamic simulations.

Micron-sized water droplets in a cryogenic flow tube were probed by IR spectroscopy. The analysis of the IR spectra suggests that there is a relative increase of about 30% in the fraction, f(L), of low density domains in water on cooling over the temperature range between 300 and 240 K. The results derived from the experiments agree qualitatively with those of molecular dynamics (MD) simulations in terms of the increase in the f(L) values. The MD simulations show that the intensities of the mode at about 100 cm(-1) for the molecules in the low density domains are reduced in comparison to the average, while the intensities and frequencies of the librational mode at 600 cm(-1) are increased. Furthermore, the reorientations (dielectric relaxation times) in these domains are found to be somewhat slower, pointing to the fact that these low density "cages" live longer than the average local molecular environments in supercooled water.

Journal Article↗
PubMed2004

Potential energy surfaces and dynamics of Ni2+ ion aqueous solution: molecular dynamics simulation of the electronic absorption spectrum.

We develop a model effective Hamiltonian for describing the electronic structures of first-row transition metals in aqueous solutions using a quasidegenerate perturbation theory. All the states consisting of 3d(n) electronic configurations are determined by diagonalizing a small effective Hamiltonian matrix, where various intermolecular interaction terms such as the electrostatic, polarization, exchange, charge transfer, and three-body interactions are effectively incorporated. This model Hamiltonian is applied to constructing the ground and triplet excited states potential energy functions of Ni(2+) in aqueous solution, based on the ab initio multiconfiguration quasidegenerate perturbation theory calculations. We perform molecular dynamics simulation calculations for the ground state of Ni(2+) aqueous solution to calculate the electronic absorption spectral shape as well as the ground state properties. Agreement between the simulation and experimental spectra is satisfactory, indicating that the present model can well describe the Ni(2+) excited state potential surfaces in aqueous solution.

Journal Article↗
PubMed2004

Dynamics of glass-forming liquids. VIII. Dielectric signature of probe rotation and bulk dynamics in branched alkanes.

We have measured the dielectric relaxation of several glass forming branched alkanes with very low dielectric loss in the frequency range 50 Hz-20 kHz. The molecular liquids of this study are 3-methylpentane, 3-methylheptane, 4-methylheptane, 2,3-dimethylpentane, and 2,4,6-trimethylheptane. All liquids display asymmetric loss peaks typical of supercooled liquids and slow beta relaxations of similar amplitudes. As an unusual feature, deliberate doping with 2-ethyl-1-hexanol, 5-methyl-2-hexanol, 2-methyl-1-butanol, 1-propanol, or 2-methyltetrahydrofuran at the 1 wt % level generates additional relaxation peaks at frequencies below those of the alpha relaxation. The relaxation times of these sub-alpha-peaks increase systematically with the size of the dopant molecules. Because these features are spectrally separate from the bulk dynamics, the rotational behavior and effective dipole moments of the probes can be studied in detail. For the alcohol guest molecules, the large relative rotational time scales and small effective dipole moments are indicative of hydrogen bonded clusters instead of individual molecules.

1-Propanol↗
PubMed2006

Calculation of the entropy and free energy of peptides by molecular dynamics simulations using the hypothetical scanning molecular dynamics method.

Hypothetical scanning (HS) is a method for calculating the absolute entropy S and free energy F from a sample generated by any simulation technique. With this approach each sample configuration is reconstructed with the help of transition probabilities (TPs) and their product leads to the configuration's probability, hence to the entropy. Recently a new way for calculating the TPs by Monte Carlo (MC) simulations has been suggested, where all system interactions are taken into account. Therefore, this method--called HSMC--is in principle exact where the only approximation is due to insufficient sampling. HSMC has been applied very successfully to liquid argon, TIP3P water, self-avoiding walks on a lattice, and peptides. Because molecular dynamics (MD) is considered to be significantly more efficient than MC for a compact polymer chain, in this paper HSMC is extended to MD simulations as applied to peptides. Like before, we study decaglycine in vacuum but for the first time also a peptide with side chains, (Val)(2)(Gly)(6)(Val)(2). The transition from MC to MD requires implementing essential changes in the reconstruction process of HSMD. Results are calculated for three microstates, helix, extended, and hairpin. HSMD leads to very stable differences in entropy TDeltaS between these microstates with small errors of 0.1-0.2 kcal/mol (T=100 K) for a wide range of calculation parameters with extremely high efficiency. Various aspects of HSMD and plans for future work are discussed.

Chemistry, Physical↗
PubMed2005

The importance of dynamic effects on the enzyme activity: X-ray structure and molecular dynamics of onconase mutants.

Onconase (ONC), a member of the RNase A superfamily extracted from oocytes of Rana pipiens, is an effective cancer killer. It is currently used in treatment of various forms of cancer. ONC antitumor properties depend on its ribonucleolytic activity that is low in comparison with other members of the superfamily. The most damaging side effect from Onconase treatment is renal toxicity, which seems to be caused by the unusual stability of the enzyme. Therefore, mutants with reduced thermal stability and/or increased catalytic activity may have significant implications for human cancer chemotherapy. In this context, we have determined the crystal structures of two Onconase mutants (M23L-ONC and C87S,des103-104-ONC) and performed molecular dynamic simulations of ONC and C87S,des103-104-ONC with the aim of explaining on structural grounds the modifications of the activity and thermal stability of the mutants. The results also provide the molecular bases to explain the lower catalytic activity of Onconase compared with RNase A and the unusually high thermal stability of the amphibian enzyme.

Animals↗
PubMed2005

Dynamic changes in histone H3 lysine 9 methylations: identification of a mitosis-specific function for dynamic methylation in chromosome congression and segregation.

Histone methylation is unique among post-translational histone modifications by virtue of its stability. It is thought to be a relatively stable and heritable epigenetic mark for gene-specific regulation. In this study, we use quantitative in situ approaches to investigate the cell cycle dynamics of methylated isoforms of histone H3 lysine 9. Contrary to the expected stability of trimethylated lysines, our results for trimethylated lysine 9 (tMeK9) of H3 demonstrate that the genomic content of this methylation undergoes significant changes as cells progress through mitosis. Unexpectedly, there is a loss of tMeK9 that appears to reflect a robust demethylase activity that is active during the period between anaphase and cytokinesis. Subsequent investigations of mitoses in tMeK9-deficient cells revealed defects in chromosome congression and segregation that are distinct from the increased cohesion at centromeres previously reported in association with the loss of tMeK9. Collectively, these results identify a mitosis-specific trimethylation of Lys9 in pericentromeric heterochromatin that functions in the faithful segregation of chromosomes.

Adenosine↗