Benchmark of Schemes for Multiscale Molecular Dynamics Simulations.

In multiscale molecular dynamics simulations the accuracy of detailed models is combined with the efficiency of a reduced representation. For several applications - namely those of sampling enhancement - it is desirable to combine fine-grained (FG) and coarse-grained (CG) approaches into a single hybrid approach with an adjustable mixing parameter. We present a benchmark of three algorithms that use a mixing of the two representation layers using a Lagrangian formalism. The three algorithms use three different approaches for keeping the particles at the FG level of representation together: 1) addition of forces, 2) mass scaling, and 3) temperature scaling. The benchmark is applied to liquid hexadecane and includes an evaluation of the average configurational entropy of the FG and CG subsystems. The temperature-scaling scheme achieved a 3-fold sampling speedup with little deviation of FG properties. The addition-of-forces scheme kept FG properties the best but provided little sampling speedup. The mass-scaling scheme yielded a 5-fold speedup but deviated the most from FG properties.

Data-driven directions for effective footwear provision for the high-risk diabetic foot.

AIMS: Custom-made footwear is used to offload the diabetic foot to prevent plantar foot ulcers. This prospective study evaluates the offloading effects of modifying custom-made footwear and aims to provide data-driven directions for the provision of effectively offloading footwear in clinical practice. METHODS: Eighty-five people with diabetic neuropathy and a recently healed plantar foot ulcer, who participated in a clinical trial on footwear effectiveness, had their custom-made footwear evaluated with in-shoe plantar pressure measurements at three-monthly intervals. Footwear was modified when peak pressure was ≥ 200 kPa. The effect of single and combined footwear modifications on in-shoe peak pressure at these high-pressure target locations was assessed. RESULTS: All footwear modifications significantly reduced peak pressure at the target locations compared with pre-modification levels (range -6.7% to -24.0%, P < 0.001). The metatarsal heads were most frequently targeted. Repositioning an existing (trans-)metatarsal pad in the shoe insole (-15.9% peak pressure relief), applying local cushioning to the insole (-15.0%) and replacing the insole top cover with Plastazote (-14.2%) were the most effective single modifications. Combining a new Plastazote top cover with a trans-metatarsal bar (-24.0% peak pressure relief) or with local cushioning (-22.0%) were the most effective combined modifications. CONCLUSIONS: In people with diabetic neuropathy and a recently healed plantar foot ulcer, significant offloading can be achieved at high-risk foot regions by modifying custom-made footwear. These results provide data-driven directions for the design and evaluation of custom-made footwear for high-risk people with diabetes, and essentially mean that each shoe prescribed should incorporate those design features that effectively offload the foot.

Stochastic Dynamics with Correct Sampling for Constrained Systems.

In this paper we discuss thermostatting using stochastic methods for molecular simulations where constraints are present. For so-called impulsive thermostats, like the Andersen thermostat, the equilibrium temperature will differ significantly from the imposed temperature when a limited number of particles are picked and constraints are applied. We analyze this problem and give two rigorous solutions for it. A correct general treatment of impulsive stochastic thermostatting, including pairwise dissipative particle dynamics and stochastic forcing in the presence of constraints, is given and it is shown that the constrained canonical distribution is sampled rigorously. We discuss implementation issues such as second order Trotter expansions. The method is shown to rigorously maintain the correct temperature for the case of extended simple point charge (SPC/E) water simulations.

Efficient Algorithms for Langevin and DPD Dynamics.

In this article, we present several algorithms for stochastic dynamics, including Langevin dynamics and different variants of Dissipative Particle Dynamics (DPD), applicable to systems with or without constraints. The algorithms are based on the impulsive application of friction and noise, thus avoiding the computational complexity of algorithms that apply continuous friction and noise. Simulation results on thermostat strength and diffusion properties for ideal gas, coarse-grained (MARTINI) water, and constrained atomic (SPC/E) water systems are discussed. We show that the measured thermal relaxation rates agree well with theoretical predictions. The influence of various parameters on the diffusion coefficient is discussed.

Completion and refinement of 3-D homology models with restricted molecular dynamics: application to targets 47, 58, and 111 in the CASP modeling competition and posterior analysis.

A method is presented to refine models built by homology by the use of restricted molecular dynamics (MD) techniques. The basic idea behind this method is the use of structure validation software to determine for each residue the likelihood that it is modeled correctly. This information is used to determine constraints and restraints in an MD simulation including explicit solvent molecules, which is used for model refinement. The procedure is based on the idea that residues that the validation software identifies as correctly positioned should be strongly constrained or restrained in the MD simulations, whereas residues that are likely to be positioned wrongly should move freely. Two different protocols are compared: one (applied to CASP3 target T58) using full structural constraints with separate optimization of each short fragment and the other (applied to T47) allowing some freedom using harmonic restraining potentials, with automatic optimization of the whole molecule. Structures along the MD trajectory that scored best in structural checks were selected for the construction of models that appeared to be successful in the CASP3 competition. Model refinement with MD in general leads to a model that is less like the experimental structure (Levitt et al. Nature Struct Biol 1999;6:108-111). Actually, refined T47 was slightly improved compared to the starting model; changes in model T58 led not to further enhancement. After the X-ray structure of the modeled proteins became known, the procedure was evaluated for two targets (T47 and the CASP4 target T111) by comparing a long simulation in water with the experimental target structures. It was found that structural improvements could be obtained on a nanosecond time scale by allowing appropriate freedom in the simulation. Structural checks applied to fast fluctuations do not appear to be informative for the correctness of the structure. However, both a simple hydrogen bond count and a simple compactness measure, if averaged over times of typically 300 ps, correlate well with structural correctness and we suggest that criteria based on these properties may be used in computational folding strategies.

DSC studies of Fusarium solani pisi cutinase: consequences for stability in the presence of surfactants.

The application of cutinase from Fusarium solani pisi as a fat-stain removing ingredient in laundry washing is hampered by its lack of stability in the presence of anionic surfactants. We postulate that the stability of cutinase towards anionics can be improved by mutations increasing its temperature stability. Thermal unfolding as measured with DSC, appears to be irreversible, though the thermograms are more symmetric than predicted by a simple irreversible model. In the presence of taurodeoxycholate (TDOC), the unfolding temperature is lower and the unfolding is reversible. We conclude that an early reversible unfolding intermediate exists in which a number of additional hydrophobic patches are exposed to the solvent, or preferentially are covered with TDOC. Improvement of the stability of cutinase with respect to both surfactants and thermal denaturation, should thus be directed toward the prevention of exposure of hydrophobic patches in the early intermediate.

Effect of tibolone and raloxifene on the tail temperature of oestrogen-deficient rats.

Oestradiol, clonidine, tibolone and raloxifene were tested for their effects on the tail temperature of oestrogen deficient rats, a potential new model that can be used to test compounds that may be of use in the treatment of hot flushes in humans. Rats underwent ovariectomies or sham operations and their tail temperature and physical activity were measured telemetrically. Oestrogen depletion affected tail temperature in the rats' active, but not their resting phase. During the transition from the resting to the active phase, tail temperature in normal rats dropped by about 6 degrees C, but only by approximately 1 degrees C after ovariectomy. Treatment of the ovariectomised rats with oestrogen, clonidine or tibolone dose-dependently restored the drop in tail temperature. However, raloxifene did not change the tail temperature of ovariectomised rats. Thus, tibolone and raloxifene have different effects on the temperature regulation in the tail. This method of measuring tail temperature free of stress in ovariectomised rats may serve as a useful procedure for selecting compounds that are of potential use in the treatment of hot flushes.

Voltage-dependent insertion of alamethicin at phospholipid/water and octane/water interfaces.

Understanding the binding and insertion of peptides in lipid bilayers is a prerequisite for understanding phenomena such as antimicrobial activity and membrane-protein folding. We describe molecular dynamics simulations of the antimicrobial peptide alamethicin in lipid/water and octane/water environments, taking into account an external electric field to mimic the membrane potential. At cis-positive potentials, alamethicin does not insert into a phospholipid bilayer in 10 ns of simulation, due to the slow dynamics of the peptide and lipids. However, in octane N-terminal insertion occurs at field strengths from 0.33 V/nm and higher, in simulations of up to 100 ns duration. Insertion of alamethicin occurs in two steps, corresponding to desolvation of the Gln7 side chain, and the backbone of Aib10 and Gly11. The proline induced helix kink angle does not change significantly during insertion. Polyalanine and alamethicin form stable helices both when inserted in octane and at the water/octane interface, where they partition in the same location. In water, both polyalanine and alamethicin partially unfold in multiple simulations. We present a detailed analysis of the insertion of alamethicin into the octane slab and the influence of the external field on the peptide structure. Our findings give new insight into the mechanism of channel formation by alamethicin and the structure and dynamics of membrane-associated helices.

['Doctor, I don't want to know that'--exploring denial in patients with lung cancer]. / 'Dokter, ik wil het niet weten'--verkenning van ontkenning bij patiënten met longkanker.

Three patients with lung cancer, a man aged 68, a woman aged 69 and a man aged 52, denied the nature or the severity of their disease in three different ways: temporary denial to evade acute emotional shock, full-blown persistent denial, and unjustified optimism respectively. The psychological mechanism of denial may become operational in patients confronted with an overwhelming disease. A less pronounced denial of medical information provided by physicians can be recognised in many patients. It may also be noticed in how individuals or groups of people sharing the same unbearable reality face up to the facts. Denial may be helpful in (temporarily) circumventing a serious problem but when the disease is serious, it may interfere in relationships with partners, relatives and friends. Denial must be differentiated from organicity, e.g. anosognosia in cerebral damage, by patient ignorance, or by vague communication from the medical community. A direct and blunt confrontation of denial may result in adverse effects due to a defensive mechanism being aggravated. Slowly providing the patient with pieces of information whilst taking into account his or her reaction, may provide a clue for gradual conformation to the medical reality.

Towards the design and computational characterization of a membrane protein.

The design of a transmembrane four-helix bundle is described. We start with an idealized four-helix bundle geometry, then use statistical information to build a plausible transmembrane bundle. Appropriate residues are chosen using database knowledge on the sequences of membrane helices and loops, then the packing of the bundle core is optimized, and favorable side chain rotamers from rotamer libraries are selected. Next, we use explicit physical knowledge from biomolecular simulation force fields and molecular dynamics simulations to test whether the designed structure is physically possible. These procedures test whether the designed protein will indeed be alpha-helical, well packed and stable over a time scale of several nanoseconds in a realistic lipid bilayer environment. We then test a modeling approach that does not include sophisticated database knowledge about proteins, but rather relies on applying our knowledge of the physics that governs protein motions. This independent validation of the design is based on simulated annealing and restrained molecular dynamics simulation in vacuo, comparable to procedures used to refine NMR and X-ray structures.

The role of serotonin in hot flushes.

Hot flushes are experienced in those periods of the female life when estrogen levels are low. Hormone replacement therapy is thus the first choice for treatment of hot flushes. However this treatment is not always accepted or contraindicated for a variety of reasons. Estrogen (and progestogen) strongly interact with a number of neurotransmitters and this has led to a range of non-hormonal treatments including compounds that act via the noradrenergic or dopaminergic systems as well as herbal remedies. These treatments (which are shortly reviewed) are not always successful. Surprisingly, apart from treatment with some selective serotonin (5-HT) reuptake inhibitors (SSRI's), up till now, little attention is given to the strong interaction of estrogens with the serotonergic system. These interactions are shortly reviewed. Based on these interactions, a hypothesis on the genesis of hot flushes is postulated. Especially the 5-HT(2A) receptor subtype may play a key role in the occurrence of hot flushes. A number of arguments that support this hypothesis are discussed.

Treatment of hot flushes with mirtazapine: four case reports.

OBJECTIVE: To evaluate the effect of mirtazapine on the severity of hot flushes and bouts of perspiration in women. METHOD: In two women with depression a reduction in hot flushes was noticed by serendipity during treatment with mirtazapine 15-30 mg/daily. On the basis of this observation clinical studies were extended with two non-depressed and non-anxious women with hot flushes. Both subjects were prescribed mirtazapine daily. RESULTS: Four cases are described as case reports. All subjects reported a practically complete disappearance of hot flushes and associated perspiration, within the first week of treatment. CONCLUSION: Mirtazapine appears to have a substantial ameliorating effect on hot flushes and perspiration bouts. It is postulated that the 5-HT(2A) blocking properties of mirtazapine is accounted in the symptomatic relief of hot flushes. In addition it is hypothesized that the serotonergic system is crucially involved in the pathogenesis of hot flushes and perspiration bouts. Further evaluation in double-blind placebo-controlled studies is encouraged.

Collective protein dynamics in relation to function.

Several techniques for the analysis of the internal motions of proteins are available - separating large collective motions from small, presumably uninteresting motions. Such descriptions are helpful in the characterization of internal motions and provide insight into the energy landscape of proteins. The real challenge, however, is to relate large collective motions to functional properties, such as binding and regulation, or to folding. These issues have been recently addressed in several papers.

A molecular dynamics study of the 41-56 beta-hairpin from B1 domain of protein G.

The structural and dynamical behavior of the 41-56 beta-hairpin from the protein G B1 domain (GB1) has been studied at different temperatures using molecular dynamics (MD) simulations in an aqueous environment. The purpose of these simulations is to establish the stability of this hairpin in view of its possible role as a nucleation site for protein folding. The conformation of the peptide in the crystallographic structure of the protein GB1 (native conformation) was lost in all simulations. The new equilibrium conformations are stable for several nanoseconds at 300K (>10 ns), 350 K (>6.5 ns), and even at 450 K (up to 2.5 ns). The new structures have very similar hairpin-like conformations with properties in agreement with available experimental nuclear Overhauser effect (NOE) data. The stability of the structure in the hydrophobic core region during the simulations is consistent with the experimental data and provides further evidence for the role played by hydrophobic interactions in hairpin structures. Essential dynamics analysis shows that the dynamics of the peptide at different temperatures spans basically the same essential subspace. The main equilibrium motions in this subspace involve large fluctuations of the residues in the turn and ends regions. Of the six interchain hydrogen bonds, the inner four remain stable during the simulations. The space spanned by the first two eigenvectors, as sampled at 450 K, includes almost all of the 47 different hairpin structures found in the database. Finally, analysis of the hydration of the 300 K average conformations shows that the hydration sites observed in the native conformation are still well hydrated in the equilibrium MD ensemble.

The mechanism of channel formation by alamethicin as viewed by molecular dynamics simulations.

Alamethicin is a 20-residue channel-forming peptide that forms a stable amphipathic alpha-helix in membrane and membrane-mimetic environments. This helix contains a kink induced by a central Gly-X-X-Pro sequence motif. Alamethicin channels are activated by a cis positive transbilayer voltage. Channel activation is suggested to correspond to voltage-induced insertion of alamethicin helices in the bilayer. Alamethicin forms multi-conductance channels in lipid bilayers. These channels are formed by parallel bundles of transmembrane helices surrounding a central pore. A change in the number of helices per bundle switches the single channel conductance level. Molecular dynamics simulations of alamethicin in a number of different environments have been used to explore its channel-forming properties. These simulations include: (i) alamethicin in solution in water and in methanol; (ii) a single alamethicin helix at the surface of a phosphatidylcholine bilayer; (iii) single alamethicin helices spanning a phosphatidylcholine bilayer; and (iv) channels formed by bundles of 5, 6, 7 or 8 alamethicin helices spanning a phosphatidylcholine bilayer. The total simulation time is c. 30 ns. Thus, these simulations provide a set of dynamic snapshots of a possible mechanism of channel formation by this peptide.

Antagonism of the 5-HT1A receptor stimulus in a conditioned taste aversion procedure.

The conditioned taste aversion procedure in mice was used to test for blockade of the drug stimulus of the 5-HT1A receptor agonists (+/-)-8-hydroxy-2-(di-n-propylamino)tetralin HBr (8-OH-DPAT), 1-(4-trifluoromethyl-2-pyridinyl)-4- [4-[2-oxo-1-pyrrolidinyl]butyl]piperazine (E)-2-butenedioate (Org 13011) and the 5-HT reuptake inhibitor fluoxetine. The conditioned taste aversion induced by 8-OH-DPAT (0.22 mg/kg) and Org 13011 (0.5 mg/kg) was readily blocked by the 5-HT1A receptor antagonist N-[2-[4-(2-methoxyphenyl)-1-piperazinyl]ethyl]-N-(2-pyridinyl) cyclohexanecarboxamide trihydrochloride (WAY-100635) (0.1 mg/kg). The conditioned taste aversion induced by fluoxetine could not be antagonized by WAY-100635 nor by the 5-HT2 receptor antagonist mianserin. It is concluded that the conditioned taste aversion induced by 8-OH-DPAT or Org 13011 is mediated via 5-HT1A receptors. The results suggest that the conditioned taste aversion induced by fluoxetine is not exclusively mediated by 5-HT1A receptors nor exclusively by 5-HT2 receptors. The results also indicate that the conditioned taste aversion paradigm can be used to test for antagonism of stimulus properties of compounds.