Interaction of water with N,N'-1,2-ethanediyl-bis(6-hydroxy-hexanamide) crystals: a simulation study

Recently it has been shown, using a variety of experimental techniques, that water can be hosted in N,N'-1,2-ethanediyl-bis(6-hydroxy-hexanamide) crystals. It forms stable interactions with the hydroxyl groups at the ends of the molecule, as well as with the amide groups. However, with experimental techniques one can not observe the exact hydrogen bonding geometries of the physically bound water molecules. Here a series of molecular dynamics simulations is presented that provide an atomistically detailed picture of the interactions of water with different parts of the crystals.

Energy utilization for control

When, on addition of a suitable substrate, a chemical potential is applied to an enzymic process such as glycolysis or respiration, whether in solution or membrane-bound, all components of the process pass into a nonequilibrium state, which might be steady or non-steady and which produces the following phenomena: (1) The reactants of each enzymic reaction are displaced from their equilibrium concentration, and energy is dissipated; (2) Part of each enzyme is transferred to a transition state of its catalytic function as well as isosteric and allosteric controlling functions, displaying local and gross conformation changes, and a rate-controlling state is generated; (3) In cyclic portions of a process futile events and chemical interconversion may occur; (4) In self- and cross-coupled portions of a process, oscillation with periodic changes of states and spatial propagation as well as instabilities may be observed; (5) At each step of a process, depending on the rate of flux and the specific enzymic function, a varying proportion of the free energy changes--which are concentration-dependent and derived from the overall potential of the system-is contributed to the control of flux rates. This will be exemplified for enzymes of bioenergetic pathways.

Properties of strange attractors in yeast glycolysis

The properties of periodic and aperiodic glycolytic oscillations observed in yeast extracts under sinusoidal glucose input were analyzed by the following methods. (1) Spectral analysis, rendering sharp peaks for periodic responses and enhanced broad-band noise for aperiodic oscillations. (2) Phase plane analysis, leading to closed and to open trajectories for periodic and aperiodic oscillations, respectively. (3) Rotation of a phase plane proportionally to time, revealing strange attractors associated with the aperiodic oscillations. (4) Stroboscopic plot on the phase plane, showing that the strange attractors follow a stretch-fold-press process, if the stroboscoping phase is varied. (5) Stroboscopic transfer plot, admitting a period of three transfer processes and thus implying chaos according to the Li-Yorke theorem. (6) Determination of the rate of information production by differentiation of the transfer plot, yielding approx. 0.21 bits per min for the chaotically glycolyzing yeast extract.

Osmotic coefficients of atomistic NaCl (aq) force fields

Solvated ions are becoming increasingly important for (bio)molecular simulations. But there are not much suitable data to validate the intermediate-range solution structure that ion-water force fields produce. We compare six selected combinations of four biomolecular Na-Cl force fields and four popular water models by means of effective ion-ion potentials. First we derive an effective potential at high dilution from simulations of two ions in explicit water. At higher ionic concentration multibody effects will become important. We propose to capture those by employing a concentration dependent dielectric permittivity. With the so obtained effective potentials we then perform implicit solvent simulations. We demonstrate that our effective potentials accurately reproduce ion-ion coordination numbers and the local structure. They allow us furthermore to calculate osmotic coefficients that can be directly compared with experimental data. We show that the osmotic coefficient is a sensitive and accurate measure for the effective ion-ion interactions and the intermediate-range structure of the solution. It is therefore a suitable and useful quantity for validating and parametrizing atomistic ion-water force fields.

Hydration Thermodynamic Properties of Amino Acid Analogues: A Systematic Comparison of Biomolecular Force Fields and Water Models

We present an extensive study on hydration thermodynamic properties of analogues of 13 amino acid side chains at 298 K and 1 atm. The hydration free energies DeltaG, entropies DeltaS, enthalpies DeltaH, and heat capacities Deltac(P)() were determined for 10 combinations of force fields and water models. The statistical sampling was extended such that precisions of 0.3, 0.8, 0.8 kJ/mol and 25 J/(mol K) were reached for DeltaG, TDeltaS, DeltaH, and Deltac(P)(), respectively. The three force fields used in this study are AMBER99, GROMOS 53A6, and OPLS-AA; the five water models are SPC, SPC/E, TIP3P, TIP4P, and TIP4P-Ew. We found that the choice of water model strongly influences the accuracy of the calculated hydration entropies, enthalpies, and heat capacities, while differences in accuracy between the force fields are small. On the basis of an analysis of the hydrophobic analogues of the amino acid side chains, we discuss what properties of the water models are responsible for the observed discrepancies between computed and experimental values. The SPC/E water model performs best with all three biomolecular force fields.

Density functional study of ion hydration for the alkali metal ions (Li+,Na+,K+) and the halide ions (F−,Br−,Cl−)

We performed first principles density functional calculations to study the effect of monovalent ions M+ (M = Li,Na,K) and A- (A = F,Cl,Br) in water with the aim of characterizing the local molecular properties of hydration. For this reason, several ion-water clusters, up to five or six water molecules were considered; such structures were optimized, and the Wannier analysis was then applied to determine the average molecular dipole moment of water. We found that with an increasing number of water molecules, the molecular polarization is determined by the water-water interaction rather than the water-ion interaction, as one would intuitively expect. These results are consistent with those obtained in previous density functional calculations and with other results obtained by employing classical polarizable water models. The main message of this work is that as one increases the number of molecules the average dipole moment of all water molecules and the ones in the first shell tends to the same value as the average of a similar sized cluster of pure water. This supports the use of nonpolarizable classical models of water in classical atomistic simulations.

Long time atomistic polymer trajectories from coarse grained simulations: bisphenol-A polycarbonate

Based on coarse grained simulations of a specially adapted model for bisphenol-A polycarbonate (BPA-PC) we generate by inverse mapping, the reintroduction of chemical details, well equilibrated all-atom conformations and time trajectories of dense polymeric melts for up to 7.8 µs. This is several orders of magnitude more than any direct all-atom simulations have reached so far. These polymer melts contain up to 68600 atoms in = 100 chains of molecular weight = 5217. By comparison with short all-atom simulations we show that these trajectories are physically meaningful, providing us with a powerful tool to compare long time simulations to experiments, which probe specific local dynamics on long time scales, such as NMR relaxation.

Modeling multibody effects in ionic solutions with a concentration dependent dielectric permittivity

We report a new strategy to parametrize effective ion-ion potentials for implicit solvent simulations of charged systems. The effective potential includes a pair term and a Coulomb term that by means of a concentration dependent dielectric permittivity takes into account multibody effects. We demonstrate that this approach allows us to accurately reproduce the solution osmotic properties and the ion coordination up to concentrations of 2.8 M aqueous NaCl.

[Health economic consequences of the use of irbesartan in patients with type 2 diabetes, hypertension and nephropathy in Switzerland]

The irbesartan in Diabetic Nephropathy Trial (IDNT) demonstrated that treatment of patients with type 2 diabetes, hypertension and nephropathy with irbesartan resulted in a 20% relative reduction of the composite endpoint of doubling serum creatinine, end-stage renal disease or death as compared with amlodipine and placebo (antihypertensive standard therapy). The objective of this study was to investigate the long-term health economic consequences of this treatment strategy in a Swiss health care setting. This analysis used a Markov model to simulate the progression of nephropathy, life-years and treatment costs over ten years for each of the three treatment options. In additon, sensitivity analyses were performed. Treatment with irbesartan will save CHF 22681/patient as compared with amlodipine and CHF 13847 as compared with standard therapy.

Reproducible Polypeptide Folding and Structure Prediction using Molecular Dynamics Simulations

The folding of a polypeptide from an extended state to a well-defined conformation is studied using microsecond classical molecular dynamics (MD) simulations and replica exchange molecular dynamics (REMD) simulations in explicit solvent and in vacuo. It is shown that the solvated peptide folds many times in the REMD simulations but only a few times in the conventional simulations. From the folding events in the classical simulations we estimate an approximate folding time of 1-2 micros. The REMD simulations allow enough sampling to deduce a detailed Gibbs free energy landscape in three dimensions. The global minimum of the energy landscape corresponds to the native state of the peptide as determined previously by nuclear magnetic resonance (NMR) experiments. Starting from an extended state it takes about 50 ns before the native structure appears in the REMD simulations, about an order of magnitude faster than conventional MD. The calculated melting curve is in good qualitative agreement with experiment. In vacuo, the peptide collapses rapidly to a conformation that is substantially different from the native state in solvent.

Preventive treatment of nephrolithiasis with alkali citrate—a critical review

Using the keywords "urolithiasis and citrate treatment", "nephrolithaisis and citrate treatment", "kidney stones and citrate treatment", a Medline search revealed 635 articles published between 1 January 1966 and 1 December 2004. For the present analysis, only studies meeting all of the following criteria were included: (1) publications in English or German, (2) studies on preventive alkali citrate treatment in patients with calcium oxalate, uric acid and infection stone disease, (3) clinical studies including at least ten subjects, and (4) treatment phases of at least 1 week duration. A total of 43 studies met the inclusion criteria and were further subclassified according to intermediate or ultimate endpoints as well as to study design. With stone recurrence as the ultimate endpoint, 21 uncontrolled studies in almost 1,000 patients demonstrated a reduction in stone forming rate by 47-100%. In four randomized controlled trials including 227 patients, 53.5% on alkali citrate vs 35% on placebo remained stone-free after at least 1 year of treatment (P<0.0005). Similar values (66% vs 27.5% for alkali citrate vs placebo, P<0.0005) were obtained in 104 patients from two randomized trials with dissolution/clearance of residual stones as endpoint. Unfortunately, up to 48% of alkali citrate treated patients left the studies prematurely, primarily due to adverse effects such as eructation, bloating, gaseousness or frank diarrhea.

GROMACS: Fast, flexible, and free

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.

Photoactivation of the photoactive yellow protein: why photon absorption triggers a trans-to-cis Isomerization of the chromophore in the protein

Atomistic QM/MM simulations have been carried out on the complete photocycle of Photoactive Yellow Protein, a bacterial photoreceptor, in which blue light triggers isomerization of a covalently bound chromophore. The "chemical role" of the protein cavity in the control of the photoisomerization step has been elucidated. Isomerization is facilitated due to preferential electrostatic stabilization of the chromophore's excited state by the guanidium group of Arg52, located just above the negatively charged chromophore ring. In vacuo isomerization does not occur. Isomerization of the double bond is enhanced relative to isomerization of a single bond due to the steric interactions between the phenyl ring of the chromophore and the side chains of Arg52 and Phe62. In the isomerized configuration (ground-state cis), a proton transfer from Glu46 to the chromophore is far more probable than in the initial configuration (ground-state trans). It is this proton transfer that initiates the conformational changes within the protein, which are believed to lead to signaling.