Timing control in regulatory networks by multisite protein modifications.

Computational and experimental studies have yielded quantitative insights into the role for multisite phosphorylation, and other protein modifications, in cell function. This work has emphasized the creation of thresholds and switches for cellular decisions. To date, the dynamics of phosphorylation events have been disregarded yet could be equally relevant for cell function.

Structure and dynamics of the UO2+ ion in aqueous solution: an ab initio QMCF-MD study.

The quantum mechanical charge field molecular dynamics (QMCF-MD) framework was applied in a simulation of the uranyl(v) ion in aqueous solution. The structure was evaluated on the basis of overall and sectorial radial distribution functions, angular distribution functions, tilt- and Theta-angle distribution functions and coordination number distributions. The cation is strongly coordinated by 4 water ligands at an average distance of 2.

[Successful treatment of a venous ulcer in an unusual manner].

Wound treatment is increasingly becoming the domain of specially trained medical personal. The flood of diverse wound treatments and bandaging techniques grows continuously. Studies which compare the effectiveness deliver such a variety of results that medical personal are starting to doubt trusted methods.

Structure and dynamics of the chromate ion in aqueous solution. An ab initio QMCF-MD simulation.

An ab initio quantum-mechanical charge-field molecular-dynamics (QMCF-MD) simulation of the chromate ion in aqueous solution at ambient temperature was performed to study the structure and dynamics of this ion and its hydration shell. In contrast to conventional quantum-mechanical molecular-mechanics molecular-dynamics (QM/MM-MD) simulations, the QMCF-MD approach offers the possibility of investigating composite systems with the accuracy of a QM/MM method but without the time-consuming construction of solute-solvent potential functions. The data of the simulation give a clear picture of the first hydration shell of the chromate anion, which consists of 14 water molecules.

The stability of [Zn(NH(3))(4)](2+) in water: A quantum mechanical/molecular mechanical molecular dynamics study.

To investigate the structural and dynamical properties of the tetraamminezinc(ii) complex (Zn-tetraamine) in aqueous solution, ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulation was performed for 50 ps at the Hartree-Fock (HF) level of theory. A predominant 4-coordinate solvation structure with a maximum probability of the Zn-N distance at approximately 2.1 A was observed, which seems to be involved in the associative mode of water exchange reactions to produce a short-lived, 5-coordinated trigonal bipyramidal structure.

Constitutively active Lck kinase in T cells drives antigen receptor signal transduction.

T cell antigen receptor (TCR) and coreceptor ligation is thought to initiate signal transduction by inducing activation of the kinase Lck. Here we showed that catalytically active Lck was present in unstimulated naive T cells and thymocytes and was readily detectable in these cells in lymphoid organs. In naive T cells up to approximately 40% of total Lck was constitutively activated, part of which was also phosphorylated on the C-terminal inhibitory site.

Mathematical modelling of DNA replication reveals a trade-off between coherence of origin activation and robustness against rereplication.

Eukaryotic genomes are duplicated from multiple replication origins exactly once per cell cycle. In Saccharomyces cerevisiae, a complex molecular network has been identified that governs the assembly of the replication machinery. Here we develop a mathematical model that links the dynamics of this network to its performance in terms of rate and coherence of origin activation events, number of activated origins, the resulting distribution of replicon sizes and robustness against DNA rereplication.

A quantum mechanical charge field molecular dynamics study of Fe(2+) and Fe(3+) ions in aqueous solutions.

Ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) simulations have been performed for aqueous solutions of Fe(2+) and Fe(3+) ions at the Hartree-Fock level of theory to describe and compare their structural and dynamical behavior. The structural features of both hydrated ions are characterized by radial distribution functions that give the maximum probability of the ion-O distance for Fe(2+) and Fe(3+) ions at 2.15 and 2.

Stochastic and reversible assembly of a multiprotein DNA repair complex ensures accurate target site recognition and efficient repair.

To understand how multiprotein complexes assemble and function on chromatin, we combined quantitative analysis of the mammalian nucleotide excision DNA repair (NER) machinery in living cells with computational modeling. We found that individual NER components exchange within tens of seconds between the bound state in repair complexes and the diffusive state in the nucleoplasm, whereas their net accumulation at repair sites evolves over several hours. Based on these in vivo data, we developed a predictive kinetic model for the assembly and function of repair complexes.

An integrated imaging approach to the study of oxidative stress generation by mitochondrial dysfunction in living cells.

Background: The mechanisms of action of many environmental agents commonly involve oxidative stress resulting from mitochondrial dysfunction. Zinc is a common environmental metallic contaminant that has been implicated in a variety of oxidant-dependent toxicological responses. Unlike ions of other transition metals such as iron, copper, and vanadium, Zn(2+) does not generate reactive oxygen species (ROS) through redox cycling.

Hydrolytic conversion of AsO(-3)4 to HAsO(-2)4: a QMCF MD study.

A quantum mechanical charge field molecular dynamics (QMCF MD) study of AsO in water was carried out to gain insight into its conversion from the hydrated anion resulting in OH(-) ions and HAsO, which occurs on the scale of a few hundred femtoseconds. The OH(-) ion undergoes further proton exchange with water molecules, while HAsO is a stable species.

Short-term memory in gene induction reveals the regulatory principle behind stochastic IL-4 expression.

Although cell-to-cell variability has been recognized as an unavoidable consequence of stochasticity in gene expression, it may also serve a functional role for tuning physiological responses within a cell population. In the immune system, remarkably large variability in the expression of cytokine genes has been observed in homogeneous populations of lymphocytes, but the underlying molecular mechanisms are incompletely understood. Here, we study the interleukin-4 gene (il4) in T-helper lymphocytes, combining mathematical modeling with the experimental quantification of expression variability and critical parameters.

Structural and dynamic aspects of hydration of HAsO4(-2): an ab initio QMCF MD simulation.

An ab initio quantum mechanical charge field simulation has been carried out in order to obtain molecular level insight into the hydration behavior of HAsO4(-2), one of the major biologically active components of As(V) oxoanion in neutral to slightly alkaline aqueous medium. Moreover, a geometrical definition of hydrogen bonding has been used to probe and characterize both solute-solvent and solvent-solvent hydrogen bonding present in the system. The asymmetry of the anion induced by the protonation of one of the oxygens of the arsenate anion causes rather irregular hydration structure.

Competing feedback loops shape IL-2 signaling between helper and regulatory T lymphocytes in cellular microenvironments.

Cytokines are pleiotropic and readily diffusible messenger molecules, raising the question of how their action can be confined to specific target cells. The T cell cytokine interleukin-2 (IL-2) is essential for the homeostasis of regulatory T (Treg) cells that suppress (auto)immunity and stimulates immune responses mediated by conventional T cells. We combined mathematical modeling and experiments to dissect the dynamics of the IL-2 signaling network that links the prototypical IL-2 producers, conventional T helper (Th) cells, and Treg cells.

Structural and dynamical aspects of the unsymmetric hydration of Sb(III): an ab initio quantum mechanical charge field molecular dynamics simulation.

An ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulation was performed to investigate the behavior of the Sb(3+) ion in aqueous solution. The simulation reveals a significant influence of the residual valence shell electron density on the solvation structure and dynamics of Sb(3+). A strong hemidirectional behavior of the ligand binding pattern is observed for the first hydration shell extending up to the second hydration layer.

Molecularly defined antibody conjugation through a selenocysteine interface.

Antibody conjugates have broad utility in basic, preclinical, and clinical applications. Conventional antibody conjugation through the amine group of lysine or the thiol group of cysteine residues yields heterogeneous products of undefined stoichiometry and considerable batch-to-batch variability. To preserve the two hallmarks of the antibody molecule, precision and predictability, methods that enable site-specific antibody conjugation are in high demand.

Ultrafine carbon particles down-regulate CYP1B1 expression in human monocytes.

Background: Cytochrome P450 monoxygenases play an important role in the defence against inhaled toxic compounds and in metabolizing a wide range of xenobiotics and environmental contaminants. In ambient aerosol the ultrafine particle fraction which penetrates deeply into the lungs is considered to be a major factor for adverse health effects. The cells mainly affected by inhaled particles are lung epithelial cells and cells of the monocyte/macrophage lineage.

Phosphorylation modulates rapid nucleocytoplasmic shuttling and cytoplasmic accumulation of Neurospora clock protein FRQ on a circadian time scale.

The Neurospora clock protein FREQUENCY (FRQ) is an essential regulator of the circadian transcription factor WHITE COLLAR COMPLEX (WCC). In the course of a circadian period, the subcellular distribution of FRQ shifts from mainly nuclear to mainly cytosolic. This shift is crucial for coordinating the negative and positive limbs of the clock.

Revisiting the hydration of Pb(II): a QMCF MD approach.

A quantum mechanical charge field (QMCF) molecular dynamics (MD) study of Pb(II) in an aqueous medium was carried out in order to gain insight into its solvation behavior, for both structural and dynamic aspects. Applying the advanced methodology and different basis sets, some new aspects concerning the solvation of Pb(II) have been revealed. One of the most interesting outcomes of the current simulation is the variation of first shell coordination number from 7 to 9 in the Pb(H2O)n(2+) complex with Pb(H2O)8(2+) as a major species.

Successful treatment for refractory convulsive status epilepticus by non-parenteral lacosamide.

Lacosamide (Vimpat) is a newly licensed novel antiepileptic drug. We report a case of refractory convulsive status epilepticus (CSE) that was successfully controlled with lacosamide. The 38-year-old male patient was admitted for a series of complex partial seizures with secondary generalization leading to refractory CSE.

Molecular networks and system-level properties.

Molecular systems biology aims to describe the functions of complex biological processes through recursive integration of molecular analysis, modeling, simulation and theory. It focuses on networks that originate from interconnection of genes, proteins and metabolites whose dynamic interactions generate, as an emergent property of the system, the corresponding function. Although evolutionary optimized, intracellular biochemical parameters, such as the expression level of gene products or the affinity between two or more proteins, must have a permissible range that gives robustness against perturbations to the system.

Structure and dynamics of the UO(2)(2+) ion in aqueous solution: an ab initio QMCF MD study.

A comprehensive theoretical investigation on the structure and dynamics of the UO(2)(2+) ion in aqueous solution using double-zeta HF level quantum mechanical charge field molecular dynamics is presented. The quantum mechanical region includes two full layers of hydration and is embedded in a large box of explicitly treated water to achieve a realistic environment. A number of different functions, including segmential, radial, and angular distribution functions, are employed together with tilt- and Theta-angle distribution functions to describe the complex structural properties of this ion.

Beryllium(II): the strongest structure-forming ion in water? A QMCF MD simulation study.

A quantum mechanical charge field (QMCF) molecular dynamics (MD) simulation including the first and second hydration shells in the QM region has been carried out to describe the structural and dynamical properties of Be(2+) in aqueous solution. In this methodology, the full first and second hydration shells are treated by ab initio quantum mechanics supplemented by a fluctuating electrostatic embedding technique. From the simulation, structural properties were extracted and were found to be in good agreement with previously published experimental and theoretical results.

Hydrated germanium (II): irregular structural and dynamical properties revealed by a quantum mechanical charge field molecular dynamics study.

Structural and dynamical properties of Ge (II) in aqueous solution have been investigated using the novel ab initio quantum mechanical charge field (QMCF) molecular dynamics (MD) formalism. The first and second hydration shells were treated by ab initio quantum mechanics at restricted Hartree-Fock (RHF) level using the cc-pVDZ-PP basis set for Ge (II) and Dunning double-zeta plus polarization basis sets for O and H. Besides ligand exchange processes and mean ligand residence times to observe dynamics, tilt- and theta-angle distributions along with an advanced structural parameter, namely radial and angular distribution functions (RAD) for different regions were also evaluated.