Biomedical subjects

Siegfried Höfinger

Publications and source records attributed to Siegfried Höfinger.

7 recordsLinked to original sources

PubMed2006

Beyond dimerization: a membrane-dependent activation model for interleukin-4 receptor-mediated signalling.

Class I cytokine receptors efficiently transfer activation signals from the extracellular space to the cytoplasm and play a dominant role in growth control and differentiation of human tissues. Although a significant body of literature is devoted to this topic, a consistent mechanistic picture for receptor activation in the membrane environment is still missing. Using the interleukin-4 receptor (IL-4R) as an example, we propose that the membrane-proximal stem-loop of the extracellular domains contains pivotal elements of a rotational switch. Interfacial energies of amino acid side-chains contained in the highly conserved WSXWS at the surface of the lipid bilayer suggest a new functional role for this motif. A generic activation mechanism for this receptor class is presented, which may impact the design of a new generation of biophysical assay systems.

Amino Acid Motifs↗

PubMed2006

A critical beta6-beta7 loop in the pleckstrin homology domain of ceramide kinase.

CerK (ceramide kinase) produces ceramide 1-phosphate, a sphingophospholipid with recognized signalling properties. It localizes to the Golgi complex and fractionates essentially between detergent-soluble and -insoluble fractions; however, the determinants are unknown. Here, we made a detailed mutagenesis study of the N-terminal PH domain (pleckstrin homology domain) of CerK, based on modelling, and identified key positively charged amino acid residues within an unusual motif in the loop interconnecting beta-strands 6 and 7. These residues are critical for CerK membrane association and polyphosphoinositide binding and activity. Their mutagenesis results in increased thermolability, sensitivity to proteolysis, reduced apparent molecular mass as well as propensity of the recombinant mutant protein to aggregate, indicating that this loop impacts the overall conformation of the CerK protein. This is in contrast with most PH domains whose function strongly relies on charges located in the beta1-beta2 loop.

Amino Acid Sequence↗

PubMed2006

Computational assessment of the entropy of solvation of small-sized hydrophobic entities.

A high level polarizable force field is used to study the temperature dependence of hydrophobic hydration of small-sized molecules from computer simulations. Molecular dynamics (MD) simulations of liquid water at various temperatures form the basis of free energy perturbation calculations that consider the onset and growth of a repulsive sphere. This repulsive sphere acts as a model construct for the hydrophobic species. In the present study, an extension is pursued for seven independent target temperatures, ranging from close to the freezing point almost up to the boiling point of liquid water under standard conditions. Care is taken to maintain proper physico-chemical model descriptions by cross-checking with experimental water densities at the selected target temperatures. The polarizable force field description of molecular water turns out to be suitable throughout the entire temperature domain considered. Derivatives of the computed free energies of hydrophobic hydration with respect to the temperature give access to the changes in entropy. In practice the entropy differential is determined from the negative of the slope of tangential lines formed at a certain target temperature in the free energy profile. The obtained changes in entropy are negative for small-sized cavities, and hence reconfirm the basic ideas of the Lum-Chandler-Weeks theory on hydrophobic hydration of small-sized solutes.

Computer Simulation↗

PubMed2005

Simple models for hydrophobic hydration.

This tutorial review compares models that describe DeltaG(cavitation). Their qualitative agreement suggests the use of the simple, time-honored Pierotti equation. Its coefficients, fine-tuned with atomistic simulations, give a revised Pierotti approach, rPA. A discussion of the extension of the rPA model to non-spherical solutes is presented and the different roles of molecular volume and surface area of the solute are brought together. The tutorial review is aimed at experimentalists and theoreticians interested in the description of solvent effects.

Hydrophobic and Hydrophilic Interactions↗

PubMed2005

The collapse of nanobubbles in water.

We use molecular dynamics to simulate the collapse of nanobubbles in water and show that the macroscopic description holds down to the nanometer size. We further give a description of the collapse in terms of stochastic growth of the density of water inside the cavity. Finally, we address the energy variation in time of the collapse in very simple terms.

Journal Article↗

PubMed2005

Solving the Poisson-Boltzmann equation with the specialized computer chip MD-GRAPE-2.

The accurate description of solvation effects is highly desirable in numerous computational chemistry applications. One widely used methodology treats the solvent as a uniform continuum ("implicit solvation"), and describes its net interaction with the solute by solving the Poisson-Boltzmann (PB) equation using the Boundary Element Method (BEM). These calculations are very time consuming using conventional computers. A new, efficient way of solving the PB equation on the special-purpose hardware chip MDGRAPE-2 is presented. The MDGRAPE-2 chip was originally developed to speed up the calculation of pairwise van der Waals and electrostatic interactions. By recasting the BEM equations and applying an iterative solution procedure, a hardware-accelerated PB solver on MDGRAPE-2 could be implemented. The performance and reliability of the method is demonstrated on three examples ranging from small peptides to large proteins, whereby the obtained acceleration factors range from 15-fold to up to 40-fold with no loss of accuracy compared to the conventional approach.

Algorithms↗

PubMed2003

On the cavitation energy of water.

Free-energy-perturbation theory from molecular dynamics calculations has been used to obtain the DeltaG of adjoining cavities' formation in water. The DeltaGs for systems with three, five and seven cavities are compared with that of a single cavity of the same volume, and found to be in good agreement. The conditions under which the analytical formulation of the energy of cavity formation proposed by Pierotti holds are discussed. The data for a single cavity have been tabulated and can lend themselves to a simple numerical implementation in standard quantum chemical packages, which can be used when high accuracy for DeltaG(cav) is required.

Journal Article↗