PAS polypeptides comprise long repetitive sequences of the small L-amino acids proline, alanine and/or serine that were developed to expand the hydrodynamic volume of conjugated pharmaceuticals and prolong their plasma half-life by retarding kidney filtration. Here, we have characterized the polymer properties both of the free polypeptides and in fusion with the biopharmaceutical IL-1Ra. Data f...

The solution properties, including hydrodynamic quantities and the radius of gyration, of globular proteins are calculated from their detailed, atomic-level structure, using bead-modeling methodologies described in our previous article (, Biophys. J. 76:3044-3057). We review how this goal has been pursued by other authors in the past. Our procedure starts from a list of atomic coordinates, from...

A new simulation strategy based on a stochastic process has been developed and tested to study the structural properties of the unfolded state of proteins at the atomistic level. The procedure combines a generation algorithm to produce representative uncorrelated atomistic microstructures and an original relaxation method to minimize repulsive non-bonded interactions. Using this methodology, a ...

We performed relativistic magnetohydrodynamic simulations of the hydrodynamic boosting mechanism for relativistic jets explored by Aloy & Rezzolla (2006) using the RAISHIN code. Simulation results show that the presence of a magnetic field changes the properties of the shock interface between the tenuous, overpressured jet (V z j ) flowing tangentially to a dense external medium. Magnetic field...

A distinct feature of wave boundaryintegral equations are the " irregular Two topics on the numerical solution of frequencies. They coincide with the eigenboundary-integral equations arising in linear frequencies of the interior Dirichlet or wave-body interactions are discussed. The Neumann problems, and are known to introduce properties of a spectral technique for the large errors in the predi...

Hydrodynamic properties as well as structural dynamics of proteins can be investigated by the well-established experimental method of fluorescence anisotropy decay. Successful use of this method depends on determination of the correct kinetic model, the extent of cross-correlation between parameters in the fitting function, and differences between the timescales of the depolarizing motions and ...

There are some hydrodynamic equations that, while their parent kinetic equation satisfies fundamental mechanical properties, appear themselves to violate mechanical or thermodynamic properties. This paper aims to shed some light on the source of this problem. Starting with diffusive volume hydrodynamic models, the microscopic temporal and spatial scales are first separated at the kinetic level ...