Temperature behavior of the velocity autocorrelation function in large MD models of water.

Velocity autocorrelation functions (VACFs) were calculated using the molecular dynamics method in the TIP4P/2005 and SPC/E water models of 157 464 molecules at temperatures ranging from 250 to 370 K. The large size of the models and the high accuracy of the calculations allow us to reliably compute the long-time tails of the VACFs, showing that they systematically change shape from hydrodynamic (argon-like) at high temperatures to that typical of supercooled liquids at low temperatures. These tails in the range of 2-10 ps can be well fitted by a combination of two power functions: At-3/2 - Bt-β (A, B > 0, β ≈ 2).

Amyloidogenicity as a driving force for the formation of functional oligomers.

Insoluble amyloid fibrils formed by self-assembly of amyloidogenic regions of proteins have a cross-β-structure. In this work, by using targeted molecular dynamics and rigid body simulation, we demonstrate that if a protein consists of an amyloidogenic region and a globular domain(s) and if the linker between them is short enough, such molecules cannot assemble into amyloid fibrils, instead, they form oligomers with a defined and limited number of β-strands in the cross-β core. We show that this blockage of the amyloid growth is due to the steric repulsion of the globular structures linked to amyloidogenic regions.

Establishment of Constraints on Amyloid Formation Imposed by Steric Exclusion of Globular Domains.

In many disease-related and functional amyloids, the amyloid-forming regions of proteins are flanked by globular domains. When located in close vicinity of the amyloid regions along the chain, the globular domains can prevent the formation of amyloids because of the steric repulsion. Experimental tests of this effect are few in number and non-systematic, and their interpretation is hampered by polymorphism of amyloid structures.

TMAO and urea in the hydration shell of the protein SNase.

We performed all-atom MD simulations of the protein SNase in aqueous solution and in the presence of two major osmolytes, trimethylamine-N-oxide (TMAO) and urea, as cosolvents at various concentrations and compositions and at different pressures and temperatures. The distributions of the cosolvent molecules and their orientation in the surroundings of the protein were analyzed in great detail. The distribution of urea is largely conserved near the protein.

Structural and entropic insights into the nature of the random-close-packing limit.

Disordered packings of equal sized spheres cannot be generated above the limiting density (fraction of volume occupied by the spheres) of rho approximately 0.64 without introducing some partial crystallization. The nature of this "random-close-packing" limit (RCP) is investigated by using both geometrical and statistical mechanics tools applied to a large set of experiments and numerical simulations of equal-sized sphere packings.