Transferable coarse-grained potential for de novo\textit{de novo} protein folding and design

Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here a novel protein model capable of simultaneously provide quantitative protein design and folding is introduced. With computer simulations it is shown that, for a large set of real protein structures, the model produces designed sequences with similar physical properties to the corresponding natural occurring sequences. The designed sequences are not yet fully realistic and require further experimental testing. For an independent set of proteins, notoriously difficult to fold, the correct folding of both the designed and the natural sequences is also demonstrated. The folding properties are characterized by free energy calculations. which not only are consistent among natural and designed proteins, but we also show a remarkable precision when the folded structures are compared to the experimentally determined ones. Ultimately, this novel coarse-grained protein model is unique in the combination of its fundamental three features: its simplicity, its ability to produce natural foldable designed sequences, and its structure prediction precision. The latter demonstrated by free energy calculations. It is also remarkable that low frustration sequences can be obtained with such a simple and universal design procedure, and that the folding of natural proteins shows funnelled free energy landscapes without the need of any potentials based on the native structure

Different regimes of the uniaxial elongation of electrically charged viscoelastic jets due to dissipative air drag

We investigate the effects of dissipative air drag on the dynamics of electrified jets in the initial stage of the electrospinning process. The main idea is to use a Brownian noise to model air drag effects on the uniaxial elongation of the jets. The developed numerical model is used to probe the dynamics of electrified polymer jets at different conditions of air drag force, showing that the dynamics of the charged jet is strongly biased by the presence of air drag forces. This study provides prospective beneficial implications for improving forthcoming electrospinning experiments.Comment: 12 pages, 6 figure

Limiting the valence: advancements and new perspectives on patchy colloids, soft functionalized nanoparticles and biomolecules

Limited bonding valence, usually accompanied by well-defined directional interactions and selective bonding mechanisms, is nowadays considered among the key ingredients to create complex structures with tailored properties: even though isotropically interacting units already guarantee access to a vast range of functional materials, anisotropic interactions can provide extra instructions to steer the assembly of specific architectures. The anisotropy of effective interactions gives rise to a wealth of self-assembled structures both in the realm of suitably synthesized nano- and micro-sized building blocks and in nature, where the isotropy of interactions is often a zero-th order description of the complicated reality. In this review, we span a vast range of systems characterized by limited bonding valence, from patchy colloids of new generation to polymer-based functionalized nanoparticles, DNA-based systems and proteins, and describe how the interaction patterns of the single building blocks can be designed to tailor the properties of the target final structures

Role of water in the selection of stable proteins at ambient and extreme thermodynamic conditions

Proteins that are functional at ambient conditions do not necessarily work at extreme conditions of temperature T and pressure P. Furthermore, there are limits of T and P above which no protein has a stable functional state. Here, we show that these limits and the selection mechanisms for working proteins depend on how the properties of the surrounding water change with T and P. We find that proteins selected at high T are superstable and are characterized by a nonextreme segregation of a hydrophilic surface and a hydrophobic core. Surprisingly, a larger segregation reduces the stability range in T and P. Our computer simulations, based on a new protein design protocol, explain the hydropathy profile of proteins as a consequence of a selection process influenced by water. Our results, potentially useful for engineering proteins and drugs working far from ambient conditions, offer an alternative rationale to the evolutionary action exerted by the environment in extreme conditions

Effects of non-linear rheology on the electrospinning process: a model study

We develop an analytical bead-spring model to investigate the role of non-linear rheology on the dynamics of electrified jets in the early stage of the electrospinning process. Qualitative arguments, parameter studies as well as numerical simulations, show that the elongation of the charged jet filament is significantly reduced in the presence of a non-zero yield stress. This may have beneficial implications for the optimal design of future electrospinning experiments