Transferable Coarse-Grained Potential for 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 we provide evidence of how a novel parametrization of the Caterpillar model may be used for both quantitative protein design and folding. 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 require further experimental testing. For an independent set of proteins, previously used as benchmark, the correct folded structure of both the designed and the natural sequences is also demonstrated. The equilibrium folding properties are characterized by free energy calculations. The resulting free energy profiles not only are consistent among natural and designed proteins, but also show a remarkable precision when the folded structures are compared to the experimentally determined ones. Ultimately, the updated Caterpillar 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. 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

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

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

Perspectives on the Future of Ice Nucleation Research: Research Needs and Unanswered Questions Identified from Two International Workshops

There has been increasing interest in ice nucleation research in the last decade. To identify important gaps in our knowledge of ice nucleation processes and their impacts, two international workshops on ice nucleation were held in Vienna, Austria in 2015 and 2016. Experts from these workshops identified the following research needs: (1) uncovering the molecular identity of active sites for ice nucleation; (2) the importance of modeling for the understanding of heterogeneous ice nucleation; (3) identifying and quantifying contributions of biological ice nuclei from natural and managed environments; (4) examining the role of aging in ice nuclei; (5) conducting targeted sampling campaigns in clouds; and (6) designing lab and field experiments to increase our understanding of the role of ice-nucleating particles in the atmosphere. Interdisciplinary teams of scientists should work together to establish and maintain a common, unified language for ice nucleation research. A number of commercial applications benefit from ice nucleation research, including the production of artificial snow, the freezing and preservation of water-containing food products, and the potential modulation of weather. Additional work is needed to increase our understanding of ice nucleation processes and potential impacts on precipitation, water availability, climate change, crop health, and feedback cycles.© 2017 by the author