Thermal unfolding of proteins

Thermal unfolding of proteins is compared to folding and mechanical stretching in a simple topology-based dynamical model. We define the unfolding time and demonstrate its low-temperature divergence. Below a characteristic temperature, contacts break at separate time scales and unfolding proceeds approximately in a way reverse to folding. Features in these scenarios agree with experiments and atomic simulations on titin.Comment: 3 figures, a text in late

What Do Our Choices Say About Our Preferences?

Taking online decisions is a part of everyday life. Think of buying a house, parking a car or taking part in an auction. We often take those decisions publicly, which may breach our privacy - a party observing our choices may learn a lot about our preferences. In this paper we investigate the online stopping algorithms from the privacy preserving perspective, using a mathematically rigorous differential privacy notion. In differentially private algorithms there is usually an issue of balancing the privacy and utility. In this regime, in most cases, having both optimality and high level of privacy at the same time is impossible. We propose a natural mechanism to achieve a controllable trade-off, quantified by a parameter, between the accuracy of the online algorithm and its privacy. Depending on the parameter, our mechanism can be optimal with weaker differential privacy or suboptimal, yet more privacy-preserving. We conduct a detailed accuracy and privacy analysis of our mechanism applied to the optimal algorithm for the classical secretary problem. Thereby the classical notions from two distinct areas - optimal stopping and differential privacy - meet for the first time.Comment: 22 pages, 6 figure

Effects of confinement and crowding on folding of model proteins

We perform molecular dynamics simulations for a simple coarse-grained model of crambin placed inside of a softly repulsive sphere of radius R. The confinement makes folding at the optimal temperature slower and affects the folding scenarios, but both effects are not dramatic. The influence of crowding on folding are studied by placing several identical proteins within the sphere, denaturing them, and then by monitoring refolding. If the interactions between the proteins are dominated by the excluded volume effects, the net folding times are essentially like for a single protein. An introduction of inter-proteinic attractive contacts hinders folding when the strength of the attraction exceeds about a half of the value of the strength of the single protein contacts. The bigger the strength of the attraction, the more likely is the occurrence of aggregation and misfolding

Untying Knots in Proteins

A shoelace can be readily untied by pulling its ends rather than its loops. Attempting to untie a native knot in a protein can also succeed or fail depending on where one pulls. However, thermal fluctuations induced by the surrounding water affect conformations stochastically and may add to the uncertainty of the outcome. When the protein is pulled by the termini, the knot can only get tightened, and any attempt at untying results in failure. We show that, by pulling specific amino acids, one may easily retract a terminal segment of the backbone from the knotting loop and untangle the knot. At still other amino acids, the outcome of pulling can go either way. We study the dependence of the untying probability on the way the protein is grasped, the pulling speed, and the temperature. Elucidation of the mechanisms underlying this dependence is critical for a successful experimental realization of protein knot untying