Folding Mechanism of Small Proteins

Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like conformations at appropriate temperatures. The results demonstrate that the folding mechanism is controlled not only by thermodynamic factors but also by kinetic factors: The way a protein folds into its native structure, is also determined by the convergence point of early folding trajectories, which cannot be obtained by the free energy surface.Comment: 11 pages, 4 figure

REPUTATION COMPUTATION IN SOCIAL NETWORKS AND ITS APPLICATIONS

This thesis focuses on a quantification of reputation and presents models which compute reputation within networked environments. Reputation manifests past behaviors of users and helps others to predict behaviors of users and therefore reduce risks in future interactions. There are two approaches in computing reputation on networks- namely, the macro-level approach and the micro-level approach. A macro-level assumes that there exists a computing entity outside of a given network who can observe the entire network including degree distributions and relationships among nodes. In a micro-level approach, the entity is one of the nodes in a network and therefore can only observe the information local to itself, such as its own neighbors behaviors. In particular, we study reputation computation algorithms in online distributed environments such as social networks and develop reputation computation algorithms to address limitations of existing models. We analyze and discuss some properties of reputation values of a large number of agents including power-law distribution and their diffusion property. Computing reputation of another within a network requires knowledge of degrees of its neighbors. We develop an algorithm for estimating degrees of each neighbor. The algorithm considers observations associated with neighbors as a Bernoulli trial and repeatedly estimate degrees of neighbors as a new observation occurs. We experimentally show that the algorithm can compute the degrees of neighbors more accurately than a simple counting of observations. Finally, we design a bayesian reputation game where reputation is used as payoffs. The game theoretic view of reputation computation reflects another level of reality in which all agents are rational in sharing reputation information of others. An interesting behavior of agents within such a game theoretic environment is that cooperation- i.e., sharing true reputation information- emerges without an explicit punishment mechanism nor a direct reward mechanisms

Anti-CRISPR Proteins: Applications in Genome Engineering

Clustered, regularly interspaced, short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) constitute a bacterial and archaeal adaptive immune system. The ongoing arms race between prokaryotic hosts and their invaders such as phages led to the emergence of anti-CRISPR proteins as countermeasures against the potent antiviral defense. Since the first examples of anti-CRISPRs were shown in a subset of CRISPR-Cas systems, we endeavored to uncover these naturally-occurring inhibitors that inactivate different types of CRISPR-Cas systems. In the first part of my thesis, we have identified and characterized Type II anti-CRISPR proteins that inactivate several Cas9 orthologs. We share mechanistic insights into anti-CRISPR inhibition and show evidence of its potential utility as an off-switch for Cas9-mediated mammalian genome editing. Although the RNA programmability of Cas9 enables facile genetic manipulation with great potential for biotechnology and therapeutics, limitations and safety issues remain. The advent of anti-CRISPR proteins presents opportunities to exploit the inhibitors to exert temporal, conditional, or spatial control over CRISPR. In the second part of my thesis, we demonstrate that anti-CRISPR proteins can serve as useful tools for Cas9 genome editing. In particular, we have demonstrated that anti-CRISPRs are effective as genome editing off-switches in the tissues of adult mammals, and we further engineered anti-CRISPR proteins to achieve tissue-specific editing in vivo. Taken together, my thesis research aimed to mine for natural anti-CRISPR protein inhibitors and repurpose these proteins to complement current Cas9 technologies in basic and clinical research