| We examine the properties of transmembrane (TM) proteins from a thermodynamic equilibrium point of view. Motivated by recent experiments that describe the Boltzmann nature of the insertion of TM segments, we construct statistical mechanical models of membrane proteins to capitalize on this finding. This is achieved using a course-grained model that treats the TM protein as a homopolymer chain. The TM segments are allowed to interact with the membrane as well as with each other once inserted. A phase diagram is constructed describing the various equilibrium phases and the transitions separating them. Next we use an approach that utilizes the full amino acid sequence of bacteriorhodopsin . We are able to do away with the coarse graining over the individual amino acid hydrophobicities by treating the TM segments as a confined fluid of rods in an external potential. Information is extracted from the sequence that supports the robustness of the TM structure against changes in temperature, chemical potential, mutations and various assembly scenarios. In the last Chapter we examine the role of the newly discovered RNA interference (RNAi) mechanism in suppressing viral growth. We analyze the competing dynamics of viral and RNAi populations and describe the conditions for which suppression can be successful at the intercellular and intracellular levels. |
