Multi-scale modeling of the structure and dynamics of macromolecules.

摘要

Biology is defined by phenomena that are inherently complex spanning multiple length and time scales. To understand these processes, there is a need for multi-scale approaches that provide a coherent framework for describing and interrogating these phenomena. Here, we employ multiple approaches to investigate specific biological systems. The first system we studied was the cytoplasmic dynein motor, a protein that walks along the microtubule tracks in cells. The major objective in the dynein motors field is to understand its mechanism. Specifically, what is dynein's structure and how does it transduce chemical energy into mechanical work? We proposed a theoretical structural model of the motor and performed normal mode analysis and molecular dynamics on the motor unit structure. These studies hypothesized new structural features in the dynein motor unit and proposed a potential mechanism for energy transduction [5,6,80]. The second system we studied was the CFTR channel, which regulates ion transport in the apical membrane of epithelial cells. Mutations in the CFTR protein are the basis of the cystic fibosis disease. One of the primary question is how a single residue deletion (Phe508) lead to ∼90% of cystic fibrosis cases. We performed molecular dynamics simulation of the first nucleotide-binding domain of CFTR and showed that the wild type and mutant exhibit a difference in their folding kinetics, in agreement with experiments. These simulations also determined the potential structural origin of this misfolding defect. We also proposed a complete model of the CFTR channel to identify the location of the Phe508 residue in the whole protein. This result is important in understanding another aspect of the DeltaF508 defect, which is the misassembly of the whole CFTR protein during its biosynthesis.