Combining Multi-scale Modeling with Multi-pronged Experiments to Unveil Conformational Changes of Macromolecular Complexes

University Of Arizona, Tucson AZ

Investigators

Abstract

Structural characterization of macromolecular complexes and their functional states is a crucial task in molecular biology, since multi-component molecular machines accomplish many important cellular functions. As these large complexes are difficult to study by X-ray crystallography, alternative low-resolution experimental techniques such as cryo-EM, SAXS and FRET are often used to characterize their conformational states. Each of these experimental approaches offers different advantages and meets with different pitfalls, artifacts and limitations. Therefore more accurate descriptions could be obtained if all pieces of experimental data were taken together to annotate conformational states. Computational methods will be developed to obtain atomic level descriptions of conformational transitions occurring in macromolecular complexes by integrating multiple data from a variety of low-resolution experiments and X-ray crystallography. Structural models will be constructed by deforming, in a physical meaningful way using molecular dynamics simulation and/or normal mode analysis, a known X-ray structure to agree with cryo-EM, SAXS and/or FRET data. The ribosome, which has been extensively characterized using multiple sets of experimental data, will serve as a test system to validate the approach with real experimental data. These methods will then be applied to study the swelling transition of a small plant virus, Tomato Bushy Stunt Virus to get a better understanding, through this model system, of the life cycle of viruses. This project will involve undergraduate and graduate students. Students will learn theories of biophysics, computational approaches and structural biology by contributing to the development, testing and subsequent applications of the methods. The newly developed tools will be distributed to the scientific community in the form of a program package that will be freely available through the Internet for download. The compelling approach with these new tools is that not only research groups could analyze their own experimental data with those algorithms, but also they could incorporate other published results into the modeling to obtain a more accurate description of the conformational transitions. The principal investigator is also involved in outreach activities to local Tucson high-school girls. The principal investigator will develop in concert with high-schools teachers an outreach program to offer research opportunities at the University to high-school girls during the summers to encourage them to pursue scientific careers.