CAREER: Cryo-EM Guided de novo Protein Fold Elucidation

Vanderbilt University, Nashville TN

Investigators

Abstract

The primary goal of this CAREER project is to integrate education and research to develop a novel protein structure prediction algorithm"EM-Fold" that advances resolution in protein structure elucidation from cryo-electron microscopy (EM) data. The concept of EM-Fold is developed with the ultimate goal of solving the structure of Ad protein IIIa. An increasing number of structural studies of large macromolecular protein complexes by cryo-electron microscopy have resulted in intermediate-resolution (5-10A) density maps. Currently no integrated approach is available to de novo build protein structures into sub-nanometer EM density maps. In aim I of the project EM-Fold is developed by deriving a protocol for consensus prediction of secondary structure elements, the development of knowledge-based scoring functions, and the implementation of the Monte Carlo assembly and refinement algorithms. Aim II focuses on testing of EM-Fold during the Critical Assessment for Techniques of protein Structure Prediction (CASP) experiment, the derivation of a rapid geometric hashing algorithm to fit structural models into cryo-EM densities, and the set up of a medium-scale experimental benchmark with simulated cryo-EM data sets. In aim III a resolution-increased cryo-EM data set for adenovirus will be recorded, the structure of adenovirus protein IIIa will be predicted, and a detailed confidence level will be assigned to the protein IIIa structure. The research carried out in this project is but one example for an increasing number of computational structural biology projects that pose interdisciplinary requirements on student education. To address this need a novel, integrated educational concept called "Research in Education RidE" is designed as a step-wise journey recruiting students through outreach activities and classroom education into their first research experiences. The outreach component consists of an annual molecular biophysics open house that brings over 100 undergraduate students to Vanderbilt University, primarily from groups underrepresented in science. The open house is complemented by a dedicated lecture series, "Protein Folding @ Home," presented at other undergraduate institutions and events. As a second educational module, the course "Protein Structure Prediction" lays the theoretical foundation for research. Course materials and workshop tutorials are made available online for usage by other teachers and students. In the third module research projects for undergraduate and high school students are aligned with tasks in the development of EM-Fold at appropriate levels of complexity.