Developing a General Description of the Unfolded State of a Protein

Michigan State University, East Lansing MI

Investigators

Abstract

The unfolded state of a protein under physiological conditions has long been modeled as a random coil polymer with negligible self-interactions. Recent measurements by nuclear magnetic resonance (NMR) have revealed substantial residual structure and transient interactions in several proteins, contradicting the classic view of the unfolded state. However, the NMR data do not describe the global conformational dynamics of these highly disordered states with much specificity. This project seeks to marry these earlier results with complementary measurements of the rate of intramolecular diffusion on the same sequences. The PI uses the novel technique of quenching of the triplet state of tryptophan by cysteine, which is measured with an optical instrument with nanosecond resolution. Intramolecular diffusion coefficients can be extracted from these measured rates using a theory by Szabo, Schulten and Schulten which requires a probability distribution of equilibrium distances between the tryptophan and cysteine in the sequence. The PI and co-PI construct such distributions using a polymer model that exploits the structural information obtained in the prior NMR studies. These distributions are compared to existing distributions constructed by the Forman-Kay and Vendruscolo labs and also to molecular dynamics simulations that will be completed as part of this project. The long-term goal is to develop sequence-specific distributions based on established polymer models, statistical structure predictors, hydrophobicity scales and measured diffusion coefficients that should lead to a general understanding of the dynamics of the unfolded state. This project encompasses aspects of structural biology, computation biology, optical spectroscopy and polymer physics. Therefore the students involved in this work will require cross-disciplinary training to accomplish the scientific goals. As part of a new graduate program in Quantitative Biology at MSU, the PI and co-PI are designing new lecture and laboratory courses to introduce physical science students to biology and biology students to quantitative methods. This project is jointly supported by the Molecular Biophysics Program in the Division of Molecular and Cellular Biosciences in the Directorate for Biological Sciences and the Division of Physics in the Mathematical and Physical Sciences Directorate.