Protein folding and dynamics are integral to many biological activities, including chaperone action, protein degradation, amyloid diseases and aging. Our goal is to combine experimental and computational studies to produce a predictive understanding of folding behavior for proteins, independent of whether they are naturally occurring, designed, unfolded, or intrinsically disordered. Our ? analysis method identifies transition states as large and native-like and, along with other data, argues that folding occurs via a process of sequential stabilization.
Aim 1 describes our planned tests of whether this mechanism applies to the whole pathway, especially the early portions. In parallel, we will advance our unifying framework for predicting both pathways and structure using only the sequence as input. Although the method is based only on basic principles of protein chemistry, it has an accuracy comparable to the best MD simulations. We will provide high-resolution data for different proteins to test our simulations and those of others, including DESRES, a collaborator.
Aim 2 delineates how we will investigate whether the unfolded state compacts under native conditions. FRET and MD simulations indicate yes, whereas small angle X-ray scattering indicates otherwise. We will probe the origins of this perplexing discrepancy that has implications to folding mechanisms, the validity of MD simulations, and biothermodynamics.
Aim 3 summarizes our proposed comparison of the folding of naturally occurring proteins and novel designed folds with complex folding kinetics. Identifying the origin of the complex kinetics both challenges our understanding and can help improve design algorithms.

Public Health Relevance

This proposal focuses on the study of protein folding and dynamics, ubiquitous processes that are integral to many biological activities. We will use knowledge gained from our experimental studies to produce a predictive understanding of folding behavior including a framework for predicting both pathways and structure using only the AA sequence as input. We will provide high-resolution data for different proteins in order to test our predictions and those of others while investigating properties of denatured proteins and the origins of the complex folding behavior of designed folds.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Macromolecular Structure and Function B Study Section (MSFB)
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Wehrle, Janna P
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University of Chicago
Schools of Medicine
United States
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Yu, Wookyung; Baxa, Michael C; Gagnon, Isabelle et al. (2016) Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange. Proc Natl Acad Sci U S A 113:4747-52
Basanta, Benjamin; Chan, Kui K; Barth, Patrick et al. (2016) Introduction of a polar core into the de novo designed protein Top7. Protein Sci 25:1299-307
Baxa, Michael C; Yu, Wookyung; Adhikari, Aashish N et al. (2015) Even with nonnative interactions, the updated folding transition states of the homologs Proteins G & L are extensive and similar. Proc Natl Acad Sci U S A 112:8302-7
Watkins, Herschel M; Simon, Anna J; Sosnick, Tobin R et al. (2015) Random coil negative control reproduces the discrepancy between scattering and FRET measurements of denatured protein dimensions. Proc Natl Acad Sci U S A 112:6631-6
Skinner, John J; Yu, Wookyung; Gichana, Elizabeth K et al. (2014) Benchmarking all-atom simulations using hydrogen exchange. Proc Natl Acad Sci U S A 111:15975-80
Zayner, Josiah P; Sosnick, Tobin R (2014) Factors that control the chemistry of the LOV domain photocycle. PLoS One 9:e87074
Baxa, Michael C; Haddadian, Esmael J; Jumper, John M et al. (2014) Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations. Proc Natl Acad Sci U S A 111:15396-401
Virtanen, J J; Sosnick, T R; Freed, K F (2014) Ionic strength independence of charge distributions in solvation of biomolecules. J Chem Phys 141:22D503
Adhikari, Aashish N; Freed, Karl F; Sosnick, Tobin R (2013) Simplified protein models: predicting folding pathways and structure using amino acid sequences. Phys Rev Lett 111:028103
Walters, Benjamin T; Mayne, Leland; Hinshaw, James R et al. (2013) Folding of a large protein at high structural resolution. Proc Natl Acad Sci U S A 110:18898-903

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