We are interested in characterizing the general principles that govern protein folding. Despite being a long studied problem, many questions remain unresolved, for example the physical folding events that dictate the pathway as well as a concise understanding of the origins of the cooperative protein folding.
Our studies are consistent with the principle of Sequential Stabilization - that protein folding is a series of smaller folding events described by the concurrent formation of secondary and tertiary structure, e.g. a turn of helix forms which buries hydrophobic surface area. This incremental accumulation of structure mostly produces native- or unfolded-like regions during folding, as suggested by the frequent observation of ψ values of 0 or 1 as well as the cooperative pattern of protection factors for hydrogen exchange (HX).
We have characterized the transition state ensembles of several proteins and have found a common feature – that is the transition state achieves 70-80% of the native topology (as defined by relative contact order - Plaxco et al., 1998). This "70% Rule" supports the belief that topology is a critical feature of the transition state and supports the correlation between folding rate and topology. Furthermore, the high threshold places a strong constraint on feasible transition state structures for a particular native topology.
Our current views on the origin of folding cooperativity and stability are challenged by our studies of snowflea anti-freeze protein (sfAFP), which has a unique fold composed of 6 polyproline 2 (PP2) helices arranged in a 3x2 stack held together by inter-helical H-bonds. Despite lacking a hydrophobic core and being 46% Glycine, sfAFP is stable and folds in a two-state manner. sfAFP highlights that while we have a good, at least qualitative understanding of folding for typical, relatively small systems, much remains to be determined, especially the proper balance of the various forces that drive folding.
J.M. Jumper, K.F. Freed, T.R. Sosnick, "Trajectory-Based Parameterization of a Coarse-Grained Forcefield for High-Throughput Protein Simulation" bioRxiv:169326.
Z.P. Gates*, M.C. Baxa*, W. Yu, J.A. Riback, H. Li, B. Roux, S.B.H. Kent, T.R. Sosnick, "Perplexing cooperative folding and stability of a low-sequence complexity, polyproline 2 protein lacking a hydrophobic core" Proc Natl Acad Sci U S A 114 (2017) 2241-6.
J.M. Jumper, K.F. Freed, T.R. Sosnick, "Maximum-likelihood, self-consistent side chain free energies with applications to protein molecular dynamics" arXiv:1610.07277 [q-bio.BM].
W. Yu, M.C. Baxa, I. Gagnon, K.F. Freed, T.R. Sosnick, "Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange" Proc Natl Acad Sci U S A 113 (2016) 4747-52.
M.C. Baxa, W. Yu, A.N. Adhikari, L. Ge, Z. Xia, R. Zhou, K.F. Freed, T.R. Sosnick, "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 (2015) 8302-7.
J.J. Skinner, W. Yu, E.K. Gichana, M.C. Baxa, J.R. Hinshaw, K.F. Freed, T.R. Sosnick, "Benchmarking all-atom simulations using hydrogen exchange" Proc Natl Acad Sci U S A 111 (2014) 15975-80.
A.T. Shandiz, M.C. Baxa, T.R. Sosnick, "A "Link-Psi" strategy using crosslinking indicates that the folding transition state of ubiquitin is not very malleable" Protein Sci 21 (2012) 819-27.
T.Y. Yoo, A. Adhikari, Z. Xia, T. Huynh, K.F. Freed, R. Zhou, T.R. Sosnick, "The folding transition state of protein L is extensive with nonnative interactions (and not small and polarized)" J Mol Biol 420 (2012) 220-34.
T.R. Sosnick, D. Barrick, "The folding of single domain proteins--have we reached a consensus?" Curr Opin Struct Biol 21 (2011) 12-24.
M.C. Baxa, K.F. Freed, T.R. Sosnick, "Psi-constrained simulations of protein folding transition states: implications for calculating φ" J Mol Biol 386 (2009) 920-8.
M.C. Baxa, K.F. Freed, T.R. Sosnick, "Quantifying the structural requirements of the folding transition state of protein A and other systems" J Mol Biol 381 (2008) 1362-81.