For many small single domain proteins, folding proceeds without the accumulation of any intermediates. It is possible though to probe the transition state by making perturbations and measuring the effects on the folding and unfolding rates.
A metal binding site can be introduced through mutation with 2 Histidine residues that in the native conformation is capable of binding a divalent metal ion, e.g. Zinc.
Measuring the effect of zinc on the folding and unfolding rates thus reports on the extent to which the two residues interact in the transition state.
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.
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.
G.L. Bosco, M. Baxa, T.R. Sosnick, "Metal binding kinetics of bi-histidine sites used in psi analysis: evidence of high-energy protein folding intermediates" Biochemistry 48 (2009) 2950-9.
J.R. Horn, T.R. Sosnick, A.A. Kossiakoff, "Principal determinants leading to transition state formation of a protein-protein complex, orientation trumps side-chain interactions" Proc Natl Acad Sci U S A 106 (2009) 2559-64.
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.
A.D. Pandit, B.A. Krantz, R.S. Dothager, T.R. Sosnick, "Characterizing protein folding transition States using Psi-analysis" Methods Mol Biol 350 (2007) 83-104.
A.D. Pandit, A. Jha, K.F. Freed, T.R. Sosnick, "Small proteins fold through transition states with native-like topologies" J Mol Biol 361 (2006) 755-70.
T.R. Sosnick, B.A. Krantz, R.S. Dothager, M.C. Baxa, "Characterizing the protein folding transition state using psi analysis" Chem Rev 106 (2006) 1862-76.
B.A. Krantz, R.S. Dothager, T.R. Sosnick, "Discerning the structure and energy of multiple transition states in protein folding using psi-analysis" J Mol Biol 337 (2004) 463-75.
T.R. Sosnick, R.S. Dothager, B.A. Krantz, "Differences in the folding transition state of ubiquitin indicated by phi and psi analyses" Proc Natl Acad Sci U S A 101 (2004) 17377-82.