Psi analysis

Psi analysis

Psi analysis

Through the introduction of metal-binding sites one can stabilize specific side chain - side chain contacts during the folding reaction. By varying the metal concentration, one can continuously tune the stabilization between the two histidines.

Approach

  • The folding transition states characterized using psi analysis are extensive with a highly native-like topology.

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.

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.

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. 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.