Posttransition state desolvation of the hydrophobic core of the src-SH3 protein domain.
The folding thermodynamics of the src-SH3 protein domain were characterized under refolding conditions through biased fully atomic molecular dynamics simulations with explicit solvent. The calculated free energy surfaces along several reaction coordinates revealed two barriers. The first, larger barrier was identified as the transition state barrier for folding, associated with the formation of the first hydrophobic sheet of the protein. phi values calculated from structures residing at the transition state barrier agree well with experimental phi values. The microscopic information obtained from our simulations allowed us to unambiguously assign intermediate phi values as the result of multiple folding pathways. The second, smaller barrier occurs later in the folding process and is associated with the cooperative expulsion of water molecules between the hydrophobic sheets of the protein. This posttransition state desolvation barrier cannot be observed through traditional folding experiments, but is found to be critical to the correct packing of the hydrophobic core in the final stages of folding. Hydrogen exchange and NMR experiments are suggested to probe this barrier.
Guo
Weihua
W
Department of Chemistry, University of California, Santa Barbara, California 93106, USA.
Lampoudi
Sotiria
S
Shea
Joan-Emma
JE
D001665:Binding Sites; D003198:Computer Simulation; D004735:Energy Transfer; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D020673:Protein Renaturation; D017434:Protein Structure, Tertiary; D012997:Solvents / Q000737:chemistry; D014867:Water / Q000737:chemistry*; D017155:Wettability; D018909:src Homology Domains; D019061:src-Family Kinases / Q000737:chemistry*
D012997:Solvents; D014867:Water; D019061:src-Family Kinases