Scanning malleable transition state ensembles: comparing theory and experiment for folding protein U1A.
Using a variational free energy functional, we calculate the characteristics of the transition state ensembles (TSE) for the folding of protein U1A and investigate how they respond to thermal and mutational changes. The functional directly yields predicted chevron plots both for the wild-type protein and for various mutants. The detailed variations of the TSE and changes in chevron plots predicted by the theory agree reasonably well with the results of the experiments. We also show how to visualize the folding nuclei using 3D isodensity plots.
Shen
Tongye
T
Department of Chemistry & Biochemistry, University of California at San Diego and Center for Theoretical Biological Physics, La Jolla, California 92093-0371.
Hofmann
Christoph P
CP
Oliveberg
Mikael
M
Wolynes
Peter G
PG
D007700:Kinetics; D008956:Models, Chemical; D009154:Mutation; D011487:Protein Conformation; D011489:Protein Denaturation / Q000235:genetics; D017510:Protein Folding; D017433:Protein Structure, Secondary; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics; D017412:Ribonucleoprotein, U1 Small Nuclear / Q000737:chemistry* / Q000235:genetics; D013696:Temperature; D013816:Thermodynamics
D016601:RNA-Binding Proteins; D017412:Ribonucleoprotein, U1 Small Nuclear; C075339:U1A protein