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Electrostatic contribution to the thermodynamic and kinetic stability of the homotrimeric coiled coil Lpp‐56: A computational study
Author(s) -
Bjelić Saša,
Wieninger Silke,
Jelesarov Ilian,
Karshikoff Andrey
Publication year - 2008
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21585
Subject(s) - chemistry , folding (dsp implementation) , electrostatics , molecular dynamics , protein folding , chemical stability , crystallography , native state , chemical physics , thermal stability , computational chemistry , biochemistry , organic chemistry , electrical engineering , engineering
The protein moiety of the Braun's E. coli outer membrane lipoprotein (Lpp‐56) is an attractive object of biophysical investigation in several aspects. It is a homotrimeric, parallel coiled coil, a class of coiled coils whose stability and folding have been studied only occasionally. Lpp‐56 possesses unique structural properties and exhibits extremely low rates of folding and unfolding. It is natural to ask how the specificity of the structure determines the extraordinary physical chemical properties of this protein. Recently, a seemingly controversial data on the stability and unfolding rate of Lpp‐56 have been published (Dragan et al. , Biochemistry 2004;43: 14891–14900; Bjelic et al. , Biochemistry 2006;45:8931–8939). The unfolding rate constant measured using GdmCl as the denaturing agent, though extremely low, was substantially higher than that obtained on the basis of thermal unfolding. If this large difference arises from the effect of screening of electrostatic interactions induced by GdmCl, electrostatic interactions would appear to be an important factor determining the unusual properties of Lpp‐56. We present here a computational analysis of the electrostatic properties of Lpp‐56 combining molecular dynamics simulations and continuum pK calculations. The pH‐dependence of the unfolding free energy is predicted in good agreement with the experimental data: the change in ΔG between pH 3 and pH 7 is ∼60 kJ mol −1 . The results suggest that the difference in the stability of the protein observed using different experimental methods is mainly because of the effect of the reduction of electrostatic interactions when the salt (GdmCl) concentration increases. We also find that the occupancy of the interhelical salt bridges is unusually high. We hypothesize that electrostatic interactions, and the interhelical salt bridges in particular, are an important factor determining the low unfolding rate of Lpp‐56. Proteins 2008. © 2007 Wiley‐Liss, Inc.