Can the stability of protein mutants be predicted by free energy calculations?
The use of free energy simulation techniques in the study of protein stability is critically evaluated. Results from two simulations of the thermostability mutation Asn218 to Ser218 in Subtilisin are presented. It is shown that components of the free energy change can be highly sensitive to the computational details of the simulation leading to the conclusion that free energy calculations cannot currently be used to reliably predict protein stability. The different factors that undermine the reliability are discussed.
Shi
Y Y
YY
Department of Biology, University of Science and Technology of China, Anhui.
Mark
A E
AE
Wang
C X
CX
Huang
F
F
Berendsen
H J
HJ
van Gunsteren
W F
WF
D001216:Asparagine / Q000737:chemistry / Q000235:genetics; D003198:Computer Simulation; D004795:Enzyme Stability; D008956:Models, Chemical; D009154:Mutation; D011506:Proteins / Q000737:chemistry*; D012694:Serine / Q000737:chemistry / Q000235:genetics; D013381:Subtilisins / Q000737:chemistry* / Q000235:genetics; D013816:Thermodynamics
D011506:Proteins; D012694:Serine; D001216:Asparagine; D013381:Subtilisins