Force field-dependent structural divergence revealed during long time simulations of Calbindin d9k.
The structural and the dynamic features of the Calbindin (CaB) protein in its holo and apo states are compared using molecular dynamics simulations under nine different force fields (FFs) (G43a1, G53a6, Opls-AA, Amber94, Amber99, Amber99p, AmberGS, AmberGSs, and Amber99sb). The results show that most FFs reproduce reasonably well the majority of the experimentally derived features of the CaB protein. However, in several cases, there are significant differences in secondary structure properties, root mean square deviations (RMSDs), root mean square fluctuations (RMSFs), and S(2) order parameters among the various FFs. What is more, in certain cases, these parameters differed from the experimentally derived values. Some of these deviations became noticeable only after 50 ns. A comparison with experimental data indicates that, for CaB, the Amber94 shows overall best agreement with the measured values, whereas several others seem to deviate from both crystal and nuclear magnetic resonance data.
Project
Elad
E
Laser Laboratory for Fast Reactions in Biology, Biochemistry, Tel Aviv University, Tel Aviv 69978, Israel.
Nachliel
Esther
E
Gutman
Menachem
M
D064026:Calbindins; D002118:Calcium / Q000737:chemistry / Q000378:metabolism; D003198:Computer Simulation; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D064030:S100 Calcium Binding Protein G / Q000737:chemistry* / Q000378:metabolism
D064026:Calbindins; D064030:S100 Calcium Binding Protein G; D002118:Calcium