TY - JOUR
T1 - Force field-dependant structural divergence revealed during long time simulations of calbindin d9k
AU - Project, Elad
AU - Nachliel, Esther
AU - Gutman, M.
PY - 2010/7/15
Y1 - 2010/7/15
N2 - 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 S2 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 widi 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.
AB - 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 S2 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 widi 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.
KW - Experimental structure
KW - Force field
KW - Molecular dynamics
KW - Protein folding
KW - Secondary structure
KW - Structural divergence
UR - http://www.scopus.com/inward/record.url?scp=77953208542&partnerID=8YFLogxK
U2 - 10.1002/jcc.21473
DO - 10.1002/jcc.21473
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AN - SCOPUS:77953208542
SN - 0192-8651
VL - 31
SP - 1864
EP - 1872
JO - Journal of Computational Chemistry
JF - Journal of Computational Chemistry
IS - 9
ER -