TY  - JOUR
AU  - Mohanty, Sandipan
AU  - Meinke, Jan
AU  - Zimmermann, Olav
TI  - Folding of Top7 in unbiased all-atom Monte Carlo simulations
JO  - Proteins
VL  - 81
IS  - 8
SN  - 0887-3585
CY  - New York, NY
PB  - Wiley-Liss
M1  - FZJ-2013-01895
SP  - 1446 - 1456
PY  - 2013
AB  - For computational studies of protein folding, proteins with both helical and β-sheet secondary structure elements are very challenging, since they expose subtle biases of the physical models. Here we present reproducible folding of a 92 residue α/β protein (residues 3–94 of Top7, PDB ID: 1QYS) in computer simulations starting from random initial conformations using a transferable physical model which has been previously shown to describe the folding and thermodynamic properties of about 20 other smaller proteins of different folds. Top7 is a de novo designed protein with two α-helices and a 5 stranded β-sheet. Experimentally it is known to be unusually stable for its size, and its folding transition distinctly deviates from the two state behaviour commonly seen in natural single domain proteins. In our all-atom implicit solvent parallel tempering Monte Carlo simulations, Top7 shows a rapid transition to a group of states with high native-like secondary structure, and a much slower subsequent transition to the native state with a root mean square deviation of about 3.5 Å from the experimentally determined structure. Consistent with experiments, we find Top7 to be thermally extremely stable, although the simulations also find a large number of very stable non-native states with high native-like secondary structure.
LB  - PUB:(DE-HGF)16
UR  - <Go to ISI:>//WOS:000329220400014
C6  - pmid:23553942
DO  - DOI:10.1002/prot.24295
UR  - https://juser.fz-juelich.de/record/133447
ER  -