Improvement on a simplified model for protein folding simulation.
Improvements were made on a simplified protein model--the Ramachandran model-to achieve better computer simulation of protein folding. To check the validity of such improvements, we chose the ultrafast folding protein Engrailed Homeodomain as an example and explored several aspects of its folding. The engrailed homeodomain is a mainly alpha-helical protein of 61 residues from Drosophila melanogaster. We found that the simplified model of Engrailed Homeodomain can fold into a global minimum state with a tertiary structure in good agreement with its native structure.
Zhang
Ming
M
Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
Chen
Changjun
C
He
Yi
Y
Xiao
Yi
Y
D000595:Amino Acid Sequence; D003198:Computer Simulation; D029721:Drosophila Proteins; D018398:Homeodomain Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017510:Protein Folding; D020539:Sequence Analysis, Protein / Q000379:methods*; D014157:Transcription Factors / Q000737:chemistry* / Q000648:ultrastructure*
D029721:Drosophila Proteins; C063459:En protein, Drosophila; D018398:Homeodomain Proteins; D014157:Transcription Factors