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|Title:||Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein||Authors:||Lazim, Raudah
|Keywords:||DRNTU::Science::Chemistry::Biochemistry||Issue Date:||2011||Source:||Lazim, R., Mei, Y., & Zhang, D. (2011). Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein. Journal of molecular modeling, 18(3), 1087-1095.||Series/Report no.:||Journal of molecular modeling||Abstract:||Replica exchange molecular dynamics (REMD) simulation provides an efficient conformational sampling tool for the study of protein folding. In this study, we explore the mechanism directing the structure variation from α/4β-fold protein to 3α-fold protein after mutation by conducting REMD simulation on 42 replicas with temperatures ranging from 270 K to 710 K. The simulation began from a protein possessing the primary structure of GA88 but the tertiary structure of GB88, two G proteins with “high sequence identity.” Albeit the large Cα-root mean square deviation (RMSD) of the folded protein (4.34 Å at 270 K and 4.75 Å at 304 K), a variation in tertiary structure was observed. Together with the analysis of secondary structure assignment, cluster analysis and principal component, it provides insights to the folding and unfolding pathway of 3α-fold protein and α/4β-fold protein respectively paving the way toward the understanding of the ongoings during conformational variation.||URI:||https://hdl.handle.net/10356/98098
|DOI:||http://dx.doi.org/10.1007/s00894-011-1147-8||Fulltext Permission:||none||Fulltext Availability:||No Fulltext|
|Appears in Collections:||SPMS Journal Articles|
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