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Title: Mechanism of CDK5 activation revealed by steered molecular dynamics simulations and energy calculations
Authors: Zhang, B. 
Su, Z.C.
Tay, T.E. 
Tan, V.B.C. 
Keywords: Cyclin-dependent kinase
Molecular dynamics
Protein-protein interaction
Steered molecular dynamics
Issue Date: Jun-2010
Citation: Zhang, B., Su, Z.C., Tay, T.E., Tan, V.B.C. (2010-06). Mechanism of CDK5 activation revealed by steered molecular dynamics simulations and energy calculations. Journal of Molecular Modeling 16 (6) : 1159-1168. ScholarBank@NUS Repository.
Abstract: In the current work, CDK5/p25 complexes were pulled apart by applying external forces with steered molecular dynamics (SMD) simulations. The crucial interactions between the kinase and the activation protein were investigated and the SMD simulations showed that several activation-relevant motifs of CDK5 leave p25 in sequence during the pulling and lead to an apo-CDK2 like CDK5 structure after separation. Based on systematic examination of hydrogen bond breaking and classical MD/molecular mechanics-generalized Born/surface area) (MM-GBSA) calculations, a CDK5 activation mechanism by p25 is suggested. This is the first step towards the systemic development of CDK inhibitors and the mechanism proposed could lead to a better understanding of the protein-protein recognition characteristics between the kinase and its activator. © Springer-Verlag 2009.
Source Title: Journal of Molecular Modeling
ISSN: 16102940
DOI: 10.1007/s00894-009-0629-4
Appears in Collections:Staff Publications

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