The effect of calciums on molecular motions of proteinase K |
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Authors: | Shu-Qun Liu Yan Tao Zhao-Hui Meng Yun-Xin Fu Ke-Qin Zhang |
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Institution: | (1) Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091 Yunnan, People’s Republic of China;(2) Library of Yunnan University, Kunming, 650091, Yunnan, People’s Republic of China;(3) Department of Cardiology, No. 1 Affiliated Hospital, Kunming Medical College, Kunming, 650032, Yunnan, People’s Republic of China;(4) Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, TX 77030, USA |
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Abstract: | The native serine protease proteinase K binds two calcium cations. It has been reported that Ca2+ removal decreased the enzyme’s thermal stability and to some extent the substrate affinity, but has discrepant effects on
catalytic activity of the enzyme. Molecular dynamics simulations were performed on the Ca2+-bound and Ca2+-free proteases to investigate the mechanism by which the calciums affect the structural stability, molecular motions, and
catalytic activity of proteinase K. Very similar structural properties were observed between these two forms of proteinase
K during simulations; and several long-lived hydrogen bonds and salt bridges common to both forms of proteinase K were found
to be crucial in maintaining the local conformations around these two Ca2+ sites. Although Ca2+ removal enhanced the overall flexibility of proteinase K, the flexibility in a limited number of segments surrounding the
substrate-binding pockets decreased. The largest differences in the equilibrium structures of the two simulations indicate
that, upon the removal of Ca2+, the large concerted motion originating from the Ca1 site can transmit to the substrate-binding regions but not to the catalytic
triad residues. In conjunction with the large overlap of the essential subspaces between the two simulations, these results
not only provide insight into the dynamics of the underlying molecular mechanism responsible for the unchanged enzymatic activity
as well as the decreased thermal stability and substrate affinity of proteinase K upon Ca2+ removal, but also complement the experimentally determined structural and biochemical data. |
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