One mechanism of regulating the catalytic activity of protein kinases is through conformational transitions. Despite great diversity in the structural changes involved in the transitions, a certain set of changes within the kinase domain (KD) has been observed for many kinases including Src and CDK2. We investigated this conformational transition computationally to identify the topological features that are energetically critical to the transition. Results from both molecular dynamics sampling and transition path optimization highlight the displacement of the αC helix as the major energy barrier, mediating the switch of the KD between the active and down-regulated states. The critical role of the αC helix is noteworthy by providing a rationale for a number of activation and deactivation mechanisms known to occur in cells. We find that kinases with the αC helix displacement exist throughout the kinome, suggesting that this feature may have emerged early in evolution.
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http://dx.doi.org/10.1021/jp301628r | DOI Listing |
Nat Chem Biol
February 2024
David Braley Centre for Antibiotics Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
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April 2023
Department of Marine Pharmacology, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China.
Outbreaks of starfish () pose a major threat to aquaculture and marine ecosystems in Qingdao, China, and no effective methods have been found to control them. A comprehensive study of collagen in starfish could be an alternative to high efficient utilization. Based on this, collagen was firstly extracted from Qingdao .
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April 2023
Rice Research Institute, Shenyang Agricultural University, Shenyang, China.
Panicle development is crucial to increase the grain yield of rice (). The molecular mechanisms of the control of panicle development in rice remain unclear. In this study, we identified a mutant with abnormal panicles, termed ().
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January 2023
State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China.
This manuscript analyzed physicochemical and structural properties of 30 different types of sorghum starches based on their apparent amylose content (AAC). Current results confirmed that sorghum starch exhibited irregular spherical or polygonal granule shape with 14.5 μm average particle size.
View Article and Find Full Text PDFFood Chem
June 2023
School of Food and Biological Engineering, Collaborative Innovation Center of Food Production and Safety, Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Zhengzhou University of Light Industry, Zhengzhou 450002, China.
The multi-scale structure and physicochemical properties of starch from five indigenous millet varieties were investigated and their correlations were revealed. Results showed that apparent amylose content (AAC) ranged from 12.3% to 27.
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