title: Positively-charged semi-tunnel is a structural and surface characteristic of polyphosphate-binding proteins: an in-silico study.
abstract: Phosphate is essential for all major life processes, especially energy metabolism and signal transduction. A linear phosphate polymer, polyphosphate (polyP), linked by high-energy phosphoanhydride bonds, can interact with various proteins, playing important roles as an energy source and regulatory factor. However, polyP-binding structures are largely unknown. Here we proposed a putative polyP binding site, a positively-charged semi-tunnel (PCST), identified by surface electrostatics analyses in polyP kinases (PPKs) and many other polyP-related proteins. We found that the PCSTs in varied proteins were folded in different secondary structure compositions. Molecular docking calculations revealed a significant value for binding affinity to polyP in PCST-containing proteins. Utilizing the PCST identified in the β subunit of PPK3, we predicted the potential polyP-binding domain of PPK3. The discovery of this feature facilitates future searches for polyP-binding proteins and discovery of the mechanisms for polyP-binding activities. This should greatly enhance the understanding of the many physiological functions of protein-bound polyP and the involvement of polyP and polyP-binding proteins in various human diseases.
authors: Neuroscience Research Institute, Peking University; Department of Neurobiology, School of Basic Medical Sciences, Peking University; Key Laboratory for Neuroscience (Peking University), Ministry of Education; Key Laboratory for Neuroscience (Peking University), National Health and Family Planning Commission, Beijing 100191, China.
authors: Zheng Zachory
authors: ZZ
authors: Wei
authors: Neuroscience Research Institute, Peking University; Department of Neurobiology, School of Basic Medical Sciences, Peking University; Key Laboratory for Neuroscience (Peking University), Ministry of Education; Key Laboratory for Neuroscience (Peking University), National Health and Family Planning Commission, Beijing 100191, China.
authors: Greg
authors: G
authors: Vatcher
authors: Neuroscience Research Institute, Peking University; Department of Neurobiology, School of Basic Medical Sciences, Peking University; Key Laboratory for Neuroscience (Peking University), Ministry of Education; Key Laboratory for Neuroscience (Peking University), National Health and Family Planning Commission, Beijing 100191, China.
authors: Alvin Hok Yan
authors: AH
authors: Tin
authors: The Key Laboratory of Cell Proliferation and Differentiation of Ministry of Education, The State Key Laboratory of Bio-membrane and Membrane Bio-engineering, College of Life Sciences, Peking University, Beijing 100871, China.
authors: Jun Lin
authors: JL
authors: Teng
authors: Department of Medical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China.
authors: Juan
authors: J
authors: Wang
authors: Department of Medical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China.
authors: Qing Hua
authors: QH
authors: Cui
authors: The Key Laboratory of Cell Proliferation and Differentiation of Ministry of Education, The State Key Laboratory of Bio-membrane and Membrane Bio-engineering, College of Life Sciences, Peking University, Beijing 100871, China.
authors: Jian Guo
authors: JG
authors: Chen
authors: Neuroscience Research Institute, Peking University; Department of Neurobiology, School of Basic Medical Sciences, Peking University; Key Laboratory for Neuroscience (Peking University), Ministry of Education; Key Laboratory for Neuroscience (Peking University), National Health and Family Planning Commission, Beijing 100191, China; Infectious Disease Center, Peking University, Beijing 100191, China; Laboratory of Translational Medicine, Institute of Systems Biomedicine, Peking University, Beijing 100191, China.
authors: Albert Cheung Hoi
authors: AC
authors: Yu
mesh_terms: D003198:Computer Simulation; D062105:Molecular Docking Simulation; D011122:Polyphosphates / Q000378:metabolism*; D011485:Protein Binding; D011506:Proteins / Q000378:metabolism*; D013499:Surface Properties
chemical_list: D011122:Polyphosphates; D011506:Proteins