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1.
PLoS One ; 10(4): e0123713, 2015.
Article in English | MEDLINE | ID: mdl-25879219

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 ß 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.


Subject(s)
Polyphosphates/metabolism , Proteins/metabolism , Computer Simulation , Molecular Docking Simulation , Protein Binding , Surface Properties
2.
DNA Cell Biol ; 31(4): 496-503, 2012 Apr.
Article in English | MEDLINE | ID: mdl-21977911

ABSTRACT

The focal adhesion-associated protein (FAAP), product of the murine D10Wsu52e gene, is involved in modulating cell adhesion dynamics. The ubiquitously expressed protein belongs to the highly conserved UPF0027 family, the newly identified RNA >p ligase family. To understand the mechanisms underlying FAAP expression and regulation, we first mapped its major transcription start site at the nucleotide 79 bp upstream of the ATG codon. The murine FAAP 2.1 kb 5'-flanking region was cloned, analyzed, and aligned with the corresponding 1.7 kb region of its human homolog HSPC117. Despite the differences in activity, cell in vitro transfection and testis in vivo electroporation identified a 0.2 kb efficient promoter region lacking a functional TATA-box. Gel shift assays confirmed the specific interaction between Yin Yang-1 (YY1) and the potential element in the proximal region of the FAAP promoter. Site mutation, truncation, RNAi, and overexpression analyses suggested that YY1 is an important regulator of the FAAP promoter.


Subject(s)
Cell Adhesion/genetics , Gene Expression Regulation/genetics , Promoter Regions, Genetic/genetics , Proteins/metabolism , YY1 Transcription Factor/metabolism , 5' Flanking Region/genetics , Amino Acyl-tRNA Synthetases , Animals , Base Sequence , Blotting, Northern , Cloning, Molecular , DNA Primers/genetics , DNA, Complementary/genetics , Electrophoretic Mobility Shift Assay , Electroporation , Male , Mice , Molecular Sequence Data , Proteins/genetics , RNA Interference , Sequence Alignment , Sequence Analysis, DNA , Sequence Homology , Testis/metabolism
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