Biology subjects

Ge, H.

Publications and source records attributed to Ge, H..

3 recordsLinked to original sources

bioRxiv2018

Expression of novel fusion antiviral proteins Ricin A Chain-Pokeweed Antiviral Proteins (RTA-PAPs) in Escherichia coli and their inhibition of protein synthesis and of hepatitis B virus in vitro

Ricin A chain (RTA) and Pokeweed antiviral proteins (PAPs) are plant-derived N-glycosidase ribosomal-inactivating proteins (RIPs) isolated from Ricinus communis and Phytolacca Americana respectively. This study was to investigate the potential antiviral value of novel fusion proteins between RTA and PAPs (RTA-PAPs). In brief, RTA-Pokeweed antiviral protein isoform 1 from seeds (RTA-PAPS1) was produced in E. coli in vivo expression system, purified from inclusion bodies using gel filtration chromatography and protein synthesis inhibitory activity assayed by comparison to the production of a control protein Luciferase. The antiviral activity of the RTA-PAPS1 against Hepatitis B virus (HBV) in HepAD38 cells was then determined using a dose response assay by quantifying supernatant HBV DNA compared to control virus infected HepAD38 cells. The cytotoxicity in HepAD38 cells was determined by measuring cell viability using a tetrazolium dye uptake assay. Results showed that RTA-PAPS1 could effectively be recovered and purified from inclusion bodies. The refolded protein was bioactive with 50% protein synthesis inhibitory concentration (IC50) of 0.06nM (3.63ng/ml). The results also showed that RTA-PAPS1 had a synergetic activity against HBV with a half-maximal response concentration value (EC50) of 0.03nM (1.82ng/ml) and a therapeutic index of >21818. The fusion protein was further optimized using in silico tools, produced in E. coli in vivo expression system, purified by three-step process from soluble lysate and protein synthesis inhibition activity assayed. Results showed that the optimized protein RTA mutant-Pokeweed antiviral protein isoform 1 from leaves (RTAM-PAP1) could be recovered and purified from soluble lysates with gain of function activity on protein synthesis inhibition with an IC50 of 0.03nM (1.82ng/ml). Collectively, our results demonstrate that RTA-PAPs are amenable to effective production and purification in native form, possess significant antiviral activity against HBV in vitro with a high therapeutic index and, thus, meriting further development as potential antiviral agents against chronic HBV infection.

synthetic biology↗

bioRxiv2018

Structure for Energy Cycle: A unique status of Second Law of Thermodynamics for living systems

Distinguishing things from beings, or matters from lives, is a fundamental question. Extending E. Schrodingers neg-entropy and I. Prigogines dissipative structure, we propose a chemical kinetic view that the earliest \"live\" process is essentially a special interaction between a pair of specific components under a corresponding, particular environmental conditions. The interaction exists as an inter-molecular-force-bond complex (IMFBC) that couples two separate chemical processes: One is the spontaneous formation of an IMFBC driven by the decrease of Gibbs free energy as a dissipative process; while the other is the disassembly of the IMFBC driven thermodynamically by free energy input from the environment. The two processes that are coupled by the IMFBC were originated independently and considered non-living on Earth, but the IMFBC coupling of the two can be considered as the earliest form of metabolism: This forms the first landmark on the path from things to a being. The dynamic formation and dissemblance of the IMFBCs, as composite individuals, follows a principle designated as \"... structure for energy for structure for energy...\", the cycle continues, shortly \"structure for energy cycle\". With additional features derived from an IMFBC, such as multiple intermediates, autocatalytic ability of one individual upon the formation of another, aqueous medium, and mutual beneficial relationship between formation of polypeptides and nucleic acids, etc., the IMFBC-centered \"live\" process spontaneously evolved into more complex living organisms with the characteristics one currently knows.

evolutionary biology↗

bioRxiv2017

Insight Into The Mechanism Of Protein Thermostability Based On The Residue Interaction Degrees

Understanding the basis of protein thermostability raises a general question: which residue with specific interaction degrees is more important to the protein thermostability? A strictly selected dataset of 131 pairs of thermophilic (TPs) and mesophilic proteins (MPs) was constructed. There were 6.4% and 8.4% of the total residues in sequences did not interact with others in TPs and MPs. The amino acid contents in sequences are closest to those with the interaction degrees of 3 according to the Chi-squared distances. Only Glu, Gln and the amide residues showed significant differences in sequences, which was the same as identified at low residue interaction degrees. However, we observed significant Phe, Lys, Leu, Gln and the charged, aliphatic, aromatic, positive charged and small residues at high interaction degree. Among them, Phe was rarely reported previously although aromatic residues were well-known contributor to protein thermostability. Finally, we took aspartate transcarbamylases as an example to explain how a residue with various interaction degrees contributed differently to their thermostability. Our results clearly demonstrated the differences of amino acids in sequence between TPs and MPs could only represent those involved in low interaction degrees. Much more residues with significant differences existed at high interaction degrees even if they had few significant amino acids in sequences. The interaction degree-based method should be an alternative tool in extracting valuable eigenvalues for predicting proteins attributes in bioinformatics. It could also provide a new perspective for studying the thermostability of proteins and engineering novel thermostable proteins.\n\nList of abbreviations

bioinformatics↗