Recommendation of Practical Learning Materials in Teaching Biochemistry / 中国生物化学与分子生物学报

The purpose of this paper is to share some practical learning materials with teachers engagedin biochemistry teaching. Students studying biochemistry can also use them directly. The materials includemultimedia such as the song “Biochemistry” and the video “The working principle of ATP synthase”, websites such as RCSB PDB protein structure database, software such as molecular imaging softwareRasmol, etc. Physical models such as the paper model of DNA double helix and the primary, secondaryand tertiary structures of tRNA are also introduced. The practicability of the materials is emphasized. Theapplication scenarios and the anticipated results of the materials are briefly described. Therecommendation levels are also denoted as stars.

Structural Modeling and Validation of Growth/Differentiation Factor 15 [NP_004855] Associated with Pregnancy Complication- Hyperemesis Gravidarum.

Background: Hyperemesis Gravidarum (HG) is acommon pregnancy complication that occurs in0.3–2% of pregnancies. Growth/Differentiation Factor(GDF) 15 serum levels are abnormally high in patientsassociated with HG. In silico analysis providesinformation about structure and function of GDF15.Aim and Objectives: The aim of this study was to enlistbiochemical and functional properties of GDF15protein and determine its three-dimensional structure,as GDF15 is known to be associated with risk of HG.Material and Methods: The PDB file of GDF15[NP_004855] was created by RaptorX structureprediction server. The UCLA-DOE server was used tovisual analysis of crystal structure of protein. Thevalidation for structure models was performed by usingPROCHECK. Model quality estimates were based onthe QMEAN and ProSA. Results: The model showedgood stereo-chemical property in terms of G-factorvalue -0.64, that indicates geometry of modelcorresponds to probability conformation with 95%residue in the favored region of Ramachandran plot,showing high accuracy of model prediction. The Zscore of -4.04 predicted by ProSA represents the goodquality of the model. The energy plot shows the localmodel quality by plotting knowledge-based energies asa function of amino acid sequence position.Conclusion: The generated model could be supportiveto understand the structure and functionalcharacteristics of Homo sapiens growth/differentiationfactor 15 [NP_004855]. As abnormal high serum levelsof GDF15 were observe in patients associated with HG.Therefore, the structure model of GDF15 [NP_004855]is useful to understand its role in development of HG. InSilico docking study could be explain the molecularassociation of GDF15 [NP_004855] with HG and newdrug designing, for that structure model is very useful.

Molecular docking studies of bioactive compounds from the leaves of Epiphyllum oxypetalum against Treponema pallidum, Zika virus and liver cirrhosis

The Epiphyllum oxypetalum is a unique plant that belongs to a cactaceae family. Traditionally, this plant mainly curessexually transmitted diseases, liver infection, and antiviral disease. The molecular docking analysis was done againstvirulent bacterial and viral enzymes. The protein responsible for bacterial and viral disease were studied and retrievedfrom Protein Data Bank. The bioactive compounds of E. oxypetalum were docked against Treponema pallidum,liver cirrhosis, and Zika virus (ZIKV). The result obtained with better binding interactions against T. pallidum wasMegastigmatrienone with −5.02Kcal/mol followed by liver cirrhosis was Megastigmatrienone with −4.58Kcal/moland against ZIKV was Testerone cypionate with −7.84Kcal/mol. Thus, the molecular docking interactions showsbetter potential of inhibition against virulent enzymes and the bioactive compounds of E. oxypetalum leave whichcould be used as a lead for treating the diseases, such as Syphilis, liver cirrhosis, and ZIKV.

Homology modeling and active site analysis of leptin receptor of homo sapiens involved in obesity.

The discovery of leptin has initiated a flurry of research into the molecular basis of weight control. In obese people levels of leptin found in the blood are normally very high and more than sufficient to suppress the appetite and increase the metabolism. This however does not happen and it is believed that obesity may be the result of a resistance to leptin. This suggests that the problem in these individuals may be related to a lack of binding of the leptin protein to its receptor. No known structure of leptin receptor is known. Therefore in present the present study we model the 3D structure of leptin receptor using MODELLER. This was done using the template GP130 of H. sapiens (PDB code: 1BQU). On the basic of results MODEL 6 was selected as the best model. The observed G-factors for the present model were -0.22 for dihedrals, -0.32 for covalent and overall -0.25. The MODEL 6 contains 88.7% of the residues in the most favored region, 11.3 % in the additional allowed and no single residue in generously allowed regions and disallowed region. The predicted model was further analyzed to locate the residues in the active sites those provide interactions with the ligand.

PDB-Metrics: a web tool for exploring the PDB contents

PDB-Metrics (http://sms.cbi.cnptia.embrapa.br/SMS/pdb_metrics/index.html) is a component of the Diamond STING suite of programs for the analysis of protein sequence, structure and function. It summarizes the characteristics of the collection of protein structure descriptions deposited in the Protein Data Bank (PDB) and provides a Web interface to search and browse the PDB, using a variety of alternative criteria. PDB-Metrics is a powerful tool for bioinformaticians to examine the data span in the PDB from several perspectives. Although other Web sites offer some similar resources to explore the PDB contents, PDB-Metrics is among those with the most complete set of such facilities, integrated into a single Web site. This program has been developed using SQLite, a C library that provides all the query facilities of a database management system

Effects of PDB on hyperglycemic animal models / 中国药理学通报

AIM To study the effects of PDB on blood glucose. METHODS 3 groups of health mice and 3 groups of model mice were administered with high, mean and low doses of PDB compatibility groups (combined with glibenclamide 0.66 mg?kg -1) respectively for 15 days. The blood goucose variation of health and model mice was observed. RESULTS A low dose of PDB compatibility group decreased obviously blood glucose in the health mice. Its mean value was(3.10?0.14), while control group's blood glucose was 4.46?0.12, P