Xiaofeng Ji

Targeting cellular apoptotic pathway with peptides from marine organisms

Apoptosis is a critical defense mechanism against the formation and progression of cancer and exhibits distinct morphological and biochemical traits. Targeting apoptotic pathways becomes an intriguing strategy for the development of chemotherapeutic agents. Peptides from marine organisms have become important sources in the discovery of antitumor drugs, especially when modern technology makes it more and more feasible to collect organisms from seas. This primer summarizes several marine peptides, based on their effects on apoptotic signaling pathways, although most of these peptides have not yet been studied in depth for their mechanisms of action. Novel peptides that induce an apoptosis signal pathway are presented in association with their pharmacological properties.

Homology Modeling and Molecular Dynamics Simulation Studies of a Marine Alkaline Protease

A cold-adapted marine alkaline protease (MP, accession no. ACY25898) was produced by a marine bacterium strain, which was isolated from Yellow Sea sediment in China. Many previous researches showed that this protease had potential application as a detergent additive. It was therefore crucial to determine the tertiary structure of MP. In this study, a homology model of MP was constructed using the multiple templates alignment method. The tools PROCHECK, ERRAT, and Verify_3D were used to check the effectiveness of the model. The result showed that 94% of residues were found in the most favored allowed regions, 6% were in the additional allowed region, and 96.50% of the residues had average 3D-1D scores of no less than 0.2. Meanwhile, the overall quality factor (ERRAT) of our model was 80.657. In this study, we also focused on elucidating the molecular mechanism of the two “flap” motions. Based on the optimized model, molecular-dynamics simulations in explicit solvent environments were carried out by using the AMBER11 package, for the entire protein, in order to characterize the dynamical behavior of the two flaps. Our results showed an open motion of the two flaps in the water solvent. This research may facilitate inhibitor virtual screening for MP and may also lay the foundationknowledge of mechanism of the inhibitors.

Cloning and Characterization of a Psychrophilic Catalase Gene from an Antarctic Bacterium

The gene of psychrophilic catalase BNC from Antarctic Bacillus sp. N2a was cloned by degenerate PCR and inverse PCR. BNC gene revealed a 1,461 bp open reading frame for a protein with 486 amino acids. The phylogenetic tree based on the amino acid sequences of BNC and representative psychrophilic microbial catalases manifested that BNC belonged to the Group III of the monofunctional catalase. The active-site residues of the structure-determined catalase were highly conserved in BNC. Comparison of the amino acid composition of BNC with its mesophilic homologue from Bacillus subtilis TE124 showed that BNC had properties of a cold-active enzyme.

Identification of latent periodicity in domains of alkaline proteases.

Internal repeats in protein sequences have wide-ranging implications for the structure and function of proteins. A keen analysis of the repeats in protein sequences may help us to better understand the structural organization of proteins and their evolutionary relations. In this paper, a mathematical method for searching for latent periodicity in protein sequences is developed. Using this method, we identified simple sequence repeats in the alkaline proteases and found that the sequences could show the same periodicity as their tertiary structures. This result may help us to reduce difficulties in the study of the relationship between sequences and their structures.

Identification of sequence repetitions in immunoglobulin folds

A lot of evidence suggests that many proteins with the symmetric structures have evolved by internal duplication and fusion. Meanwhile many internal sequence repeats correspond to functional and structural units. These proteins, which have internal structural symmetry, this means that their sequences should be made up of identical repeats. However, many of these repeat signals can only be seen at the structural level yet. We have developed a de novo algorithm, modified recurrence correlation analysis, to detect the symmetries in the primary sequences of immunoglobulin folds (Ig folds), which adopt highly symmetrical tertiary structures while their sequences appear nearly random. Using this method, we show that the internal repetitions of the immunoglobulin folds could be identified directly at the sequence level. These results may give us some help to study the hypotheses about the origin of Ig folds by duplication of simpler fragments and it may also give us some helps to understand the relationship between the sequences and their tertiary structures.

Expression, purification, crystallization and diffraction analysis of a selenomethionyl lipase Lip8 from Yarrowia lipolytica

ABSTRACT Yarrowia lipolytica is a nonconventional model micro-organism with multiple biotechnological applications. It is also considered to be an excellent producer for lipase. Genome survey shows that Y. lipolytica possesses various paralogs of genes coding for extracellular, cell-bound, and intracellular lipolytic enzymes. However, little structural information on these isoenzymes is available. With the aim to facilitate crystal structure solution of Lip8, one of the most valuable lipases from Y. lipolytica, a less conventional protein expression technique—selenomethionyl protein expression was used to produce recombinant selenomethionine (SeMet)-Lip8 in Escherichia coli. Finally, three Met residues of Lip8 were all substituted with SeMet. A total of 72 mg of SeMet-Lip8 was obtained from a liter of the SeMet medium. Using sodium acetate as a precipitant and ammonium sulfate as an additive, crystals of the SeMet-Lip8 with 1.9 Å were successfully cultured through hanging-drop vapor diffusion method. The estimated crystal dimensions were 0.11 × 0.11 × 0.14 mm2. The crystal belonged to the space group I4 with unit cell parameters a = b = 128.87 Å, c = 171.77 Å, α = β = γ = 90°. It is the second member of lipase crystal family from Y. lipolytica. This work will provide a platform for further studying lipases from a structural insight.