Biomedical subjects

Yi Ding

Publications and source records attributed to Yi Ding.

At least 109 records · Page 6Linked to original sources

PubMed2003

Design and structure-based study of new potential FKBP12 inhibitors.

Based on the structure of FKBP12 complexed with FK506 or rapamycin, with computer-aided design, two neurotrophic ligands, (3R)-4-(p-Toluenesulfonyl)-1,4-thiazane-3-carboxylic acid-L-Leucine ethyl ester and (3R)-4-(p-Toluenesulfonyl)-1,4-thiazane-3-carboxylic acid-L-phenylalanine benzyl ester, were designed and synthesized. Fluorescence experiments were used to detect the binding affinity between FKBP12 and these two ligands. Complex structures of FKBP12 with these two ligands were obtained by x-ray crystallography. In comparing FKBP12-rapamycin complex and FKBP12-FK506 complex as well as FKBP12-GPI-1046 solution structure with these new complexes, significant volume and surface area effects and obvious contact changes were detected which are expected to cause their different binding energies-showing these two novel ligands will become more effective neuron regeneration drugs than GPI-1046, which is currently undergoing phase II clinical trail as a neurotrophic drug. Analysis of volume and surface area effects also gives a new clue for structure-based drug design.

Binding Sites↗

PubMed2003

Design and analysis of post-fusion 6-helix bundle of heptad repeat regions from Newcastle disease virus F protein.

Fusion of paramyxovirus to the cell involves receptor binding of the HN glycoprotein and a number of conformational changes of F glycoprotein. The F protein is expressed as a homotrimer on the virus surface. In the present model, there are at least three conformations of F protein, i.e. native form, pre-hairpin intermediate and the post-fusion state. In the post-fusion state, the two highly conserved heptad repeat (HR) regions of F protein form a stable 6-helix coiled-coil bundle. However, no crystal structure is known for this state for the Newcastle disease virus, although the crystal structure of the F protein native form has been solved recently. Here we deployed an Escherichia coli in vitro expression system to engineer this 6-helix bundle by fusion of either the two HR regions (HR1, linker and HR2) or linking the 6-helix [3 x (HR1, linker and HR2)] together as a single chain. Subsequently, both of them form a stable 6-helix bundle in vitro judging by gel filtration and chemical cross-linking and the proteins show salient features of an alpha-helix structure. Crystals diffracting X-rays have been obtained from both protein preparations and the structure determination is under way. This method could be used for crystallization of the post-fusion state HR structures of other viruses.

Amino Acid Sequence↗

PubMed2003

The structural basis of Trp192 and the C-terminal region in trichosanthin for activity and conformational stability.

Trichosanthin (TCS) is a type I ribosome-inactivating protein (RIP) possessing N-glycosidase activity. TCS has various pharmacological properties, including immunomodulatory, anti-tumor and anti-HIV activities. Up to seven C-terminal residues of TCS (TCS-C7) can be deleted resulting in lower antigenicity with minimal effects on its activity. However, an additional problem is that the minimal effects on activity are higher than the reduction in antigenicity. In the present work, the crystal structure of TCS-C7 was determined. It shows the details of the C-terminal residues of TCS-C7, and in particular the hydrogen bonds between P35 and L240, S196 and L240, and W192 and L239, which play an important role in maintaining the structure of TCS-C7. Further analysis shows that the hydrogen bonds related to Leu240 are key in maintaining the relationship between N- and C-terminal domains. The major role of the C-terminal tail appears to stabilize the structure of TCS. The conformation between helix H7 at the N-terminal domain and the C-terminal tail at the C-terminal domain is also revealed. Two mutants, TCS-W192F and TCS-C7-W192F, were prepared and crystal structures were determined. These variants have greatly reduced ribosome-inactivating activities compared with TCS and TCS-C7, respectively, and TCS-W192F and TCS-C7-W192F have a similar stability in guanidine hydrochloride compared with TCS-C7. This suggests that Trp192 can affect the ribosome-inactivating activity of TCS.

Crystallography, X-Ray↗

PubMed2003

Site-directed mutagenesis and preliminary x-ray crystallographic studies of the tabtoxin resistance protein.

Tabtoxin resistance protein (TTR) is an enzyme that catalyzes the acetylation of tabtoxin rendering tabtoxin-producing pathogens tolerant to their own phytotoxins. According to the structure based detoxification mechanism of TTR, three site-directed mutants Y141F, D130N and Y141F-D130N were constructed and overexpressed in E. coli. The products were then purified and their properties were analyzed by CD and DLS. Crystallization trials of two mutants Y141F andY141F-D130N were preformed.

Acetylation↗

PubMed2003

Methylation and mutation analysis of p16 gene in gastric cancer.

AIM: To study methylation, frequencies of homozygous deletion and mutation of p16 gene in gastric carcinoma. METHODS: The methylation pattern in exon 1 and exon 2 of p16 gene was studied with polymerase chain reaction (PCR), using methylation sensitive restriction endonuclease HpaII and methylation insensitive restriction endonuclease MspI. PCR technique was used to detect homozygous deletions of exon 1 and exon 2 of p16 gene and single strand conformation polymorphism (SSCP) technique was used to detect the mutation of the gene. RESULTS: Hypermethylation changes in exon 1 and exon 2 of p16 gene were observed in 25 % and 45 % of 20 gastric cancer tissues, respectively, while no methylation abnormality was found in normal tissues. The homozygous deletion frequency of exon 1 and exon 2 of p16 gene in 20 gastric cancer tissues was 20 % and 10 %, respectively. No mutation was found in exon 1 of p16 gene, while abnormal single strands were found in 2 (10 %) cases in exon 2 as detected by SSCP. CONCLUSION: The results suggest that hypermethylation and abnormality of p16 gene may play a key role in the progress of gastric cancer. Hypermethylation of exon 2 of p16 gene may have effects on the carcinogenesis of gastric mucosa and may be a later event.

DNA Methylation↗

PubMed2003

Studies on microsatellite instability in p16 gene and expression of hMSH2 mRNA in human gastric cancer tissues.

AIM: To detect the loss of heterozygosity (LOH) frequency of microsatellite sites D9s171, D9s1604 of p16 gene and expression of hMSH2 mRNA in various differentiated types of gastric cancer, adjacent cancer tissues and normal gastric mucosa. METHODS: LOH was detected by polymerase chain reaction (PCR)-denaturing polyacrylamide gel electrophoresis-silver staining. The expression of hMSH2 mRNA was examined with in situ hybridization. RESULTS: The frequency rate of LOH was significantly higher in gastric cancers than that in adjacent cancer tissues (P=0.032). No significant difference was noted among various differentiated types and various clinical stages of gastric cancers. The significantly reduced expression of hMSH2 mRNA positive signal cells exhibited in gastric cancers, in comparison with that in the adjacent cancer tissues and normal gastric mucosa, respectively (P=0.001). No significant difference was noted among various clinical stages of gastric cancers (P>0.05). The difference of positive signal cells in poorly differentiated cancers and those in well and moderately differentiated cancers were significant (P<0.001). CONCLUSION: The frequencies of LOH in two microsatellite sites, D9s171 and D9s1604, in p16 genome were associated with development of gastric cancer and no significant correlation was demonstrated between the LOH frequency and the cell differentiated types of tumor cells or clinical stages. There was a positive relationship between the expression of hMSH2 mRNA and the differentiated types of gastric cancer.

DNA-Binding Proteins↗

PubMed2003

[In vitro and in vivo functional evaluation of anti-human bladder tumor human-mouse chimeric antibody ch-BDI].

OBJECTIVE: To evaluate the in vitro and in vivo function of anti-human bladder tumor human-mouse chimeric antibody ch-BDI and its future clinical application. METHODS: With ch-BDI in high-expression cell-line medium, affinity chromatography was used for the purification. Labeled with (99m)Tc through reduction method, its immunoreactive fraction and association constant were measured. The constant was injected into nude mice with xenografted human bladder tumor. The biodistribution of the labeled ch-BDI was studied with radioimmunoimaging. RESULTS: ch-BDI showed desirable immunoreactive fraction (76%) and association constant (3.56 x 10(9) M(-1)) in vitro and a terrific specific targeting effect in vivo. CONCLUSION: ch-BDI has fairly good function against human bladder tumor both in vitro and in vivo, and is promising in clinical use.

Animals↗

PubMed2003

[Surgical management of metastatic disease of long bone].

OBJECTIVE: To improve the life quality of cancer patients with metastasis to long bone and to select suitable surgical treatment. METHODS: Fifty two patients with metastasis 27 men and 25 women, were treated from 1990 to 1999. Their average age was 56.8 years (33 - 74). In 16 patients with multiple lesions, underwent surgery at bone shaft (29 patients) and bone epiphysis (26). Thirty patients were treated for pathologic fracture and the rest for impending fracture. Operations included limb-salvage (51 patients) and amputation (4) Limb salvage consisted of intralesional curettage (3 patients), intramedullary nailing reconstruction (29), endoprosthesis (18), and temporary spacer (1). 21 patients accepted postoperative chemotherapy or radiotherapy. RESULTS: Follow-up of 52 patients for a mean of 28.2 months (2 - 122 months) showed pain relief (41 patients), (75%) and full or part weight-bearing stability (36) 69%. Local tumor recurrence occurred in 11 patients. CONCLUSIONS: Surgical treatment can effectively improve the life quality of patients with metastasis to long bone. The metastatic lesions should be resected with wide or radical margin for the patients with kidney, breast, prostate and thyroid cancer.

Adult↗

PubMed2003

[The effect of pulsed Nd:YAG laser used as an adjunct to subgingival scaling and root planning].

OBJECTIVE: This study was to observe and compare the microbiological effects of laser therapy combined with ultrasonic subgingival scaling and root planning (SRP) versus SRP alone. METHODS: 26 contra lateral teeth were randomly assigned to the test group (laser + SRP) or the control group (SRP alone). Subgingival microbial samples were collected, cultured and analyzed at baseline, then repeated immediately after laser treatment at week 1, week 2 and week 4. RESULTS: Although both groups had significant increase in G+/G- ratio (P < 0.01), the changes of G+ and G- were more obvious in the test group till week 1(P < 0.05). The total CFU of test group diminished significantly just after laser irradiation (P < 0.05). That revealed the laser therapy followed by SRP appeared to have a stronger effect on converting the subgingival micro-ecosystem to healthy status. CONCLUSION: Laser appeared to have a stronger bactericidal action in vivo. especially on the dark-pigmented G- rods associated with periodontal disease.

Bacteria↗

PubMed2003

[Parosteal osteosarcoma: a clinical study of 48 cases].

OBJECTIVE: To investigate the way of diagnosis and therapy of parosteal osteosarcoma. METHODS: A retrospective review was conducted of 48 patients treated at our department between June 1964 and December 2001. The average age of patients in this study was 29.2 years (13 - 47 years). Thirty-two of the patients were female; sixteen were male. The single most common site is the posterior aspect of the distal femur (in 36 patients), followed by the femur shaft (in 6 patients), the proximal tibia (in 2 patients), etc. Nine patients had been operated on before referral to our department. RESULTS: The average follow-up period from the first operation was 5.2 (0.25 - 24) years. In 36 of the 39 patients in whom a limb-salvage procedure was performed, a segment of the tumor-bearing bone was excised along with the tumor, whereas in 3 patients only the subadjacent cortex was excised with the tumor. In the limb-sparing group, the reconstruction was achieved by means of attenuated tumor bone or allograft in 23 cases, by endoprosthetic replacement in 9 cases, and by allograft replacement in 4 cases. The local resections were wide in 35 cases, and marginal in 13 cases. After marginal surgery, local recurrence occurred in 5/13 patients, whereas it occurred in 3/35 patients treated with wide resection. Pulmonary metastases developed in 6 patients, four patients died, and 2 patients are alive with disease. There were 4 cases of fractures of bone grafts. Four patients developed an infection. Long-term survival rate is 85.8%. For tumors that invaded the medullary canal there was no statistical association with local recurrence or metastasis. There is statistical significance between surgical margin and local recurrence. CONCLUSIONS: Wide surgical excision alone is adequate treatment for patients with conventional parosteal osteosarcoma. A tumor-free margin remains the critical factor determining overall prognosis. When a marginal excision was knowingly done to preserve a major neurovascular bundle, the risk of recurrence was less than when it was done to shell-out a presumptively benign lesion. Repeated recurrence probably increases the risk of dedifferentiation and thereby worsens the prognosis. Recurrent lesions with multiple soft-tissue satellite nodules or involvement of the neurovascular structures may however require amputation to provide sufficient local control when a wide margin cannot be achieved. An individualized resection will be performed in the future probably under the help of the advanced technique of image to distinguish the reactive zone from the normal tissue precisely.

Adolescent↗

PubMed2003

[Study on chemical constituents in rhizome of Smilax perfoliate].

OBJECTIVE: To investigate the components of Smilax perfoliate. METHOD: The chemical components were isolated by solvent extraction and column chromatography. The chemical structures were identified on the base of physical and spectral data. RESULT: Nine compounds were isolated and identified as palmitic acid(I), beta-sitosterol(II), delta 7-5 alpha-cholesten-3-beta-ol(III), naringenin(IV), succinic acid(V), apigenin(VI), resveratrol(VII), daucosterol(VIII) and juncusyl ester B(IX). CONCLUSION: Compound(I), (III), (IV), (VI) and (IX) were obtained from the genus Smilax for the first time.

Apigenin↗

PubMed2002

Structure of the N-terminal domain of human FKBP52.

FKBP52 is a member of the FK506-binding protein family (FKBPs). The N-terminal domain of FKBP52 (FKBP52-N; residues 1-140) is responsible for peptidyl-prolyl isomerase activity and binding of FK506. Here, the crystal structure of FKBP52-N has been determined by molecular replacement to 2.4 A. FKBP52-N is defined by a six-stranded antiparallel beta-sheet wrapping with a right-handed twist around a short alpha-helix, an architecture similar to that of FKBP12. FKBP52-N is able to bind FK506 in a similar way to FKBP12. The variability in two loop regions (residues 70-76 and 108-127) is the principal reason for the specificity differences between FKBP52-N and FKBP12. The Pro120 change corresponding to Gly89 in FKBP12 limits the conformational adaptation between the loop (residues 108-127) and FK506 and decreases the FK506 affinity, while the Lys121 substitution corresponding to Ile90 of FKBP12 destroys a key interaction between FKBP52-N and calcineurin. It can be inferred from the locations of strictly conserved amino acids in the polypeptide chain that the maintenance of the overall conformation of the PPIase domains of FKBPs is essential for the PPIase activity. The N-terminal region and beta-sheets of FKBP52-N forms a hydrophobic patch which may be responsible for the binding of target proteins such as dynein or PAHX.

Amino Acid Sequence↗

PubMed2002

Crystallization and preliminary X-ray diffraction analysis of FKBP52 N-terminal domain.

FKBP52 is a FK506-binding protein which was first discovered in the heterocomplex composed of HSP90 and inactive steroid receptor. Here, the N-terminal domain (residues 1-140) of FKBP52 has been overexpressed, purified and crystallized using the hanging-drop vapour-diffusion technique. Crystals with a 2.4 A resolution limit were obtained using ammonium sulfate as precipitant at pH 8.5. The crystals belong to space group P2(1), with unit-cell parameters a = 27.8, b = 58.4, c = 70.9 A, beta = 98.3 degrees. Assuming two molecules per asymmetric unit, the solvent content is calculated to be 40%.

Crystallization↗

PubMed2002

Crystallographic study of a naturally occurring trans-splicing intein from Synechocystis sp. PCC 6803.

A naturally occurring split intein from the dnaE gene of Synechocystis sp. PCC6803 (Ssp DnaE intein) has been purified and crystallized using PEG 8K as precipitant. The crystal belongs to space group P3(1)21 or P3(2)21, with unit-cell parameters a = b = 58.5, c = 70.2 A. It has one molecule per asymmetric unit and diffracts to beyond 2.9 A under cryoconditions (110 K) using a Cu rotating-anode X-ray generator in-house.

Alternative Splicing↗

PubMed2002

Purification and initial crystallization studies of a DnaB intein from Synechocystis sp. PCC 6803.

A 154-residue mini-intein from the dnaB gene of Synechocystis sp. PCC 6803 (Ssp DnaB intein) has been purified and crystallized using PEG 4000 as a precipitant. The crystal belongs to space group P3(1)21 or P3(2)21, with unit-cell parameters a = b = 58.2, c = 70.3 A. It has one molecule per asymmetric unit and diffracts to beyond 2.0 A under cryoconditions (100 K) using a rotating copper anode X-ray generator.

Bacterial Proteins↗

PubMed2002

Crystallization and preliminary crystallographic studies on the chromo shadow domain (CSD) of mouse heterochromatin protein M31.

Members of the heterochromatin protein 1 (HP1) class of non-histone chromosomal proteins are components of heterochromatin and are involved in the epigenetic regulation of the genome. HP1 proteins are modular and consist of two sequence-related domains called the chromodomain (CD) and the chromo shadow domain (CSD). In order to investigate the role of the murine HP1-like protein M31 in heterochromatin formation and gene silencing, recombinant CSD was overexpressed in Escherichia coli and crystallized using the hanging-drop vapour-diffusion method with PEG 4000 as precipitant. Diffraction data to 2.9 A were collected from a native crystal belonging to space group C222(1), with unit-cell parameters a = 60.0, b = 95.6, c = 91.7 A, alpha = beta = gamma = 90 degrees.

Animals↗

PubMed2002

Crystallization and preliminary crystallographic analysis of acylamino-acid releasing enzyme from the hyperthermophilic archaeon Aeropyrum pernix.

Crystals of acylamino-acid releasing enzyme from the hyperthermophilic archaeon Aeropyrum pernix strain K1 have been grown at 291 K using ammonium phosphate as a precipitant. The diffraction pattern of the crystal extends to 2.4 A resolution at 100 K using Cu Kalpha radiation. The crystal belongs to space group P1, with unit-cell parameters a = 107.5, b = 109.9, c = 119.4 A, alpha = 108.1, beta = 109.8, gamma = 91.9 degrees. The presence of eight molecules per asymmetric unit gives a crystal volume per protein mass (V(M)) of 2.4 A(3) Da(-1) and a solvent content of 48% by volume. A full set of X-ray diffraction data was collected to 2.9 A from the native crystal.

Archaeal Proteins↗

PubMed2002

Purification, crystallization and preliminary X-ray diffraction studies of a Ca2+-binding protein, human S100P.

S100P, a Ca(2+)-binding protein, is a member of the S100 family. Its presence is associated with the development of prostate cancer, but its cellular function is not known. Recombinant human S100P has been expressed and purified in bacterial cells and crystals of human S100P in the calcium-bound state have been grown using the vapour-diffusion technique with PEG 4000 as precipitant. Diffraction data have been obtained to a resolution of 2.0 A from a single frozen S100P crystal which belongs to the space group P4(1)2(1)2, with unit-cell parameters a = b = 60.8, c = 47.6 A.

Calcium-Binding Proteins↗