Biomedical subjects

Lanfen Li

Publications and source records attributed to Lanfen Li.

10 recordsLinked to original sources

PubMed2006

Preparation, crystallization and preliminary X-ray analysis of protein YtlP from Bacillus subtilis.

Bacillus subtilis YtlP is a protein that is predicted to belong to the bacterial and archael 2'-5' RNA-ligase family. It contains 183 residues and two copies of the HXTX sequence motif conserved among proteins belonging to this family. In order to determine the structure of YtlP and to compare it with the paralogue YjcG and identified 2'-5' RNA ligases, the gene ytlP was amplified from B. subtilis genomic DNA and cloned into expression vector pET-21a. The soluble protein was produced in Escherichia coli, purified to homogeneity and crystals suitable for X-ray analysis were obtained. The crystal diffracted to 2.0 A and belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 34.16, b = 48.54, c = 105.75 A.

Amino Acid Sequence↗

PubMed2006

A large-scale, high-efficiency and low-cost platform for structural genomics studies.

A large-scale, high-efficiency and low-cost platform based on a Beckman Coulter Biomek FX and custom-made automation systems for structural genomics has been set up at Peking University, Beijing, People's Republic of China. This platform has the capacity to process up to 2000 genes per year for structural and functional analyses. Bacillus subtilis, a model organism for Gram-positive bacteria, and Streptococcus mutans, a major pathogen of dental caries, were selected as the main targets. To date, more than 470 B. subtilis and 1200 S. mutans proteins and hundreds of proteins from other sources, including human liver proteins, have been selected as targets for this platform. The selected genes are mainly related to important metabolism pathways and/or have potential relevance for drug design. To date, 40 independent structures have been determined; of these 11 are in the category of novel structures by the criterion of having less than 30% sequence identity to known structures. More than 13 structures were determined by SAD/MAD phasing. The macromolecular crystallography beamline at the Beijing Synchrotron Radiation Facility and modern phasing programs have been crucial components of the operation of the platform. The idea and practice of the genomic approach have been successfully adopted in a moderately funded structural biology program and it is believed this adaptation will greatly improve the production of protein structures. The goal is to be able to solve a protein structure of moderate difficulty at a cost about US 10,000 dollars.

Bacillus subtilis↗

PubMed2005

Protein preparation, crystallization and preliminary X-ray crystallographic analysis of Smu.1475c from caries pathogen Streptococcus mutans.

The gene smu.1475c encodes a putative protein of 211 residues in Streptococcus mutans, a primary pathogen for human dental caries. In this work, smu.1475c was cloned into pET28a and expressed in good amount from the E. coli strain BL21 (DE3). Smu.1475c protein was purified to homogeneity in a two-step procedure of Ni2+ chelating and size exclusion chromatography. Crystals were obtained by hanging-drop vapor-diffusion method and diffracted to 2.7 angstroms resolution. The crystal belongs to orthorhombic space group P2(1)2(1)2(1) with cell dimension of a = 68.3 angstroms, b = 105.9 angstroms, c = 136.2 angstroms. The asymmetric unit is expected to contain four molecules with solvent content of 49.4%.

Amino Acid Sequence↗

PubMed2005

Protein preparation, crystallization and preliminary X-ray analysis of imidazolonepropionase from Bacillus subtilis.

Imidazolonepropionase (EC 3.5.2.7) is the third enzyme of the histidine degradation pathway that has been conserved from bacteria to eukaryotes. The enzyme is the only one with unknown three-dimensional structure in this pathway. In this work, Bacillus subtilis imidazolonepropionase (HutI) was expressed in E. coli and purified to homogeneity. After thrombin digestion, high quality crystals were obtained by hanging-drop vapor diffusion method. The best crystal diffracted to 2.0 A and belonged to the space group P2(1) with unit-cell parameters a = 57.73 A, b = 106.34 A, c = 66.47 A, beta = 89.93 degrees .

Amidohydrolases↗

PubMed2005

Preparation, crystallization and preliminary X-ray analysis of YjcG protein from Bacillus subtilis.

Bacillus subtilis YjcG is a functionally uncharacterized protein with 171 residues that has no structural homologue in the Protein Data Bank. However, it shows sequence homology to bacterial and archaeal 2'-5' RNA ligases. In order to identify its exact function via structural studies, the yjcG gene was amplified from B. subtilis genomic DNA and cloned into the expression vector pET21-DEST. The protein was expressed in a soluble form in Escherichia coli and was purified to homogeneity. Crystals suitable for X-ray analysis were obtained that diffracted to 2.3 A and belonged to space group C2, with unit-cell parameters a = 99.66, b = 73.93, c = 61.77 A, beta = 113.56 degrees.

Amino Acid Sequence↗

PubMed2005

The crystal structure of human adenylate kinase 6: An adenylate kinase localized to the cell nucleus.

Adenylate kinases (AKs) play important roles in nucleotide metabolism in all organisms and in cellular energetics by means of phosphotransfer networks in eukaryotes. The crystal structure of a human AK named AK6 was determined by in-house sulfur single-wavelength anomalous dispersion phasing methods and refined to 2.0-A resolution with a free R factor of 21.8%. Sequence analyses revealed that human AK6 belongs to a distinct subfamily of AKs present in all eukaryotic organisms sequenced so far. Enzymatic assays show that human AK6 has properties similar with other AKs, particularly with AK5. Fluorescence microscopy showed that human AK6 is localized predominantly to the nucleus of HeLa cells. The identification of a nuclear-localized AK sheds light on nucleotide metabolism in the nucleus and the energetic communication between mitochondria and nucleus by means of phosphotransfer networks.

Active Transport, Cell Nucleus↗

PubMed2005

Protein preparation, crystallization and preliminary X-ray crystallographic studies of dihydroorotase from Bacillus subtilis.

B. subtilis dihydroorotase is an important enzyme in de novo pyrimidine biosynthesis pathway and encoded by pyrC gene in pyr operon. pyrC was amplified from B. subtilis genomic DNA and cloned into expression vector pET21-DEST. Dihydroorotase was expressed soluble form in E. coli and purified. The protein was crystallized and diffracted to 2.2 A. The crystal belongs to P2(1)2(1)2(1) space-group, with unit cell parameters a = 48.864 A, b = 84.99 A, c = 203.05 A. There are 2 molecules per asymmetry unit.

Amino Acid Sequence↗

PubMed2005

Protein expression, crystallization and preliminary X-ray crystallographic studies of YjbK from Bacillus subtilis.

B. subtilis YjbK is a protein with 190 residues of uncharacterized function, it has been annotated by Pfam database as a member of adenylate cyclase family (EC: 4.6.1.1). In order to identify its exact function via structural studies, yjbK gene was amplified from B. subtilis genomic DNA and cloned into expression vector pET21-DEST. The protein was expressed in a soluble form in E. coli and purified to homogeneity. YjbK was crystallized and diffracted to a resolution of 2.0 A in-house. The crystals belong to P1 space group, with unit cell parameters a = 32.38 A, b = 34.69 A, c = 46.02 A, alpha = 96.560 degrees, beta = 99.683 degrees, gamma = 111.333 degrees. There is one molecule per asymmetric unit.

Amino Acid Sequence↗

PubMed2004

Protein preparation, crystallization and preliminary X-ray analysis of human adrenal gland protein AD-004.

The adrenal gland protein AD-004 was identified in the human adrenal gland. Full-length AD-004 contains 172 amino acids, with a predicted molecular weight of about 20 kDa. In attempts to crystallize human AD-004, the gene was subcloned into a modified pET vector, pET21-DEST, with an N-terminal His(5) tag using the Gateway cloning system, followed by protein expression in Escherichia coli strain BL21(DE3). The protein was purified in two steps to near-homogeneity and was crystallized. The crystals belong to space group P6(1) or P6(5), with unit-cell parameters a = b = 99.56, c = 57.19 A. A complete 2.0 A data set has been collected at a rotating-anode X-ray source and structure determination is under way.

Adrenal Glands↗

PubMed2002

[Clinical study of severe complications during hysteroscopic surgeries].

OBJECTIVE: To investigate the clinical characteristics, treatment and prevention methods of severe complications during hysteroscopic procedures. METHODS: From January 1995 to January 2001, seventeen cases with uterine perforation, heavy bleeding and fluid overload respectively were encountered during hysteroscopic procedures. This analysis focuses on their diagnosis and clinical management as well as prevention methods. RESULTS: Three cases with uterine perforation and seven with incomplete perforation followed transcervical resection of myoma (TCRM), transcervical resection of adhesion, transcervical resection of septum and transcervical removal of foreign body respectively, which were diagnosed by both B ultrasonography and laparoscopy and treated laparoscopically. Four cases with heavy bleeding were encountered during TCRM. Foley catheter was inserted into uterine cavity to stop the bleeding successfully. Three cases with fluid overload were cured by diuretic agent and saline infusion. There were no serious consequence happened. CONCLUSIONS: It is a potential high risk factor of resulting in complications that performing complicated procedures inside uterine cavity during hysteroscopic operations. Pre-treatment with gonadotropin-releasing-a and guiding with B ultrasound/laparoscopy as well as controlling irrigation pressure are necessary for preventing above complications.

Adult↗