Biomedical subjects

Haitao Yang

Publications and source records attributed to Haitao Yang.

16 recordsLinked to original sources

PubMed2026

Genomic distribution characteristics and interspecific differences of microsatellite landscapes in Felidae.

BACKGROUND: Microsatellites within genomes play crucial roles in regulating gene expression, DNA replication, and chromosomal structure and function. Analyzing the composition and distribution patterns of microsatellites in closely related species not only reveals their evolutionary dynamics and adaptive mechanisms but also provides essential technical support for applications in genetic breeding, species conservation, and disease research. As one of the world's most captivating animal groups, the landscape patterns of microsatellites across feline genomes remain to be systematically characterized. RESULTS: This study utilized high-quality genomic data to conduct a systematic comparative analysis of microsatellite landscape distribution patterns across the genomes of 13 felid species. The findings revealed that microsatellite abundance and distribution exhibit species-specific characteristics, with a non-random genomic distribution and a negative correlation between microsatellite abundance and repeat length. The predominant distribution pattern followed the sequence: single > double > quadruple > triple > quintuple > sextuple nucleotide repeats. Microsatellite abundance peaked in intergenic regions, whereas trinucleotide repeats were more prevalent within exons. Coding regions showed a marked preference for trinucleotide and hexanucleotide repeats. Enrichment analysis of GO and KEGG pathways indicated that coding sequences containing microsatellites were primarily involved in transcription and translation processes. CONCLUSIONS: Our study elucidates the distribution patterns and characteristics of microsatellites across diverse feline species, providing significant insights into their evolutionary mechanisms and functional roles. Furthermore, these findings establish a valuable reference and foundational dataset for the future development of high-quality, species-specific microsatellite markers in felids.

Animals↗

PubMed2006

Production of authentic SARS-CoV M(pro) with enhanced activity: application as a novel tag-cleavage endopeptidase for protein overproduction.

The viral proteases have proven to be the most selective and useful for removing the fusion tags in fusion protein expression systems. As a key enzyme in the viral life-cycle, the main protease (M(pro)) is most attractive for drug design targeting the SARS coronavirus (SARS-CoV), the etiological agent responsible for the outbreak of severe acute respiratory syndrome (SARS) in 2003. In this study, SARS-CoV M(pro) was used to specifically remove the GST tag in a new fusion protein expression system. We report a new method to produce wild-type (WT) SARS-CoV M(pro) with authentic N and C termini, and compare the activity of WT protease with those of three different types of SARS-CoV M(pro) with additional residues at the N or C terminus. Our results show that additional residues at the N terminus, but not at the C terminus, of M(pro) are detrimental to enzyme activity. To explain this, the crystal structures of WT SARS-CoV M(pro) and its complex with a Michael acceptor inhibitor were determined to 1.6 Angstroms and 1.95 Angstroms resolution respectively. These crystal structures reveal that the first residue of this protease is important for sustaining the substrate-binding pocket and inhibitor binding. This study suggests that SARS-CoV M(pro) could serve as a new tag-cleavage endopeptidase for protein overproduction, and the WT SARS-CoV M(pro) is more appropriate for mechanistic characterization and inhibitor design.

Calbindins↗

PubMed2006

Expression, crystallization and preliminary X-ray studies of the immunoglobulin-like domain 3 of human palladin.

Palladin is a member of the recently discovered palladin/myotilin/myopalladin family, the members of which associate with alpha-actinin. Palladin may play important roles in actin stress-fibre formation, cell adhesion and migration. The immunoglobulin-like domain 3 of human palladin has been overexpressed in Escherichia coli and crystallized suitable for X-ray crystallographic study. Crystals have been obtained using the vapour-diffusion method and belong to space group P2(1). X-ray diffraction data were collected in-house to 1.8 A resolution from a single crystal. The unit-cell parameters are a = 40.9, b = 33.3, c = 34.8 A, beta = 90.3 degrees . One molecule was predicted to be present in the asymmetric unit.

Cloning, Molecular↗

PubMed2006

Experimental study of multi-slice spiral CT perfusion imaging in VX2 soft-tissue tumor of rabbits.

An experimental animal model of malignant soft-tissue tumor was established to investigate the applied value of multi-slice spiral CT perfusion imaging preliminarily. Ten New Zealand white rabbits which were implanted with VX2 tumor in either proximal thigh were subjected to CT plain scan and perfusion scan two weeks later respectively, then the original perfusion images were transmitted to AW4.0 Workstation. The functional maps and perfusion parameters including blood flow (BF), blood volume (BV), mean transit time (MTT) and permeability surface (PS) were computed and analyzed. All the values of BF, BV and PS in VX2 soft-tissue tumors were obviously higher while the MTT-values were lower than those in the normal muscular tissues significantly. It was suggested that multi-slice spiral CT perfusion imaging is an accurate, convenient and relatively safe functional imaging technique, and can give a quantitative assessment to angiogenesis and blood perfusion of soft-tissue tumors.

Animals↗

PubMed2006

High prevalence of sexually transmitted diseases among men who have sex with men in Jiangsu Province, China.

OBJECTIVE: : The objective of this study was to investigate the prevalence of sexually transmitted diseases (STDs), including HIV infection, and sexual risk behaviors among men who have sex with men (MSM) in Jiangsu Province, China. DESIGN: : The authors conducted a cross-sectional study. METHODS: : From February to July 2003, men who attended 10 participating gay bars in five cities in Jiangsu Province were asked to complete a self-administered questionnaire, including measures of alcohol use and sexual risk behaviors. Blood samples and urethral swabs were taken to examine the presence of STDs, including HIV infection. RESULTS: : A total of 144 men were recruited in the study. Forty-six percent of men reported unprotected anal intercourse with their male sexual partners in the past 3 months. No one was found to be HIV-infected, but the prevalence of STDs was high: gonorrhea 2.7%, chlamydial infection 8.0%, nonchlamydial nongonococcal urethritis 27.7%, active syphilis 6.9%, hepatitis B virus infection 9.1%, herpes simplex virus-2 infection 7.8%, and genital warts 13.2%. CONCLUSIONS: : Given that HIV prevalence among MSM in some other parts of China has been as high as 3%, STDs facilitate the transmission of HIV, and high prevalence of STDs and sexual risk behaviors among MSM exist in Jiangsu Province, the potential for the future spread of HIV is of concern, and it is urgent to provide MSMs with STD healthcare services and HIV/AIDS/STD prevention education and intervention.

Adolescent↗

PubMed2006

Dodecamer structure of severe acute respiratory syndrome coronavirus nonstructural protein nsp10.

The severe acute respiratory syndrome coronavirus (SARS-CoV) nonstructural proteins nsp1 to nsp16 have been implicated by genetic analysis in the assembly of a functional replication/transcription complex. We report the crystal structure of nsp10 from SARS-CoV at 2.1-A resolution. The nsp10 structure has a novel fold, and 12 identical subunits assemble to form a unique spherical dodecameric architecture. Two zinc fingers have been identified from the nsp10 monomer structure with the sequence motifs C-(X)2-C-(X)5-H-(X)6-C and C-(X)2-C-(X)7-C-(X)-C. The nsp10 crystal structure is the first of a new class of zinc finger protein three-dimensional structures to be revealed experimentally. The zinc finger sequence motifs are conserved among all three coronavirus antigenic groups, implicating an essential function for nsp10 in all coronaviruses. Based on the structure, we propose that nsp10 is a transcription factor for coronavirus replication/transcription.

Amino Acid Sequence↗

PubMed2006

Drug design targeting the main protease, the Achilles' heel of coronaviruses.

Coronaviruses (CoVs), a genus containing about 26 known species to date, cause highly prevalent diseases and are often severe or fatal in humans and animals. In 2003, a previously unknown coronavirus was identified to be the etiological agent of a global outbreak of a form of life-threatening pneumonia called severe acute respiratory syndrome (SARS). No efficacious therapy is currently available, and vaccines and drugs are under development to prevent SARS-CoV infection in many countries. The CoV main protease (M(pro)), which plays a pivotal role in viral gene expression and replication through a highly complex cascade involving the proteolytic processing of replicase polyproteins, is an attractive target for drug design. This review summarizes the recent advances in biological and structural studies, together with development of inhibitors targeting CoV M(pro)s. It is expected that inhibitors targeting CoV M(pro)s could be developed into wide-spectrum antiviral drugs against existing and possible future emerging CoV-associated diseases.

Amino Acid Sequence↗

PubMed2005

Structural insights into SARS coronavirus proteins.

The SARS coronavirus was identified as the pathogen of a global outbreak of SARS (severe acute respiratory syndrome) in 2003. Its large RNA genome encodes four structural proteins, sixteen non-structural proteins and eight accessory proteins. The availability of structures of SARS coronavirus macromolecules has enabled the elucidation of their important functions, such as mediating the fusion of viral and host cellular membranes, and in replication and transcription. In particular, the spike protein fusion core and the main protease have been the most extensively studied, with the aim of designing anti-SARS therapeutics. Attention is now being focused on replicase proteins, which should enhance our understanding of the replication and transcription machinery. The structures and functions of most SARS proteins remain unknown, and further structural studies will be important for revealing their functions and for designing potential anti-SARS therapeutics.

Membrane Proteins↗

PubMed2005

Design of wide-spectrum inhibitors targeting coronavirus main proteases.

The genus Coronavirus contains about 25 species of coronaviruses (CoVs), which are important pathogens causing highly prevalent diseases and often severe or fatal in humans and animals. No licensed specific drugs are available to prevent their infection. Different host receptors for cellular entry, poorly conserved structural proteins (antigens), and the high mutation and recombination rates of CoVs pose a significant problem in the development of wide-spectrum anti-CoV drugs and vaccines. CoV main proteases (M(pro)s), which are key enzymes in viral gene expression and replication, were revealed to share a highly conservative substrate-recognition pocket by comparison of four crystal structures and a homology model representing all three genetic clusters of the genus Coronavirus. This conclusion was further supported by enzyme activity assays. Mechanism-based irreversible inhibitors were designed, based on this conserved structural region, and a uniform inhibition mechanism was elucidated from the structures of Mpro-inhibitor complexes from severe acute respiratory syndrome-CoV and porcine transmissible gastroenteritis virus. A structure-assisted optimization program has yielded compounds with fast in vitro inactivation of multiple CoV M(pro)s, potent antiviral activity, and extremely low cellular toxicity in cell-based assays. Further modification could rapidly lead to the discovery of a single agent with clinical potential against existing and possible future emerging CoV-related diseases.

Animals↗

PubMed2004

Crystallization and preliminary crystallographic analysis of a native chitinase from the fungal pathogen Aspergillus fumigatus YJ-407.

Chitinase hydrolyzes chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine (NAG), and plays a variety of roles in the biological world. In addition to endo- and exo-hydrolytic activities, transglycosyl activity has also been observed in the extracellular chitinase (afCHI) from the airborne saprophytic fungi Aspergillus fumigatus YJ-407. Crystals of this native chitinase have been grown at 291 K using PEG 3350 as a precipitant. The diffraction data from the crystal extend to 1.7 A resolution at BSRF, China. The crystal belongs to space group P2(1)2(1)2(1), with unit-cell parameters a = 95.7, b = 100.5, c = 134.3 A. The presence of two molecules per asymmetric unit gives a crystal volume per protein mass (V(M)) of 3.6 A(3) Da(-1) and a solvent content of 65% by volume. A full set of X-ray diffraction data was collected to 2.1 A resolution.

Aspergillus fumigatus↗

PubMed2004

Crystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1.

Acylpeptide hydrolases (APH; also known as acylamino acid releasing enzyme) catalyze the removal of an N-acylated amino acid from blocked peptides. The crystal structure of an APH from the thermophilic archaeon Aeropyrum pernix K1 to 2.1 A resolution confirms it to be a member of the prolyl oligopeptidase family of serine proteases. The structure of apAPH is a symmetric homodimer with each subunit comprised of two domains. The N-terminal domain is a regular seven-bladed beta-propeller, while the C-terminal domain has a canonical alpha/beta hydrolase fold and includes the active site and a conserved Ser445-Asp524-His556 catalytic triad. The complex structure of apAPH with an organophosphorus substrate, p-nitrophenyl phosphate, has also been determined. The complex structure unambiguously maps out the substrate binding pocket and provides a basis for substrate recognition by apAPH. A conserved mechanism for protein degradation from archaea to mammals is suggested by the structural features of apAPH.

Aeropyrum↗

PubMed2003

The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor.

A newly identified severe acute respiratory syndrome coronavirus (SARS-CoV), is the etiological agent responsible for the outbreak of SARS. The SARS-CoV main protease, which is a 33.8-kDa protease (also called the 3C-like protease), plays a pivotal role in mediating viral replication and transcription functions through extensive proteolytic processing of two replicase polyproteins, pp1a (486 kDa) and pp1ab (790 kDa). Here, we report the crystal structures of the SARS-CoV main protease at different pH values and in complex with a specific inhibitor. The protease structure has a fold that can be described as an augmented serine-protease, but with a Cys-His at the active site. This series of crystal structures, which is the first, to our knowledge, of any protein from the SARS virus, reveal substantial pH-dependent conformational changes, and an unexpected mode of inhibitor binding, providing a structural basis for rational drug design.

Amino Acid Chloromethyl Ketones↗

PubMed2003

Determination of Simvastatin in human plasma by liquid chromatography-mass spectrometry.

A simple, sensitive and selective liquid chromatography coupled with electrospray ionization mass spectrometry (LC/ESI/MS) method for the determination of simvastatin (I) has been developed. After extraction by ethyl acetate, using lovastatin (II) as internal standard, solutes are separated on a C(18) column with a mobile phase consisting of methanol-water (9:1). Detection is performed on an atmospheric pressure ionization single quadruple mass spectrometer equipped with an ESI interface and operates in positive ionization mode. Simvastatin quantification was realized by computing peak area ratio (I/II) of the extracts analyzed in SIM mode (m/z: 441 and m/z: 427 for I and II, respectively) and comparing them with calibration curve (r=0.9997). Accuracy and precision for the assay were determined by calculating the intra-batch and inter-batch variation at three concentrations 0.1, 5.0, 10.0 ng/ml; the intra batch relative standard deviation (RSD) was less than 10% and ranged from 1.8 to 8.5%, respectively; the inter-batch RSD was less than 20% and ranged from 4.1 to 16.5%. The limit of detection was 0.05 ng/ml.

Adult↗

PubMed2003

Crystal structure of a DNA binding protein from the hyperthermophilic euryarchaeon Methanococcus jannaschii.

The Sac10b family consists of a group of highly conserved DNA binding proteins from both the euryarchaeotal and the crenarchaeotal branches of Archaea. The proteins have been suggested to play an architectural role in the chromosomal organization in these organisms. Previous studies have mainly focused on the Sac10b proteins from the crenarchaeota. Here, we report the 2.0 A resolution crystal structure of Mja10b from the euryarchaeon Methanococcus jannaschii. The model of Mja10b has been refined to an R-factor of 20.9%. The crystal structure of an Mja10b monomer reveals an alpha/beta structure of four beta-strands and two alpha-helices, and Mja10b assembles into a dimer via an extensive hydrophobic interface. Mja10b has a similar topology to that of its crenarchaeota counterpart Sso10b (also known as Alba). Structural comparison between the two proteins suggests that structural features such as hydrophobic inner core, acetylation sites, dimer interface, and DNA binding surface are conserved among Sac10b proteins. Structural differences between the two proteins were found in the loops. To understand the structural basis for the thermostability of Mja10b, the Mja10b structure was compared to other proteins with similar topology. Our data suggest that extensive ion-pair networks, optimized accessible surface area and the dimerization via hydrophobic interactions may contribute to the enhanced thermostability of Mja10b.

Amino Acid Motifs↗

PubMed2002

Expression, purification, crystallization and preliminary X-ray analysis of a DNA-binding protein from Methanococcus jannaschii.

A small DNA-binding protein of 87 amino-acid residues from the hyperthermophilic archaeon Methanococcus jannaschii (Mja10b) was cloned and overexpressed in Escherichia coli. The protein was crystallized and the crystals belong to the space group P6(1)22/P6(5)22, with unit-cell parameters a = b = 50.85, c = 124.02 A, alpha = beta = 90, gamma = 120 degrees. The crystals diffracted to a maximum resolution of 2.2 A at 100 K using Cu Kalpha radiation. The presence of one molecule per asymmetric unit gives a crystal volume per protein mass (V(M)) of 2.4 A(3) Da(-1) and a solvent content of 49% by volume. A full set of X-ray diffraction data was collected to 2.2 A from the native crystal.

Crystallography, X-Ray↗

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↗