Biomedical subjects

Hailong Zhang

Publications and source records attributed to Hailong Zhang.

11 recordsLinked to original sources

PubMed2025

Identification and validation of the important role of KIF11 in the development and progression of endometrial cancer.

BACKGROUND: Human kinesin family member 11 (KIF11) plays a vital role in regulating the cell cycle and is implicated in the tumorigenesis and progression of various cancers, but its role in endometrial cancer (EC) is still unclear. Our current research explored the prognostic value, biological function and targeting strategy of KIF11 in EC through approaches including bioinformatics, machine learning and experimental studies. METHODS: The GSE17025 dataset from the GEO database was analyzed via the limma package to identify differentially expressed genes (DEGs) in EC. Functional enrichment analysis of the DEGs was conducted using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. DEGs were further screened for hub genes through protein-protein interaction (PPI) network analysis and machine learning. The role of the hub gene KIF11 in EC was analyzed using clinical data from the TCGA database. The expression of KIF11 in EC was subsequently validated in clinical samples. In vitro experiments were utilized to evaluate the effects of KIF11 on biological functions such as proliferation, migration, apoptosis, and the cell cycle in endometrial cancer cells. RESULTS: A total of 877 DEGs, which are widely involved in important biological processes such as cell division, tubulin binding, and the cell cycle, were identified. Through PPI network analysis and machine learning, KIF11 was selected as the hub gene for subsequent analysis and experimental validation. An analysis of TCGA data revealed that KIF11 is highly expressed in EC and is associated with tumor grade, stage, and a low survival rate. The overexpression of KIF11 in tumor tissues was further confirmed in EC patient samples. KIF11 knockdown had inhibitory effects on cell proliferation, migration and invasion. Flow cytometry analysis revealed that KIF11 knockdown induced G2/M phase arrest and promoted apoptosis in EC cells. CONCLUSION: Our study demonstrated that KIF11 was upregulated in EC and was strongly associated with a poor prognosis. Notably, we found that reduced KIF11 expression inhibited EC cell proliferation, migration and invasion. KIF11 knockdown caused more EC cells to arrest in the G2/M phase and undergo apoptosis. The findings of our study emphasized that KIF11 may be a promising prognostic biomarker and therapeutic target for EC patients.

Humans↗

PubMed2005

Congruent strategies for carbohydrate sequencing. 2. FragLib: an MSn spectral library.

A bottom-up approach to achieve full oligosaccharide and glycan characterization has been described that is based on an MSn fragment spectral library and associated tools. The library, identified as FragLib, was initiated with known standards and commercially available oligomers prepared as methylated derivatives. As a component of this effort a set of software tools has been written for storing, organizing, and comparing spectral files, including the identification of isobaric mixtures. These tools provide a facile and objective evaluation of structural details including interresidue linkage, monomer identification, anomeric configuration, and branching. The tools are components of a web-based data sharing interface for sample tracking, spectral searching, and structural confirmation. Applications have been detailed with unknown samples and previously characterized glycoconjugates.

Carbohydrate Sequence↗

PubMed2005

Congruent strategies for carbohydrate sequencing. 3. OSCAR: an algorithm for assigning oligosaccharide topology from MSn data.

This is the third in a sequence of reports devoted to the development of congruent strategies for carbohydrate sequencing. Two previous reports outlined the strategies for observing structural detail from MSn data and introduced tools that compile, search, and compare fragment spectra in a bottom-up approach to oligosaccharide sequencing. In this third report, we introduce the operational details of an algorithm that we define as the Oligosaccharide Subtree Constraint Algorithm (OSCAR). This algorithm assimilates analyst-selected MSn ion fragmentation pathways into oligosaccharide topology (branching and linkage) using what may be considered a top-down sequencing strategy. Guided by a series of logical constraints, this de novo algorithm provides molecular topology without presumed biosynthetic constraints or external comparisons. In this introductory study, OSCAR is applied to a series of permethylated oligomers and isomeric glycans, and topologies are assigned in a few hundredths of a second.

Algorithms↗

PubMed2005

Direct measurement of interactions between adsorbed vitronectin layers: the influence of ionic strength and pH.

Vitronectin (Vn) is an adhesive protein in the plasma serum and plays an important role in cell attachment, spreading, and proliferation. The interactions between protein bovine vitronectin layers adsorbed onto a silica probe and a mica surface have been investigated with the use of atomic force microscopy (AFM). Adsorption of vitronectin was confirmed by XPS surface analysis. The force-separation curves and pull-off forces were measured as a function of ionic strength and solution pH. The pull-off force (adhesion force) decreased as the salt concentration increased, which suggests that some binding domains of this protein may associate with the ionic species and reduce its binding ability. Discrete jumps, or discontinuities, in the separation force curve were observed to extend to a maximum of 300 nm, evidence that the protein molecules bridge between the surfaces. As a function of pH, the adhesion force on separation of the protein-coated surfaces showed a maximum at pH 5 (i.e.p. of vitronectin), decreasing in magnitude at lower and higher pH values. At pH 5, the approaching curves illustrated a jump-in force; whereas for pH values away from 5, the approaching force curves were repulsive. Correlation of the interaction forces with Vn conformational changes in different pH environments, directly visualized with the use of AFM imaging, was developed. In its i.e.p. region, the Vn molecular conformation appeared to be dense and compact. Significantly, at wounds/injured sites the pH is low (approximately 5) which this study discovered to facilitate adsorption and formation of vitronectin aggregates, known to trigger their subsequent biological functions.

Adhesiveness↗

PubMed2004

Structural basis of the alpha1-beta subunit interaction of voltage-gated Ca2+ channels.

High-voltage-activated Ca2+ channels are essential for diverse biological processes. They are composed of four or five subunits, including alpha1, alpha2-delta, beta and gamma (ref. 1). Their expression and function are critically dependent on the beta-subunit, which transports alpha1 to the surface membrane and regulates diverse channel properties. It is believed that the beta-subunit interacts with alpha1 primarily through the beta-interaction domain (BID), which binds directly to the alpha-interaction domain (AID) of alpha1; however, the molecular mechanism of the alpha1-beta interaction is largely unclear. Here we report the crystal structures of the conserved core region of beta3, alone and in complex with AID, and of beta4 alone. The structures show that the beta-subunit core contains two interacting domains: a Src homology 3 (SH3) domain and a guanylate kinase (GK) domain. The AID binds to a hydrophobic groove in the GK domain through extensive interactions, conferring extremely high affinity between alpha1 and beta-subunits. The BID is essential both for the structural integrity of and for bridging the SH3 and GK domains, but it does not participate directly in binding alpha1. The presence of multiple protein-interacting modules in the beta-subunit opens a new dimension to its function as a multi-functional protein.

Amino Acid Sequence↗

PubMed2004

Molecular basis for the inhibition of the carboxyltransferase domain of acetyl-coenzyme-A carboxylase by haloxyfop and diclofop.

Acetyl-CoA carboxylases (ACCs) are crucial for the metabolism of fatty acids, making these enzymes important targets for the development of therapeutics against obesity, diabetes, and other diseases. The carboxyltransferase (CT) domain of ACC is the site of action of commercial herbicides, such as haloxyfop, diclofop, and sethoxydim. We have determined the crystal structures at up to 2.5-A resolution of the CT domain of yeast ACC in complex with the herbicide haloxyfop or diclofop. The inhibitors are bound in the active site, at the interface of the dimer of the CT domain. Unexpectedly, inhibitor binding requires large conformational changes for several residues in this interface, which create a highly conserved hydrophobic pocket that extends deeply into the core of the dimer. Two residues that affect herbicide sensitivity are located in this binding site, and mutation of these residues disrupts the structure of the domain. Other residues in the binding site are strictly conserved among the CT domains.

Acetyl-CoA Carboxylase↗

PubMed2004

Vitronectin adsorption on surfaces visualized by tapping mode atomic force microscopy.

Vitronectin (Vn) is an abundant glycoprotein present in plasma and the extracellular matrix of most tissue and is an important medium required for bone cells to attach and spread on biomaterial surfaces. Hence, Vn adsorption is an initial and key step in implantation. In this study, adsorption of Vn molecules on mica and oxidized titanium substrates in Milli-Q water (pH 5.6) and in simulated body fluid (SBF, pH 7.4) has been investigated using tapping mode atomic force microscopy. Conformation of the adsorbed proteins was determined from the images. The effect of adsorption time was investigated on mica surfaces. The protein first attaches to the surface, then immediately spreads out with different lateral dimensions of adsorbed protein and becomes aggregated. After 15 min of adsorption, globular Vn molecules form clusters of aggregates in extended chains on the mica surface. Globular Vn molecules appear flatter (i.e., oblate ellipsoids) and coalesce on the ridges of the uneven oxidized titanium surface. From cross-sectional analyses of the Vn images, it was found that the contact areas of Vn molecules associated with Ti surfaces are larger than those with mica surfaces. This suggests that the different surface properties of substrates contribute to this different conformation of adsorbed Vn molecules. The larger contact areas of Vn associated with Ti substrates indicates higher affinity for the biomaterial oxidized titanium surface than for mica. In SBF, Vn interacted weakly with the mica surfaces and Vn molecules were easily desorbed during the imaging process. On oxidized titanium substrates, after 3 h of incubation time in Vn-SBF solution, images can be obtained showing adsorbed Vn aggregates on the oxidized titanium surface. In this case, the protein colloids are strongly adherent, with increased lateral dimensions compared with the adsorption on mica.

Adsorption↗

PubMed2004

Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase in complex with CP-640186.

Acetyl-coenzyme A carboxylases (ACCs) are important targets for the development of therapeutic agents against obesity, diabetes, and other diseases. CP-640186 is a potent inhibitor of mammalian ACCs and can reduce body weight and improve insulin sensitivity in test animals. It is believed to target the carboxyltransferase (CT) domain of these enzymes. Here we report the crystal structure of the yeast CT domain in complex with CP-640186. The inhibitor is bound in the active site at the interface of a dimer of the CT domain. CP-640186 has tight interactions with the putative biotin binding site in the CT domain and demonstrates a distinct mode of inhibiting the CT activity as compared to the herbicides that inhibit plant ACCs. The affinity of inhibitors for the CT domain has been assessed using kinetic and fluorescence anisotropy binding studies. The structural information identifies three regions for drug binding in the active site of CT.

Acetyl-CoA Carboxylase↗

PubMed2003

Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase.

Acetyl-coenzyme A carboxylases (ACCs) are required for the biosynthesis and oxidation of long-chain fatty acids. They are targets for therapeutics against obesity and diabetes, and several herbicides function by inhibiting their carboxyltransferase (CT) domain. We determined the crystal structure of the free enzyme and the coenzyme A complex of yeast CT at 2.7 angstrom resolution and found that it comprises two domains, both belonging to the crotonase/ClpP superfamily. The active site is at the interface of a dimer. Mutagenesis and kinetic studies reveal the functional roles of conserved residues here. The herbicides target the active site of CT, providing a lead for inhibitor development against human ACCs.

Acetyl-CoA Carboxylase↗

PubMed2002

Structural studies of the pigeon cytosolic NADP(+)-dependent malic enzyme.

Malic enzymes are widely distributed in nature, and have important biological functions. They catalyze the oxidative decarboxylation of malate to produce pyruvate and CO(2) in the presence of divalent cations (Mg(2+), Mn(2+)). Most malic enzymes have a clear selectivity for the dinucleotide cofactor, being able to use either NAD(+) or NADP(+), but not both. Structural studies of the human mitochondrial NAD(+)-dependent malic enzyme established that malic enzymes belong to a new class of oxidative decarboxylases. Here we report the crystal structure of the pigeon cytosolic NADP(+)-dependent malic enzyme, in a closed form, in a quaternary complex with NADP(+), Mn(2+), and oxalate. This represents the first structural information on an NADP(+)-dependent malic enzyme. Despite the sequence conservation, there are large differences in several regions of the pigeon enzyme structure compared to the human enzyme. One region of such differences is at the binding site for the 2'-phosphate group of the NADP(+) cofactor, which helps define the cofactor selectivity of the enzymes. Specifically, the structural information suggests Lys362 may have an important role in the NADP(+) selectivity of the pigeon enzyme, confirming our earlier kinetic observations on the K362A mutant. Our structural studies also revealed differences in the organization of the tetramer between the pigeon and the human enzymes, although the pigeon enzyme still obeys 222 symmetry.

Amino Acid Sequence↗

PubMed2001

Structure of an acidic phospholipase A2 from the venom of Deinagkistrodon acutus.

An acidic phospholipase A(2) was purified from Deinagkistrodon acutus (Agkistrodon acutus) which displays an inhibitory effect on platelet aggregation. The three-dimensional structure of the enzyme was determined by molecular replacement at 2.6 A resolution with a crystallographic R factor of 18.40% (R(free) = 22.50%) and reasonable stereochemistry. Two molecules in the asymmetric unit form a dimer and the dimer formation accompanies a significant conformational adaptation of segment 14-23, a constituent of the 'interface recognition site' (IRS). This probably reflects the inherent structural flexibility of the IRS. The possible expansion of the site for inhibiting platelet aggregation as proposed previously [Wang et al. (1996), J. Mol. Biol. 255, 669-676] is discussed.

Agkistrodon↗