Biomedical subjects

Xiao Hui Ma

Publications and source records attributed to Xiao Hui Ma.

9 recordsLinked to original sources

PubMed2006

Prediction of the binding mode between BMS-378806 and HIV-1 gp120 by docking and molecular dynamics simulation.

BMS-378806 is a newly discovered small molecule that effectively blocks the binding of CD4 with gp120. The binding mode of this kind of inhibitor remains unknown. In this paper, AutoDock 3.0 in conjunction with molecular dynamics simulation, accommodating the receptor's flexibility, was used to explore the binding mode between BMS-378806 and gp120. Two structures, Mode I and Mode II, with the lowest docking energy were selected as different representative binding modes. The analysis of the results from the molecular dynamics simulation indicated that the binding of BMS-348806 in Mode II is more stable. The average structure of Mode II was analyzed and compared with the experimental data. The conclusion was that BMS-378806 inserts the azaindole ring deeply into the PHE43 cavity and makes contact with a number of residues in the cavity, on the cavity and near the cavity. This study benefits the understanding of the mechanism of this kind of inhibitor and may provide useful information for rational drug design.

Binding Sites↗

PubMed2005

Biologically enhanced sampling geometric docking and backbone flexibility treatment with multiconformational superposition.

An efficient biologically enhanced sampling geometric docking method is presented based on the FTDock algorithm to predict the protein-protein binding modes. The active site data from different sources, such as biochemical and biophysical experiments or theoretical analyses of sequence data, can be incorporated in the rotation-translation scan. When discretizing a protein onto a 3-dimensional (3D) grid, a zero value is given to grid points outside a sphere centered on the geometric center of specified residues. In this way, docking solutions are biased toward modes where the interface region is inside the sphere. We also adopt a multiconformational superposition scheme to represent backbone flexibility in the proteins. When these procedures were applied to the targets of CAPRI, a larger number of hits and smaller ligand root-mean-square deviations (RMSDs) were obtained at the conformational search stage in all cases, and especially Target 19. With Target 18, only 1 near-native structure was retained by the biologically enhanced sampling geometric docking method, but this number increased to 53 and the least ligand RMSD decreased from 8.1 A to 2.9 A after performing multiconformational superposition. These results were obtained after the CAPRI prediction deadlines.

Algorithms↗

PubMed2003

A soft docking algorithm for predicting the structure of antibody-antigen complexes.

An efficient soft docking algorithm is described for predicting the mode of binding between an antibody and its antigen based on the three-dimensional structures of the molecules. The basic tools are the "simplified protein" model and the docking algorithm of Wodak and Janin. The side-chain flexibility of Arg, Lys, Asp, Glu, and Met residues on the protein surface is taken into account. A combined filtering technique is used to select candidate binding modes. After energy minimization, we calculate a scoring function, which includes electrostatic and desolvation energy terms. This procedure was applied to targets 04, 05, and 06 of CAPRI, which are complexes of three different camelid antibody VHH variable domains with pig alpha-amylase. For target 06, two native-like structures with a root-mean-square deviation < 4.0 A relative to the X-ray structure were found within the five top ranking structures. For targets 04 and 05, our procedure produced models where more than half of the antigen residues forming the epitope were correctly predicted, albeit with a wrong VHH domain orientation. Thus, our soft docking algorithm is a promising tool for predicting antibody-antigen recognition.

Algorithms↗

PubMed2003

A protein-protein docking algorithm dependent on the type of complexes.

An efficient 'soft docking' algorithm is described to assist the prediction of protein-protein association using three-dimensional structures of molecules. The basic tools are the 'simplified protein' model and the docking algorithm of Wodak and Janin. The side chain flexibility of Arg, Lys, Asp, Glu and Met residues at the protein surface is taken into account. The complex type-dependent filtering technique on the basis of the geometric matching, hydrophobicity and electrostatic complementarity is used to select candidate binding modes. Subsequently, we calculate a scoring function which includes electrostatic and desolvation energy terms. In the 44 complexes tested including enzyme-inhibitor, antibody-antigen and other complexes, native-like structures were all found, of which 30 were ranked in the top 20. Thus, our soft docking algorithm has the potential to predict protein-protein recognition.

Algorithms↗

PubMed2002

Hyperglycemia induces PAI-1 gene expression in adipose tissue by activation of the hexosamine biosynthetic pathway.

We examined whether acute in vivo increases in either plasma glucose or insulin concentrations stimulate PAI-1 gene expression in fat tissue. We studied chronically catheterized unstressed and awake, lean (approximately 300 g, n=12) and obese (approximately 450 g, n=12) Sprague-Dawley rats. Hyperglycemia (approximately 18mM) was induced for 3 h by glucose infusion during a pancreatic clamp (somatostatin inhibited endogenous insulin secretion). Compared with equivalent saline infusion, hyperglycemia induced a 6-7 fold increase in PAI-1 gene expression in both lean and obese rats (P<0.001). When the rate of cellular glucose uptake was matched during a euglycemic hyperinsulinemic (approximately 60 microU/ml) clamp, PAI-1 gene expression in both obese and lean rats was proportionately and significantly increased (P<0.001). We further examined whether induction of the hexosamine biosynthetic pathway would mimic the effects of hyperglycemia and hyperinsulinemia on PAI-1 gene expression. Indeed, infusion of glucosamine (GlcN, 30 micromol/kg/min), induced a approximately 3-4 fold increase (P<0.01) in PAI-1 gene expression in both lean and obese animals. While obese rats had a four times greater fat mass then the lean rats, PAI-1 gene expression remained significantly higher when expressed as per gram fat. Our results support the hypothesis that increased glucose uptake induces PAI-1 gene expression in adipose tissue, probably through the activation of the hexosamine biosynthetic pathway. These findings may account for some of the fibrinolytic alterations seen in obese type 2 diabetic humans.

Adipose Tissue↗

PubMed2002

Aging is associated with resistance to effects of leptin on fat distribution and insulin action.

Leptin has been shown to modulate total body fat and visceral fat distribution and to enhance insulin action in young rats. We hypothesize that failure of leptin action may contribute to the increase in visceral fat and insulin resistance in aging. By chronic subcutaneous infusion of leptin over 7 days, we increased leptin levels in young rats to match the levels in aging ad libitum fed rats. Leptin induced an approximately 50% decrease in food intake compared with saline controls, an approximately 50% decrease in visceral fat, and improved hepatic (fourfold) and peripheral (30%) insulin action (euglycemic hyperinsulinemic clamp technique) compared with the pair-fed group (p <.001). Although the plasma leptin level was doubled in aging rats, leptin failed to produce a significant change in food intake, in fat mass and its distribution, and in hepatic and peripheral insulin action. Increasing plasma leptin levels failed to suppress leptin gene expression in aging rats as compared with the approximately 50% suppression seen in young rats (p <.01). We propose that leptin resistance may play a causative role in the metabolic decline seen with aging.

Adipose Tissue↗

PubMed2002

A fast empirical approach to binding free energy calculations based on protein interface information.

Three useful variables from the interfaces of 20 protein-protein complexes were investigated. These variables are the side-chain accessible number (N(b)), the number of hydrophilic pairs (N(pair)) and buried a polar solvent accessible surface areas (DeltaDeltaASA(apol)). An empirical model based on the three variables was developed to describe the free energy of protein associations. As the results show, the side-chain accessible numbers characterize the loss of side-chain conformational entropy of protein interactions and the effective empirical function presented here has great capability for estimating the binding free energy. It was found that the variables of interface information capture most of the significant features of protein-protein association. Also, we applied the model based on the variables as a rescoring function to docking simulations and found that it has the potential to distinguish the 'true' binding mode. It is clear that the simple and empirical scale developed here is an attractive target function for calculating binding free energy for various biological processes to rational protein design.

Algorithms↗

PubMed2002

Removal of visceral fat prevents insulin resistance and glucose intolerance of aging: an adipokine-mediated process?

Age-dependent changes in insulin action and body fat distribution are risk factors for the development of type 2 diabetes. To examine whether the accumulation of visceral fat (VF) could play a direct role in the pathophysiology of insulin resistance and type 2 diabetes, we monitored insulin action, glucose tolerance, and the expression of adipo-derived peptides after surgical removal of VF in aging (20-month-old) F344/Brown Norway (FBN) and in Zucker Diabetic Fatty (ZDF) rats. As expected, peripheral and hepatic insulin action were markedly impaired in aging FBN rats, and extraction of VF (accounting for approximately 18% of their total body fat) was sufficient to restore peripheral and hepatic insulin action to the levels of young rats. When examined at the mechanistic level, removal of VF in ZDF rats prevented the progressive decrease in insulin action and delayed the onset of diabetes, but VF extraction did not alter plasma free fatty acid levels. However, the expression of tumor necrosis factor-alpha and leptin in subcutaneous (SC) adipose tissue were markedly decreased after VF removal (by approximately three- and twofold, respectively). Finally, extracted VF retained approximately 15-fold higher resistin mRNA compared with SC fat. Our data suggest that insulin resistance and the development of diabetes can be significantly reduced in aging rats by preventing the age-dependent accumulation of VF. This study documents a cause-and-effect relationship between VF and major components of the metabolic syndrome.

Abdomen↗

PubMed2002

Leptin resistance during aging is independent of fat mass.

Increased fat mass, abdominal adiposity, and insulin resistance are typical findings in aging mammals and are frequently associated with leptin resistance and increased plasma leptin levels. To examine whether leptin's failure in aging is due to aging per se or to changes in body fat mass or distribution, we studied aging rats that underwent calorie restriction throughout their lives, maintaining their youthful body fat pattern and metabolic profile. Leptin's action was assessed by measuring its ability to regulate food intake, fat mass and its distribution, peripheral and hepatic insulin action, and its own gene expression in fat. Our results show that leptin's action is markedly diminished in aging rats, independently of their body fat pattern. Leptin's failure in this model suggests its causative role in the metabolic decline seen with aging.

Adipose Tissue↗