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Jiyao Wang

Publications and source records attributed to Jiyao Wang.

16 recordsLinked to original sources
PubMed2025

IgStrand: A universal residue numbering scheme for the immunoglobulin-fold (Ig-fold) to study Ig-proteomes and Ig-interactomes.

The Immunoglobulin fold (Ig-fold) is found in proteins from all domains of life and represents the most populous fold in the human genome, with current estimates ranging from 2 to 3% of protein coding regions. That proportion is much higher in the surfaceome where Ig and Ig-like domains orchestrate cell-cell recognition, adhesion and signaling. The ability of Ig-domains to reliably fold and self-assemble through highly specific interfaces represents a remarkable property of these domains, making them key elements of molecular interaction systems: the immune system, the nervous system, the vascular system and the muscular system. We define a universal residue numbering scheme, common to all domains sharing the Ig-fold in order to study the wide spectrum of Ig-domain variants constituting the Ig-proteome and Ig-Ig interactomes at the heart of these systems. The "IgStrand numbering scheme" enables the identification of Ig structural proteomes and interactomes in and between any species, and comparative structural, functional, and evolutionary analyses. We review how Ig-domains are classified today as topological and structural variants and highlight the "Ig-fold irreducible structural signature" shared by all of them. The IgStrand numbering scheme lays the foundation for the systematic annotation of structural proteomes by detecting and accurately labeling Ig-, Ig-like and Ig-extended domains in proteins, which are poorly annotated in current databases and opens the door to accurate machine learning. Importantly, it sheds light on the robust Ig protein folding algorithm used by nature to form beta sandwich supersecondary structures. The numbering scheme powers an algorithm implemented in the interactive structural analysis software iCn3D to systematically recognize Ig-domains, annotate them and perform detailed analyses comparing any domain sharing the Ig-fold in sequence, topology and structure, regardless of their diverse topologies or origin. The scheme provides a robust fold detection and labeling mechanism that reveals unsuspected structural homologies among protein structures beyond currently identified Ig- and Ig-like domain variants. Indeed, multiple folds classified independently contain a common structural signature, in particular jelly-rolls. Examples of folds that harbor an "Ig-extended" architecture are given. Applications in protein engineering around the Ig-architecture are straightforward based on the universal numbering.

Humans↗
PubMed2006

The role of electrostatics in protein-membrane interactions.

Many experimental, structural and computational studies have established the importance of nonspecific electrostatics as a driving force for peripheral membrane association. Here we focus on this component of protein/membrane interactions by using examples ranging from phosphoinositide signaling to retroviral assembly. We stress the utility of the collaboration of experiment and theory in identifying and quantifying the role of electrostatics not only in contributing to membrane association, but also in affecting subcellular targeting, in the control of membrane binding, and in the organization of proteins and lipids at membrane surfaces.

Animals↗
PubMed2006

Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials.

The absolute (standard) binding free energy of eight FK506-related ligands to FKBP12 is calculated using free energy perturbation molecular dynamics (FEP/MD) simulations with explicit solvent. A number of features are implemented to improve the accuracy and enhance the convergence of the calculations. First, the absolute binding free energy is decomposed into sequential steps during which the ligand-surrounding interactions as well as various biasing potentials restraining the translation, orientation, and conformation of the ligand are turned "on" and "off." Second, sampling of the ligand conformation is enforced by a restraining potential based on the root mean-square deviation relative to the bound state conformation. The effect of all the restraining potentials is rigorously unbiased, and it is shown explicitly that the final results are independent of all artificial restraints. Third, the repulsive and dispersive free energy contribution arising from the Lennard-Jones interactions of the ligand with its surrounding (protein and solvent) is calculated using the Weeks-Chandler-Andersen separation. This separation also improves convergence of the FEP/MD calculations. Fourth, to decrease the computational cost, only a small number of atoms in the vicinity of the binding site are simulated explicitly, while all the influence of the remaining atoms is incorporated implicitly using the generalized solvent boundary potential (GSBP) method. With GSBP, the size of the simulated FKBP12/ligand systems is significantly reduced, from approximately 25,000 to 2500. The computations are very efficient and the statistical error is small ( approximately 1 kcal/mol). The calculated binding free energies are generally in good agreement with available experimental data and previous calculations (within approximately 2 kcal/mol). The present results indicate that a strategy based on FEP/MD simulations of a reduced GSBP atomic model sampled with conformational, translational, and orientational restraining potentials can be computationally inexpensive and accurate.

Computer Simulation↗
PubMed2006

Prognostic analysis in chronic hepatitis B patients: a retrospective study of 216 cases about Scheuer scores, in situ expression of viral antigens and tissue hepatitis B virus DNA levels.

BACKGROUND: Most of the previous studies of patients with chronic hepatitis B virus (HBV) infection concentrated on serum samples. Liver biopsy specimens for HBV have not been systematically analyzed. This study was performed to analyze some histopathological indicators (Scheuer scores, the expression of HBV antigens in situ, HBV DNA quantification) in the biopsy samples and showed the relationship among them and the prognosis of chronic hepatitis. METHODS: A total of 216 consecutive chronic HBV-infected patients were followed up by clinical and laboratory data and classified into two groups at first: carcinogenesis and non-carcinogenesis. The non-carcinogenesis also included two groups: cirrhosis and non-cirrhosis. The non-cirrhosis was still divided into fluctuation and normalization at last. Histological activity index was described by Scheuer scores. Two-step immunohistochemical staining showed the expression of viral antigens in situ. Tissue HBV DNA levels were determined by fluorescence quantitative real-time PCR. RESULTS: Regression analysis revealed significant positive correlations between the expression of hepatitis B e antigen (HBeAg) and grading, as well as between hepatitis Bx (HBx) protein and grading or staging of Scheuer scores. Positive correlations between grading or staging and prognosis were statistically significant. The expressions of HBeAg and HBx protein were higher in patients with cirrhosis than those without cirrhosis. Scheuer score was the most important indicator of prognosis. CONCLUSIONS: HBeAg and HBx protein can be used as indicators of hepatitis activity and their positive expressions increase the risk for cirrhosis remarkably. In addition to be a marker of liver damage, Scheuer score is the most reliable indicator of the prognosis.

Adult↗
PubMed2005

The origin of C1A-C2 interdomain interactions in protein kinase Calpha.

The regulatory domain of protein kinase Calpha (PKCalpha) contains three membrane-targeting modules, two C1 domains (C1A and C1B) that bind diacylglycerol and phorbol ester, and the C2 domain that is responsible for the Ca2+-dependent membrane binding. Accumulating evidence suggests that C1A and C2 domains of PKCalpha are tethered in the resting state and that the tethering is released upon binding to the membrane containing phosphatidylserine. The homology modeling and the docking analysis of C1A and C2 domains of PKCalpha revealed a highly complementary interface that comprises Asp55-Arg252 and Arg42-Glu282 ion pairs and a Phe72-Phe255 aromatic pair. Mutations of these residues in the predicted C1A-C2 interface showed large effects on in vitro membrane binding, enzyme activity, phosphatidylserine selectivity, and cellular membrane translocation of PKCalpha, supporting their involvement in interdomain interactions. In particular, D55A (or D55K) and R252A (or R252E) mutants showed much higher basal membrane affinity and enzyme activity and faster subcellular translocation than wild type, whereas a double charge-reversal mutant (D55K/R252E) behaved analogously to wild type, indicating that a direct electrostatic interaction between the two residues is essential for the C1A-C2 tethering. Collectively, these studies provide new structural insight into PKCalpha C1A-C2 interdomain interactions and the mechanism of lipid-mediated PKCalpha activation.

Animals↗
PubMed2005

Retroviral matrix domains share electrostatic homology: models for membrane binding function throughout the viral life cycle.

The matrix domain (MA) of Gag polyproteins performs multiple functions throughout the retroviral life cycle. MA structures have an electropositive surface patch that is implicated in membrane association. Here, we use computational methods to demonstrate that electrostatic control of membrane binding is a central characteristic of all retroviruses. We are able to explain a wide range of experimental observations and provide a level of quantitative and molecular detail that has been inaccessible to experiment. We further predict that MA may exist in a variety of oligomerization states and propose mechanistic models for the effects of phosphoinositides and phosphorylation. The calculations provide a conceptual model for how non-myristoylated and myristoylated MAs behave similarly in assembly and disassembly. Hence, they provide a unified quantitative picture of the structural and energetic origins of the entire range of MA function and thus enhance, extend, and integrate previous observations on individual stages of the process.

Cell Membrane↗
PubMed2004

A computational model for the electrostatic sequestration of PI(4,5)P2 by membrane-adsorbed basic peptides.

The multivalent acidic phospholipid phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) plays a key role in many biological processes. Recent studies show that unstructured clusters of basic residues from a number of peripheral proteins can laterally sequester PI(4,5)P2 in membranes. Specifically, experiments suggest that the basic effector domain of the myristoylated alanine-rich C kinase substrate (MARCKS), or a peptide corresponding to this domain, MARCKS(151-175), sequesters several PI(4,5)P2 and that this sequestration is due to nonspecific electrostatic interactions. Here, we use the finite difference Poisson-Boltzmann method to test this hypothesis by calculating the electrostatic free energy of lateral sequestration of PI(4,5)P2 by membrane-adsorbed basic peptides: Lys-7, Lys-13, and FA-MARCKS(151-175), a peptide based on MARCKS(151-175). In agreement with experiments, we find that the electrostatic free energy becomes more favorable when: 1), Lys-13 and FA-MARCKS(151-175) sequester several PI(4,5)P2; 2), the linear charge density of the basic peptide increases; 3), the mol percent monovalent acidic lipid in the membrane decreases; and 4), the ionic strength of the solution decreases. In addition, the electrostatic sequestration free energy is in excess of the entropic penalty associated with localizing PI(4,5)P2. Our calculations, thus, provide a structural and quantitative description of the observed interaction of PI(4,5)P2 with membrane-adsorbed basic sequences.

Algorithms↗
PubMed2004

Electrostatic sequestration of PIP2 on phospholipid membranes by basic/aromatic regions of proteins.

The basic effector domain of myristoylated alanine-rich C kinase substrate (MARCKS), a major protein kinase C substrate, binds electrostatically to acidic lipids on the inner leaflet of the plasma membrane; interaction with Ca2+/calmodulin or protein kinase C phosphorylation reverses this binding. Our working hypothesis is that the effector domain of MARCKS reversibly sequesters a significant fraction of the L-alpha-phosphatidyl-D-myo-inositol 4,5-bisphosphate (PIP2) on the plasma membrane. To test this, we utilize three techniques that measure the ability of a peptide corresponding to its effector domain, MARCKS(151-175), to sequester PIP2 in model membranes containing physiologically relevant fractions (15-30%) of the monovalent acidic lipid phosphatidylserine. First, we measure fluorescence resonance energy transfer from Bodipy-TMR-PIP2 to Texas Red MARCKS(151-175) adsorbed to large unilamellar vesicles. Second, we detect quenching of Bodipy-TMR-PIP2 in large unilamellar vesicles when unlabeled MARCKS(151-175) binds to vesicles. Third, we identify line broadening in the electron paramagnetic resonance spectra of spin-labeled PIP2 as unlabeled MARCKS(151-175) adsorbs to vesicles. Theoretical calculations (applying the Poisson-Boltzmann relation to atomic models of the peptide and bilayer) and experimental results (fluorescence resonance energy transfer and quenching at different salt concentrations) suggest that nonspecific electrostatic interactions produce this sequestration. Finally, we show that the PLC-delta1-catalyzed hydrolysis of PIP2, but not binding of its PH domain to PIP2, decreases markedly as MARCKS(151-175) sequesters most of the PIP2.

Amino Acid Sequence↗
PubMed2002

Dual role for phosphoinositides in regulation of yeast and mammalian phospholipase D enzymes.

Phospholipase D (PLD) generates lipid signals that coordinate membrane trafficking with cellular signaling. PLD activity in vitro and in vivo is dependent on phosphoinositides with a vicinal 4,5-phosphate pair. Yeast and mammalian PLDs contain an NH2-terminal pleckstrin homology (PH) domain that has been speculated to specify both subcellular localization and regulation of PLD activity through interaction with phosphatidylinositol 4,5-bisphosphate (PI[4,5]P2). We report that mutation of the PH domains of yeast and mammalian PLD enzymes generates catalytically active PI(4,5)P2-regulated enzymes with impaired biological functions. Disruption of the PH domain of mammalian PLD2 results in relocalization of the protein from the PI(4,5)P2-containing plasma membrane to endosomes. As a result of this mislocalization, mutations within the PH domain render the protein unresponsive to activation in vivo. Furthermore, the integrity of the PH domain is vital for yeast PLD function in both meiosis and secretion. Binding of PLD2 to model membranes is enhanced by acidic phospholipids. Studies with PLD2-derived peptides suggest that this binding involves a previously identified polybasic motif that mediates activation of the enzyme by PI(4,5)P2. By comparison, the PLD2 PH domain binds PI(4,5)P2 with lower affinity but sufficient selectivity to function in concert with the polybasic motif to target the protein to PI(4,5)P2-rich membranes. Phosphoinositides therefore have a dual role in PLD regulation: membrane targeting mediated by the PH domain and stimulation of catalysis mediated by the polybasic motif.

Amino Acid Motifs↗
PubMed2002

[Effects of antisense transforming growth factor beta receptor-I expressing plasmid on pig serum-induced rat liver fibrosis].

OBJECTIVE: To observe the effects of antisense transforming growth factor beta receptor-I (TbetaRI) expressing plasmid on rat liver fibrosis. METHODS: RT-nested-PCR and gene recombinant techniques were used to construct the rat antisense TbetaRI recombinant plasmid which can be expressed in eucaryotic cells. The recombinant plasmid and blanx vector (pcDNA3) were encapsulated by glycosyl-poly-L-lysine and then transducted into rats of pig serum-induced liver fibrosis model respectively. Expression of exogenous transfected plasmid was assessed by Northern blot, RT-PCR, Western blot and immunohistochemistry. Serum TGF-beta(1) was determined by ELISA. The content of hepatic hydroxyproline was tested. Immunohistochemistry was used to test type I and III collagen. VG staining was used for pathological study. RESULTS: The exogenous antisense TbetaRI could be expressed in vivo, and could block the mRNA and protein expression of TbetaRI in the fibrotic liver induced by pig serum. Its expression also reduced the level of TGF-beta(1) (P < 0.05) and decreased the the contents of hepatic hydroxyproline and the deposition of collagens type I and type III (P < 0.01). And its expression also improved the pathologic classification of liver fibrosis models (P < 0.01). CONCLUSIONS: The results demonstrate that the antisense TbetaRI recombinant plasmid has certain extern reverse effect on liver fibrosis and make it as a possible candidate for use in future gene therapy.

Activin Receptors, Type I↗
PubMed2002

Lateral sequestration of phosphatidylinositol 4,5-bisphosphate by the basic effector domain of myristoylated alanine-rich C kinase substrate is due to nonspecific electrostatic interactions.

A peptide corresponding to the basic (+13), unstructured effector domain of myristoylated alanine-rich C kinase substrate (MARCKS) binds strongly to membranes containing phosphatidylinositol 4,5-bisphosphate (PIP(2)). Although aromatic residues contribute to the binding, three experiments suggest the binding is driven mainly by nonspecific local electrostatic interactions. First, peptides with 13 basic residues, Lys-13 and Arg-13, bind to PIP(2)-containing vesicles with the same high affinity as the effector domain peptide. Second, removing basic residues from the effector domain peptide reduces the binding energy by an amount that correlates with the number of charges removed. Third, peptides corresponding to a basic region in GAP43 and MARCKS effector domain-like regions in other proteins (e.g. MacMARCKS, adducin, Drosophila A kinase anchor protein 200, and N-methyl-d-aspartate receptor) also bind with an energy that correlates with the number of basic residues. Kinetic measurements suggest the effector domain binds to several PIP(2). Theoretical calculations show the effector domain produces a local positive potential, even when bound to a bilayer with 33% monovalent acidic lipids, and should thus sequester PIP(2) laterally. This electrostatic sequestration was observed experimentally using a phospholipase C assay. Our results are consistent with the hypothesis that MARCKS could reversibly sequester much of the PIP(2) in the plasma membrane.

Amino Acid Sequence↗
PubMed2002

[Relationship between plasma carbon monoxide and blood-brain barrier permeability in cirrhotic rats].

OBJECTIVE: To explore the relationship between plasma levels of carbon monoxide and blood-brain permeability in cirrhotic rats. METHODS: We measured mean arterial pressure (MAP), heart rate, plasma levels of carbon monoxide and amount of Evans blue in the brain tissue taken as the index of blood-brain permeability in cirrhotic rats (n=10) and controls (n=10). RESULTS: Cirrhotic rats showed significant increases in plasma carbon monoxide and amount of Evans blue in brain tissue compared with controls [(18.37 +/- 1.79) micromol/L,(18.52 +.- 1.39) ng/mg vs (10.27 +/- 1.21) micromol/L, (15.08 +/- 1.06) ng/mg; P< 0.01]. Carbon monoxide levels in cirrhotic rats correlated positively with blood-brain barrier permeability and inversely with MAP (r=0.72, P< 0.01; r= -0.67, P< 0.05). CONCLUSIONS: Carbon monoxide, involving in the occurrence of hypotension and the increase of blood-brain barrier permeability, may play a role in the development of hepatic encephalopathy.

Alanine Transaminase↗
PubMed2002

[Clinical and pathological characteristics of primary biliary cirrhosis].

OBJECTIVE: In order to improve the cognition and early diagnosis of primary biliary cirrhosis (PBC), we investigated clinical and pathological characteristics of PBC. METHODS: Clinical data of 37 PBC patients together with pathological findings of 20 PBC patients were reviewed. RESULTS: Among the 37 patients, 35 were women and the mean age at diagnosis was (53.4 8.9) years. The most frequent clinical presentations were jaundice (70.3%), fatigue (70.3%), and pruritus (56.8%). Serum glutamyl transpeptidase (GGT) and alkaline phosphatase (ALP) levels were markedly elevated in all patients (P50 was 467.50 U/L and 424.00 U/L, respectively). Among the 37 cases, 35 (94.6%) had total bile acids elevation, 32 (86.5%) had serum cholesterol elevation and 32 (86.5%) serum IgM elevation, 34 (91.9%) were positive for anti-mitochondrial antibody (AMA) and/or AMA-M2. Liver biopsy in 20 PBC patients mainly found: fibrosis in 17 cases (85%), interlobular bile duct lesions in 13 (65%), lobular mononuclear inflammation in 13 (65%), lymphocytic hepatocellular piecemeal necrosis in 10 (50%), and bile pigment accumulation in 9 (45%). The results of nonparametric test showed that GGT was related with pathological stage (P=0.002) and interlobular bile duct lesions (P=0.01). CONCLUSIONS: PBC is mostly found in middle-aged women. Accurate and prompt diagnosis of PBC should be based on the clinical presentation, biochemical and immunological indexes, and hepatic pathological changes. The level of GGT may partly reflect the severity of the histological lesions

Bile Acids and Salts↗
PubMed2002

[The effectiveness of an intervention program in the promotion of condom use among sexually transmitted disease patients].

OBJECTIVE: To assess the effectiveness of an educational intervention program in sexually transmitted disease (STD) and condom-related knowledge and promoting condom use among STD patients. METHODS: STD clinic patients were randomly assigned to three groups (A, control group; B, video viewing group; group C, video viewing plus education with talk) after administered with baseline questionnaire. Each patient was then scheduled to complete the questionnaire regarding the change of STD knowledge and use of condom in two weeks and 3 months. RESULTS: Six hundred and forty-eight patients entered the study. More than half of the patients were aware of STD-related knowledge. However the rate of condom use was very low. When having intercourse with the casual sexual partners the percentage of condom use was only 20%. Seventeen per cent of the patients knew nothing about how to use condom correctly. Follow up results showed that the education program increased the knowledge about STD to some degree. However the percentage of condom use in the latest sexual intercourse increased greatly both in intervention and control groups, but more in intervention groups (P < 0.05). CONCLUSION: STD education should be focused on advocating and correcting condom use.

Adult↗
PubMed2001

PIP(2) and proteins: interactions, organization, and information flow.

We review the physical properties of phosphatidylinositol 4,5-bisphosphate (PIP2) that determine both its specific interactions with protein domains of known structure and its nonspecific electrostatic sequestration by unstructured domains. Several investigators have postulated the existence of distinct pools of PIP2 within the cell to account for the myriad functions of this lipid. Recent experimental work indicates certain regions of the plasma membrane-membrane ruffles and nascent phagosomes-do indeed concentrate PIP2. We consider two mechanisms that could account for this phenomenon: local synthesis and electrostatic sequestration. We conclude by considering the hypothesis that proteins such as MARCKS bind a significant fraction of the PIP2 in a cell, helping to sequester it in lateral membrane domains, then release this lipid in response to local signals such as an increased concentration of Ca(++)/calmodulin or activation of protein kinase C.

Animals↗