Interaction between human interleukin-16 and CD4 receptor of HIV-1

AIM: To study the interaction between human interleukin-16 (IL-16) and the receptor CD4 (T-lymphocyte differentiation antigen) of human immunodeficiency virus type 1 (HIV-1). METHODS: Two structurally con served regions (SCRs) of human IL-16 were built by the SYBYL/Biopolymer module using the corresponding transmembrane (TM) domain of human interleukin-1 (HIL-4) and HIL-2 as the templates. The coordinates for amino-terminal residue sequence, carboxyl-terminal residue sequences, and cytoplasm loops were generated using Biopolymer's LOOP SEARCH algorithm. RESULTS: HIL-16 first formed a homodimer, then contacted with CD4 dimer further forming a dimeric complex. Subsequently, the dimeric complex constructed the tetrameric complex by two disulfide bridges between the cysteines of HIL-16 (Cys31-Cys31). CONCLUSION: The interaction model is useful to propose the action mechanism of HIL-16 and is beneficial for rational designing of novel anti-HIV drugs.

Structural and functional characterization of the human CCR5 receptor in complex with HIV gp120 envelope glycoprotein and CD4 receptor by molecular modeling studies

The entry of human immunodeficiency virus (HIV) into cells depends on a sequential interaction of the gp120 envelope glycoprotein with the cellular receptors CD4 and members of the chemokine receptor family. The CC chemokine receptor CCR5 is such a receptor for several chemokines and a major coreceptor for the entry of R5 HIV type-1 (HIV-1) into cells. Although many studies focus on the interaction of CCR5 with HIV-1, the corresponding interaction sites in CCR5 and gp120 have not been matched. Here we used an approach combining protein structure modeling, docking and molecular dynamics simulation to build a series of structural models of the CCR5 in complexes with gp120 and CD4. Interactions such as hydrogen bonds, salt bridges and van der Waals contacts between CCR5 and gp120 were investigated. Three snapshots of CCR5-gp120-CD4 models revealed that the initial interactions of CCR5 with gp120 are involved in the negatively charged N-terminus (Nt) region of CCR5 and positively charged bridging sheet region of gp120. Further interactions occurred between extracellular loop2 (ECL2) of CCR5 and the base of V3 loop regions of gp120. These interactions may induce the conformational changes in gp120 and lead to the final entry of HIV into the cell. These results not only strongly support the two-step gp120-CCR5 binding mechanism, but also rationalize extensive biological data about the role of CCR5 in HIV-1 gp120 binding and entry, and may guide efforts to design novel inhibitors.

On-line policy optimisation of spoken dialogue systems via live interaction with human subjects

Statistical dialogue models have required a large number of dialogues to optimise the dialogue policy, relying on the use of a simulated user. This results in a mismatch between training and live conditions, and significant development costs for the simulator thereby mitigating many of the claimed benefits of such models. Recent work on Gaussian process reinforcement learning, has shown that learning can be substantially accelerated. This paper reports on an experiment to learn a policy for a real-world task directly from human interaction using rewards provided by users. It shows that a usable policy can be learnt in just a few hundred dialogues without needing a user simulator and, using a learning strategy that reduces the risk of taking bad actions. The paper also investigates adaptation behaviour when the system continues learning for several thousand dialogues and highlights the need for robustness to noisy rewards. © 2011 IEEE.

On-line policy optimisation of Bayesian spoken dialogue systems via human interaction

A partially observable Markov decision process has been proposed as a dialogue model that enables robustness to speech recognition errors and automatic policy optimisation using reinforcement learning (RL). However, conventional RL algorithms require a very large number of dialogues, necessitating a user simulator. Recently, Gaussian processes have been shown to substantially speed up the optimisation, making it possible to learn directly from interaction with human users. However, early studies have been limited to very low dimensional spaces and the learning has exhibited convergence problems. Here we investigate learning from human interaction using the Bayesian Update of Dialogue State system. This dynamic Bayesian network based system has an optimisation space covering more than one hundred features, allowing a wide range of behaviours to be learned. Using an improved policy model and a more robust reward function, we show that stable learning can be achieved that significantly outperforms a simulator trained policy. © 2013 IEEE.

Computer simulation of Gd(III) speciation in human interstitial fluid

The speciation and distribution of Gd(III) in human interstitial fluid was studied by computer simulation. The results show that at the background concentration, all the Gd(III) species are soluble and no precipitates appear. However as the total concentration of Gd(III) rises above 2.610 x 10(-9) mol/l the insoluble species become predominant. GdPO4 is formed first as a precipitate and then Gd-2(CO3)(3). Among soluble species, free Gd(III), [Gd(HSA)], [Gd(Ox)] and the ternary complexes of Gd(III) with citrate as the primary ligand are main species when the total concentration of Gd(III) is below 2.074 x 10(-2) mol/l. With the total concentration of Gd(III) further rising, [Gd-3(OH)(4)] begins to appear and gradually becomes a predominant species.

Computer simulation of Zn(II) speciation and effect of Gd(III) on Zn(II) speciation in human blood plasma

The speciation and distribution of Zn(II) and the effect of Gd(III) on Zn(II) speciation in human blood plasma were studied by computer simulation. The results show that, in normal blood plasma, the most predominant species of Zn(II) are [Zn(HSA)] (58.2%), [Zn(IgG)](20.1%), [Zn(Tf)] (10.4%), ternary complexes of [Zn(Cit)(Cys)] (6.6%) and of [Zn(Cys)(His)H] (1.6%), and the binary complex of [Zn(CYS)(2)H] (1.2%). When zinc is deficient, the distribution of Zn(II) species is similar to that in normal blood plasma. Then, the distribution changes with increasing zinc(II) total concentration. Overloading Zn(II) is initially mainly bound to human serum albumin (HSA). As the available amount of HSA is exceeded, phosphate metal and carbonate metal species are established. Gd(III) entering human blood plasma predominantly competes for phosphate and carbonate to form precipitate species. However, Zn(II) complexes with phosphate and carbonate are negligible in normal blood plasma, so Gd(III) only have a little effect on zinc(II) species in human blood plasma at a concentration above 1.0x10(-4) M.

Computer simulation for effect of Pr(III) on Ca(II) speciation in human interstitial fluid

A multiphase model of metal ion speciation in human interstitial fluid was constructed and the effect of Pr(III) on Ca(II) speciation was studied. Results show that free Ca2+, [Ca(HCO3)], and [Ca(Lac)] are the main species of Ca(II). Because of the competition of Pr(III) for ligands with Ca(II), the percentages of free Ca2+, [Ca(Lac)], and [Ca(His)(Thr)H-3] increase gradually and the percentages of CaHPO4(aq) and [Ca(Cit)(His)H-2] decrease gradually with the increase in the total concentration of Pr(III). However, the percentages of [Ca(HCO3)] and CaCO3(aq) first increase and then begin to decrease when the total concentration of Pr(III) exceeds 6.070 x 10(-4) M.

Computer simulation of Gd(III) speciation in human interstitial fluid

The speciation and distribution of Gd(III) in human interstitial fluid was studied by computer simulation. Meantime artificial neural network was applied to the estimation of log beta values of complexes. The results show that the precipitate species, GdPO4 and Gd-2(CO3)(3), are the predominant species. Among soluble species, the free Gd(III), [Gd(HSA)], [Gd(Ox)] and then the ternary complexes of Gd(III) with citrate arc main species and [Gd-3(OH)(4)] becomes the predominant species at the Gd(III) total concentration or 2.2x10(-2)mol/L.

Computer Simulation Tb(lll) Speciation in Human Blood Plasma

A multi phase model of human blood plasma was developed and the Tb(Ⅲ) speciation in this system was studied. The results show that the speciation of Tb(Ⅲ) depends on the concentration of Tb(Ⅲ). When the concentration of Tb(Ⅲ) is below 4.000×10 -8 mol/L, most of Tb(Ⅲ) exists as soluble species while the concentration of Tb(Ⅲ) is in between 4.000 ×10 -8 mol/L and 1.667×10 -2 mol/L, precipitates(TbPO 4 and Tb 2 (CO 3 ) 3 ) are the dominant species of Tb(Ⅲ). Among soluble Tb(Ⅲ) ...

Computer simulation for effect of Tb3+ on Ca2+ speciation in human plasma

Effect of Tb3+ on Ca2+ speciation in human plasma was studied by means of the computer program of MINTEQA2. When Tb3+ ions are not added into the system, Ca2+ ions mostly distribute in free Ca2+ (74.7%) and the surplus distributes in Ca2+ complexes, such as [CaHCO3](+) (7.9%),[Ca(Lac)](+) (6.4%), CaHPO4 (1.3%), [CaHistidinateThreoninateH(3)](3+) (2.4%), [CaCitrateHistidinateH(2)] (2.3%) and CaCO3 (1.1%). Tb3+ can compete with Ca2+ for inorganic as well as biological ligands. An increase of concentration of Tb3+ in the system results in an increase of content of free Ca2+ and a decrease of contents of Ca2+ complexes.

The interaction of aldolase with the cytoplasmic domain of human erythrocyte band 3 inhibited by lanthanum ions

The effect of lanthanum ions on the activity of the cytoplasmic domain of human erythrocyte band 3 (CDB3), which was measured according to the inhibition to aldolase, was studied. In the presence of low concentration of lanthanum ions, the function of CDB3 to inhibit aldolase activity decreased significantly. It indicated that lanthanum ions in the erythrocyte would change the conformation of CDB3 and influence the control on aldolase activity.

Computer simulation of insoluble Pr(III) speciation in human interstitial fluid

A multi-phase model of Pr(III) speciation in human interstitial fluid was constructed and insoluble Pr(III) speciation was studied. When the total concentration of Pr(III) is below 8.401E-10 mol/L, soluble Pr(III) species are main species. With rising the total concentration of Pr(III), Pr(III) is firstly bound to phosphate to form precipitate of PrPO4, then bound to carbonate and another precipitate of Pr-2(CO3)(3) was obtained. When the total concentration is between 1.583E-9 mol/L and 4.000E-3 mol/L, the insoluble species are predominant Pr(III) species.

Computer simulation of human iodothyronine deiodinase single-chain antibody

Iodothyronine plays a major role in growth, basic metabolism and organ formation. It has an extremely limited source in the body. In this thesis, we designed iodothyronine(T4) as hapten. Then a single chain antibody displayed on phange was obtained from a human phage displaying a single chain antibody library. The specific genes of E3 was subcloned in P-5E vector. According to its amino acid sequences, we simulate its three dimention structure by computer. It has never been reported in PDB.

Amplified immunoassay of human IgG using real-time biomolecular interaction analysis (BIA) technology

An automated biomolecular interaction analysis instrument (BI-Acore) based on surface plasmon resonance (SPR) has been used to determine human immunoglobulin G (IgG) in real time. Polyclonal anti-human IgG antibody was covalently immobilized to a carboxymethyldextran modified gold film surface. The samples of human IgG prepared in HBS buffer were poured over the immobilized surface. The signal amplification antibody was applied to amplify the response signal. After each measurement, the surface was regenerated with 0.1 mol/L H3PO4. The assay was rapid, requiring only 30 min for antibody immobilization and 20 min for each subsequent process of immune binding, antibody amplification and regeneration. The antibody immobilized surface had good response to human IgG in the range of 0.12-60 nmol/L with a detection limit of 60 pmol/L. The same antibody immobilized surface could be used for more than 110 cycles of binding, amplification and regeneration. The results demonstrate that the sensitivity, specificity and reproducibility of amplified immunoassay using real-time BIA technology are satisfactory.