Molecular modeling on human CCR5 receptors and complex with CD4 antigens and HIV-1 envelope glycoprotein gp120

AIM: To investigate the interaction between human CCR5 receptors (CCR5) and HIV-1 envelope glycoprotein gp120 (HIV-1 gp120) and HIV-1 receptor CD4 antigens (CD4). METHODS: The structurally con served regions (SCR) of human CCR5 was built by the SYBYL/Biopolymer module using the corresponding transmembrane (TM) domain of bacteriorhodopsin (bR) as the template. The coordinates for amino-ter minal residue sequence, and carboxyl-terminal residue sequence, extracellular and cytoplasmic loops were generated using LOOP SEARCH algorithm. Subsequently the structural model was merged into the complex with HIV-1 gp120 and CD4. RESULTS: Human CCR5 interacted with both an HIV-1 gp120 and CD4. The N-terminal residues (especially Met1 and Gln4) of human CCR5, contacted with CD4 residues, mainly 7Nith one span (56 - 59) of CD4 in electrostatic interaction and hydrogen-bonds. The binding sites of human CCR5 were buried in a hydrophobic center surrounded by a highly basic periphery. On the other hand, direct interatomic contacts were made between ? CCR5 residues and 6 gp120 amino-acid residues, which included van der Waals contacts, hydrophobic interaction, and hydrogen bonds. CONCLUSION: The interaction model should be helpful for rational design 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.

小麦高分子量谷蛋白新亚基基因1Dx5’的克隆与分子标记

小麦是世界第一大粮食作物, 而HMW- GS 是直接影响小麦品质的重要因子。我国小麦面粉的烘烤品质普遍较差, 这与我国品种缺少优质的HMW- GS 有关，因此创造与发掘新的优质谷蛋白亚基编码基因，并开展相关生化、农学、分子生物学等方面研究、探讨优质的分子机理，对于培育优质小麦新品种具有重要意义。W958是我们培育的种间远缘杂交（T.durum Desf. ×T.aestivum L）优良品系，该品系在1D染色体上具有父母本没有的新型亚基，由于此亚基在SDS- PAGE电泳中具有和1Dx5亚基一样的电泳迁移率, 因此我们将该亚基命名为1Dx5’亚基。为了进一步从分子水平确证该亚基为新亚基和在育种中利用该亚基，本研究对该亚基的遗传规律、基因分子结构、品质特性和农艺性状等进行了分析。结果表明1Dx5’亚基在品质上与1Dx5亚基一样优质，对于品质的贡献大于1Dx2亚基。1Dx5’亚基具有特异的遗传规律，在分离群体中，此亚基占有极大的比例，该特性十分有利于将其导入高产小麦遗传背景中。此外，本研究扩增出了1Dx5’亚基基因的启动子区域、N－端区域和部分中间重复区域，并比较了1Dx5’和传统的1Dx5、1Dx2亚基在此区域氨基酸序列。结果进一步证明了1Dx5’是一个新的基因。通过蛋白质结构模拟分析，认为1Dx5’亚基的优良特性可能是由于1Dx5’亚基的的中部重复区域能形成分子间较强的氢键，加大了分子间的相互作用，使1Dx5’亚基的面团具有优良的品质，这为1Dx5’亚基的应用提供了理论基础。同时，本研究还设计用于区分1Dx5’和1Dx5等位基因的分子标记，解决了利用SDS-PAGE生化标记难以将二者区分的问题。Wheat is one of the major crops utilized worldwide. Nevertheless, due to the lackof the superior HMW- GS, the wheat quality in China is not satisfying. Therefore,identification and characterization of the superior HMW- GS will lay good foundation to the wheat breeding.W958 is a new bread wheat line developed by interspecific cross (T.durum Desf.×T.aestivum L). It contains a novel HMW- GS. We have designated such subunit as1Dx5’ here for its unique character. To confirm that such subunit is innovative andbeneficial for wheat breeding program on the molecular level, we have investigated itin terms of inheritance, DNA and protein sequence, dough property and agronomictrait associated with it. The result shows that 1Dx5’is as superior as 1Dx5 in terms of dough property.In addition, we have cloned the promoter, N- terminal as well as partial centralrepetitive domain of the allele coding for this subunit. Comparison of the amino acidsequence of 1Dx5’ with that of 1Dx5 and 1Dx2 showed that the superior quality of1Dx5’ subunit may result from the degree of conservation of the repetitive sequencesby which the glutenin polymers interact via inter-chain hydrogen bonds formedbetween the subunit repetitive domains with longer subunits forming more stableinteractions. In addition, we have developed two dominant molecular markers tofacilitate the discrimination of 1Dx5’ and 1Dx5 which could no be achieved by SDS-PAGE.

Self-assembly of p-sulfonatocalix[4]arene and a Ag-hmt coordination polymer into a porous structure

A novel porous material constructed from p-sulfonatocalix[4]arene molecules and a Ag-I coordination polymer has been structurally characterized. The porous supramolecular complex features a bilayer arrangement of p-sulfonatocalix[4]arene molecules linked by a Ag-I-hmt (hmt: hexamethylene- tetramine) coordination polymer through metal-ligand bonding, hydrogen bonding and host-guest interactions.

Preparation and Characterization of Interpenetration Polymer Network Films Based on Poly(vinyl alcohol) and Poly(acrylic acid) for Drug Delivery

A series of full interpenetrating polymer network (full-IPN) films of poly(acrylic acid) (PAA)/poly (vinyl alcohol) (PVA) were prepared by radical solution polymerization and sequential IPN technology. Attenuated total reflectance-Fourier transform infrared spectroscopy, swelling properties, mechanical properties, morphology, and glass transition temperature of the films were investigated. FTIR spectra analysis showed that new interaction hydrogen bonds between PVA and PAA were formed. Swelling property of the films in distilled water and different pH buffer solution was studied. Swelling ratio increased with increasing PAA content of IPN films in all media, and swelling ratio decreased with increasing PVA crosslink degree. Tensile strength and elongation at break related not only to the constitution of IPNs but also to the swelling ratio of IPNs.

Crystal packing motifs of oligothiophenes end-capped with N-containing aryls

Oligothiophenes (OThs) end-capped with 3-quinolyl or pyridyl with nitrogen atom at meta-, ortho- or para-position were synthesized. The single-crystal structures of the resulting molecules, i.e., o-PyTh4, m-PyTh4, p-PyTh4, QuTh2, and QuTh3, were successfully determined by single-crystal X-ray analysis. Pyridyl end-capped OThs; o-PyTh4, m-PyTh4, and p-PyTh4, adopt the different herringbone packing arrangement in crystals depending on the position of the nitrogen atom because of the presence of weak C-H center dot center dot center dot N hydrogen bonds. The p-PyTh4 molecules are linked each other along the long axis of the molecules to form the extended chains by C-H center dot center dot center dot N dimer synthon. For m-PyTh4, the C-H center dot center dot center dot N interactions two-dimensionally extend through C-H center dot center dot center dot N trimer synthon.

Type I collagen-mediated synthesis of noble metallic nanoparticles networks and the applications in Surface-Enhanced Raman Scattering and electrochemistry

In this paper, we demonstrated an effective enviromentally friendly synthesis route to prepare noble metallic (Au, Ag, Pt and Pd) nanoparticles (NPs) networks mediated by type I collagen in the absence of any seeds or surfactants. In the reactions, type I collagen served as stabilizing agent and assembly template for the synthesized metallic NPs. The hydrophobic interaction between collagen and mica interface as well as the hydrogen bonds between inter- and intra-collagen molecules play important roles in the formation of collagen-metallic NPs networks. The noble metallic NPs networks have many advantages in the applications of Surface-Enhanced Raman Scattering (SERS) and electrochemistry detection. Typically, the as-prepared Ag NPs networks reveal great Raman enhancement activity for 4-ATP, and can even be used to detect low concentration of DNA base, adenine.

A ternary supramolecular compound of p-sulfonatocalix[8]arene with 1D channels

A ternary supramolecular complex of [Ni(bipy)(2)(H2O)](4)(C8AS)center dot 17.6(H2O) (bipy=4,4'-dimethyl-2,2'-bipyridine and C8AS = p-sulfonatocalix[8]arene) has been synthesized by a hydrothermal method and characterized by FT-IR spectroscopy, TG-DTA analysis and single crystal X-ray diffraction. In the structure. the water-soluble p-sulfonatocalix[8]arene molecule adopts a double partial cone conformation and is coordinated by four nickel atoms each of which is bonded by two 4,4'-dimethyl-2,2'-bipyridine molecules and one water molecule at the same time. The tetranuclear Subunits are stacked into an extended 3D structure with 1D water-filled channels via hydrogen bonds and C-H center dot center dot center dot pi interactions.

Poly[[diaqua-mu-4,4 '-bipyridine-dinitratodi-mu-L-tyrosinato-dicopper(II)]: a chiral two-dimensional coordination polymer

The title compound, [Cu-2(C9H10NO3)(2)(NO3)(2)(C10H8N2)-(H2O)(2)](n), contains Cu-II atoms and L-tyrosinate (L-tyr) and 4,4'-bipyridine (4,4'-bipy) ligands in a 2:2:1 ratio. Each Cu atom is coordinated by one amino N atom and two carboxylate O atoms from two L-tyr ligands, one N atom from a 4,4'-bipy ligand, a monodentate nitrate ion and a water molecule in an elongated octahedral geometry. Adjacent Cu atoms are bridged by the bidentate carboxylate groups into a chain. These chains are further linked by the bridging 4,4'-bipy ligands, forming an undulated chiral two-dimensional sheet. O-H center dot center dot center dot O and N-H center dot center dot center dot O hydrogen bonds connect the sheets in the [100] direction. This study offers useful information for the engineering of chiral coordination polymers with amino acids and 4,4'-bipy ligands by considering the ratios of the metal ion and organic components.

A polymorph of diaquabis(pyrazine-2-carboxylato-kappa N-2(1),O)copper(II)

The title compound, [Cu(C5H3N2O2)(2)(H2O)(2)], is a new polymorph of the previously reported compound [Klein et al. (1982). Inorg. Chem. 21, 1891-1897]. The Cu-II atom, lying on an inversion center, is coordinated by two N atoms and two O atoms from two pyrazine-2-carboxylate ligands and by two water molecules in a distorted octahedral geometry with the water molecules occupying the axial sites. Intermolecular O-H center dot center dot center dot O, O-H center dot center dot center dot N and C-H center dot center dot center dot O hydrogen bonds connect the complex molecules into a two-dimensional layer parallel to (10 (1) over bar), whereas the previously reported polymorph exhibits a three-dimensional hydrogen-bonded network.

Hydrothermal synthesis, crystal structure and electrochemical properties of a novel 3D Dawson-type polyoxometalate supramolecular network

A novel Dawson-type polyoxometalate supramolecular architecture of the formula [4,4'-H(2)bipy](2.5)center dot[4,4'-Hbipy]center dot[P2W18O62]center dot 6.25H(2)O (4,4'-bipy = 4,4'-bipyridine) has been hydrothermally synthesised and characterised by means of elemental analysis, IR, CV and X-ray single-crystal diffraction. X-ray crystallography indicates that the title compound consists of Dawson-type polyoxoaions [P2W18O62](6-), water molecules and 4,4'-bipy units. The polyoxoanion clusters together with 4,4'-bipy units and water molecules to construct the three-dimensional supramolecular network through hydrogen bonds. The crystal structure analyses reveal that water molecules and 4,4'-bipy units play the important role on the packing arrangements of crystals. Cyclic voltammetry shows that the title compound exhibits three chemically reversible steps

Affinity and Specificity of Levamlodipine-Human Serum Albumin Interactions: Insights into Its Carrier Function

The affinity and specificity of drugs with human serum albumin (HSA) are crucial factors influencing the bioactivity of drugs. To gain insight into the carrier function of HSA, the binding of levamlodipine with HSA has been investigated as a model system by a combined experimental and theoretical/computational approach. The fluorescence properties of HSA and the binding parameters of levamlodipine indicate that the binding is characterized by one binding site with static quenching mechanism, which is related to the energy transfer. As indicated by the thermodynamic analysis, hydrophobic interaction is the predominant force in levamiodipine-HSA complex, which is in agreement with the computational results. And the hydrogen bonds can be confirmed by computational approach between levamlodipine and HSA. Compared to predicted binding energies and binding energy spectra at seven sites on HSA, levamlodipine binding HSA at site I has a high affinity regime and the highest specificity characterized by the largest intrinsic specificity ratio (ISR). The binding characteristics at site I guarantee that drugs can be carried and released from HSA to carry out their specific bioactivity.

Spectroscopic Study on Water Diffusion in Poly(ester urethane) Block Copolymer Matrix

The diffusion of water in a phase-separated biodegradable poly(ester urethane) shape-memory polymer with poly(E-caprolactone) (PCL) as the soft segment was investigated using time-resolved FTIR-ATR. On the basis of the band fitting and water ordering in drawn films, the broad water band in the 3800-2800 cm(-1) region was decomposed into four bands located at 3620, 3510, 3400, and 3260 cm(-1), and the first two components at 3620 and 35 10 cm(-1) were assigned to the vibrations of antisymmetric and symmetric stretching of water hydrogen bonded with the C=O group of the soft segment. The other two were associated with water bonded to the urethane hard segments in the forms of N-H:O-H:O=C bridge hydrogen bond and double hydrogen bonds with two C=O groups, respectively. Furthermore, band fitting and two-dimensional correlation analyses revealed that in the diffusion process, water first diffuses into the continuous soft-rich PCL phase and then into the hard-rich urethane domains, forming double hydrogen bonds with two C=O groups prior to the bridge hydrogen bond in the form of N-H:O-H:O=C.