Functionally relevant protein motions: extracting basin-specific collective coordinates from molecular dynamics trajectories

Functionally relevant motion of proteins has been associated with a number of atoms moving in a concerted fashion along so-called "collective coordinates." We present an approach to extract collective coordinates from conformations obtained from molecular dynamics simulations. The power of this technique for differentiating local structural fluctuations between classes of conformers obtained by clustering is illustrated by analyzing nanosecond-long trajectories for the response regulator protein Spo0F of Bacillus subtilis, generated both in vacuo and using an implicit-solvent representation. Conformational clustering is performed using automated histogram filtering of the inter-C(alpha) distances. Orthogonal (varimax) rotation of the vectors obtained by principal component analysis of these interresidue distances for the members of individual clusters is key to the interpretation of collective coordinates dominating each conformational class. The rotated loadings plots isolate significant variation in interresidue distances, and these are associated with entire mobile secondary structure elements. From this we infer concerted motions of these structural elements. For the Spo0F simulations employing an implicit-solvent representation, collective coordinates obtained in this fashion are consistent with the location of the protein's known active sites and experimentally determined mobile regions.     

Organic Crystal Rings Formed in Template Polymer Pores by Evaporation of Solvent

Summary: The fabrication of organic crystals into useful forms might play an important role in future electronics technology. A method for fabricating organic crystal rings has been developed. The self‐assembly of six‐armed poly(methyl methacrylate) with a triphenylene core leads to the formation of pores homogeneously distributed in the polymer film. Because the solubility of this polymer in tetrahydrofuran (THF) is lower than that of 2,3,6,7,10,11‐hexamethacrylate triphenylene (HMTP), the holes initially formed and distributed in the polymer film are filled with a THF solution of HMTP. Crystallization nucleation occurs at the edge of holes and HMPT crystals grow at the contact line to form organic crystal rings.

Schematic illustration of crystal‐ring formation.     

Photoinduced electron transfer across linearly fused oligo-norbornyl structures

The rates of photoinduced electron transfer (ET) reactions across two oligo-norbornyl spacer groups (S), that is, structure 1 fused by two norbornadiene (NBD) units and structure 2 fused by three NBD units, are examined. Substituted naphthalene acted as an electron donor (D), whilst ethylene-1,2-dicarboxylate as an electron acceptor (A). ET rates were measured by fluorescence quenching experiments on these D-S-A dyads, and the results were correlated with reaction free energies according to the Marcus relationship. It was found that naphthalene with phenyl substituents showed relatively slower ET rates. The conformational flexibility of phenyl substituents may cause a hindrance on the electronic coupling between D and A. Another salient feature was the abnormally high quenching rates observed in nonpolar solvents such as cyclohexane, the results of which may be ascribed to a competing energy transfer process.     

MOLECULAR ENGINEERING STUDIES ON NONTHROMBOGENIC BIOMATERIALS——A NOVEL CLASS OF NONTHROMBOGENIC BIOMATERIALS WITH ZWITTERIONIC STRUCTURE OF CARBOXYBETAINES

N,N-dimethyl-N-methacryloyloxyethyl-N-carboxyethyl ammonium (DMMCA) was graft-copolymerized onto the surface of segmented poly(ether urethane) (SPEU) and PE film. The carboxybetaine structure on SPEU and PE film surfaces was confirmed by ATR-FTIR, XPS and water contact angle measurements. Through the experiments with platelet adhesion and protein adhesion assay in vitro, the two materials studied, including poly-DMMCA gel, all show excellent nonthrombogenicity. This confirms once again that the zwitterionic molecular structure on the surfaces of materials is essential for improving their nonthrombogenicity and biocompatibility.     

Carboxylic Acids from <Emphasis Type="Italic">Phyllanthus urinaria</Emphasis>

Five compounds, terephthalic acid mono-[2-(4-carboxy-phenoxycarbonyl)-vinyl] ester (1), (E)-3-(5′-hydroperoxy-2,2′-dihydroxy[1,1′-biphenyl]-4-yl)-2-propenoic acid (2), 3,4,5-trihydroxybenzoic acid (3), succinic acid (or butanedioic acid) (4), and 2,3,4,5,6-pentahydroxybenzoic acid (5), were isolated from Phyllanthus urinaria. The structures of these compounds were elucidated by means of spectral techniques including IR, MS, and 1D/2D NMR. 1 and 2 are new compounds.__________Published in Khimiya Prirodnykh Soedinenii, No. 1, pp. 14–17, January–February, 2005.     

Synthesis and crystal structure of two novel nickel (imidazole) complexes having hydrogen-bonded networks

Two nickel (imidazole) complexes, Ni(im)₆Cl₂·4H₂O (1) and Ni(im)₆(NO₃)₂ (2) (im=imidazole) have been synthesized and characterized by elemental analysis, IR, UV, TG and single crystal X-ray diffraction. 1 crystallizes in the triclinic space group P-1 with a=8.800(6) Å, b=9.081(6) Å, c=10.565(7) Å, =75.058(9)°, β=83.143(8)°, γ=61.722(8)°, V=718.3(8) Å³, Z=1 and R₁ (wR₂)=0.0469 (0.1497). 2 crystallizes in the trigonal space group R-3 with a=12.370(6) Å, b=12.370(6) Å, c=14.782(14) Å, =90.00°, β=90.00°, γ=120.00°, V=1959(2) Å³, Z=3 and R₁ (wR₂)=0.0358 (0.0955). 1 and 2 exhibit different supramolecular network due to their different counter anions and different hydrogen bonding connection. In compound 1, [Ni(im)₆]²⁺ cation and counter anions Cl⁻ alternatively array in an ABAB fashion via N–HCl hydrogen bonding. In compound 2, the plane of each NO₃²⁻ is almost parallel and each NO₃²⁻ connect three different [Ni(im)₆]²⁺ cations via N–HO hydrogen bonding.     

荧光光谱法研究钙试剂羧酸钠与牛血清白蛋白结合反应特征

不同温度下,研究了钙试剂羧酸钠与牛血清白蛋白作用的荧光猝灭光谱、同步荧光光谱、三维荧光光谱和紫外可见吸收光谱特征;分别用SternVolmer方程和LineweaverBurk双倒数方程等处理实验数据,得到了26℃时反应的结合常数为7.664×104mol/L,结合位点数为1.522,结合反应的标准焓变、标准熵变和标准吉布斯自由能变分别为-58.36kJ/mol,-101.7J/K和-27.958kJ/mol;分析所得光谱,证实了在实验浓度和温度范围内,CCS与BSA反应可形成具有一定结构的复合物,获得了CCS对BSA构型的影响等重要信息。     

纳米TiO2膜用于光催化氧化测定化学需氧量的研究

A photocatalytic oxidation method for determination of chemical oxygen demand （COD） using nano-TiO2 film, based on the use of a nano-TiO2-Ce（SO4）2 system and electrochemical detection, was proposed. The technique was originated from the direct determination of the Ce（Ⅲ） concentration change resulting from photocatalytic oxidation of organic compounds. Ce（Ⅲ）, which was produced by photocatalytic reduction of Ce（SO4）2, could be measured at a multi-walled carbon nanotubes （MWNT） chemically modified electrode （CME）. The COD values by this method were calculated from the differential pulse voltammetry （DPV） current of Ce（Ⅲ） at the CME. Under the optimal operation conditions, the detection limit of 0.5 mg·L^-1 COD with the linear range of 1-600 mg·L^-1 was achieved. This method was also applied to determination of various COD of ground water and wastewater samples. The resuits were in good agreement with those from the conventional COD methods, i.e., permanganate and dichromate ones.     

Two Novel Olean Triterpenoids from Celastrus hypoleucus

Two new triterpenoids, (3β)‐olean‐12‐ene‐3,23‐diol ( 1 ) and (6α)‐6‐hydroxyolean‐12‐en‐3‐one ( 2 ) were isolated from the MeOH extract of the stalks of Celastrus hypoleucus (Oliv .) Warb ., together with the seven known compounds (3β,22α)‐3,22‐dihydroxyolean‐12‐en‐29‐oic acid, β‐amyrin and β‐amyrin palmitate, wilforlide A, wilforilide B, palmitic acid, and β‐sitosterol. Their structures were elucidated on the basis of spectroscopic data and, in the case of 2 , by X‐ray crystallography. Compound 1 showed moderate cytotoxicity against human cervical squamous carcinoma (Hela) cells.     

Nitrophenol Derivatives Oxidized by Cerium(IV) Ammonium Nitrate (CAN) and Their Cytotoxicity

Oxidation of a series of phenols with cerium(IV) ammonium nitrate (CAN) in acetonitrile under mild conditions yields the mixture of corresponding nitrophenols. In the cases of methylphenols and hydroxy ‐carboxylic acids, the steric effect may reduce the nitration reaction. Compounds 3a and 4b showed selective activities to Hep 3B and Hep G2 cancer cell lines, respectively. Compound 2c showed selective activities to Hep G2 and MDA‐MB‐231 cancer cell lines. Furthermore, compound 10b showed selective activities to Hep G2, Hep 3B, MCF‐7 and MDA‐MB‐231 cancer cell lines.