基于结合位点的辅酶A结合蛋白家族的分类

发展了一种基于分子相互识别的蛋白质分类方法, 应用数据挖掘策略与统计学聚类, 根据辅酶A (coenzyme-A, CoA)结合蛋白的结合模式特征数据, 通过对比和分析多种分类方法对该体系的分类准确度, 对这类体内重要的蛋白进行了分类方法学研究, 选择了最优的两步聚类法. 本研究工作设计和建立了一个分类参数, 可以简洁有效地评价出各个结合特征的显著性与重要性, 并以此为依据从所有特征中筛选出决定性的特征变量. 研究结果所得到的CoA结合蛋白的三个分类, 都具有显著的氢键与疏水结合特征; CoA可以与多个生物活性关键氨基酸残基形成氢键作用. 这些相互作用的共性及分类上的差异, 说明了配体与不同受体相互作用过程中结合模式上的细微差别, 对于以CoA结合蛋白为靶点的选择性调控分子设计具有重要的参考意义与指导作用.     

Structural and Binding Effects of Chemical Modifications on Thrombin Binding Aptamer (TBA)

The thrombin binding aptamer (TBA) is a promising nucleic acid-based anticoagulant. We studied the effects of chemical modifications, such as dendrimer Trebler and NHS carboxy group, on TBA with respect to its structures and thrombin binding affinity. The two dendrimer modifications were incorporated into the TBA at the 5′ end and the NHS carboxy group was added into the thymine residues in the thrombin binding site of the TBA G-quadruplex (at T4, T13 and both T4/T13) using solid phase oligonucleotide synthesis. Circular dichroism (CD) spectroscopy confirmed that all of these modified TBA variants fold into a stable G-quadruplex. The binding affinity of TBA variants with thrombin was measured by surface plasmon resonance (SPR). The binding patterns and equilibrium dissociation constants (K_D) of the modified TBAs are very similar to that of the native TBA. Molecular dynamics simulations studies indicate that the additional interactions or stability enhancement introduced by the modifications are minimized either by the disruption of TBA–thrombin interactions or destabilization elsewhere in the aptamer, providing a rational explanation for our experimental data. Overall, this study identifies potential positions on the TBA that can be modified without adversely affecting its structure and thrombin binding preference, which could be useful in the design and development of more functional TBA analogues.     

Moco Carrier and Binding Proteins

The molybdenum cofactor (Moco) is the active site prosthetic group found in numerous vitally important enzymes (Mo-enzymes), which predominantly catalyze 2 electron transfer reactions. Moco is synthesized by an evolutionary old and highly conserved multi-step pathway, whereby the metal insertion reaction is the ultimate reaction step here. Moco and its intermediates are highly sensitive towards oxidative damage and considering this, they are believed to be permanently protein bound during synthesis and also after Moco maturation. In plants, a cellular Moco transfer and storage system was identified, which comprises proteins that are capable of Moco binding and release but do not possess a Moco-dependent enzymatic activity. The first protein described that exhibited these properties was the Moco carrier protein (MCP) from the green alga Chlamydomonas reinhardtii. However, MCPs and similar proteins have meanwhile been described in various plant species. This review will summarize the current knowledge of the cellular Moco distribution system.     

Study on Synthesis and Binding Ability of a New Anion Receptor Containing NH Binding Sites

A new colorimetric recognition receptor 1 based on the dual capability containing NH binding sites of selectively sensing anionic guest species has been synthesized. Compared with other halide anions, its UV/Vis absorption spectrum in dimethyl sulfoxide showed the response toward the presence of fluoride anion with high selectivity, and also displayed dramatic color changes from colorless to yellow in the presence of TBAF （5 × 10^-5 mol/L）. The similar UV/Vis absorption spectrum change also occurred when 1 was treated with AcO^- while a little change with H2PO^-4 and OH^-. Receptor 1 has almost not affinity abilities to Cl^-, Br^- and I^-. The binding ability of receptor 1 to fluoride with high selectivity over other halides contributes to the anion size and the ability of forming hydrogen bonding. While the different ability of binding with geometrically triangular （AcO^-）, tetrahedral （H2PO^-4 ） and linear （OH^-） anions maybe result from their geometry configuration.     

Binding of Ionic Species: A General Approach To Measuring Binding Constants and Assessing Affinities

Bound together : The association of receptors with ionic species cannot be assimilated to the binding of neutral guests. When dealing with salts, both ion pairing and binding to the free and the ion‐paired ionic guest determine the actual association pattern (see figure). The general issue of measuring association constants and assessing affinities for ions is addressed and validated in two cases of anion binding.

     

Binding properties of alginic acid and chitin

The binding properties of granular alginic acid(H-alg.) and chitin to iodine, bromine, cadmium ion, calcium ion and cholesterol were investigated. Chitin-iodine and chitin-bromine compounds closely resemble those of H-alg. The amount of iodine included by these polysaccharides increased with a decrease in the concentration of potassium iodide (KI). The number of sugar residues bound to one iodine molecule extrapolated to 0 g of KI was around 6.0 for H-alg. and 6.4 for chitin. These saccharides, which do not form a gel in water, were found to also absorb KI and radioactive iodide or iodine in aqueous solution. H-alg. did not show as much affinity to cadmium ion and calcium ion and cholesterol in iso-propyl alcohol as metalalginates.Presented at the Fourth International Symposium on Inclusion Phenomena and the Third International Symposium on Cyclodextrins, Lancaster, U.K., 20–25 July 1986.     

Supramolecular Metallacycles and Their Binding of Fullerenes

The synthesis of a new triaminoguanidinium-based ligand with three tris-chelating [NNO]-binding pockets and C₃ symmetry is described. The reaction of tris-(2-pyridinylene-N-oxide)triaminoguanidinium salts with zinc(II) formate leads to the formation of cyclic supramolecular coordination compounds which in solution bind fullerenes in their spherical cavities. The rapid encapsulation of C₆₀ can be observed by NMR spectroscopy and single-crystal X-ray diffraction and is verified using computation.     

Binding properties of octaaminocryptands

Complexation and protonation equilibria were studied in aqueous solution for a new range of aminocryptand ligands, N(CH2CH2NHCH2RCH2NHCH2CH2)3N, (R = m-xylyl, p-xylyl, 2,5-furan, 2,6-pyridine) and demonstrate that stability constants for first transition series ions Co2+ to Zn2+ are relatively high. X-ray crystallography shows that the cryptands are reasonably well preorganized for complexation. The furan-spaced cryptand L6.H2O crystallizes in the rhomobohedral space group R3 (no. 148) with a = 14.645(1), b = 14.645(1), and c = 25.530(4) A, whereas the m-xylyl-spaced cryptand L4 crystallizes in the triclinic space group P1 (no. 2) with a = 9.517(1), b = 15.584(2), and c = 23.617(4) A. The highest formation constant (log beta21 = 33.07) is observed for the dicopper cryptate of a pyridine-spaced cryptand, suggesting involvement in complexation of donors from the spacer link. This pyridine-spaced host also shows good selectivity for copper(II) over zinc(II), making it a possible candidate for treatment of copper-excess pathology.     

麻黄碱的分子烙印聚合物的制备方法及其结合性能

分子烙印;麻黄碱;结合能力;紫外光谱;功能单体     

Local Unfolding of Fatty Acid Binding Protein to Allow Ligand Entry for Binding

Fatty acid binding proteins are responsible for the transportation of fatty acids in biology. Despite intensive studies, the molecular mechanism of fatty acid entry to and exit from the protein cavity is still unclear. Here a cap‐closed variant of human intestinal fatty acid binding protein was generated by mutagenesis, in which the helical cap is locked to the β‐barrel by a disulfide linkage. Structure determination shows that this variant adopts a closed conformation, but still uptakes fatty acids. Stopped‐flow experiments indicate that a rate‐limiting step exists before the ligand association and this step corresponds to the conversion of the closed form to the open one. NMR relaxation dispersion and H‐D exchange data demonstrate the presence of two excited states: one is native‐like, but the other adopts a locally unfolded structure. Local unfolding of helix 2 generates an opening for ligands to enter the protein cavity, and thus controls the ligand association rate.     

金属配合物键合DNA的研究进展*

本文对金属配合物键合DNA 研究领域的背景、内容、潜在应用及发展前景作了综述, 详尽地介绍了国际上在金属配合物与DNA 作用过程、机制等方面的最新研究进展。     

Rugulosin对N-Hsp90的抑制与结合作用

经Docking模拟发现Rugulosin能与Hsp90N端的ATPase活性结构域结合,体外实验表明,其抑制Hsp90的ATPase活性的IC50为22.77μM。应用荧光,圆二色,紫外－可见吸收等光谱法及SPR技术研究Rugulosin与Hsp90N端蛋白（N-Terminal of Hsp90,NHsp90）的相互作用机制．荧光光谱实验结果表明Rugulosin对Hsp90的内源荧光具有较强的猝灭作用,其猝灭方式为静态猝灭。热力学计算得知,Rugulosin通过静电引力与NHsp90结合, 解离常数为22.4±0.17μM。圆二色光谱检测发现, Rugulosin会影响NHsp90的α-螺旋数, Rugulosin浓度的增加,NHsp90蛋白的α-螺旋减少。本研究结果表明Rugulosin可以与Hsp90结合,进而抑制其ATPase活性。Ruglulosin可能是潜在的Hsp90的抑制剂。     

Binding Mode of Insulin Receptor and Agonist Peptide

LI Wei Introduction In1986,Geysen[1]foundthatshortpeptidescon tainingthekeyresiduesofaproteincanmimicthede terminantoftheprotein;mostofthebindingenergybe tweenproteinsresultsfromthenoncovalentinteractions ofsomekeyresidues.Thesesmallpeptidesgenerally have…     

三联吡啶-萘酰亚胺二元化合物的合成及其与DNA的相互作用

本文合成了两种三联吡啶修饰的萘酰亚胺化合物NPI1和NPI2,并利用紫外-可见吸收光谱(UV-Vis)、圆二色光谱(CD)、荧光共振能量转移(FRET)等方法研究了它们与双链CT DNA和Htelo G-四链体DNA的相互作用。实验结果表明,化合物NPI1和NPI2对G-四链体DNA具有很好的结合能力和选择性,溶液中的碱金属离子种类和萘酰亚胺基团上的取代基对NPI1和NPI2与DNA的作用有很大的影响。在含K+的缓冲液中,NPI2与G-四链体的结合常数达到1.06×108 L/mol,是与双链CT DNA结合常数的268倍。圆二色谱结果表明在不含碱金属离子的溶液中,NPI1和NPI2可诱导Htelo DNA形成反平行结构G-四链体。Autodock分子对接模拟表明NPI1和NPI2可以通过堆积作用、静电作用、氢键等作用方式与G-四链体结合,使得它们对G-四链体具有很高亲和性(Ka>107 L/mol)。     

Synthesis and Binding of Mannose-Specific Synthetic Carbohydrate Receptors

Synthetic carbohydrate receptors (SCRs) that selectively recognize cell-surface glycans could be used for detection, drug delivery, or as therapeutics. Here we report the synthesis of seven new C_2h symmetric tetrapodal SCRs. The structures of these SCRs possess a conserved biaryl core, and they vary in the four heterocyclic binding groups that are linked to the biaryl core via secondary amines. Supramolecular association between these SCRs and five biologically relevant C¹-O-octyloxy glycans, α/β-glucoside ( α/β-Glc ), α/β-mannoside ( α/β-Man ), and β-galactoside ( β-Gal ), was studied by mass spectrometry, ¹H NMR titrations, and molecular modeling. These studies revealed that selectivity can be achieved in these tetrapodal SCRs by varying the heterocyclic binding group. We found that SCR017 (3-pyrrole), SCR021 (3-pyridine), and SCR022 (2-phenol) bind only to β-Glc. SCR019 (3-indole) binds only to β-Man. SCR020 (2-pyridine) binds β-Man and α-Man with a preference to the latter. SCR018 (2-indole) binds α-Man and β-Gal with a preference to the former. The glycan guests bound within their SCR hosts in one of three supramolecular geometries: center-parallel, center-perpendicular, and off-center. Many host–guest combinations formed higher stoichiometry complexes, 2:1 glycan⋅SCR or 1:2 glycan⋅SCR , where the former are driven by positive allosteric cooperativity induced by glycan–glycan contacts.     

米托蒽醌与生物大分子DNA结合平衡的研究

米托蒽醌(MX)是一个广谱高效的葸醌类抗癌新药(下式),核酸是该类药物的主要细胞作用靶位,它通过与DNA结合,影响DNA的转译和复制,从而起到抗癌作用。研究这类药物与核酸的作用对于阐明抗癌机理具有重要意义,为此,广泛地开展了这方面的研究。     

Binding of sulfonamides to erythrocytes and their components

Binding of zonisamide, a new antiepileptic sulfonamide derivative, was examined to human erythrocytes, their lysate and their carbonic anhydrase by centrifugation for cells or by ultrafiltration for the others. Scatchard plots revealed that the binding to intact and lysed cells was composed of high- and low-affinity components and that to carbonic anhydrase, of the high-affinity component alone. Parameters for high-affinity binding were similar in all three preparations and those for low-affinity binding were similar in the former two preparations. Dissociation constants for these bindings to erythrocytes were smaller than the dissociation constant for serum albumin. These results may explain the concentration of sulfonamides in red cells, and suggest the participation of cellular protein component(s) in addition to previously known carbonic anhydrase in the binding. Acetazolamide, sulthiame, zonisamide, hydrochlorothiazide and sulfanilamide inhibited carbonic anhydrase in a non-competitive manner to different extents. The Ki values of these sulfonamides were of the order of 0.1--0.2 of their respective Kd values determined by ultrafiltration, suggesting that under the present conditions, physicochemical interactions between sulfonamides and carbonic anhydrase primarily occur at common sites that affect the activity of the enzyme.     

磺化冠醚的分子键合与组装

冠醚作为第一代大环主体分子,具有柔性的空腔,因其对金属离子、有机阳离子的络合作用而被广泛用于构筑超分子组装体。磺化冠醚是一种水溶性良好的阴离子型冠醚衍生物,相比于冠醚,它具有更多的键合位点,对金属离子、有机阳离子具有更强的键合和良好的选择性。本文从磺化冠醚的合成,对碱金属离子、镧系金属的络合,对有机阳离子客体的组装等方面介绍了磺化冠醚的研究进展。然后从热力学、晶体结构学的角度综合分析了磺化冠醚键合与组装的模式及驱动力。最后讨论了磺化冠醚的分子键合与组装发展所面临的挑战,并对其应用前景进行了展望。