ATP合酶中α亚基推动γ亚基旋转的可能机制

F1F0-ATP合酶是一种分子马达,它能够利用跨膜的质子浓度梯度推动γ亚基旋转,进而在α/β亚基界面上催化合成ATP,也能够利用ATP水解推动γ亚基旋转,将ATP中蕴藏的化学能转变成为机械能.ATP水解发生在α/β亚基界面上.但是在ATP水解过程中,高能磷酸键断裂释放的能量如何传递给γ亚基,使之旋转?什么原因导致了α/β亚基产生相对运动?本文提出的假说认为:ATP在与α/β界面上的关键氨基酸αArg376、βArg182的相互作用过程中,使Arg的结构由原来的卷曲型转变为伸展型,从而引发催化活性区域的空间构象发生变化,进而推动α/β亚基的相对运动.α/β亚基之间的相对运动传递给γ亚基并使之旋转.     

多种精氨酸衍生物与ＡＴＰ作用及其催化ＡＴＰ水解的影响研究

分别使用荧光光谱法、 ~1H和~(31)P核磁方法对腺苷-5′-三磷酸(ATP)和多种L-精氨酸衍生物(L)的相互作用做了系统的研究, 得到了一些有意义的结果.在荧光滴定实验中, L对ATP有很强的荧光猝灭作用, 说明两者有较强的相互作用. ~1H和~(31)P核磁结果进一步证实了L与ATP的识别位点在ATP的嘌呤环和磷酸链上, 结合力为氢键和静电作用. 另外, 用~(31)P 核磁滴定的方法考察了L对ATP水解的影响, 发现不同的精氨酸衍生物对ATP水解的催化影响有很大的差异, 说明L对ATP的识别和催化其水解作用有较强的选择性. 此识别及催化作用的研究对深入理解精氨酸残基在ATP合酶中起到"触点"作用有一定的参考价值.     

ATP与对甲基苯磺酰-L-精氨酸甲酯盐酸盐的弱相互作用光谱法研究

本文分别使用荧光猝灭光谱法、荧光滴定实验及FT-IR光谱法对腺苷-5´-三磷酸（ATP）和对甲基苯磺酰-L-精氨酸甲酯盐酸盐（TAME）的相互识别作用做了系统的研究，并得出了一些有意义的结果。在荧光实验中，发现TAME对ATP有很强的荧光猝灭作用，同时为了进一步验证TAME与ATP的相互作用又利用红外光谱法，推测出两者的识别作用位点是在TAME的主链胍基和ATP的磷酸根基团上，结合力为氢键和静电相互作用力。另一方面，本文又分别考察了TAME同ADP和AMP的作用，用Stern-Volmer方程分别计算出相应的猝灭常数，发现TAME与ADP和AMP的作用非常弱，说明TAME对ATP的识别作用有较强的选择性。这种识别作用的发生，对深入理解在ATP合成和水解过程中，ATP合酶中精氨酸残基如何起到“触点”的作用有一定的参考价值。     

结核分枝杆菌EPSP合酶与草甘膦的分子对接研究

采用Autodock4.2分子对接软件包,对结核分枝杆菌5-烯醇式丙酮酰莽草酸-3-磷酸合酶(5-Enolpyruvylshikimate-3-phosphate synthase,简称EPSP合酶)和草甘膦的相互作用机制进行了分子对接研究.研究结果表明,草甘膦与结核分枝杆菌EPSP合酶结合能为-28.27kcal/mol;结合位点位于该酶底物磷酸烯醇式丙酮酸(PEP)的结合位点上,并与底物形成竞争性结合;草甘膦能与结核分枝杆菌EPSP合酶中位于活性空腔的Glu311,His340,Thr97及Arg124等11个氨基酸残基及酶底物S3P形成疏水作用;结核分枝杆菌EPSP合酶中Arg385,Arg344,His384,Lys23,Gly96,Arg124,Lys410,Glu341 8个氨基酸残基能与草甘膦上的羧基及磷酸基团形成10个氢键,推测草甘膦的羧基及磷酸基团是草甘膦对EPSP合酶抑制作用的物质基础;草甘膦与结核分枝杆菌EPSP合酶结合的主要推动力为氢键、疏水作用及静电作用力.研究结果可为草甘膦的结构改良及EPSP合酶基因的改造提供理论参考,并为通过对莽草酸途径的抑制作用这一崭新方法来研发新型抗结核药物提供科学依据.     

Cd(Ⅱ)和ATP的结合位点的NMR研究

用NMR方法研究了金属镉离子在ATP(嘌呤三磷酸腺苷)上的配位点.测量了不同pH值时由于Cd²⁺的存在而引起的¹H,¹⁵N及³¹P的化学位移和³¹P－³¹P中的偶合常数的变化以及由ATP的存在所引起的¹¹³Cd的化学位移的变化.结果表明,在pH＞4.5的条件下,ATP主要以磷酸根和N₇同时对Cd²⁺配位;在pH值2.5～4.5的条件下,ATP主要以磷酸根和N₁同时对Cd²⁺配位,还存在少量的磷酸根和N₇同时配位的模式;而在酸性非常强的条件下(pH＜2.5),ATP不再与Cd²⁺相互作用。     

Aerolysin纳米孔核酸检测灵敏区域的协同相互作用探索研究

纳米孔单分子检测技术以其简便、快速、高通量及无需标记等特点, 应用于DNA及蛋白质测序, 更有望实现单分子动态构象变化的研究. Aerolysin(气单胞菌溶素)纳米孔道由于其特有的较长的β-桶限域区(β-barrel)及孔内壁丰富的带电荷氨基酸残基, 在单个寡聚核苷酸分子分析中展现出极高的灵敏性. 本设计利用dA₁₄-4-X, dA₁₄-11-X, dA₁₄-4-X-11-X (X=C, T, G)等单个寡聚核苷酸探针分子, 研究了Aerolysin的两个灵敏区域R1和R2, 探索了R1灵敏区域对单个碱基弱相互作用的差异, 实现区分单个碱基差异. 进一步实验证明, R1灵敏区域对单个碱基类型差异的灵敏区分不受R2灵敏区域被碱基A、C、T占位所影响. 然而, 当R2区域被碱基G占位时, 会使R1区域丧失对整个孔道电流的主导性. 本研究有助于理解Aerolysin对单个寡聚核苷酸分子的超灵敏测量机制.     

NaY沸石超笼中合成12-钼磷杂多酸

针对负载杂多酸催化剂在极性反应体系中活性组分易溶脱的难题, 用“瓶中造船(ship in the bottle)”的方法在NaY沸石超笼中合成了12-钼磷酸. 将机械混和的MoO₃晶体和NaY沸石在高温下焙烧, 使MoO₃在沸石表面高度分散, 以此复合物在磷酸水溶液中反应, 得到的固体样品用X射线衍射仪(XRD)、³¹P核磁共振谱(³¹P NMR)和红外光谱(IR)进行了表征, 并测试了其在醋酸和正丁醇的酯化反应中的催化性能. 结果表明, MoO₃质量分数为10%的MoO₃/NaY 中载体仍保持Y沸石的结构, 以此为原料合成的样品呈现出Keggin结构杂多酸的红外特征峰, 并且在核磁共振磷谱中杂多酸的化学位移峰向负值方向发生了较大程度的位移, 说明杂多阴离子与Y沸石羟基发生了强相互作用, 样品在醋酸与正丁醇的酯化反应中显示出了较高的催化活性和优异的重复使用性能. 这些充分说明在NaY沸石超笼中成功合成了12-钼磷酸.     

人参二醇类皂苷的生物转化动态及人参稀有皂苷C-K或F2的制备

为了低成本有效制备人参稀有皂苷C-K或F₂, 将A. niger g.848菌酶用于转化含有人参皂苷(质量分数)分别为49.6% Rb₁, 25.9% Rd, 19.3% Rc和5.23% Rb₂的西洋参二醇混合皂苷. 霉菌发酵时, 采用人参二醇皂苷诱导物比人参提取液诱导物的产酶总活力提高10%~15%. 所产的2种诱导酶均能水解人参二醇皂苷的3-O-和20-O-多种糖基, 均为人参皂苷酶Ⅰ型; 但是人参二醇皂苷诱导物所产酶几乎全部转化人参二醇皂苷为C-K, 而人参提取液诱导物所产酶则残留中间产物. 使用黑曲霉人参二醇皂苷诱导所产酶, 在转化西洋参二醇皂苷的动态研究中发现, 酶反应1.5~2.5 h, 主要为产物F₂; 酶反应12 h后, 主要产物为C-K皂苷. 基于此, 40 g人参二醇类皂苷在45 ℃粗酶反应24 h, 经处理得到含C-K质量分数为87%的23 g酶反应产物, C-K转化率达85%(摩尔分数). 用40 g西洋参二醇皂苷在45 ℃粗酶反应2.5 h, 经处理得到含有质量分数为58%的F₂和27%的C-K的26 g酶反应产物, F₂转化率为50.4%, C-K转化率为29.5%. 通过人参二醇皂苷诱导的黑曲霉粗酶转化人参二醇类皂苷动态研究, 建立了C-K转化率为85%, F₂转化率为50%的制备方法, 为大批量制备提供了基础依据.     

烷基修饰寡聚脱氧核苷酸磷酸残基的化学合成及稳定性研究

分别采用格氏试剂和三氯化磷三步取代法合成了4个新的烷基修饰磷酸残基的亚磷酸酰胺单体, 其结构经1H NMR和31P NMR表征. 利用这些单体合成模型序列5'-dTTTx TT-3', 考察了单体及寡聚核苷酸序列在DNA/RNA合成条件下的稳定性, 提出了固相合成含有烷基修饰磷酸残基的寡聚核苷酸序列裂解及脱保护条件.     

肌球蛋白中金属离子与ATP相互作用及其催化ATP水解的研究进展

生物体内细胞在氧化物质的过程中释放出的大量自由能,这些能量先形成高能磷酸化合物三磷酸腺苷（adenosine 5′-triphosphate,ATP）,当ATP水解为ADP（二磷酸腺苷,adenosine 5′-diphosphate）和无机磷酸时.     

Sequence-Tunable Phase Behavior and Intrinsic Fluorescence in Dynamically Interacting Peptides

A conceptual framework towards understanding biological condensed phases is emerging, derived from biological, biomimetic, and synthetic sequences. However, de novo peptide condensate design remains a challenge due to an incomplete understanding of the structural and interactive complexity. We designed peptide modules based on a simple repeat motif composed of tripeptide spacers (GSG, SGS, GLG) interspersed with adhesive amino acids (R/H and Y). We show, using sequence editing and a combination of computation and experiment, that n→π* interactions in GLG backbones are a dominant factor in providing sufficient backbone structure, which in turn regulates the water interface, collectively promoting liquid droplet formation. Moreover, these R(GLG)Y and H(GLG)Y condensates unexpectedly display sequence-dependent emission that is a consequence of their non-covalent network interactions, and readily observable by confocal microscopy.     

Multiple intermolecular interaction modes of positively charged residues with adenine in ATP-binding proteins

Adenosine 5'-triphosphate (ATP) plays an essential role in all forms of life. Molecular recognition of ATP in ATP-binding proteins is a subject of great importance for understanding enzymatic mechanisms and for drug design. We have carried out a large-scale data mining of the Protein Data Bank (PDB) to analyze molecular determinants for recognition of ATP, in particular, the adenine base, by ATP-binding proteins. A novel distribution pattern of charged residues around the adenine base was discovered: lysine residues tend to occupy the major groove N7 side of the adenine base, and the arginine residues situate preferentially above or below the adenine bases. Such an arrangement is advantageous because it facilitates multiple modes of intermolecular interactions, that is, cation-pi interactions and a hydrogen bond between lysine and adenine, and cation-pi and pi-pi stacking interactions between arginine and adenine. For the two representative Lys...Adenine and Arg...Adenine interactions, intermolecular interaction energies were subsequently analyzed by means of the supermolecular approach at the MP2 level with solvation free energy correction using the SM5.42R model of Cramer and Truhlar, which gave rise to significant interaction strengths.     

Investigating the Broad Matrix-Gate Network in the Mitochondrial ADP/ATP Carrier through Molecular Dynamics Simulations

The mitochondrial ADP/ATP carrier (AAC) exports ATP and imports ADP through alternating between cytosol-open (c-) and matrix-open (m-) states. The salt bridge networks near the matrix side (m-gate) and cytosol side (c-gate) are thought to be crucial for state transitions, yet our knowledge on these networks is still limited. In the current work, we focus on more conserved m-gate network in the c-state AAC. All-atom molecular dynamics (MD) simulations on a variety of mutants and the CATR-AAC complex have revealed that: (1) without involvement of other positive residues, the charged residues from the three Px[DE]xx[KR] motifs only are prone to form symmetrical inter-helical network; (2) R235 plays a determinant role for the asymmetry in m-gate network of AAC; (3) R235 significantly strengthens the interactions between H3 and H5; (4) R79 exhibits more significant impact on m-gate than R279; (5) CATR promotes symmetry in m-gate mainly through separating R234 from D231 and fixing R79; (6) vulnerability of the H2-H3 interface near matrix side could be functionally important. Our results provide new insights into the highly conserved yet variable m-gate network in the big mitochondrial carrier family.     

Role of the D-loops in allosteric control of ATP hydrolysis in an ABC transporter

ABC transporters couple ATP hydrolysis to movement of substrates across cell membranes. They comprise two transmembrane domains and two cytosolic nucleotide-binding domains forming two active sites that hydrolyze ATP cooperatively. The mechanism of ATP hydrolysis is controversial and the structural dynamic basis of its allosteric control unknown. Here we report molecular dynamics simulations of the ATP/apo and ATP/ADP states of the bacterial ABC exporter Sav1866, in which the cytoplasmic region of the protein was simulated in explicit water for 150 ns. In the simulation of the ATP/apo state, we observed, for the first time, conformers of the active site with the canonical geometry for an in-line nucleophilic attack on the ATP γ-phosphate. The conserved glutamate immediately downstream of the Walker B motif is the catalytic base, forming a dyad with the H-loop histidine, whereas the Q-loop glutamine has an organizing role. Each D-loop provides a coordinating residue of the attacking water, and comparison with the simulation of the ATP/ADP state suggests that via their flexibility, the D-loops modulate formation of the hydrolysis-competent state. A global switch involving a coupling helix delineates the signal transmission route by which allosteric control of ATP hydrolysis in ABC transporters is mediated.     

官能团化的手性联芳基单齿膦配体在不对称均相金催化反应中的应用

自2005年以来, 不对称均相金催化反应研究取得了显著的进展, 并在有机合成中得到了广泛应用. 近年来, 官能团化的联芳基单齿膦配体在金催化反应中显露头角, 为不对称金催化反应提供了新的发展思路. 本文综合评述了这一领域的研究进展, 着重介绍了近年来利用这类配体实现的金催化不对称反应及反应过程中配体与底物间相互作用.     

PO2X…PX3/PH2X(X=F,Cl, Br,CH3, NH2)复合物中π-hole磷键作用的电子密度拓扑分析

磷键作为一种新型的分子键合力,因在晶体工程和超分子合成等方面的重要作用而越来越多地引起科研工作者的广泛关注。本文采用量子化学从头算和电子密度拓扑分析等方法,在MP2/aug-cc-pVTZ理论水平上,对PO₂X…PX₃和PO₂X…PH₂X (X = F, Cl, Br, CH₃, NH₂) π型复合物的结构和磷键性质进行了理论研究。研究表明:π-hole磷键复合物存在A和B两种稳定构型,分别以P…P和P…X磷键作用为主。分子中原子(AIM)、非共价作用(NCI)、电子定域函数(ELF)及适应性自然密度划分(AdNDP)分析表明,不同取代基对该类磷键作用的性质产生很大影响:当取代基为给电子基(CH₃, NH₂)时,磷键具有明显的共价作用特征;当取代基为吸电子基(F, Cl, Br)时,构型和取代基不同的磷键分别表现为非共价、部分共价或共价作用特征。自然键轨道(NBO)分析指出,分子间磷键的Wiberg键级的数值越大,磷键的共价性越强,磷键的作用强度越大。构型B的电荷转移主要是PX₃/PH₂X中X原子上的孤对电子转移到PO₂X中π^*(P=O)反键空轨道。     

g-CN体系的准粒子能带结构和光学特性

利用多体格林函数理论,本文研究了二维CN体系(包括triazine和tri-s-triazine)的激发态特性。通过GW方法,我们计算了准粒子的能量。考虑电子-空穴相互作用,通过求解Bethe-Salpeter方程,我们获得了激发态能量和光谱。我们发现,在这两种CN体系的价带中,σ轨道和π轨道之间的交换作用非常强烈。由于占据的σ轨道和π轨道之间的准粒子修正量非常不同,因此,为了得到准确的带隙值和光谱,我们需要对这两种轨道开展精确的GW计算。与单层的CN体系相比,双层结构中层与层之间的范德华相互作用使带隙值降低了0.6 eV,而光吸收谱红移了0.2 eV,这是由于双层结构具有更小的激子束缚能。我们计算的吸收峰的位置与实验结果符合很好。实验中的吸收峰主要是由深能级的π轨道到π^*轨道的跃迁形成的。π→π^*跃迁和σ→π^*跃迁之间的耦合能够在长波长范围产生弱的吸收尾巴,如果调整入射光的极化方向,由σ→π^*跃迁产生的高强度的吸收峰将会在更低能量处出现。     

异氰酸苯酯诱导的类胶原多肽自组装

Synthetic matrices provide powerful tools for dissecting molecular interactions involved in the organization of the extracellular matrix (ECM), establishment of cell axis polarity, and suppression of neoplasticity in pre-cancerous endothelial cells. Collagen is the most abundant protein in extracellular matrix. A de novo approach is essential for the synthesis of collagen matrices which can have a broad impact on the understanding of matrix biology and our capacity to construct safe and medically useful biomaterials. Conventionally, the ECM has been studied by an analytical "top-down" approach, where the individual components of the matrix are first isolated and then characterized to explore their biochemical and functional properties. Since native collagen is difficult to modify and can engender pathogenic and immunological side effects, its application on tissue regeneration is limited. Therefore, we attempted to synthesize artificial collagen directly through small organic molecule recognition. The collagen-like peptides possess various benefits such as being clean, programmable, and easy to modify; therefore, in recent years, they have been used as ideal substrates for the synthesis of collagen nanomaterials. The self-assembly of collagen-like peptides is mainly driven by various non-covalent interactions such as electrostatic attraction, π-π stacking, and metal coordination. This renders a difficulty in the rational design of uniform nanostructures from short synthesized peptides and demands a novel strategy. To date, small organic molecules have been rarely used for the self-assembly of collagen-like peptides. In the present study, we attempted to use the small organic molecules for the combined supramolecular self-assembly of collagen-like peptides. Initially, the collagen-like peptides, (POG)₆ and (POG)₈, synthesized by the solid-phase synthesis technique, were both modified chemically using 4, 4'-methylene bis(phenyl isocyanate) to obtain the collagen-like hybrid peptides, AP₆ and AP₈, respectively. Phenyl isocyanate contributes to the formation of potential weak forces, such as hydrogen bonds and π-π stacking at the N-terminal regions of the collagen-like hybrid peptides. The purity and molecular weight of the collagen-like hybrid peptides were analyzed using analytical high-performance liquid chromatography (HPLC) and matrix-assisted laser desorption ionization time of flight (MALDI-TOF), respectively. The stability of AP₆ and AP₈ triple helices was analyzed by circular dichroism (CD) spectroscopy. The small organic molecule 4, 4'-methylene bis(phenyl isocyanate) promoted the unfolding of (POG)₆ and increased the melting temperature (T_m) of (POG)₈ from 37.7 to 58.8 ℃to form a triple helix. The hydrodynamic radii of collagen-like hybrid peptides were measured by dynamic light scattering (DLS). Atomic force microscopy (AFM) and transmission electron microscopy (TEM) were used to analyze the morphology of the aggregation states. AFM results showed that the collagen-like hybrid peptides, AP₆ and AP₈, formed nanofibers spontaneously. Consistent with the AFM results, TEM showed that the AP₆ and AP₈ collagen-like hybrid peptides also formed nanofiber structures. The formation of stable complexes was attributed to the presence of multiple weak interactions such as hydrogen bonding, π-π stacking, and hydrophobic interactions. In the present study, we demonstrated that the chemical modification of collagen-like polypeptides at the N-terminus via the small organic molecule, 4, 4'-methylene bis(phenyl isocyanate), promoted the intramolecular and intermolecular assembly of collagen-like peptides. A simple and effective strategy has been developed in this study to promote the self-assembly of collagen-like peptides.     

Synthesis and Crystal Structure Characterization of [Zr(HPO_4)(PO_4)F_2]·1.5H_3NCH_2CH_2NH_3

Thesynthesisofcrystallinezirconiumphosphateswasfirstreportedinl964byClearfieldandStynes['J,whodeterminedtheformulaasZr(HPO,),.H,O(a-ZrP)basedonchemicalcomposition,dehydrationandion-exchangebe-haviour'Sincethen,manyothercrystallinezirconiumphosphate,suchasZr(HPO,)(g-ZrP),Zr(HPO'),.H,O(Y-ZrP),havebeenprepared['.'1.Thesephosphatesconsistedofalternate,cross-linkedlayersofZrO,octahedraandPO'tetrahedrawithwatermoleculesaccommodatedininterlamellarfashion.a-Zirco-niumphosphate,Zr(HPO'),.…