蛋白质相互作用界面中磷酸酪氨酸质子化状态的判定研究

蛋白质相互作用界面上磷酸酪氨酸的质子化状态对蛋白质相互作用具有重要影响, 在进行相关结构的计算研究时, 必须对其进行准确判定. 采用AMBER/parm99力场和广义波恩(GBobc)隐式水模型, 以SHC1 (src homology 2 domain-containing transforming protein C1)的SH2 (Src homology 2)结构域与磷酸化激活的T细胞受体CD247链的相互作用核磁结构为例, 首次以热力学积分方法对相互作用界面上磷酸酪氨酸的质子化状态进行判定研究, 结果显示该方法计算精确, 判定结果与实验结果一致. 表明该方法不仅为涉及磷酸酪氨酸的蛋白质相互作用的计算结构研究奠定了基础, 在其它具有可电离基团的氨基酸的质子化状态判定中也将具有潜在的推广应用价值.     

分子动力学模拟研究质子化态在HIV-1 Protease-Indinavir复合物中的作用

I 型人体免疫缺陷病毒(HIV-1)蛋白酶中Asp25/Asp25'的质子化对于理论研究HIV-1 蛋白酶和抑制剂的作用机制
以及氨基酸变异对抗药性的影响有重要意义. 分别对Protease-Indinavir (PR-IDV)复合物的六种可能的质子化态进行了
5 ns 的分子动力学模拟, 分析了不同状态对动力学特征和结构的影响, 用molecular mechanics/Possion-Boltzman surface
area (MM-PBSA)方法计算了PR 和IDV 在各种状态下的结合自由能. 计算结果说明A 链Asp25 的OD2 的质子化是最
为可能的状态. 对PR-IDV 复合物中起到媒介作用的水分子与PR-IDV 复合物形成的氢键进行了分析, 分析结果说明不
同的质子化态对水分子在PR-IDV 复合物中所起的媒介作用没有影响, 这一结果与我们先前对PR-BEA369 复合物的研
究不同. 我们的研究结果为更高效的PR 抑制剂的设计以及PR 氨基酸变异对药物抗药性的研究提供了理论上的指导.     

The Controlled Formation and Cleavage of an Intramolecular d8–d8 Pt–Pt Interaction in a Dinuclear Cycloplatinated Molecular “Pivot‐Hinge”

The bis(diphenylphosphino)methane (dppm)‐bridged dinuclear cycloplatinated complex {[Pt(L)]₂(μ‐dppm)}²⁺ (Pt₂ ? dppm; HL: 2‐phenyl‐6‐(1H‐pyrazol‐3‐yl)‐pyridine) demonstrates interesting reversible “pivot‐hinge”‐like intramolecular motions in response to the protonation/deprotonation of L. In its protonated “closed” configuration, the two platinum(II) centers are held in position by intramolecular d⁸–d⁸ Pt–Pt interaction. In its deprotonated “open” configuration, such Pt–Pt interaction is cleaved. To further understand the mechanism behind this hingelike motion, an analogous dinuclear cycloplatinated complex, {[Pt(L)]₂(μ‐dchpm)}²⁺ (Pt₂ ? dchpm) with bis(dicyclohexylphosphino)methane (dchpm) as the bridging ligand, was synthesized. From its protonation/deprotonation responses, it was revealed that aromatic π–π interactions between the phenyl moieties of the μ‐dppm and the deprotonated pyrazolyl rings of L was essential to the reversible cleavage of the intramolecular Pt–Pt interaction in Pt₂ ? dppm. In the case of Pt₂ ? dchpm, spectroscopic and spectrofluorometric titrations as well as X‐ray crystallography indicated that the distance between the two platinum(II) centers shrank upon deprotonation, thus causing a redshift in its room‐temperature triplet metal–metal‐to‐ligand charge‐transfer emission from 614 to 625 nm. Ab initio calculations revealed the presence of intramolecular hydrogen bonding between the deprotonated and negatively charged 1‐pyrazolyl‐N moiety and the methylene CH and phenyl C–H of the μ‐dppm. The “open” configuration of the deprotonated Pt₂ ? dppm was estimated to be 19 kcal mol^?1 more stable than its alternative “closed” configuration. On the other hand, the open configuration of the deprotonated Pt₂ ? dchpm was 6 kcal mol^?1 less stable than its alternative closed configuration.     

Protonation of ferrocene,ruthenocene, and osmocene: a density functional study

Protonated forms of the ferrocene, ruthenocene, and osmocene molecules in the gas phase were calculated using the density functional approach with the Becke—Lee—Young—Parr functional. The proton affinity energies of ferrocene, ruthenocene, and osmocene were estimated at 214.2, 220.3, and 229.7 kcal mol^–1, respectively. The addition of a proton to carbon atoms of the cyclopentadienyl ring in the ferrocene molecule and to the metal atom in the ruthenocene and osmocene molecules is more energetically favorable. No minimum corresponding to ring protonation was located on the potential energy surface of protonated osmocene. The C—H _endo bond in the ring-protonated [C₁₀H₁₁M]⁺ (M = Fe, Ru) cations is involved in agostic interaction with the metal atom. Transition states of interconversions between the ring-protonated and metal-protonated forms were identified. A specific group of protonated forms of the ferrocene and ruthenocene molecules includes four types of structures, viz., ring-protonated (1a,b) and metal-protonated (2a,b) structures, transition states of the 1 2 interconversion (3a,b), as well as ring-protonated structures with the cyclopentadiene ring folded along the C(2)—C(5) line so that the M—H _endo interaction is virtually negligible. The latter structures are required for [1,5]-sigmatropic shift of the exo-hydrogen atom in the Cp ring to occur. The results obtained were used for the interpretation of the available schemes of electrophilic substitution reactions in metallocenes and of the sigmatropic shift mechanisms.     

Catalytic ionic hydrogenations

Catalytic ionic hydrogenation of ketones occurs by proton transfer to a ketone from a cationic metal dihydride, followed by hydride transfer from a neutral metal hydride. This contrasts with traditional catalysts for ketone hydrogenation that require binding of the ketone to the metal and subsequent insertion of the ketone into a M-H bond. Ionic hydrogenation catalysts based on the inexpensive metals molybdenum and tungsten have been developed based on mechanistic understanding of the individual steps required in the catalytic reaction.     

不同pH值的酸处理DNA溶液的拉曼光谱分析

通过拉曼光谱研究了经不同pH值的酸处理后的DNA溶液．小牛胸腺DNA被配制成pH6．0、pH5．0、pH4．0、pH3．0、pH2．0、pH1．0的酸性溶液，经24h充分水合后测试其拉曼光谱．实验结果表明，DNA分子内部产生了明显的质子化，其拉曼特征频率和强度均发生了变化，而且不同的pH值致使它们的变化程度也不同．对DNA分子结构的影响包括磷酸骨架基团，脱氧核糖及碱基．随着酸性的增强，DNA的构型也发生变化：在pH6．0、pH5．0时DNA溶液为标准B构型，而在pH4．0、pH3．0、pH2，0的DNA溶液出现B和C构型共存，到pH1．0时出现了Z构型．从pH3．0碱基开始质子化，逐渐地GC碱基对之间形成了Hoogsteen型氢键，AT碱基对之间的氢键发生断裂，双螺旋结构遭到破坏，而脱氧核糖也受到不同程度的损伤．     

Strontium-mediated selective protonation of unsaturated linkage of aromatic hydrocarbons and these derivatives

The selective protonation of aromatic hydrocarbons with at least two or more aromatic rings and aromatic compounds bearing unsaturated linkages can be achieved by metallic strontium metal with ammonium chloride and iodine, or ammonium iodide in tetrahydrofuran. The reaction system is ammonia-free in room temperature and the reaction proceeds high selectivity in moderate to good yields.