过氧亚硝酸与酪氨酸的反应机理

用密度泛函理论(DFT)研究了过氧亚硝酸与酪氨酸的反应机理. 在B3LYP/6-311G(d,p)水平上对该反应体系的反应物、中间体、过渡态和产物进行了几何构型优化并计算了振动频率和能量. 计算结果表明, 过氧亚硝酸不易直接与酪氨酸反应, 而是先分解产生自由基(·OH和·NO2), 而后再与酪氨酸分步作用. 过氧亚硝酸与酪氨酸的反应生成两种主要产物, 分别为3-羟基酪氨酸和3-硝基酪氨酸, 这一结论与实验所得到的结果一致. 此外在同一计算水平上采用SCRF(PCM)方法计算了溶剂化效应, 结果表明, 极性溶剂可以增加自由基结合的稳定化能, 并降低反应通道的活化能, 有利于反应的进行.     

蛋白质相互作用: 界面分析, 结合自由能计算与相互作用设计

蛋白质相互作用在生命活动中起着重要作用. 研究蛋白质间相互作用的本质有助于了解生命活动中这些基本单元的作用. 本文主要综述了近期蛋白质相互作用研究的进展, 包括蛋白质相互作用界面的基本性质, 蛋白质结合自由能的计算方法, 不同相互作用在蛋白质结合/解离中的角色和差异, 以及上述知识在蛋白质相互作用设计中的应用. 蛋白质相互作用界面的特性, 例如界面大小、保守性以及结构的动态性质, 使得具有生物功能的蛋白质相互作用界面区别于非特异性的晶体堆积界面. 生物功能界面的一个重要结构特征是界面上存在着关键残基以及相对独立的相互作用模块. 利用多种方法, 如MM-PBSA、统计平均势以及不同的相互作用自由能模型, 可以在不同的精度上计算蛋白质相互作用自由能. 利用蛋白质相互作用界面的特点, 从不同的角度进行蛋白质相互作用对的设计与改造, 近年来已经有了不少成功的例子, 但还存在着很大的挑战. 我们认为在今后的蛋白质相互作用设计中, 考虑各种因素对蛋白质结合与解离的动力学过程的影响将有助于提高人类控制蛋白质相互作用的能力.     

蛋白质酪氨酸硝化的研究

蛋白质酪氨酸硝基化是一种重要的蛋白质翻译后修饰,与多种病症相关.经由过氧亚硝酸根(ONOO-)和NO2-/H2O2/血红素过氧化物酶体系是促使蛋白质硝化最主要的两种途径,其反应为自由基机理.本文对体内蛋白质硝基化的途径、机制及其生物学意义作了综述,指出蛋白质的硝化具有选择性,特定酪氨酸残基发生硝化能够改变蛋白质的结构和功能,影响其免疫应答和可能涉及的信号转导过程,从而具有重要的生物学意义.     

蛋白质-RNA相互作用界面预测与设计

蛋白质-RNA之间的相互作用是蛋白质在细胞里面行使功能的重要方式之一. 结构生物学家利用实验手段可以得到蛋白质-RNA复合物的三维结构, 通过原子水平的晶体结构来解释蛋白质与RNA的识别过程. 但实验取得蛋白质-RNA的复合物结构非常困难, 耗钱、耗时, 同时受限于其相互作用强度. 因而利用理论的方法对蛋白质-RNA相互作用界面进行预测与设计在生物医学研究中十分重要. 本文主要综述了近期蛋白质-RNA相互作用界面预测与设计方面的进展, 包括以下几个方面: (1) 蛋白质-RNA分子对接算法以及对接前后存在的构象变化的处理; (2) 蛋白质-RNA 识别机制的研究; (3) 基于蛋白质-RNA 相互作用界面的分子设计. 蛋白质-RNA分子对接算法逐步完善将有助于我们对大量未知功能的蛋白质与RNA进行功能注释, 而基于生物大分子相互作用界面的分子设计将在药物设计领域中有广阔的应用前景.     

蛋白质相互作用预测、设计与调控

蛋白质相互作用是生命活动在分子水平上的基本事件. 蛋白质相互作用的三维图像可以给出关键生命活动过程的分子细节. 了解蛋白质相互作用的原理有助于揭示生命活动的机制, 并在此基础上开展有重要价值的蛋白质设计. 本文对于蛋白质相互作用预测、设计和调控研究的近期进展进行了总结归纳, 介绍了作者实验室在相关领域的研究进展, 并对今后的研究方向进行了展望. 主要包括: (1) 蛋白质相互作用网络、蛋白质相互作用机制和蛋白质复合物结构计算分析; (2) 基于序列、结合位点以及复合物结构的蛋白质相互作用预测; (3)蛋白质相互作用设计方法; (4) 利用化学分子调控蛋白质相互作用的方法; (5) 针对蛋白质相互作用的蛋白质药物设计方法.     

蛋白质-蛋白质相互作用界面统计分析

以作者开发的从蛋白质结合部位推导出其界面所具有的疏水性质和氢键性质的计算程序PP_SITE为基础,利用蛋白质结构数据库(PDB),对蛋白质-蛋白质相互作用界面进行了统计分析.从PDB中挑出非冗余的链间相互作用对,计算出这个数据集中所有链间界面的疏水和氢键相互作用特征.对得到的界面特征进行统计分析,寻找能够明显聚类的界面特征.结果表明，界面大小、氢键和疏水相互作用在界面所占比例以及疏水相互作用的集中程度可以作为分类的依据.     

阴离子表面活性剂存在下光系统Ⅱ中酪氨酸残基的性能研究

通过荧光光谱和富立叶变换红外(FT-IR)光谱研究了阴离子型表面活性剂-十二烷基硫酸钠(SDS)与光系统Ⅱ(PSⅡ)的相互作用.结果表明,PSⅡ表现出酪氨酸荧光的特性.在PSⅡ蛋白质内部,存在着232 nm处的组分与酪氮酸之间以及这两种氨基酸残基与叶绿素a之间的能量传递.SDS的存在会使这些能量传递以及PSⅡ中蛋白的骨架结构和酪氨酸残基的结构发生改变,而变化方式又明显受SDS在溶液中聚集状态的影响.低于其临界胶束浓度(cmc)时,SDS会促进蛋白质中232 nm处的组分与酪氨酸之间的能量传递,并且使酪氨酸残基处于极性更小的环境;而大于cmc时,SDS却产生相反的效应.但不同浓度的SDS均会抑制酪氨酸残基至叶绿素a的能量传递.     

酪氨酸激酶抑制剂的三维定量构效关系研究

利用柔性原子受体模型(FLARM)方法对一系列的异黄酮和喹诺酮衍生物表皮生长因子受体酪氨酸激酶抑制剂进行了三维定量构效关系研究，得到了合理的构效关系模型.FLARM方法的计算结果还给出了虚拟的受体模型，该模型说明了抑制剂与受体之间可能的相互作用.由该虚拟受体模型得到的受体-配体相互作用与Novartis药效团模型比较类似.     

蛋白质酪氨酸硝化的研究

蛋白质酪氨酸硝基化是一种重要的蛋白质翻译后修饰,与多种病症相关。经由过氧亚硝酸根(ONOO-)和NO2-/H2O2/血红素过氧化物酶体系是促使蛋白质硝化最主要的两种途径,其反应为自由基机理。本文对体内蛋白质硝基化的途径、机制及其生物学意义作了综述,指出蛋白质的硝化具有选择性,特定酪氨酸残基发生硝化能够改变蛋白质的结构和功能,影响其免疫应答和可能涉及的信号转导过程,从而具有重要的生物学意义。     

阴离子表面活性剂存在下光系统II中酪氨酸残基的性能研究

通过荧光光谱和富立叶变换红外(FT-IR)光谱研究了阴离子型表面活性剂－十 二烷基硫酸钠（SDS）与光系统II（PSII）的相互作用。结果表明,PSII表现出酪 氨酸荧光的特性。在PSII蛋白质内部,存在着232 nm处的组分与酪氨酸之间以及这 两种氨基酸列基与叶绿素a之间的能量传递。SDS的存在会使这些能量传递以及 PSII中蛋白的骨架结构和酪氨酸残基的结构发生改变,而变化方式又明显受SDS在 溶液中聚集状态的影响。低于其临界胶束浓度(cmc)时,SDS会促进蛋白质中232 nm外的组分与酪氨酸之间的能量传递,并且使酪氨酸残基外于极性更小的环境; 而大于cmc时,SDS却产生相反的效应。但不同浓度的SDS均会抑制酪氨酸残基至叶 绿素a的能量传递。     

A minimalist model for exploring conformational effects on the electrospray charge state distribution of proteins

The electrospray ionization (ESI) charge state distribution of proteins is highly sensitive to the protein structure in solution. Unfolded conformations generally form higher charge states than tightly folded structures. The current study employs a minimalist molecular dynamics model for simulating the final stages of the ESI process in order to gain insights into the physical reasons underlying this empirical relationship. The protein is described as a string of 27 beads ("residues"), 9 of which are negatively charged and represent possible protonation sites. The unfolded state of this bead string is a random coil, whereas the native conformation adopts a compact fold. The ESI process is simulated by placing the protein inside a solvent droplet with a 2.5 nm radius consisting of 1600 Lennard-Jones particles. In addition, the droplet contains 14 protons which are modeled as highly mobile point charges. Disintegration of the droplet rapidly releases the protein into the gas phase, resulting in average charge states of 4.8+ and 7.4+ for the folded and unfolded conformation, respectively. The protonation probabilities of individual residues in the folded state reveal a characteristic pattern, with values ranging from 0.2 to 0.8. In contrast, the protonation probabilities of the unfolded protein are more uniform and cover the range from 0.8 to 1.0. The origin of these differences can be traced back to a combination of steric and electrostatic effects. Residues exhibiting a small accessible surface area are less likely to capture a proton, an effect that is exacerbated by partial electrostatic shielding from nearby positive residues. Conversely, sites that are sterically exposed are associated with electrostatic funnels that greatly increase the likelihood of protonation. Unfolding enhances the steric and electrostatic exposure of protonation sites, thereby causing the protein to capture a greater number of protons during the droplet disintegration process.     

Solvation of p-coumaric acid in water

The photoactive yellow protein (PYP) is an important model protein for many (photoactive) signaling proteins. Key steps in the PYP photocycle are the isomerization and protonation of its chromophore, p-coumaric acid (pCA). In the ground state of the protein, this chromophore is in the trans configuration with its phenolic oxygen deprotonated. For this paper, we studied four different configurations of pCA solvated in water with ab initio molecular dynamics simulations as implemented in CP2K/Quickstep. We researched the influence of the protonation and isomerization state of pCA on its hydrogen-bonding properties and on the Mulliken charges of the atoms in the simulation. The chromophore isomerization state influenced the hydrogen-bonding less than its protonation state. In general, more charge yielded a higher hydrogen-bond coordination number. Where deprotonation increases both the coordination number and the residence time of the water molecules around the chromophore, protonation showed a somewhat lower coordination number on two of the three pCA oxygens but much higher residence times on all of them. This could be explained by the increased polarization of the OH groups of the molecule. The presence of the chromophore also influenced the charge and polarization of the water molecules around it. This effect was different in the four systems studied and mainly localized in the first solvation shell. We also performed a proton-transfer reaction from hydronium through various other water molecules to the chromophore. In this small charge-separated system, the protonation occurred within 6.5 ps. We identified the transition state for the final step in this protonation series.     

Protonation of the chromophore in the photoactive yellow protein

The photoactive yellow protein (PYP) acts as a light sensor to its bacterial host: it responds to light by changing shape. After excitation by blue light, PYP undergoes several transformations, to partially unfold into its signaling state. One of the crucial steps in this photocycle is the protonation of p-coumaric acid after excitation and isomerization of this chromophore. Experimentalists still debate on the nature of the proton donor and on whether it donates the hydrogen directly or indirectly. To obtain better knowledge of the mechanism, we studied this proton transfer using Car-Parrinello molecular dynamics, classical molecular dynamics, and computer simulations combining these two methods (quantum mechanics/molecular mechanics, QMMM). The simulations reproduce the chromophore structure and hydrogen-bond network of the protein measured by X-ray crystallography and NMR. When the chromophore is protonated, it leaves the assumed proton donor, glutamic acid 46, with a negative charge in a hydrophobic environment. We show that the stabilization of this charge is a very important factor in the mechanism of protonation. Protonation frequently occurs in simplified ab initio simulations of the chromophore binding pocket in vacuum, where amino acids can easily hydrogen bond to Glu46. When the complete protein environment is incorporated in a QMMM simulation on the complete protein, no proton transfer is observed within 14 ps. The hydrogen-bond rearrangements in this time span are not sufficient to stabilize the new protonation state. Force field molecular dynamics simulations on a much longer time scale have shown which internal rearrangements of the protein are needed. Combining these simulations with more QMMM calculations enabled us to check the stability of protonation states and clarify the initial requirements for the proton transfer in PYP.     

Quantum mechanical models of the resting state of the vanadium-dependent haloperoxidase

Density functional theory has been used to investigate structural and electronic properties of complexes related to the resting form of the active site of vanadium haloperoxidase as a function of environment and protonation state. Results obtained by studying models of varying size and complexity highlight the influence of environment and protonation state on the structure and stability of the metal cofactor. The study shows that, in the trigonal bipyramidal active site, where one axial position is occupied by a key histidine, the trans position cannot contain a terminal oxo group. Further, a highly negatively charged vanadate unit is not stable. Protonation of at least one equatorial oxo ligand appears necessary to stabilize the metal cofactor. The study also indicates that, while at rest within the protein, the vanadate unit is most likely an anion with an axial hydroxide and an equatorial plane containing two oxos and a hydroxide. For the neutral, protonated state of the vanadate unit, there were two minima found. The first structure is characterized by an axial water with two oxo and one hydroxo group in the equatorial plane. The second structure contains an axial hydroxo group and an equatorial plane composed of one oxo and two hydroxo oxygen atoms. These two species are not significantly different in energy, indicating that either form may be important during the catalytic cycle. These data support the initial crystallographic assignment of an axially bound hydroxide, but an axial water is also a possibility. This study also shows that the protonation state of the vanadate ion is most likely greater than previously proposed.     

Protonation of the oxygen axial ligand in galactose oxidase model compounds as seen with high resolution X-ray emission experiments and FEFF simulations

X-ray Emission Spectroscopy (XES) crossover peaks were shown to be sensitive to the protonation state of solvent molecules in the Zn protein carbonic anhydrase and its model compounds. Here we extend such studies to galactose oxidase models i.e. Cu(ii) open d-shell systems, illustrating that XES combined with FEFF8 simulations reflect changes in the protonation state of the phenolate ligand for the copper center.     

NMR chemical shifts of the rhodopsin chromophore in the dark state and in bathorhodopsin: a hybrid QM/MM molecular dynamics study

We investigate nuclear magnetic resonance (NMR) parameters of the rhodopsin chromophore in the dark state of the protein and in the early photointermediate bathorhodopsin via first-principles molecular dynamics simulations and NMR chemical shift calculations in a hybrid quantum/classical (QM/MM) framework. NMR parameters are particularly sensitive to structural properties and to the chemical environment, which allows us to address different questions about the retinal chromophore in situ. Our calculations show that both the 13C and the 1H NMR chemical shifts are rather insensitive to the protonation state of Glu181, an ionizable amino acid side chain located in the vicinity of the isomerizing 11-cis bond. Thus, other techniques should be better suited to establish its protonation state. The calculated chemical shifts for bathorhodopsin further support our previously published theoretical structure, which is in very good agreement with more recent X-ray data.     

Low-temperature chromophore isomerization reveals the photoswitching mechanism of the fluorescent protein Padron

Photoactivatable fluorescent proteins are essential players in nanoscopy approaches based on the super-localization of single molecules. The subclass of reversibly photoswitchable fluorescent proteins typically activate through isomerization of the chromophore coupled with a change in its protonation state. However, the interplay between these two events, the details of photoswitching pathways, and the role of protein dynamics remain incompletely understood. Here, by using a combination of structural and spectroscopic approaches, we discovered two fluorescent intermediate states along the on-switching pathway of the fluorescent protein Padron. The first intermediate can be populated at temperatures as low as 100 K and results from a remarkable trans-cis isomerization of the anionic chromophore taking place within a protein matrix essentially deprived of conformational flexibility. This intermediate evolves in the dark at cryotemperatures to a second structurally similar but spectroscopically distinct anionic intermediate. The final fluorescent state, which consists of a mixture of anionic and neutral chromophores in the cis configuration, is only reached above the glass transition temperature, suggesting that chromophore protonation involves solvent interactions mediated by pronounced dynamical breathing of the protein scaffold. The possibility of efficiently and reversibly photoactivating Padron at cryotemperatures will facilitate the development of advanced super-resolution imaging modalities such as cryonanoscopy.     

Electronic excitations of the green fluorescent protein chromophore in its protonation states: SAC/SAC-CI study

Two ground-state protonation forms causing different absorption peaks of the green fluorescent protein chromophore were investigated by the quantum mechanical SAC/SAC-CI method with regard to the excitation energy, fluorescence energy, and ground-state stability. The environmental effect was taken into account by a continuum spherical cavity model. The first excited state, HOMO-LUMO excitation, has the largest transition moment and thus is thought to be the source of the absorption. The neutral and anionic forms were assigned to the protonation states for the experimental A- and B-forms, respectively. The present results support the previous experimental observations.     

Determination of chromophore charge states in the low pH color transition of the fluorescent protein Rtms5 via time-dependent DFT

The red fluorescent protein Rtms5^H146S displays a transition from blue (absorbance λ_max 590 nm) to yellow (absorbance λ_max 453 nm) upon titration to low pH. The pK_a of the reaction depends on the concentration of halide, offering promise for new expressible halide sensors. The protonation state involved in the low pH form of the chromophore remains, however, ambiguous. We report calculated excitation energies of different protonation states of an RFP chromophore model. These suggest that the relevant titration site is the phenoxy moiety of the chromophore, and the relevant base and conjugate acid are anionic and neutral chromophore species, respectively.     

Multiple protonation equilibria in electrostatics of protein-protein binding

All proteins contain groups capable of exchanging protons with their environment. We present here an approach, based on a rigorous thermodynamic cycle and the partition functions for energy levels characterizing protonation states of the associating proteins and their complex, to compute the electrostatic pH-dependent contribution to the free energy of protein-protein binding. The computed electrostatic binding free energies include the pH of the solution as the variable of state, mutual "polarization" of associating proteins reflected as changes in the distribution of their protonation states upon binding and fluctuations between available protonation states. The only fixed property of both proteins is the conformation; the structure of the monomers is kept in the same conformation as they have in the complex structure. As a reference, we use the electrostatic binding free energies obtained from the traditional Poisson-Boltzmann model, computed for a single macromolecular conformation fixed in a given protonation state, appropriate for given solution conditions. The new approach was tested for 12 protein-protein complexes. It is shown that explicit inclusion of protonation degrees of freedom might lead to a substantially different estimation of the electrostatic contribution to the binding free energy than that based on the traditional Poisson-Boltzmann model. This has important implications for the balancing of different contributions to the energetics of protein-protein binding and other related problems, for example, the choice of protein models for Brownian dynamics simulations of their association. Our procedure can be generalized to include conformational degrees of freedom by combining it with molecular dynamics simulations at constant pH. Unfortunately, in practice, a prohibitive factor is an enormous requirement for computer time and power. However, there may be some hope for solving this problem by combining existing constant pH molecular dynamics algorithms with so-called accelerated molecular dynamics algorithms.