分子动力学模拟Cu2+对α-突触核蛋白(1-17)肽段构象变化的影响

利用分子动力学模拟研究铜离子(Cu2+)对α-突触核蛋白1-17号氨基酸肽段(α-synuclein(1-17))构象变化的影响,采用GROMOS 43A1力场对Cu2+-α-synuclein(1-17)复合体和α-synuclein(1-17)肽段单体分别进行了6组独立的分子动力学模拟,每组模拟时间为500ns,总模拟时间为3μs.研究结果表明:Cu2+与α-synuclein(1-17)肽段结合使其更易向β折叠片结构折叠,促进了其二级结构的形成,增强了构象的稳定性;Cu2+增大了α-synuclein肽段疏水残基的溶剂可及表面积,增强了其疏水残基的暴露程度.自由能分析指出,Cu2+-α-synuclein(1-17)复合体的自由能比α-synuclein(1-17)肽段低,构象稳定,采样空间紧密,其自由能极小构象为β折叠片结构.构象聚类分析进一步表明,Cu2+使得α-synuclein(1-17)肽段构象趋于稳定.总之,Cu2+诱导固有无序蛋白α-synuclein(1-17)肽段由无序向有序转变,降低了构象的自由能,同时Cu2+增强了α-synuclein(1-17)肽段的疏水性,使得α-synuclein肽段因疏水作用更倾向于形成β折叠片结构,加速其疏水性聚集.     

分子动力学模拟极端嗜热核糖结合蛋白的热力学稳定性

采用分子动力学模拟方法研究极端嗜热性核糖结合蛋白(tteRBP)的嗜热机理.在常温(300 K)和最佳活性温度(375 K)时,分别对tteRBP分子进行动力学模拟,结果表明,整体分子均保持结构稳定,但分子内部的协调运动不同.在375 K时蛋白整体柔性显著提高,使分子能够局部调整构象以适应极端高温.蛋白结构变化的分析也确认了高温时构象局部微调对蛋白极端高温稳定性的关键作用.     

海藻糖抑制淀粉质多肽42构象转变的分子动力学模拟

应用分子动力学模拟方法研究了海藻糖抑制淀粉质多肽42(Aβ42)构象转变的分子机理.结果表明,海藻糖溶液浓度对Aβ42构象转变具有非常重要的影响.在水和低浓度海藻糖溶液(0.18mol·L-1)中,Aβ42可由初始的α-螺旋结构转变成β-折叠的二级结构;但海藻糖浓度为0.37mol·L-1时即可有效抑制Aβ42的构象转变.这是因为海藻糖利用其优先排阻作用使水分子在多肽周围0.2nm内富集,而其自身却在距离多肽0.4nm的位置附近团聚.另外,海藻糖还可通过降低多肽间的疏水相互作用,减少多肽分子内远距离的接触,有效抑制多肽的疏水塌缩和构象转变.上述分子模拟的结果对于进一步合理设计阿尔茨海默病的高效抑制剂具有非常重要的理论指导意义.     

盐酸胍诱导的变性卵清溶菌酶分子重折叠过程及其各稳定构象态的分布和过渡

采用变性和非变性电泳、 高效凝胶排阻色谱、 内源荧光发射光谱和荧光相图以及生物活性测定等方法, 研究了盐酸胍诱导的变性卵清溶菌酶分子的重折叠过程及此过程中卵清溶菌酶分子各稳定构象态的分布和过渡. 结果表明, 当复性液中盐酸胍浓度分别约为5.0和2.4 mol/L时, 变性卵清溶菌酶分子的重折叠过程各存在1个稳定折叠中间态, 重折叠过程符合"四态模型". 在卵清溶菌酶分子四态重折叠过程基础上, 结合盐酸胍与卵清溶菌酶分子之间的缔合-解离平衡, 给出了一个定量描述变性剂诱导的蛋白质分子复性过程中蛋白质分子复性率随溶液中变性剂浓度变化的方程. 该方程包含2个特征折叠参数, 一个是蛋白质分子从一个稳定构象态过渡到另一个稳定构象态的热力学过渡平衡常数k; 另一个是在此过程中平均每个蛋白质分子所结合的变性剂分子数目m. 通过这2个特征折叠参数能够定量描述盐酸胍诱导的变性卵清溶菌酶完全去折叠态、 折叠中间态和天然态分子随复性液中盐酸胍浓度变化的分布和过渡情况.     

自组装小肽RADA16-1的构象研究

研究自组装小肽RADA16-1的稳定构象具有一定挑战性,为了解决这个问题,分别利用经典分子动力学(MD)模拟方法和温度副本交换分子动力学(REMD)模拟方法进行对比研究.采用CHARMM力场参数,研究小肽RADA16-1在生理温度310 K左右的稳定构象.其中利用REMD完成26 ns时长水溶性小肽RADA16-1的模拟,利用MD完成3次160 ns时长小肽的模拟.之后,对比分析了RADA16-1小肽能量、氢键、回转半径(RGYR)和溶剂可及表面积(SASA)的变化特征.通过模拟结果的对比,发现REMD计算较MD计算能够使用更少的计算量搜索到相对明确的稳定构象信息,从而通过对能量、氢键、RGYR和SASA的结果分析,确定疏水作用和氢键相互作用共同稳定小肽的空间构象.     

血红蛋白和细胞色素c构象去折叠行为研究

利用紫外-可见吸收和荧光光谱法研究了血红蛋白(Hb)与细胞色素c(Cytc)两种血红素蛋白的去折叠行为。采用化学变性剂盐酸胍(GdHCl)和尿素(Urea)诱导两种蛋白构象去折叠,阐述了两种蛋白的去折叠机理。Hb的血红素(Heme)辅基通过与卟啉铁原子和组氨酸配位,与肽链键合的稳定性较差,在3.0 mol/L的盐酸胍作用下即发生解离。而Cyt c的Heme辅基通过卟啉与半胱氨酸形成二硫键呈现较强的稳定性,盐酸胍浓度达到6.0 mol/L也难使其发生解离。该研究为阐释蛋白构象与功能之间的关系提供了重要依据。     

β发卡多肽Trpzip4折叠的副本交换分子动力学模拟

采用副本交换分子动力学对β发卡Trpzip4重折叠进行研究,结果表明,构象空间存在较大能垒时,副本交换分子动力学(REMD)表现出比分子动力学(MD)更优的抽样效率.288 K下,Trpzip4势能、骨架均方根偏差、溶剂可及表面积(SASA)在REMD中呈逐渐降低趋势.采样得到两种特定形态的低势能构象:β发卡和螺旋-卷曲.β发卡中,第3组氢键Asp46容易与Thr49形成氢键;转角Thr49的羟基(OH)倾向于与Asp46的羧基(COO-)或主链上的C=O形成氢键,强化了Asp46与Thr49的相互作用,导致转角形成折回弯度;与Thr49相比,Thr51的羟基倾向与水分子作用,甲基朝内,因此与Asp46的侧链作用微小.螺旋-卷曲中,吲哚环-甲基为主要疏水形式.Trpzip4在折叠成β发卡过程中,转角氢键影响整个β发卡构象的形成.转角氢键具有距离优势和强侧链相互作用,最先形成.     

虎纹捕鸟蛛毒素-Ⅴ去折叠过程的色谱分析

 将纯化的天然虎纹捕鸟蛛毒素-Ⅴ经盐酸胍变性30 min后,在pH 3.0、反应温度为37 ℃的条件下与三羧甲基磷酸(TCEP)反应12 min,用反相高效液相色谱分离得到其全部去折叠中间体,通过基体辅助激光解吸电离飞行时间质谱(MALDI-TOF MS)进行鉴定,并利用烷基化反应对这些去折叠中间体予以进一步确证。 根据其保留时间,分析虎纹毒素-Ⅴ各去折叠中间体的色谱行为,初步探讨了多肽或蛋白质构象异构体反相色谱行为的多样性。     

恢复蛋白Recoverin正则模式分析的理论研究

采用旋转平移块方法对Ca2+/豆蔻酰基开关进行了正则模式分析(NMA). 研究结果表明, 恢复蛋白(Recoverin)的T态的N-末端与C-末端易于发生刚体逆向旋转, 一旦结合Ca2+, 很容易发生构象变化, 形成具有双向构象转变特征的I态. I态是一个中间结构, 既可以发生构象回转到T态, 又可以继续相对旋转到R态, 使豆蔻酰基完全暴露, 从而行使其信号传导生物功能. 从低频振动模式分析可以看出, 恢复蛋白具有构象转变这一本质属性.     

H2CCC光谱性质的从头算研究

采用全活化空间自洽场方法(CASSCF)在C2v对称性和ANO-S基组水平下, 研究了H2CCC自由基及其阴阳离子的基态和低激发态性质. 为了进一步考虑动态电子相关效应, 采用多组态二级微扰理论(CASPT2)获得了更加精确的能量值. 计算得到X1A1 → 1A2, X1A1 → 1B1和X1A1 → 21A1在159.0, 216.5和476.4 kJ/mol处的激发可分别归因于π(b2)→π*(b1), n(a1)→π*(b1)和π(b1)→π*(b1)的跃迁, 理论波长与紫外吸收光谱得到的实验数据一致. 计算得到的电子亲和势与实验值也非常接近.     

Energetic basis of human telomeric DNA folding into G-quadruplex structures

Recent theoretical studies performed on the folding/unfolding mechanism of the model telomeric human DNA, 5'-AGGGTTAGGGTTAGGGTTAGGG-3' (Tel22), have indicated that in the presence of K(+) ions Tel22 folds into two hybrid G-quadruplex structures characterized by one double and two reversal TTA loops arranged in a different way. They predicted a new unfolding pathway from the initial mixture of hybrid G-quadruplexes via the corresponding intermediate triplex structures into the final, fully unfolded state. Significantly, no experimental evidence supporting the suggested pathway has been reported. In the current work, we performed a comprehensive global thermodynamic analysis of calorimetric (DSC, ITC) and spectroscopic (CD) data obtained on monitoring the folding/unfolding of Tel22 induced by changes of temperature and K(+) concentration. We show that unfolding of Tel22 may be described as a monomolecular equilibrium three-state process that involves thermodynamically distinguishable folded (F), intermediate (I), and unfolded (U) state. Considering that calorimetric methods cannot distinguish between energetically similar G-quadruplex or triplex conformations predicted by the theoretical model one can conclude that our results represent the first experimental support of the suggested unfolding/folding mechanism of Tel22. This conclusion is confirmed by the fact that the estimated number of K(+) ions released upon each unfolding step in our thermodynamic model agrees well with the corresponding values predicted by the theoretical model and that the observed changes in enthalpy, entropy, and heat capacity accompanying the F → I and I → U transitions can be reasonably explained only if the intermediate state I is considered to be a triplex structural conformation.     

A foldamer at the liquid/graphite interface: the effect of interfacial interactions, solvent, concentration, and temperature

The unfolding process and self-assembly of a foldable oligomer (foldamer 1) at the liquid/graphite interface were investigated by scanning tunnelling microscopy. At the level of molecular conformation, we identified several molecular conformations (A(z), B, C, D, E) that represent intermediate states during unfolding, which may help to elucidate the unfolding process at the liquid/graphite interface. Adsorption at the interface traps the intermediate states of the unfolding process, and STM has proved to be a powerful technique for investigating folding and unfolding of a foldamer at the molecular level, which are not accessible by other methods. The STM observations also revealed that varying the solvent and/or concentration results in different self-assemblies of foldamer 1 as a result of variations in molecular conformations. The solvent and concentration effects were attributed to the changes in existing states (extended or folded) of foldamers in solution, which in turn affect the distribution of adsorbed molecular conformations at the interface. This mechanism is quite different from other systems in which solvent and concentration effects were also observed.     

Observation of entropic effect on conformation changes of complex systems under well-controlled temperature conditions

We report direct observation of an entropic effect in determining the folding of a linear dicarboxylate dianion with a flexible aliphatic chain [(-)O(2)C-(CH(2))(6)-CO(2)(-)] by photoelectron spectroscopy as a function of temperature (18-300 K) and degree of solvation from 1 to 18 water molecules. A folding transition is observed to occur at 16 solvent water molecules at room temperature and at 14 solvent molecules below 120 K due to the entropic effect. The (-)O(2)C-(CH(2))(6)-CO(2)(-)(H(2)O)(14) hydrated cluster exhibits interesting temperature-dependent behaviors, and its ratio of folded over linear conformations can be precisely controlled as a function of temperature, yielding the enthalpy and entropy differences between the two conformations. A folding barrier is observed at very low temperatures, resulting in kinetic trapping of the linear conformation. The current work provides a simple model system to study the dynamics and entropic effect in complex systems and may be important for understanding the hydration and conformation changes of biological molecules.     

14-helical folding in a cyclobutane-containing beta-tetrapeptide

The efficient synthesis of tetrapeptide 5 containing, in alternation, cyclobutane and beta-alanine residues is described. NMR experiments both at low temperature in CDCl(3) and at 298 K in DMSO-d(6) solutions show the contribution of a strong hydrogen bond in the folded major conformation of 5. Temperature coefficients and diffusion times point out a hydrogen bond involving the NH proton from the cyclobutane residue 1 whereas NOEs manifest the high rigidity of the central fragment of the molecule and are compatible with a 14-membered macrocycle. Theoretical calculations predict a most stable folded conformation corresponding to a 14-helix stabilized by a hydrogen bond between NH(10) in the first residue and OC(25) in the third residue. This structure remains unaltered during the molecular dynamics simulation at 298 K in chloroform. All these results provide evidence for a 14-helical folding and reveal the ability of cis-2-aminocyclobutane carboxylic acid residues to promote folded conformations when incorporated into beta-peptides.     

Structural Insights into the Trp‐Cage Folding Intermediate Formation

The 20 residue long Trp‐cage is the smallest protein known, and thus has been the subject of several in vitro and in silico folding studies. Here, we report the multistate folding scenario of the miniprotein in atomic detail. We detected and characterized different intermediate states by temperature dependent NMR measurements of the ¹⁵N and ¹³C/¹⁵N labeled protein, both at neutral and acidic pH values. We developed a deconvolution technique to characterize the invisible—fully folded, unfolded and intermediate—fast exchanging states. Using nonlinear fitting methods we can obtain both the thermodynamic parameters (ΔH^F–I, T_m^F–I, ΔC_p^F–I and ΔH^I–U, T_m^I–U, ΔC_p^I–U) and the NMR chemical shifts of the conformers of the multistate unfolding process. During the unfolding of Trp‐cage distinct intermediates evolve: a fast‐exchanging intermediate is present under neutral conditions, whereas a slow‐exchanging intermediate‐pair emerges at acidic pH. The fast‐exchanging intermediate has a native‐like structure with a short α‐helix in the G¹¹–G¹⁵ segment, whereas the slow‐exchanging intermediate‐pair presents elevated dynamics, with no detectable native‐like residue contacts in which the G¹¹? P¹² peptide bond has either cis or trans conformation. Heteronuclear relaxation studies combined with MD simulations revealed the source of backbone mobility and the nature of structural rearrangements during these transitions. The ability to detect structural and dynamic information about folding intermediates in vitro provides an excellent opportunity to gain new insights into the energetic aspects of the energy landscape of protein folding. Our new experimental data offer exceptional testing ground for further computational simulations.     

Folding pathways of human telomeric type-1 and type-2 G-quadruplex structures

We have investigated new folding pathways of human telomeric type-1 and type-2 G-quadruplex conformations via intermediate hairpin and triplex structures. The stabilization energies calculated by ab initio methods evidenced the formation of a hairpin structure with Hoogsteen GG base pairs. Further calculations revealed that the G-triplet is more stable than the hairpin conformation and equally stable when compared to the G-tetrad. This indicated the possibility of a triplex intermediate. The overall folding is facilitated by K(+) association in each step, as it decreases the electrostatic repulsion. The K(+) binding site was identified by molecular dynamics simulations. We then focused on the syn/anti arrangement and found that the anti conformation of deoxyguanosine is more stable than the syn conformation, which indicated that folding would increase the number of anti conformations. The K(+) binding to a hairpin near the second lateral TTA loop was found to be preferable, considering entropic effects. Stacking of G-tetrads with the same conformation (anti/anti or syn/syn) is more stable than mixed stacking (anti/syn and vice versa). These results suggest the formation of type-1 and type-2 G-quadruplex structures with the possibility of hairpin and triplex intermediates.     

Do Charge State Signatures Guarantee Protein Conformations?

The extent to which proteins in the gas phase retain their condensed-phase structure is a hotly debated issue. Closely related to this is the degree to which the observed charge state reflects protein conformation. Evidence from electron capture dissociation, hydrogen/deuterium exchange, ion mobility, and molecular dynamics shows clearly that there is often a strong correlation between the degree of folding and charge state, with the most compact conformations observed for the lowest charge states. In this article, we address recent controversies surrounding the relationship between charge states and folding, focussing also on the manipulation of charge in solution and its effect on conformation. 'Supercharging' reagents that have been used to effect change in charge state can promote unfolding in the electrospray droplet. However for several protein complexes, supercharging does not appear to perturb the structure in that unfolding is not detected. Consequently, a higher charge state does not necessarily imply unfolding. Whilst the effect of charge manipulation on conformation remains controversial, there is strong evidence that a folded, compact state of a protein can survive in the gas phase, at least on a millisecond timescale. The exact nature of the side-chain packing and secondary structural elements in these compact states, however, remains elusive and prompts further research.     

Protonation/deprotonation effects on the stability of the Trp-cage miniprotein

The Trp-cage miniprotein is a 20 amino acid peptide that exhibits many of the properties of globular proteins. In this protein, the hydrophobic core is formed by a buried Trp side chain. The folded state is stabilized by an ion pair between aspartic acid and an arginine side chain. The effect of protonating the aspartic acid on the Trp-cage miniprotein folding/unfolding equilibrium is studied by explicit solvent molecular dynamics simulations of the protein in the charged and protonated Asp9 states. Unbiased Replica Exchange Molecular Dynamics (REMD) simulations, spanning a wide temperature range, are carried out to the microsecond time scale, using the AMBER99SB forcefield in explicit TIP3P water. The protein structural ensembles are studied in terms of various order parameters that differentiate the folded and unfolded states. We observe that in the folded state the root mean square distance (rmsd) from the backbone of the NMR structure shows two highly populated basins close to the native state with peaks at 0.06 nm and 0.16 nm, which are consistent with previous simulations using the same forcefield. The fraction of folded replicas shows a drastic decrease because of the absence of the salt bridge. However, significant populations of conformations with the arginine side chain exposed to the solvent, but within the folded basin, are found. This shows the possibility to reach the folded state without formation of the ion pair. We also characterize changes in the unfolded state. The equilibrium populations of the folded and unfolded states are used to characterize the thermodynamics of the system. We find that the change in free energy difference due to the protonation of the Asp amino acid is 3 kJ mol(-1) at 297 K, favoring the charged state, and resulting in ΔpK(1) = 0.5 units for Asp9. We also study the differences in the unfolded state ensembles for the two charge states and find significant changes at low temperature, where the protonated Asp side chain makes multiple hydrogen bonds to the protein backbone.