不同螺旋结构类蛋白质分子管道传输动力学研究

采用动态蒙特卡洛模拟(Dynamical Monte Carlo,DMC)对不同螺旋结构的类蛋白质分子穿越管道的动力学过程进行了研究.计算了不同螺旋能参数下类蛋白质链的传输时间,传输成功率,管道内单体数目,形状因子<δ>,均方位移g等.结果发现螺旋能较小的链传输时间较短,变化不明显,而螺旋能较大的链随着螺旋能的增强传输时间迅速增大.计算表明相同类型的分子链其传输成功率随着电场的增大而减小.而对于不同螺旋结构的链,螺旋能参数εh=0的链传输成功率最大,达到80%左右,略小于自避链;而εh=-0.5的类蛋白质链传输成功率突然减小.随着螺旋能的增强,传输成功率又开始增大.另外的计算表明自避链的传输过程比类蛋白质链平稳.<δ>在传输过程中的变化都存在了最大值,说明链在传输时有一个最松散的构象.对于均方位移的计算得到εh=0的链均方位移变化最快,说明传输过程中扩散最快.同时发现εh=-3.0的链比εh=-1.5的链均方位移扩散快.形状因子和均方位移的趋势均能很好的解释不同螺旋参数下的类蛋白质链不同的传输性质.这些研究对生物大分子的输运行为有一定的指导意义.     

类蛋白质分子的二级结构对力学行为的影响

采用Kolinski等建立的类蛋白质分子的格点模型,研究了由典型的(HHPPHPP)x重复单元构成、含有α螺旋结构的类蛋白质分子链在拉伸过程中的构象性质和力学行为.发现不同强度的α螺旋相互作用会直接影响其拉伸过程.α螺旋相互作用强的类蛋白质分子链,具有更低的内能,更小的应力,在拉伸过程中更容易失去紧密接触对,同时也更容易被拉成“棒状”结构,但在整个拉伸过程中,α螺旋结构且能保持稳定;还发现类蛋白质分子的链长对拉伸也有影响,对较长的类蛋白质分子链,其内能更低,弹性力更小,自由能更大,紧密接触对的含量比例也更高,而“棒状化”程度较小.这些研究能够帮助我们加深对蛋白质分子的构象和弹性力学行为的理解.     

类蛋白质分子形成紧密接触对的速率研究

采用Kolinski等建立的类蛋白质分子的格点模型,通过计算类蛋白质分子的末端距分布函数P(r)来研究类蛋白质分子形成紧密接触对的速率k .发现不同的氨基酸序列,其分布函数P(r)不同.对于序列(H) x和(P) x,分布函数P(r)有二个峰值;而对于序列(HP) x,分布函数P(r)只有一个峰值.对于类蛋白质分子形成紧密接触对的速率k ,当链长N <11,随着N的增加而增加;当N >11,形成紧密接触对的速率k随着N的增加而减少,这个趋势与实验结果一致,并存在关系k～N-α(N >11) ,系数α与氨基酸序列有关.这些研究能够帮助我们加深对蛋白质结构形成的了解.     

β-turn预测的新方法

蛋白质二级结构由一些重复单元和非重复单元组成:前者主要包括α螺旋和β折叠,后者则包括tight turn、bulges和random coil等结构.Tight turn属于不规则结构,大部分结构中至少含有一个氢键,该结构由2～6个残基构成,根据残基个数的不同可将其分为δ-turn、γ-turn、β-turn、α-turn、π-turn五种类型.     

季铵盐高分子抗菌剂的工艺优化与抗菌性能研究

采用正交实验设计,进行公斤级批量制备DMAEMA-DB季铵盐单体和抗菌聚合物的研究,对影响单体合成的关键因素以及聚合的条件进行优化,并采用FT-IR和NMR等方法对所合成的单体和聚合物分别进行了结构表征,通过平板活菌计数法测定了单体以及聚合物的抗菌性能.结果表明,DMAEMA-DB单体的优化合成条件为:反应温度55℃,反应时间30h,反应物浓度为V<,s>:V<,l>=1:1,反应物配比为DMAEMA:DB=1:1.1.Poly(AAm/DMAEMA-DB)的最佳合成工艺条件为:聚合温度70℃,聚合时间8h,单体浓度为0.4mol/L,引发剂用量为单体用量的0.4mol%,在该条件下合成的聚合物平均得率达89%.将它们用于杀灭大肠杆菌时,接触时间5min对大肠杆菌的抑菌率可达99%,接触时间30min抑菌率达到100%.     

圆二色光谱法研究环境因素对细胞红蛋白二级结构的影响

采用远紫外圆二色光谱法系统地研究了细胞红蛋白(cytoglobin, Cygb)的浓度、环境温度、溶液的pH值和溶剂性质对细胞红蛋白二级结构的影响.结果表明: 当Cygb浓度<1 μmol/L时,它主要以α-螺旋形式存在,其α-螺旋含量>60%; 当Cygb浓度从0.3 μmol/L增大到2.0 μmol/L时,其α-螺旋含量迅速降低;当Cygb浓度>2.0 μmol/L时,其α-螺旋含量随浓度的增大变化很小(约30%).随着温度的升高,Cygb的α-螺旋含量逐渐减小,但既使温度达到368 K,它仍保持有20%的α-螺旋结构,说明该蛋白具有较高的热稳定性.在弱酸性和弱碱性溶液中,Cygb的二级结构都会有不同程度的破坏.在甲醇和乙醇中,Cygb的α-螺旋含量明显增加,这说明醇类可以诱导其α-螺旋的生成.     

ε-聚赖氨酸吸附条件的优化

以吸附率为指标,通过单因素试验比较了5种不同的树脂类型、p H值、溶质浓度和树脂量对ε-聚赖氨酸(ε-PL)的吸附效果,进一步采用响应面设计优化了HZD-3B和D155树脂的吸附条件,分析了两种树脂吸附ε-PL的吸附等温线以及吸附动力学曲线。结果表明,试验的5种树脂中,HZD-3B和D155树脂的吸附效果较好。HZD-3B最佳静态吸附条件为:溶液起始p H 8.5、起始浓度40g/L、树脂用量150g/L、温度25℃、吸附13h,ε-PL的最大吸附率是97.69%;D155最佳静态吸附条件为:溶液起始p H 8、起始浓度40g/L、树脂用量150g/L、温度25℃、吸附14h,ε-PL的最大吸附率是96.84%;等温线数据拟合均较符合Freundlich方程,动力学数据拟合均较符合二级动力学方程。发酵液验证试验结果显示,ε-PL最大吸附量与纯品吸附量基本一致。     

聚赖氨酸为主链的牙刷状分子刷的可控合成

设计合成了溴基功能化的赖氨酸单体(Br-lys)并通过关环反应制备了对应的溴代L-赖氨酸N-羧酸酐(Br-Lys-NCA)单体.利用过渡金属引发剂Ni(COD)depe调控的NCA活性开环聚合和顺序添加单体的方法,得到了组成和结构明确的聚(ε苄氧羰基L-赖氨酸)-b-PBrLL(PZLL-PBrLL)两嵌段共聚肽.利用PZLL-b-PBrLL两嵌段共聚肽为大分子引发剂,通过ATRP引发甲基丙烯酸寡聚乙二醇酯(EGMA),合成了以聚赖氨酸为骨架的牙刷状分子刷.研究发现PZLL-PBrLL两嵌段在四氢呋喃中形成α-螺旋结构,螺旋度随着PBrLL链段的增长而降低,而PZLL-b-(PBrLL-g-PEGMA)形成部分α-螺旋构象,螺旋度随侧链PEGMA增长而减小.     

δ-FeOOH对刚果红的吸附及光催化降解EI北大核心CSCD

通过化学还原法合成了δ-FeOOH,对其物理性质和微观结构进行了表征。以偶氮废水中的刚果红(CR)为模拟污染物,研究了CR初始质量浓度、催化剂用量、反应时间和H2O2投入量对δ-FeOOH吸附及光催化降解CR活性的影响。实验结果表明:δ-FeOOH为非晶态、呈片状,比表面积高达402.5 m^(2)/g;在CR质量浓度250 mg/L、δ-FeOOH用量20 mg时,6 h后CR的脱除率为100%,吸附量为1225 mg/g,可循环吸附5次;在CR质量浓度为250 mg/L的废水中,δ-FeOOH用量为30 mg时,在可见光下照射40 min,CR的降解率达99%以上,经5次循环使用后,光催化降解率仍可达99%。     

侧基对N-炔丙基酰胺螺旋共聚物光学活性的影响

设计并合成了5个系列的带有不同侧基的手性-非手性N-炔丙基酰胺共聚物,以铑有机配合物为催化剂对单体实施聚合反应得到高产率(>95%)的共聚物,聚合物具有高立构规整性(cis-含量高于94%).利用圆二色(CD)及紫外-可见吸收(UV-Vis)光谱技术对共聚物的二级结构及光学活性进行了表征,当非手性单体的酰胺侧基体积适中时,共聚物具有较高的光学活性,部分共聚物的光学活性甚至高于纯手性聚合物.表明通过选择合适的手性-非手性共聚单体及单体配比,可获得具有高光学活性的螺旋聚合物.     

The effect of crystal structure on the thermal reactivity of CL-20 and its C4 bonded explosives (I): thermodynamic properties and decomposition kinetics

The crystal structure, thermal behavior, and decomposition kinetics of ε-CL-20, RS-ε-CL-20, α-CL-20, ε-CL-20/C4, and RS-ε-CL-20/C4 were investigated by nonisothermal FTIR, TG, and DSC techniques. It was found that the thermal decomposition of α-CL-20, ε-CL-20/C4, and RS-ε-CL-20/C4 could be considered as a two-step process and the initial step is partly controlled by crystal structure. However, the crystal structure could only affect the initial step of decomposition and the total heat release, and the heat release of RS-ε-CL-20 is the highest compared with α- and normal ε-CL-20. In addition, the activation energy of studied materials was calculated by Kissinger method and modified KAS method, which was compared with the results obtained by other researchers. It was indicated that the obtained activation energy of ε-CL-20 by Kissinger method is about 176.0 kJ mol^?1, which is almost the same with the results from the literatures by STABIL and Noniso-TG methods. It was noticed that the crystal structure has significant effect on the initial activation energy distribution of CL-20, while in case of second stage (α = 0.30–0.85) this effect is relatively small, resulting in identical decomposition mechanism. Moreover, the kinetic compensation effects show that the studied materials could be divided into two groups, one including ε-CL-20, RS-ε-CL-20, α-CL-20, and ε-CL-20/C4 which decompose at solid state and another including ε-CL-20/Formex and RS-ε-CL-20/C4 which decompose at partial liquid state, resulting in different kinetic compensation effects. It reveals that the C4 base could affect the distribution of activation energy of ε-CL-20 and RS-ε-CL-20 in a totally different way.     

The effect of crystal structure on the thermal reactivity of CL-20 and its C4-bonded explosives

The critical temperature and mechanism functions for thermal decomposition of ε-CL-20, RS-ε-CL-20, α-CL-20, ε-CL-20/C4, and RS-ε-CL-20/C4 were evaluated based on non-isothermal TG data. A two-step mechanism has been found for thermal decomposition of α-CL-20, ε-CL-20/C4, and RS-ε-CL-20/C4, where the initial step is partly controlled by crystal structure of CL-20. The more reasonable mean activation energies could be obtained after peak separation for each individual steps. In fact, the activation energy for the post integrated process is almost equivalent with that of the second step, indicating that the total activation energy at the main decomposition process is dominated by thermolysis of CL-20 molecular. Besides, it has been found that the decomposition of C4 matrix does not affect the decomposition of normal ε-CL-20, resulting in identical activation energy and reaction model. However, the interaction between the C4 matrix and RS-ε-CL-20 is significant especially at the initial stage, where the activation energy of RS-ε-CL-20/C4 was overestimated before peak separation, while the activation energy for the second step due to thermolysis of CL-20 molecular is underestimated. The first decomposition step for α-CL-20, ε-CL-20/C4, and RS-ε-CL-20/C4 could be considered as autocatalytic process (AC model), whereas the second as JMA model, which is also applicable to that of pure ε-CL-20 and RS-ε-CL-20. Moreover, The critical temperatures of thermal explosion (T _b) are obtained as 205.6, 205.5, 209.4, 214.4, and 227.5 °C for α-CL-20, ε-CL-20, RS-ε-CL-20, ε-CL-20/C4, and RS-ε-CL-20/C4, respectively. It proves that the C4 matrix could stabilize ε-CL-20 while the crystal form of CL-20 has little effect on its thermal stability.     

Elastic Behaviors of Adsorbed Protein-like Chains

Elastic behaviors of protein-like chains are investigated by Pruned-Enriched-Rosenbluth method and modified orientation-dependent monomer-monomer interactions model. The protein-like chain is pulled away from the attractive surface slowly with elastic force acting on it. Strong adsorption interaction and no adsorption interaction are both considered. We calculate the characteristic ratio and shape factor of protein-like chains in the process of elongation. The conformation change of the protein-like chain is well depicted. The shape of chain changes from “rod” to “sphere” at the beginning of elongation. Then, the shape changes from “sphere” to “rod”. In the end, the shape becomes a “sphere” as the chain leaves away from the surface. In the meantime, we discuss average Helmoholtz free energy per bond, average energy per bond, average adsorbed energy per bond, average α-helical energy per bond, average β-sheet energy per bond and average contact energy per bond.On the other hand, elastic force is also studied. It is found that elastic force has a long plateau during the tensile elongation when there exists adsorption interaction. This result is consistent with SMFS experiment of general polymers. Energy contribution to elastic force and contact energy contribution to elastic force are both discussed. These investigations can provide some insights into the elastic behaviors of adsorbed protein chains.     

EFFECTS OF SECONDARY STRUCTURE ON ELASTIC BEHAVIOR OF PROTEIN-LIKE CHAINS

The elastic behavior of protein-like chains was investigated by using the Pruned-Enriched-Rosenbluth Method (PERM).Three typical protein-like chains such as all-α,all-β,and α+β(α/β) proteins were studied in our modified orientation dependent monomer-monomer interaction (ODI) model.We calculated the ratio of /N and shape factor <δ*> of protein-like chains in the process of elongation.In the meantime,we discussed the average energy per bond ＜U＞/N,average contact energy per bond ＜U＞c/N,average helical energy per bond ＜U＞h/N and average sheet energy per bond ＜U＞b/N.Three maps of contact formation,α-helix formation,β-sheet formation were depicted.All the results educe a view that the helix structure is the most stable structure,while the other two structures are easy to be destroyed.Besides,the average Helmholtz free energy per bond ＜A＞/Nis was presented.The force f obtained from the free energy was also discussed.It was shown that the chain extended itself spontaneously first.The force was studied in the process of elongation.Lastly,the energy contribution to elastic force fu was calculated too.It was noted that fu for all-β chains increased first,and then decreased with x0 increasing.     

Mesoscopic dynamic Monte Carlo simulations of the adsorption of proteinlike HP chains within laterally constricted spaces

Two-dimensional dynamic Monte Carlo simulations are applied to the protein-like HP chain model to investigate the influence of lateral confinement of the adsorbed chain on adsorption thermodynamics and the ensemble of accessible chain conformations. The structure of the model makes it possible to enumerate all possible chain conformations and thereby define with precision the relation between adsorption thermodynamics and changes in accessible chain conformations resulting from the adsorption process. Lateral confinement of the adsorbed chain is shown to dramatically reduce the number of accessible energy states and unique chain conformations such that, under certain conditions, adsorption is predicted to actually stabilize the chain against denaturation. Lateral confinement preferentially eliminates expanded conformations of the adsorbed chain, shifting the equilibrium from the unfolded state toward the native state. As a result, the conformational entropy of the adsorbed chain is predicted to be lower than that of the chain free in solution. The protein-like HP chain responds to an increase in the hydrophobicity of the sorbent surface by strongly favoring those conformations that minimize the overall internal energy of the system. As a result, adsorption severely destabilizes the native-state conformation. The ability of our simulation results to provide insights into underlying mechanisms for nonspecific protein adsorption is illustrated through qualitative comparison with activity data for hen egg-white lysozyme adsorbed on silica at different surface concentrations.     

The influence of the binding of low molecular weight surfactants on the thermal stability and secondary structure of IgG

The effect of low molecular weight surfactants on the thermal stability of immunoglobulin G is studied by differential scanning calorimetry. The corresponding change in the secondary structure is investigated using circular dichroism spectroscopy and the rate of aggregate formation, both in the presence and absence of surfactant, is monitored by dynamic light scattering. At low surfactant concentrations (SDS/Tween 20 mixture) the thermal stability of the protein was not affected. With increasing surfactant concentration the protein structure is perturbed, most probably due to hydrophobic interaction with the surfactant, leading to a lower thermal stability. At even higher concentrations the surfactant molecules encapsulate the protein molecules, so that the unfolded state is strongly suppressed due to restricted conformational freedom in a confined volume. Interaction with the surfactant mixture at intermediate concentration influences the secondary structure of IgG strongly, i.e. α-helix and random coil conformations are promoted and the amounts of β-sheets and β-turns are reduced.     

Hairpin folding behavior of mixed α/β-peptides in aqueous solution

The invention of new strategies for the design of protein-mimetic oligomers that manifest the folding encoded in natural amino acid sequences is a significant challenge. In contrast to the α-helix, mimicry of protein β-sheets is less understood. We report here the aqueous folding behavior of a prototype α-peptide hairpin model sequence varied at cross-strand positions by incorporation of 16 different β-amino acid monomers. Our results provide a folding propensity scale for β-residues in a protein β-sheet context as well as high-resolution structures of several mixed-backbone α/β-peptide hairpins in water.     

Local protein backbone folds determined by calculated NMR chemical shifts

NMR chemical shifts (CSs: δN(NH), δC(α), δC(β), δC', δH(NH), and δH(α)) were computed for the amino acid backbone conformers (α(L), β(L), γ(L), δ(L), ε(L), α(D), γ(D), δ(D), and ε(D) [Perczel et al., J Am Chem Soc 1991, 113, 6256]) modeled by oligoalanine structures. Topological differences of the extended fold were investigated on single β-strands, hairpins with type I and II β-turns, as well as double- and triple-stranded β-sheet models. The so-called "capping effect" was analyzed: residues at the termini of a homoconformer sequence unit usually have different CSs than the central residues of an adequately long homoconformer model. In heteroconformer sequences capping effect ruins the direct applicability of several chemical shift types (δH(NH), δC', and δN(NH)) for backbone structure determination of the parent residue. Experimental δH(α), δC(α), and δC(β) values retrieved from protein database are in good agreement with the relevant computed data in the case of the common backbone conformers (α(L), β(L), γ(L), and ε(L)), even though neighboring residue effects were not accounted for. Experimental and computed ΔδH(α)-ΔδC(α), ΔδH(α)-ΔδC(β), and ΔδC(α)-ΔδC(β) maps give qualitatively the same picture, that is, the positions of the backbone conformers relative to each other are very similar. This indicates that the H(α), C(α), and C(β) chemical shifts of alanine depend considerably on the backbone fold of the parent residue also in proteins. We provide tabulated CSs of the chiral amino acids that may predict the various structures of the residues.